Source: UNIVERSITY OF ARKANSAS submitted to
DEVELOPING GENETIC AND MOLECULAR RESOURCES TO IMPROVE SPINACH PRODUCTION AND MANAGEMENT
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
OTHER GRANTS
Reporting Frequency
Annual
Accession No.
1013082
Grant No.
2017-51181-26830
Cumulative Award Amt.
$2,447,432.00
Proposal No.
2017-03188
Multistate No.
(N/A)
Project Start Date
Sep 1, 2017
Project End Date
Jun 30, 2022
Grant Year
2017
Program Code
[SCRI]- Specialty Crop Research Initiative
Project Director
Shi, A.
Recipient Organization
UNIVERSITY OF ARKANSAS
(N/A)
FAYETTEVILLE,AR 72703
Performing Department
Horticulture
Non Technical Summary
In the last 20 years, the US spinach industry has seen a dramatic increase in the popularity of spinach, and as a result, increased production and consumption. In order to keep up with the demand, the spinach industry requires continuous development of improved and adapted cultivars to meet numerous disease constraints to satisfy consumer demands. Spinach breeding presents some unique challenges, and efforts to improve and expedite the selection process would greatly accelerate the release of new, improved, and durably disease resistant cultivars. The proposed project is a multi-state and multi-agency collaboration to develop tools for molecular breeding and outreach activities to directly benefit stakeholders. The effort will accelerate the introgression of critically important traits into breeding populations for improved spinach cultivar development and establish a set of outreach activities to communicate information and impact industry stakeholders. We propose to develop SNP markers associated with the three most economically important diseases affecting spinach (downy mildew, white rust, and Fusarium wilt) as a tool for spinach breeders, in both public and private sectors, to select resistant germplasm through marker-assisted selection. As a direct consequence, spinach resources for resistance to downy mildew, white rust, and Fusarium wilt will be characterized and developed for release to spinach breeding programs. This project will address the areas of the USDA SCRI program: (1) "Research in plant breeding, genetics, genomics, and other methods to improve crop characteristics"; and (2) "Efforts to identify and address threats from pests and diseases, including threats to specialty crop pollinators".
Animal Health Component
60%
Research Effort Categories
Basic
20%
Applied
60%
Developmental
20%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2011430108150%
2021430108050%
Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms; 202 - Plant Genetic Resources;

Subject Of Investigation
1430 - Greens and leafy vegetables;

Field Of Science
1081 - Breeding; 1080 - Genetics;
Goals / Objectives
Spinach (Spinacia oleracea L.) has become an increasingly important economic vegetable crop worldwide with an estimated annual value of $11.8 billion (Correll et al. 2011, van Deynze 2015). The US is the second largest producer of spinach after China with over 550,000 tons harvested, valued at over $300 million annually (Correll et al. 2011; NASS 2015). In addition to its economic importance, spinach is one of the healthiest vegetables in the human diet due to its high concentration of nutrients and health-promoting compounds (Dicoteau 2000; Morelock and Correll 2008). During the last 15 years, the US spinach industry has seen a dramatic increase (double) in fresh market demand (NASS 2015). This requires development of new, improved cultivars to increase production. The major yield-limiting diseases in spinach production in the US are downy mildew (DM), white rust (WR), and Fusarium wilt (FW).The purpose of this project is to build a molecular breeding platform integrated into a classical breeding approach in spinach. With improved next generation sequencing (NGS) and the decreasing cost of sequencing, it is becoming feasible to discover millions of single-nucleotide-polymorphisms (SNPs) for any plant and connect these markers to desirable phenotypic traits. Spinach is a very popular vegetable crop which can greatly benefit from the development of molecular tools to improve commercial cultivars. The overall goal of this proposal is to develop genetic, molecular, and management resources to improve US spinach production by combining molecular and conventional breeding to expedite breeding procedures and speed up genetic gains for the release of spinach cultivars adapted to the main regions of spinach production.The specific research objectives of this proposal are: (1) Genetic mapping and SNP marker identification for downy mildew and white rust resistance in spinach; (2) Evaluation, QTL and association mapping and SNP marker identification for Fusarium wilt resistance in spinach; (3) Introgression of downy mildew and white rust resistance into spinach lines with diverse leaf quality characteristics to satisfy market demand; and (4) Construction of high density SNP consensus genetic maps of six chromosomes in spinach using whole genome resequencing.
Project Methods
Downy mildew evaluation: (1) For the 384 spinach genotypes of the association panel, downy mildew resistance will be evaluated under both greenhouse and growth chamber as previously described (Irish et al. 2008; Feng et al. 2014) and field conditions (Correll et al. 2016), and we will also use Pfs race 10 and race 16 to evaluate the 384 spinach genotypes. (2) For the five F2 populations, we will also evaluate them under both greenhouse (growth chamber) and field conditions but use one Pfs race due to single plant in F2 as the unit of phenotyping.The evaluation of white rust resistance will be evaluated at Del Monte White Rust Nursery, TX where heavy disease pressure has consistently been observed for 30 years in winter 2017-2018 and winter 2018-2019. We will also evaluate white rust resistance at the University of Arkansas Vegetable Research Station in Alma, AR in the spring 2018 and spring 2019 through inoculating with white rust pathogen twice in seedling stage and once in adult stage during each growth season.Fusarium wilt resistance screening of the 384 genotypes will be carried out in the greenhouses at the Washington State University (WSU) Mount Vernon NWREC. The protocol used in the spinach Fusarium wilt soil bioassay and the parent line screening developed by du Toit's program will be used to quantify the level of Fusarium wilt resistance.DNA extraction, whole-genome resequencing (WGR) and SNP discovery: Genomic DNA will be extracted from freeze dry leaves of spinach plants using the CTAB method (Kisha et al., 1997). Before DNA sequencing, qualified DNA for each sample is cut into 350bp fragment by Covaris Ultrasonic Processor randomly. The construction of the DNA libraries are through the process of end repairing, adding A to tails, purification, PCR amplification (van Dijk et al. 2014b) and the DNA library for each sample will be constructed in Novogene (http://en.novogene.com/). Pair-end sequencing libraries (read length 350bp) will be sequenced by Illumina HiSeq X Ten machine (http://www.illumina.com/systems/hiseq-x-sequencing-system/system.html). The short-read sequences data (350bp) will be analyzed using SOAP family software (Li 2011; Li et al. 2009; Li et al. 2010; http://soap.genomics.org.cn/) for SNP discovery.Genetic map construction: Linkage maps will be constructed for each F2 population using JoinMap 4 (van Ooijen 2006) and MSTmap (Wu et al. 2007, 2008a; http://www.mstmap.org/). The consensus genetic maps for the ten F2 populations will be constructed by MergeMap (Wu et al. 2008b; http://138.23.178.42/mgmap/).QTL analysis: Linkage maps will be constructed for each F2 population using JoinMap 4 (van Ooijen 2006). Single marker regression (SMR), interval mapping (IM), composite interval mapping (CIM), and multiple-interval mapping (MIM) analyses will be conducted for QTL mapping using Windows QTL Cartographer V2.5 (Wang et al. 2006) and QGene (Joehanes et al. 2008); and variance components, QTL heritability and QTL effects will be estimated by QTLNetworkv2.1 (Yang et al. 2008). The QTL maps will be drawn with MapChart (Voorrips 2002).Genetic diversity analysis will conducted for the association panels using MAGA 7 (Kumar et al. 2016) and population structure will be analyzed using the model-based program STUCTURE 2.3.4 (Pritchard et al., 2000)Association analysis: Genome-wide association study (GWAS) will be conducted with the mixed linear model method as described in TASSEL 5 (Bradbury et al. 2007) and the analysis will be also performed with compressed mixed linear model (Zhang et al. 2010) implemented in the GAPIT R package (Lipka et al. 2012) and in FarmCPU (Liu et al., 2016).SNP marker validation: The SNP markers identified from QTL and association mapping will be validated through KASP SNP genotyping in 960 individuals of spinach genotypes including germplasm, cultivars and breeding lines and also in other segregating populations with phenotypic data.

Progress 09/01/17 to 06/30/22

Outputs
Target Audience: Nothing Reported Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?1. A course Hort6033 "Molecular Plant Breeding (Genetic Techniques in Plant Breeding)" has been developed for training students and scientists in molecular breeding at University of Arkansas, Fayetteville and it has been opened the class in Fall 2017 and Fall 2019 and taught by Ainong Shi. 2. Sanjaya Gyawali, the postdoc in Toit's lab organized a workshop and taught the population structure and genome wide association studies (GWAS) on 23-24 May 2019 at the WSU Mount Vernon NWREC, where there were ten participants and three observers, including graduate students and professional staff from WSU in the workshop. 3. Gyawali participated a workshop as the main instructor to teach the population structure and genome wide association studies (GWAS) from 17-22 June 2019 at the International Center for Agricultural Research in Dry Areas (ICARDA), Rabat, Morocco, where there were nineteen participants, including graduate students (PhD and MS), and research scientists (pathologists, breeders, and gene bank managers) from India, Ghana, Rwanda, Tunisia, and Morocco. 4. Dr. Avila was invited as a panelist in a workshop organized by the Vegetable Breeding interest group of the American Society for Horticultural Sciences (ASHS) during the annual meeting held on August 11th, 2020. Avila gave a presentation to attendees (online audience) about current efforts in his program to develop and utilize high-throughput phenotyping in vegetable breeding. 5. Five postdoctoral research associates have been working on this project: one at Shi's lab, one at Correll's lab, one at Avila's lab, one at Mou's lab and one at du Toit's lab. Two PhD students and one MS student Research Assistant were graduated from both Shi's and Correll's labs. How have the results been disseminated to communities of interest?1. Spinach breeding lines: spinach lines have been released to Bowery Farming; 20 lines to 80 Acres Farms, and 30 lines to Clemson University for spinach production testing. 2. Molecular markers: Molecular markers associated with DM, white rust, and Fusarium with were relieved to spinach seed companies breeders, and scientists for utilizing in spinach molecular breeding. 3. Spinach field days for downy mildew disease: Dr. Correll organized the multiple stakeholder Spinach Field Days with over 150 attendees for each meeting. The Spinach Field Days were hold on October 9th, 2019 at Salinas, CA; hold on February 20, 2019, February 26, 2020, and March 15, 2021 at Yuma, AZ; and at University of Massachusetts Amherst, UMass Extension on Jan 28, 2021 (https://ucanr.edu/blogs/blogcore/postdetail.cfm?postnum=31421; https://desertagsolutions.org/events/377-spinach-field-day; https://desertagsolutions.org/events/427-2020-spinach-field-day; https://extension.arizona.edu/2021-downy-mildew-field-day; https://ag.umass.edu/vegetable/events/field-day-winter-greens-diseases-variety-trials). 4. Spinach field day in Texas: Two field days were organized by Larry Stein in the winter seasons on February 19, 2020 and February 25, 2021 at Tiro Tres Farms, Crystal City, TX with the presence of more than 50 producers and spinach industry representatives. Field days include fungicide trials against white rust and anthrachnose. In addition, commercial cultivars were demonstrated to attendees. Avila and Stein gave talks about spinach white rust evaluation and fungicide tests to local producers and spinach industry representatives in the field days. Avila talked about white rust evaluations, research objectives and potential benefits expected resistant varieties receiving a positive feedback and interest from producers (Avila 2020b). In addition, results were presented including white rust disease evaluation trials on commercial and USDA accessions, Stemphylium evaluation, and commercial cultivar trials. A booklet having evaluation results were given to attendees and sent by email to producers and stakeholders that were not able to attend to the field days. 5. Extension and outreach for Fusarium wilt: Several talks by Lindsey du Toit and her lab members were presented at the Western Washington Seed Workshop held at the Washington State University (WSU) Mount Vernon Northwestern Washington Research and Extension Center (NWREC) on Jan. 11, 2019 and Jan. 10, 2020; and in the WSU Mount Vernon NWREC Field Day on July 11, 2019, March 2, 2020, 2021. The information was shared with representatives of all the seed companies that contract with growers in western WA to produce seed crops of these vegetables, as well as seed growers, students, researchers, extension specialists, and public. 6. Extension and outreach for white rust: Carlos Avila and Larry Stein have built two new white rust screening plots (nursery) at the Rio Grande Valley and in Wintergarden area of TX and spinach was planted during 2018-2019, 2019-2020, 2020-2021 winter seasons. The new white evaluation nursey allowed to screen more spinach lines at multiple locations. Outreach included spinach grower/industry meetings to discuss the various spinach white rust and other disease challenges being faced in the Rio Grande Valley and Wintergarden region of TX including Stemphylium leaf spot and Anthracnose in spinach production. 7. Spinach extension and outreach activities in Larry Stein's lab: Dr. Stein traveled to California and Washington State on July 7 to 11, 2019 to examine growing practices and seed production fields; worked with Peterson Brother's Nursery in San Antonio to prepare a leafy greens display for the HEB produce convention for their produce buyers; extension was instrumental in making this happen during an odd time of the year to try to grow leafy greens; and plants delivered 31 July 2019; held a series of 7 am breakfast meetings with producers to map out strategies for the upcoming growing season on July 22, August 6, and September 2, 16, and 25 in 2019; and hosted several spinach field days in cooperation with Tiro Tres Farms and the Wintergarden Spinach Producers Board and conducted white rust screening for the various companies in the winter seasons since 2016. 8. Spinach breeding and California Leafy Greens Research Program: Beiquan Mou attended and presented spinach breeding and production ten-times from 2017 to 2022 (Mou, 2020, 2019a, b, c, d, 2018a, b, 2017a, b, c). 9. Economic estimation: Robert Hogan has been working on review trends and seasonality associated with fresh market spinach in 2018 and spinach varieties to be planted in years 2019 and 2020. 10. International Spinach Conference: Jim Correll has hosted several meeting of International Spinach Conferences and Field Day (https://spinach.uark.edu/meetings-2/). The recent one was hold on February, 2018 on Murcia, Spain and several members at PIs' labs gave presentations in the meeting (https://spinach.uark.edu/spain-presentations/). Due to COVID-19, the one planned in 2020 was cancelled and the next one will be in Feb/March 2022 in Belle Glade, FL. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? I. Genetic mapping and SNP marker identification for downy mildew and white rust resistance in spinach 1. Downy mildew (DM) evaluation in commercial cultivars/hybrids: 70 spinach cultivars were evaluated for downy mildew (DM) resistance (Peronospora effusa, Pfs) at the Salinas Valley, CA and at Yuma, AZ during six winter seasons from 2017 to 2022 (Correll et al. 2019a, b, 2017; Dhillon et al. 2020a, b; Matheron et al. 2019) and evaluated reactions to 10 DM races under greenhouse/growth chamber conditions (Dotun et al. 2020, 2021; Feng et al. 2021). 2. DM field evaluation in spinach germplasm: 440 spinach genotypes were evaluated DM resistance at Salinas, CA and Yuma, AZ (Bhattarai et al. 2019e), and 300 accessions was evaluated in Crystal City and Weslaco, TX (Bhattarai et al., 2020c). 3. Molecular markers for DM resistance: Thirteen, two and eight molecular markers have been developed for three loci, RPF1, RPF2 and RPF3, of DM resistance, respectively (Feng et al. 2018b). 4. DM resistance QTL/ gene mapping and genome-wide association study (GWAS): - GWAS was conducted using 9,783 GBS-generated SNPs on a panel of 174 spinach genotypes to identify the genetic loci governing the resistance to DM pathogen Pfs race 13 and the resistance gene alleles were mapped to spinach chromosome (chr) 3 within a 0.5 M region for resistance to Pfs (Bhattarai et al. 2020a) - Association analysis was performed in 172 spinach genotypes using 10,788 GBS (genotyping by sequencing) generated SNPs in the population derived from a cross of Whale and Lazio segregating for Pfs 16 resistance and SNP markers were identified (Bhattarai et al. 2021a). - The F2 populations derived from Viroflay x Whale inoculated with Pfs 5 were genotyped following a low-coverage genome resequencing approach mapped the resistance on the 1.2 Mb region of chr 3 (Bhattarai et al., 2022b). - GWAS performed under greenhouse/growth chamber condition for resistance to Pfs 5 in 251 genotypes; the major QTL/alleles was mapped near the previously mapped region on chr. 3; 14 SNP markers were strongly associated with DM resistance; and the prediction accuracy (r-value) was 0.81 - 0.90 when 14 SNP markers were used (Olaoye 2021 MS Thesis; Olaoye et al. 2022b). 5. GWAS of DM resistance in spinach under field condition: GWAS has been performed in 434 spinach lines in a multi-year and multi-location DM screening in Salinas, CA and Yuma, AZ (Bhattarai et al. 2020b, Bhattarai et al., 2022a) and in Wintergarden area in southern Texas (Bhattarai et al. 2020c, 2020e). 6. Evaluation and GWAS for white rust resistance in spinach commercial cultivars/hybrids: A total of 522 spinach lines from Pop Vriends, Enza Zaden, Rijk Zwaan, Sakata, and the University of Arkansas were evaluated white rust resistance and performed GWAS (Shi et al. 2020, 2019, 2018a, b). 7. GWAS and Genomic prediction (GP) for white rust resistance in USDA spinach germplasm: GWAS and GP was performed in 346 USDA germplasm accessions for white rust resistance (Shi et al. 2022). 8. White rust susceptibility in spinach germplasm: Minor alleles were identified to be associated with white rust susceptibility in spinach (Awika et al. 2020a, 2019b, 2018) and a new phenotyping was developed to do white rust phenotyping in the field (Awika et al. 2021b, 2019a, 2018). II. Evaluation, QTL and association mapping and SNP marker identification for Fusarium wilt resistance in spinach 1. Fusarium wilt resistance evaluation: 68 spinach commercial cultivars was evaluated for Fusarium wilt resistance under greenhouse. (Gyawali et al. 2019 a, b, c, 2021). 2. QTL mapping of Fusarium wilt resistance: A bi-parental spinach population if 192 genotypes of Viroflay/AS10-1512F were phenotyped and genoptyped and SNP markers were identified (Gyawali et al. 2019b). 3. GWAS for Fusarium wilt resistance: The reactions of 351 USDA spinach accessions to a mixture of three Fos isolates (Fus058, Fus254, and Fus322) were performed for a GWAS of spinach Fusarium wilt resistance (Gyawali et al. 2019a). 4. Evaluation, GWAS and GP of Fusarium wilt resistance in wild spinach species S. turkestanica: GWAS of Fusarium wilt in 75 S. turkestanica accessions revealed major QTL on chr 4, 5, and 6 for Fusarium wilt resistance and 33-associated SNP markers were identified. The prediction accuracy (r-value) was >0.6 based on six GP models. III. Introgression of DM and white rust resistance into spinach lines with diverse leaf quality characteristics to satisfy market demand 1. Crosses were made among cultivars with different DM-resistant genes to combine their resistances. Progenies from 34 crosses; 16 populations were developed; 12 populations showed decreases of DM incidences; and 6 populations dropped DM incidences to 0%. 2. For white rust, over 50 spinach lines were evaluated their white rust resistance in the field of Crystal City, TA and showed these lines are white rust resistant; and 30 crosses have been made between AR spinach lines with white rust resistance with commercial spinach cultivars with DM resistance in order to release cultivars resistant to both diseases. Thirty-advanced spinach breeding with white rust resistance were selected. 3. 66 spinach lines have been released to Bowery Farming; 20 lines to 80 Acres Farms, and 30 lines to Clemson University for spinach production testing. 4. Twenty new crosses between Arkansas white rust resistant, USDA white rust resistant, and susceptible lines with different leaf characteristics were made. IV. Construction of high-density SNP consensus genetic maps of six chromosomes in spinach using whole genome resequencing Ten F2 populations were developed from Viroflay, a spinach cultivar with high susceptibility to all three diseases of DM, white rust, and Fusarium wilt, crossed to ten other spinach lines including seven DM resistant lines (Lazio, Whale, Boeing, Califlay, Campania, NIL1, and NIL3), two white rust resistant lines (F415 and F380), and one Fusarium wilt resistant line (AS10-1512F). So far, five F2 populations with a total of 960 F2 individuals were phenotyped and genotyped using low-coverage WGR in Texas A&M Bioinformatics Center. Over half million SNPs were identified in the seven F2 populations. The consensus genetic maps of the spinach six genomes has been analyzing and manuscript is being written. V. Other spinach research 1. Whole genome sequencing (WGS) and whole genome resequencing (WGR): - The spinach line NIL1, a Viroflay-background, near isogenic line with the RPF1 DM resistance gene, was subjected to de novo assembly with 92.8% whole genome coverage. - 480 spinach genotypes have been sequenced using WGRwith 10X coverage, and the sequence data have been deposited at NCBI SRA with BioProject: PRJNA860974 and > 10 million SNPs were found. 2. SSR discovery in spinach: Genome-wide SSRs were discovered (Bhattarai et al. 2021b). 3. Gene-expression for resistance to DM pathogen (P. effuse): Transcriptome profile was studies in the DM resistant and susceptible spinach cultivars, Solomon and Viroflay using RNAseq (Kandel et al. 2019, 2020);NIL1 and Viroflay (Zia et al. 2021); and NIL6 and Viroflay (Bhattarai and Shi 2021c). 4. Spinach leaf spot evaluation: 271 spinach genotypes were evaluated for Stemphylium vesicarium resistance under the greenhouse and associated SNP markers were identified (Liu et al. 2020, 2021; Bhattarai et al. 2022). 5. Anthrachnose leaf spot evaluation: Resistance to anthracnose (Colletotrichum dematium) was evaluated in 276 spinach accessions and associated SNP markers were identified (Awika et al 2020a). 6. High-throughput phenotyping in spinach: A high-throughput phenotyping (HTP) technology has been developed for fast phenotyping in spinach (Avila et al. 2020a, 2019, 2018; Awika et al. 2019a, b) and has been used to identify molecular markers associated to plant growth parameters, biomass (yield), water-use efficiency, and abiotic stress (Awika et al. 2021a, b, c).

Publications

  • Type: Journal Articles Status: Published Year Published: 2021 Citation: " Awika, H.O., A.K. Mishra, H. Gill, J. DiPiazza, C.A. Avila, and V. Joshi*. 2021a. Selection of Nitrogen Responsive Root Architectural Traits in Spinach Using Machine Learning and Genetic Correlations. Scientific Reports 11:9536. https://doi.org/10.1038/s41598-021-87870-z " Awika, H.O., J. Solorzano, U.C. Rivera, A. Shi, J. Enciso, and C.A. Avila*. 2021b. Prediction modeling for yield and water-use efficiency in spinach using remote sensing via an unmanned aerial system. Smart Agriculture Technology 1, 100006. https://doi.org/10.1016/j.atech.2021.100006 " Batson, A.M.*, Fokkens, L., Rep, M., and du Toit, L.J. 2021. Putative effector genes distinguish two pathogenicity groups of Fusarium oxysporum f. sp. spinaciae. Molecular Plant-Microbe Interactions 34:141-156. https://doi.org/10.1094/MPMI-06-20-0145-R o Bhattarai, G., W. Yang, A. Shi*, C. Feng, B. Dhillon, J.C. Correll*, and B. Mou*. 2021a. Mapping and candidate gene identification of downy mildew race 16 resistance in spinach. BMC Genomics 22-478. https://doi.org/10.1186/s12864-021-07788-8 o Bhattarai, G., A. Shi*, D.R. Kandel, N. Soli?s-Gracia, J.A. da Silva, and C.A. Avila*. 2021b. Genome-wide simple sequence repeats (SSR) markers discovered from whole-genome sequence comparisons of multiple spinach accessions. Scientific Reports, 11, 9999. https://doi.org/10.1038/s41598-021-89473-0 o Bhattarai, G.*, and A. Shi*. 2021c. Research advances and prospects of spinach breeding, genetics, and genomics. Vegetable Research 1:9. http://www.maxapress.com/article/doi/10.48130/VR-2021-0009. o Clark, K. J., Feng, C., Zima, H. V., Poudel-Ward, B., Slinski, S. L., Porchas, P. Klosterman; S. J., and J.C. Correll*. 2021. Evaluation of spinach cultivars for downy mildew resistance in Yuma, AZ 2021. Plant Disease Management Reports. Report No. 15:V112. https://www.plantmanagementnetwork.org/pub/trial/pdmr/volume15/abstracts/v112.asp o Gyawali, S., M.L. Derie, E.W. Gatch, D. Sharma-Poudyal, and L.J. du Toit*. 2021a. Lessons from 10 years of stakeholder adoption of a soil bioassay for assessing the risk of spinach Fusarium wilt. Plant Pathology 70:778-792. https://doi.org/10.1111/ppa.13335 o Gyawali, S., G. Bhattarai, A. Shi*, C. Kik, and L. du Toit*. 2021b. Early stages of allopatric speciation in Spinacia turkestanica and the domestication of cultivated spinach. Frontiers in Genetics 12:740437. https://doi.org/10.3389/fgene.2021.740437 o Hulse-Kemp, A.M., Bostan, H., Chen, S., Ashrafi, H., Stoffel, K., Sanseverino, W., Li, L., Cheng, S., Schatz, M.C., Garvin, T., du Toit, L.J., Tseng, E., Chin, J., Iorizzo, M., and van Deynze, A.* 2021. An anchored chromosome-scale genome assembly of spinach (Spinacia oleracea) improves annotation and reveals extensive gene rearrangements in euasterids. Plant Genome 14:e20101. https://doi.org/10.1002/tpg2.20101 o Liu, B., L. Stein, K. Cochran, L.J. du Toit, C. Feng, and J.C. Correll*. 2021a. Three New Fungal Leaf Spot Diseases of Spinach in the United States and the Evaluation of Fungicide Efficacy for Disease Management. Plant Disease 105:316-323. https://doi.org/10.1094/pdis-04-20-0918-re o Liu, Z., Lu, T., Feng, C., Zhang, H., Li, G., Xu, Z., Correll, J. C., Qian, W.*, 2021b. Fine mapping and molecular marker development of the Fs gene controlling fruit spines in spinach (Spinacia olereace L). Theoretical and Applied Genetics 134:1319-1328. https://doi:10.1007/s00122-021-03772-8 o McDonald, M.R., Collins, B., du Toit, L.J., and Adusei-Fosu, K. 2021. Soil amendments for the management of Fusarium wilt of bunching spinach in Ontario, Canada. Crop Protection 145:105646. https://doi.org/10.1016/j.cropro.2021.105646
  • Type: Theses/Dissertations Status: Published Year Published: 2021 Citation: o Olaoye, D. 2021. Resistance Screening and Association Analysis of Downy Mildew Resistance in Spinach (MS Thesis at Shis and Corrells Lab), University of Arkansas. o Zia, B. 2021a. Genetic Resistance to the Downy Mildew Pathogen and Breeding towards Durable Disease Management in Spinach (PhD Dissertation at Shis lab), University of Arkansas.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: " Awika, H, Cochran, V. Joshi, R. Bedre, K.K. Mandadi, C.A. Avila*. 2020a. Single-marker and haplotype-based association analysis of anthracnose (Colletotrichum dematium) resistance in Spinach (Spinacia oleracea). Plant Breeding 139:402-418. https://doi.org/10.1111/pbr.12773 o Bhattarai, G., A. Shi*, C. Feng, B. Dhillon, B. Mou*, J.C. Correll*. 2020a. Genome-wide association studies in multiple spinach breeding populations refine downy mildew race 13 resistance genes. Frontiers in Plant Science, doi:10.3389/fpls.2020.563187. https://www.frontiersin.org/articles/10.3389/fpls.2020.563187/full. o Bhattarai, G., C. Feng, B. Dhillon, A. Shi, M. Villarroel-Zeballos, J.C. Correll*. 2020b. Detached leaf inoculation assay for evaluating resistance to the spinach downy mildew pathogen. European Journal of Plant Pathology, 158:511520. https://doi.org/10.1007/s10658-020-02096-5 o Clark, K.J., Feng, C., Dhillon, B., Kandel, S.L., Poudel, B., Mou, B., Klosterman, S.J., Correll, J.C.* 2020. Evaluation of spinach cultivars for downy mildew resistance in Yuma, AZ 2020. Plant Disease Management Reports. 14. Article V146. o Dhillon, B., C. Feng, G. Bhattarai, B. Poudel, M. E Matheron, and J. C. Correll*. 2020a. Evaluation of spinach varieties for downy mildew resistance, Yuma, AZ 2019. Plant Disease Management Reports. o Kandel, S.L., A.M. Hulse-Kemp, K. Stoffel, S.T. Koike, A. Shi, B. Mou, A. Van Deynze*, and S.J. Klosterman*. 2020. Transcriptional analyses of resistant and susceptible spinach cultivars in response to the downy mildew pathogen, Peronospora effuse. Scientific Reports 10:6719. https://doi.org/10.1038/s41598-020-63668-3. o Liu, B., L. Stein, K. Cochran, L.J. du Toit, C. Feng, B. Dhillon, and J.C. Correll*. 2020a. Characterization of Leaf Spot Pathogens from Several Spinach Production Areas in the United States. Plant Disease 104(7): 1994-2004. https://doi.org/10.1094/pdis-11-19-2450-re o Spawton, K.A., McGrath, M., and du Toit, L.J. 2020. First report of Stemphylium leaf spot of spinach in New York caused by Stemphylium beticola. Plant Disease 104:3068. https://doi.org/10.1094/PDIS-02-20-0343-PDN o Synoground, T., Batson, A., Derie, M., Koenick, L.B., Pethybridge, S.J., and du Toit, L.J.* 2020. First report of Cercospora leaf spot caused by Cercospora chenopodii on Spinacia oleracea in the USA. Plant Disease 104:976. https://doi.org/10.1094/PDIS-09-19-1924-PDN
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: " Batson, A.*, Spawton, K, Katz, R., and du Toit, L.J. 2022. Cladosporium leaf spot, caused by Cladosporium variabile, in winter high tunnel production of spinach (Spinacia oleracea) in Maine, United States. Plant Disease, Published Online:20 Jul 2022https://doi.org/10.1094/PDIS-11-21-2424-PDN " Bhattarai, G.*, A. Shi*, B. Mou*, and J. Correll*. 2022. Resequencing worldwide spinach germplasm identifies downy mildew field tolerance QTLs and genomic prediction tools. Horticulture Research, Published: 13 September 2022, uhac205, https://doi.org/10.1093/hr/uhac205; https://academic.oup.com/hr/advance-article/doi/10.1093/hr/uhac205/6696976 " Bhattarai, G., D. Olaoye, B. Mou*, J. C. Correll*, A. Shi*. 2022. Mapping and selection of downy mildew resistance locus RPF3 in spinach by low coverage whole genome sequencing. Frontiers in Plant Science (Accepted). " Clark, K.J., Anchieta, A.G., da Silva, M.B., Kandel, S.L., Choi, Y.-J., Martin, F.N., Correll, J.C., Van Denyze, A., Brummer, E.C., and Klosterman, S.J.* 2022. Early detection of the spinach downy mildew pathogen in leaves by recombinase polymerase amplification. Plant Disease. https://doi.org10.1094/PDIS-11-21-2398-RE. " Fletcher, K., Shin, O. H., Clark, K. J., Feng, C., Putman, A.I., Correll, J. C., Klosterman, S. J., Van Deynze, A., Michelmore, R.* 2022. A telomere-to-telomere reference genome assembly for the Peronosporaceae. Molecular Plant Microbe Interactions. https://doi.org10.1094/MPMI-09-21-0227-R " Joshi, V.*, A. Shi*, A.K Mishra, H. Gill, and J. DiPiazza. 2022. Genetic dissection of nitrogen induced changes in the shoot and root biomass in spinach. Scientific Reports (2022) 12:13751 | https://doi.org/10.1038/s41598-022-18134-7 " Rueda, D., H.O. Awika, R. Bedre, D.R. Kandel, K.K. Mandadi, K. Crosby, C.A. Avila*. 2022. Phenotypic diversity and association mapping of spinach content in spinach. Frontiers in Genetic. 12:752313. https://doi.org/10.3389/fgene.2021.752313 " Shi, A.*, G. Bhattarai, H. Xiong, A. Carlos*, C. Feng, B. Liu, V. J. Joshi, L. Stein*, B. Mou*, L.J. du Toit*, J.C. Correll*. 2022. Genome-wide association study and genomic prediction of white rust resistance in USDA GRIN Spinach Germplasm. Horticulture Research, Volume 9, 2022, uhac069, https://doi.org/10.1093/hr/uhac069.
  • Type: Journal Articles Status: Other Year Published: 2022 Citation: " Bhattarai, G., Liu, B., Shi, A.*, Correll, J.C*. 2022b. Genome-wide association analysis and genomic selection of Stemphylium vesicarium leaf spot resistance in USDA spinach germplasm. Preparing to submit in Frontiers in Plant Science, in an internal review. " Gyawali, S., & L.J. du Toit*, et al. 2022. Identification of major QTLs associated with Fusarium wilt resistance in wild spinach, Spinacia turkestanica (in preparation). " Feng, C., K. Lamour, B.D.S, Dhillon, M.I. Villarroel-Zeballos, V.L. Castroagudin, B. Liu, B.H. Bluhm, A. Shi, A. Rojas, and J.C. Correll*. 2022. Genetic diversity of the spinach downy mildew pathogen based on hierarchical sampling (https://www.biorxiv.org/content/10.1101/2020.02.18.953661v1). " Olaoye, D., A. Shi*, J.C. Correll* et al. 2022a. Resistance Characterization to the Downy Mildew Pathogen in Spinach (Preparation for Euphytica). " Olaoye, D., A. Shi*, J.C. Correll* et al. 2022b. Genome-wide association study and genomic prediction of resistance to downy mildew race 15 in spinach (preparation for Frontiers in Plant Science). " Zia, B., B. Dhillon, C. Feng, J.C. Correll*, and A. Shi*. 2022. Gene expression profiling to identify genes associated with resistance to the downy mildew pathogen Peronospora effusa in spinach (in preparation).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Bhattarai, G., A. Shi, B. Mou and J.C. Correll. 2022. Molecular Breeding Effort Using Genome Resequencing in Spinach for Resistance to Economically Important Pathogens. 2022 ASHS annual conference July 30  August 3, Chicago, IL. https://ashs.confex.com/ashs/2022/meetingapp.cgi/Paper/37526
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: " Awika, H, R. Bedre, J. Yeom, T.G. Marconi, J. Enciso, K.K. Mandadi, J. Jung, C.A. Avila*. 2019a. Developing Growth-Associated Molecular Markers via High-Throughput Phenotyping in Spinach. The Plant Genome 12(3):1-19. https://doi.org/10.3835/plantgenome2019.03.0027 " Awika, H.O., T.G. Marconi, R. Bedre, K.K. Mandadi, C.A. Avila*. 2019b. Minor Alleles are Associated with White Rust Susceptibility in Spinach. Horticulture Research 6:129. https://doi.org/10.1038/s41438-019-0214-7 " Bhattarai, G. 2019a. Genetic resistance to the downy mildew pathogen and mapping the RPF resistance loci in spinach (PhD Dissertation at Shis and Corrells lab). Available at: https://scholarworks.uark.edu/etd/3442. " Correll, J. C.*, Feng, F., Matheron, M. E., Koike, S. T. 2019a. Evaluation of spinach varieties for downy mildew resistance, Yuma, AZ, 2018. Plant Disease Management Reports. " Correll, J.C.*, Feng, F., Matheron, M.E., Koike, S. T. 2019b. Evaluation of spinach varieties for downy mildew resistance, Monterey County, CA, 2018. Plant Disease Management Reports. " Dhillon, B.D., C. Feng, G. Bhattarai, B. Wodka, and J.C. Correll* 2019a. Evaluation of spinach varieties for downy mildew resistance, San Juan Bautista, CA 2018. Plant Disease Management Reports 13:V017. " Kandel, S.L., K.V. Subbarao, A. Shi, B. Mou*, and S.J. Klosterman. 2019a. Evaluation of biopesticides for managing downy mildew of spinach in organic production systems 2017 and 2018. Plant Disease Management Report 13: V171. " Kandel, S., B. Mou*, N. Shishkoff, A. Shi, K. Subbarao, and S. Klosterman. 2019b. Spinach downy mildew: Advances in our understanding of the disease cycle and prospects for disease management. Plant Disease 103: 791-803. https://doi.org/10.1094/PDIS-10-18-1720-FE. " Matheron, M. E., J.C. Correll*, M. Porchas, and C. Feng. 2019. Evaluation of fungicides for management of downy mildew of spinach. Plant Disease Management Reports.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: o Feng, C., K. Saito, B. Liu, A. Manley, K. Kammeijer, S.J. Mauzey, S. Koike, and J.C. Correll*. 2018a. New Races and Novel Strains of the Spinach Downy Mildew Pathogen Peronospora effusa. Plant Disease 102:613-618. https://doi.org/10.1094/pdis-05-17-0781-re o Feng, C., B.H. Bluhm, A. Shi, J.C. Correll*. 2018b. Molecular markers linked to three spinach downy mildew disease resistance loci. Euphytica 214: 174. https://doi.org/10.1007/s10681-018-2258-4. o Feng, C., Lamour, K. H., Bluhm, B. H., Sharma, S. Shrestha, S., Dhillon, B. D. S., and Correll, J. C.*. 2018c. Genome sequences resources of three races of Peronospora effusa: a resource for studying the evolution of the spinach downy mildew pathogen. Molecular Plant Molecular Interactions 31 (12):1230-1231. https://doi.org/10.1094/mpmi-04-18-0085-a o Liu, B., C. Feng, M.E. Matheron, and J.C. Correll*. 2018a. Characterization of foliar web blight of spinach, caused by Pythium aphanidermatum, in the desert Southwest of the United States. Plant Disease 102(3):608-612. https://doi.org/10.1094/pdis-06-17-0859-re o She, H., W. Qian, H. Zhang, Z. Liu, X. Wang, J. Wu, C. Feng, J.C. Correll*, and Z. Xu. 2018. Fine mapping and candidate gene screening of the downy mildew resistance gene RPF1 in spinach. Theoretical and Applied Genetics 2018 Dec;131(12):2529-2541. https://doi.org/10.1007/s00122-018-3169-4
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: o Correll, J.C.*, C. Feng, and B. Liu. 2017. First report of white rust (Albugo occidentalis) of spinach in Mexico. Plant Disease 101(3):511. https://doi.org/10.1094/PDIS-06-16-0905-PDN o Correll, J.C.*, C. Feng, M.E. Matheron, and M. Porchas, and S.T. Koike. 2017. Evaluation of spinach varieties for downy mildew resistance. Plant Disease Management Reports 11:V108. " Matheron, M. E., J.C. Correll*, M. Porchas, C. Feng. 2017. Assessment of fungicides for managing downy mildew of spinach, 2017. Plant Disease Management Reports 11:V108. " Qin, J., A. Shi*, B. Mou*, M.A, Grusak, Y. Weng, W. Ravelombola, G. Bhattarai, L. Dong, and W. Yang. 2017. Genetic diversity and association mapping of mineral element concentrations in spinach leaves. BMC Genomics 18:941. https://doi.org/10.1186/s12864-017-4297-y. " Shi, A.*, J. Qin, B. Mou*, J. Correll*, Y. Weng, D. Brenner, C. Feng, D. Motes, W. Yang, L. Dong, and G. Bhattarai, and W. Ravelombola. 2017. Genetic diversity and population structure analysis of spinach by single-nucleotide polymorphisms identified through genotyping-by-sequencing. PLOS ONE, https://doi.org/10.1371/journal.pone.0188745
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Bhattarai, G., and A. Shi. 2021d. Comparative Transcriptome and Proteome Analysis of Resistant and Susceptible Spinach in Response to Downy Mildew Pathogen. 2021 ASHS International Conference, August 5-9, Denver, Colorado. https://ashs.confex.com/ashs/2021/meetingapp.cgi/Paper/35991 " Correll, J., D. Smilde, and A. K�nigs. 2021. Two New Races of Downy Mildew in Spinach, Pfs 18 and Pfs 19. https://vegetableswest.com/2021/04/19/two-new-races-of-downy-mildew-in-spinach/; http://cemonterey.ucdavis.edu/?blogpost=46392&blogasset=32041 " Gyawali, S., G. Bhattarai, A. Shi, C. Kik, and L.J. du Toit. 2021c. Genetic Diversity and population Structure of Spinacia turkestanica, a Wild Progenitor of Cultivated Spinach, Spinacia oleracea. 2021 ASHS International Conference, August 5-9, Denver, Colorado. https://ashs.confex.com/ashs/2021/meetingapp.cgi/Paper/35994
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: " Feng, C., J. Correll, and B. Bluhm. 2017. Characterization and marker development for three resistance loci to the spinach downy mildew pathogen. Phytopathology 107. " Mou, B. 2017a. Spinach breeding at USDA-ARS, Salinas, CA. Mid-year Meeting of the California Leafy Greens Research Program, Salinas, CA, October 10, 2017. " Mou, B. 2017b. Spinach Breeding at USDA-ARS, Salinas, CA, presented to about 150 spinach growers, producers, shippers, processors, researchers, breeders, and other leafy vegetable industry personnel attending the California Leafy Greens Research Program (CLGRP) annual meeting, Pismo Beach, CA, 14 March. " Mou, B. 2017c. Spinach Breeding at USDA-ARS, Salinas, CA, presented to about 40 CLGRP Board members, spinach growers, producers, processors, researchers, and breeders attending the California Leafy Greens Research Program mid-year meeting, Salinas, CA, 10 October.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: " Avila, C.A. 2020a. High throughput phenotyping in Vegetable breeding. Vegetable Breeding Interest Group Workshop. 2020 ASHS Annual Conference, August 9  13 ZOOM meeting https://ashs.confex.com/ashs/2020/meetingapp.cgi/Paper/33980 " Avila C.A. 2020b. Wintergarden field day (Feb 2020). Dr. Avila presented results of white rust resistance evaluation to local producers and spinach industry representatives during field day on February 19th 2020 at Tiro Tres Farms near Crystal City, TX. " Avila, C.A. D. Kandel, and H.O. Awika. 2019. Development of Molecular and Phenotyping Selection Tools for Spinach Breeding. American Society for Horticultural Sciences Annual Meeting, Las Vegas, NV July 21-25. " Awika, H.O., J. Solorzano, U.C Rivera, A. Laredo, J. Enciso, C.A. Avila. 2020b. Using RGB and multispectral sensors to assess growth rate and water use efficiency in spinach. Annual meeting of the American Society for Horticultural Sciences (ASHS). Orlando, Florida. August, 2020 (Virtual Meeting). https://ashs.confex.com/ashs/2020/meetingapp.cgi/Paper/32819. " Batson, A., Gyawali, S., and du Toit, L. 2020. Evaluation of spinach and Beta vulgaris cultivars for differential susceptibility to two pathogenicity groups of Fusarium oxysporum f. sp. spinaciae. Phytopathology 110: In press. Abstract of poster presented at Plant Health 2020 Online, the Annual Meeting of American Phytopathological Society, 10-14 Aug. 2020. " Bhattarai, G., Shi, A., Correll, J. C., and Feng, C. 2020c. Field evaluation and genome-wide association analysis of downy mildew resistance in spinach. HortScience 55, S227. (Abstr.). Available at: https://ashs.confex.com/ashs/2020/meetingapp.cgi/Paper/33056. " Bhattarai, G., Shi, A., and Correll, J. C. 2020d. Identification of genomic regions associated with bolting and flowering time in spinach. HortScience 55, S108. (Abstr.). Available at: https://ashs.confex.com/ashs/2020/meetingapp.cgi/Paper/33055. " Bhattarai, G., Shi, A., Avila, C. A., and Stein, L. A. 2020e. GWAS on USDA Spinach Germplasm Evaluated for Downy Mildew in the Texas Wintergarden Production Area. HortScience 55, S227. (Abstr.). Available at: https://ashs.confex.com/ashs/2020/meetingapp.cgi/Paper/33070. " Bhattarai, G., Liu, B., Shi, A., Feng, C., and Correll, J. C. (2020f). Genome-wide association of leaf spot (Stemphylium vesicarium) resistance in USDA spinach germplasm. HortScience 55, S351. (Abstr.). Available at: https://ashs.confex.com/ashs/2020/meetingapp.cgi/Paper/33054. " Correll, J. C., C. Feng, B.D.S. Dhillo. 2020. Update on downy mildew of spinach. IWGP, Goude, Netherlands, February 4, 2020. " Liu, B., G Bhattarai, A Shi, J Correll, and C. Feng. 2020b. Evaluation of resistance of USDA spinach germplasm to Stemphylium vesicarium, Plant Health 2020 Online, https://apsnet.confex.com/apsnet/2020/meetingapp.cgi/Paper/16594. " Mou, B. 2020. Spinach breeding. California Leafy Greens Research Program Year-end Meeting, March 17, 2020, Virtual. " Olaoye, D., G. Bhattarai, C. Feng, J.C. Correll, and A. Shi. 2020. Genome-Wide Association Study and Genomic Selection for Downy Mildew Resistance in Spinach. 2020 ASHS Annual Conference, August 9  13 ZOOM meetinghttps://ashs.confex.com/ashs/2020/meetingapp.cgi/Paper/33121 " Shi, A., J. Correll, G. Bhattarai, B. Liu, C. Feng, H. Awika, C.A. Avila, and B. Mou. 2020. Evaluation and Genome-wide Association Study for White Rust Resistance in USDA Spinach Germplasm. ASHS 2020 Annual Conference. August 9-13, 2020, Orlando, FL. " Zia, B., and A. Shi. 2020. Differential Gene Expression to Identify Potential Genetic Elements Involved in Disease Resistance to Downy Mildew Pathogen in Spinach Cultivars. 2020 ASHS Annual Conference, August 9  13 at Orlando, Florida. https://ashs.confex.com/ashs/2020/meetingapp.cgi/Paper/33219
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Awika, H., T.G. Marconi, R. Bedre, K.K. Mandadi and C.A. Avila. 2019c. White Rust Resistance in Spinach Is Multigenic and Non-Chromosome Specific. American Society for Horticultural Sciences Annual Meeting, Las Vegas, NV July 21-25. " Bhattarai, G., A. Shi, J.C. Correll, and B. Mou. 2019b. Mapping Resistance to Race of Downy Mildew in Multiple Spinach Populations. 2019 ASA-CSSA-SSSA International Annual Meeting,| Nov. 10-13, San Antonio, Texas. https://scisoc.confex.com/scisoc/2019am/meetingapp.cgi/Paper/122853 " Bhattarai, G., C, Feng, B. Dhillon, A. Shi, and J.C. Correll. 2019c. Evaluation of a Detached Leaf Inoculation Method to Screen for Resistance to Downy Mildew in Spinach. ASHS 2019 Annual Conference. July 21-25, Las Vegas Nevada. https://ashs.confex.com/ashs/2019/meetingapp.cgi/Paper/30872. " Bhattarai, G., A. Shi, J.C. Correll, and B. Mou. 2019d. Mapping of Resistance to Downy Mildew Race 16 in Spinach Cultivar Whale. ASHS 2019 Annual Conference. July 21-25, Las Vegas Nevada. https://ashs.confex.com/ashs/2019/meetingapp.cgi/Paper/30873. " Bhattarai, G., A. Shi, J.C. Correll, C. Feng, B. Dhillon, J. Qin, and B. Mou. 2019e. Field Evaluation, Association Mapping, and QTL Analysis to Dissect Downy Mildew Resistance in Spinach. ASHS 2019 Annual Conference. July 21-25, Las Vegas Nevada. https://ashs.confex.com/ashs/2019/meetingapp.cgi/Paper/30874. " Correll, J. C., C. Feng, B.D.S. Dhillon, A. Shi, B. Liu, G. Bhattarai, and M. Villarroel-Zeballos. 2019c. Economically Important Spinach Diseases: An Evolving Problem. Eucarpia Leafy Greens Meeting. Czech Republic June 22, 2019. " Correll, J. C. 2019d. New races and novel strains of the downy mildew pathogen of spinach. January 5.International Working Group on Peronospora. Goude, Netherlands. " Correll, J. C. 2019e. Emerging diseases of spinach of economic importance. January 12. International Spinach Field Day. Murcia, Spain. " Correll, J. C. 2019f. Epidemiology of spinach downy mildew under tunnel house production. March 3. University of Massachusetts. Amherst, MA. " Dhillon, B., C. Feng, M. Villarroel-Zeballos, V.L. Castroagudin, and J.C. Correll. 2019b. Primary inoculum, etiology, and oospore production of the spinach downy mildew pathogen, Peronospora effusa. Phytopathlogy 108. " Feng, C., K. Lamour, B. Dhillon, M.Villarroel-Zeballos, V.L. Castroagudin, B. Liu, B. Bluhm, A. Shi, A. Rojas, and J. C. Correll. 2019. Genetic diversity of the spinach downy mildew pathogen based on hierarchical sampling. Phytopathology 108. " Gyawali, S., L. du Toit, J.C. Correll, and A. Shi. 2019a. Genome wide association studies of Fusarium wilt resistance in spinach (Spinacia oleracea L.). Poster presented at the American Phytopathological Society (APS) Annual Meeting, Plant Health 2019, 3-7 August 2019, Cleveland, OH. Abstract. https://apsnet.confex.com/apsnet/2019/meetingapp.cgi/Paper/13443. " Gyawali, S., and L. du Toit. 2019b. Spinach Fusarium wilt resistance assessment and mapping of QTL associated with wilt resistance. Western Washington Seed Workshop held at the Washington State University (WSU) Mount Vernon Northwestern Washington Research and Extension Center (NWREC) on 11 January 2019. " Gyawali, S., and L. du Toit. 2019c. Progress of Fusarium wilt components of this spinach SCRI project in the WSU Mount Vernon NWREC Field Day on 11 July 2019. " Kandel, S.L., A. Hulse-Kemp, B. Mou, A. Van Deynze, and S.J. Klosterman. 2019c. Transcriptional analysis of spinach cultivars during resistant and susceptible interactions with the downy mildew pathogen, Peronospora effusa. American Phytopathological Society Annual Meeting, August 3-7, 2019, Cleveland, Ohio. Available: https://apsnet.confex.com/apsnet/2019/meetingapp.cgi/Paper/14429.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Mou, B. 2019a. Spinach breeding. California Leafy Greens Research Program Year-end Meeting, March 19, 2019, Pismo Beach, CA. " Mou, B. 2019b. Spinach production and consumption in the United States. The EUCARPIA Leafy Vegetables International Conference, June 25, 2019, Palacky University in Olomouc, Czech Republic. " Mou, B. 2019c. Genetic variation and improvement of nutritional traits in lettuce and spinach. The EUCARPIA Leafy Vegetables International Conference, June 26, 2019, Palacky University in Olomouc, Czech Republic. " Mou, B. 2019d. Spinach breeding. California Leafy Greens Research Program Mid-Year Meeting, October 8, 2019, Salinas, CA " Olaoye, D., G. Bhattarai, C. Feng, A. Shi, and J. Correll. 2019. Evaluation of Incomplete Dominance in a Spinach Downy Mildew Resistance Locus. 2019 ASA-CSSA-SSSA International Annual Meeting. Nov. 10-13, San Antonio, Texas. https://scisoc.confex.com/scisoc/2019am/meetingapp.cgi/Paper/122831 " Qin, J., A. Shi, J. Correll, C.A. Avila, C. Feng, B. Liu, G. Bhattarai, B. Zia and W. Ravelombola. 2019a. Genome-Wide Association Study and Genomic Selection for White Rust Resistance in Spinach. ASHS 2019 Annual Conference. July 21-25, Las Vegas Nevada. https://ashs.confex.com/ashs/2019/meetingapp.cgi/Paper/30001. " Qin, J., A. Shi, J. Correll, G. Bhattarai, B. Zia, and W. Ravelombola. 2019b. Genome-wide study for white rust resistance in spinach. 2019 Plant & Animal Genomics XXVI on January 12-16, 2019 at San Diego, CA, USA. PE1112 at https://www.intlpag.org/2019/images/pdf/2019/PAGXXVII-abstracts-posters.pdf. " Shi, A., J. Correll, C. Feng, B. Mou, C.A. Avila, L.A. Stein, R. Hogan, L. du Toit, J. Qin, G. Bhattarai, H. Awika, S. Gyawali, and S. Kandel. 2019. Progress at Developing Genetic and Molecular Resources to Improve Spinach Production and Management. HortScience 54, S137. (Abstr.). ASHS 2019 Annual Conference. July 21-25, Las Vegas Nevada. (https://ashs.confex.com/ashs/2019/meetingapp.cgi/Paper/29998). " Smilde, D., and J.C. Correll. 2019. A future-proof differential set for Peronospora effusa in spinach. International Eucarpia Meeting. June 24. Czech Republic. " Spawton, K.A., M.L. Derie, J.C. Correll, L.A. Stein, G. Olaya, R.N. Raid, G.V. Sandoya, T.L. Peever, and L.J. du Toit. 2019. Characterization of Stemphylium spp. from spinach based on molecular data, host response, and azoxystrobin sensitivity. APS annual meeting Cleveland, OH August 3-7.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Avila, C.A. 2018. Texas A&M AgriLife Spinach Breeding Program: Selection tools for cultivar development. Texas A&M AgriLife Research and Extension Center. Uvalde, TX May 11th, 2018. Target audience: Wintergarden producers, extension specialists, and faculty members (Project PI). " Awika, H, T.G. Marconi, J. Enciso, J. Jung, and C.A. Avila. 2018. Development of Molecular Markers Associated to Spinach Growth Parameters. American Society for Horticultural Sciences Annual Meeting, Washington D.C. July 31st to August, 3rd 2018. " Bhattarai, G., B. Zia, W. Zhou, C. Feng, J. Qin, W. Ravelombola, Y. Weng, J. Correll, A. Shi, and B. Mou. 2018a. Field phenotyping and genome wide association analysis for downy mildew resistance in USDA spinach germplasm. 2018 ASHS Annual Conference on July 30-August 3, Washington, DC. https://ashs.confex.com/ashs/2018/meetingapp.cgi/Paper/28214. " Bhattarai, G., B. Zia, W. Zhou, J. Qin, W. Ravelombola, Y. Weng, C. Feng, J. Correll, A. Shi, and B. Mou. 2018b. Development of Genome-wide Simple Sequence Repeat (SSR) Markers in Spinach. 2018 ASHS Annual Conference on July 30-August 3, Washington, DC. https://ashs.confex.com/ashs/2018/meetingapp.cgi/Paper/28558. " Correll, J., C. Feng, and A. Shi. 2018a. White rust: beyond borders. The 2018 International Spinach Conference, 02/14-02/15, 2018 in Murcia, Spain. " Correll, J., and C. Feng. 2018b. Overview of downy mildew disease resistance and race diversity. International Spinach Conference, Murcia, Spain. February 14. " Correll, J.C., C. Feng, D.D.S. Dhillon, A. Shi, K.H. Lamour, B. Liu, G. Bhattarai, V. Castroagudin, and M. Villarroel-Zeballos. 2018c. Spinach downy mildew. Mitigating a conundrum. Soilborne Oomycete International Conference. December 2018. " Deep, B., S. Dhillon, C. Feng, A. Shi, Q. Pan, and J. Correll. 2018 Spinach genome sequence overview including NIL1 and candidate resistance genes. The 2018 International Spinach Conference, 02/14-02/15, 2018 in Murcia, Spain. " Dhillon, B., C. Feng, A. Shi, Q. Pan, J.C. Correll. 2018. Genome sequencing of spinach Near Isogenic Line 1 and candidate resistance genes. International Spinach Conference, Murcia, Spain. February 14. " Feng, C. and J.C. Correll. 2018f. PurGrow: a novel methodology for cleaning seed and managing diseases. International Spinach Conference, Murcia, Spain. February 14. " Feng, C., B. Liu, B. Dhillon, M. Villarroel-Zeballos, B. Bluhm, A. Shi, J. Correll. 2018f. Molecular markers for spinach sex determination gene. The 2018 International Spinach Conference, 02/14-02/15, 2018 in Murcia, Spain. " Lamour, K., K. Shrestha, B. Liu, C. Feng, and J.C. Correll. 2018. Whole genome variation in 2016 field populations of spinach downy mildew. International Spinach Conference, Murcia, Spain. February 14. " Liu, B., C. Feng, and J.C. Correll. 2018b. Evaluation of oospores on spinach seed. International Spinach Conference, Murcia, Spain. February 14. " Mou, B. 2018a. Spinach breeding. California Leafy Greens Research Program Mid-Year Meeting, October 9, 2018, Salinas, CA. " Mou, B. 2018b. Spinach breeding at USDA-ARS, Salinas, CA. Year-end Meeting of the California Leafy Greens Research Program, Pismo Beach, CA, March 27, 2018. " Qin, J., A. Shi, B. Mou, and M. Grusak. 2018a. Phenotypic and genetic diversity and association study of mineral components in spinach. 2018 Plant & Animal Genomics XXVI on January 13-17, 2018 at San Diego, CA, USA. " Qin, J., A. Shi, W. Zhou, Y. Weng, W. Ravelombola, G. Bhattarai, and B. Zia. 2018b. A SNP Set for Spinach Cultivar Determination. 2018b. ASHS Annual Conference on July 30-August 3, Washington, DC. https://ashs.confex.com/ashs/2018/meetingapp.cgi/Paper/28251.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Shi, A. 2018a. Genome-wide association study and genomic selection in spinach. Gust talk on February 23, 2018 at ABI, Arkansas State University, Jonesboro, AR. " Shi, A., J. Qin, Y. Weng, J. Correll, C. Feng, G. Bhattarai, W. Ravelombola, B. Zia, W. Zhou, and B. Mou. 2018b. Genetic diversity, genome-wide association study and genomic selection in spinach. The 2018 International Spinach Conference, 02/14-02/15, 2018 in Murcia, Spain. " Shi, A., J. Qin, Y. Weng, G. Bhattarai, W. Ravelombola, B. Zia, W. Zhou, J. Correll, and B. Mou. 2018c. Genetic diversity and genome-wide association study in spinach. 2018 SR-ASHS conference on February 2-4, Jacksonville, FL. " Shi, A., J. Qin, B. Mou, and J. Correll. 2018d. Phenotypic and genetic diversity of spinach USDA germplasm accessions. 2018 Plant & Animal Genomics XXVI on January 13-17, 2018 at San Diego, CA, USA. " Shi, A., J. Qin , J. Correll, W. Zhou, G. Bhattarai, B. Zia, W. Ravelombola, Y. Weng, C. Feng, B. Liu , C. Avila, and B. Mou. 2018d. Enhance Spinach Development through Molecular Breeding. 2018 ASHS Annual Conference on July 30-August 3, Washington, DC. https://ashs.confex.com/ashs/2018/meetingapp.cgi/Paper/28869. " Shi, A., J. Correll, C. Feng, B. Mou, C. Avila, L. du Toit, L. Stein, R. Hogan, J. Qin, W. Zhou, G. Bhattarai, B. Zia, W. Ravelombola, Y. Weng, B. Liu, S. Gyawali, and S. Kandel. 2018e. Developing Genetic and Molecular Resources to Improve Spinach Production and Management. 2018 ASHS Annual Conference on July 30-August 3, Washington, DC. https://ashs.confex.com/ashs/2018/meetingapp.cgi/Paper/28249. " Shyam, L.K., B. Mou, S. Kunjeti, K. Subbarao, S. Klosterman. 2018. Downy mildew of Spinach: Oospore production, viability, and incidence on seed. International Spinach Conference, Murcia, Spain, February 14-15, 2018. " Villarroel-Zeballos, M., B. Dhillon, C. Feng, and J.C. Correll. 2018. Tissue culture approaches for spinach research on disease resistance. International Spinach Conference, Murcia, Spain. February 14. " Zia, B., G. Bhattarai, C, Feng, W. Zhou, J. Qin, M.I. Villarroel-Zeballos, Y. Weng, W. Ravelombola, Jim Correll, A. Shi, and B. Mou. 2018. Evaluation and Association Analysis of Downy Mildew Resistance in USDA Spinach Germplasm (submitted to 2018 ASHS Annual Conference on July 30-August 3, Washington, DC. https://ashs.confex.com/ashs/2018/meetingapp.cgi/Paper/28047.


Progress 09/01/20 to 08/31/21

Outputs
Target Audience: Nothing Reported Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? A course Hort6033 "Molecular Plant Breeding (Genetic Techniques in Plant Breeding)" has been developed for training students and scientists in molecular breeding at University of Arkansas, Fayetteville. Five postdoctoral research associates have been working on this project: one at Shi's lab, one at Correll's lab, one at Avila's lab, one at Mou's lab and one at du Toit's lab. Two PhD students and one MS student Research Assistant were graduated. How have the results been disseminated to communities of interest?New spinach breeding varieties/lines are available for companies through Material Transfer Agreements (MTAs). SNP markers associated with each of the three diseases, downy mildew, white rust, and Fusarium in spinach have been made available for both public and private sections to use and several manuscripts with the SNP markers have been written and will be published in 2020 and 2021. PCR markers for three alleles of downy mildew resistance and SNP markers associated with the three disease resistance have been and will be published in refereed journals such as Euphytica, Frontiers in Plant Sciences, and BMC Genomics. What do you plan to do during the next reporting period to accomplish the goals? QTL mapping of downy mildew resistance: Two GWAS panels have been phenotyped for downy mildew resistance under field conditions in Salinas CA and Texas Wintergarden area and genotyped by WGR and we will conduct GWAS and GP and identify the SNP markers for downy mildew resistance in the two panels. We plan to add other 3 available F2 populations for identifying QTL of downy mildew resistance. SNP consensus genetic maps of the spinach six genomes: So far, five F2 populations with 960 individuals have been done genotyping using low-coverage WGR. The preliminary analysis showed that although the sequencing results are good but not good enough for us to build an excellent SNP genetic consensus maps for spinach. We would like to add other 3-5 available F2 populations to build an excellent SNP consensus genetic maps in spinach. Selecting and developing downy mildew resistant lines: We will continue selecting and breeding new spinach lines for downy mildew resistance in both the USDA facility in Salinas, CA and University of Arkansas at Fayetteville, AR. Selecting and developing white rust resistant lines: We will continue selecting and breeding new spinach lines for white rust resistance at both the University of Arkansas at Fayetteville, AR and Texas A&M AgriLife Research and Extension Center in Weslaco, TX.

Impacts
What was accomplished under these goals? I. Genetic mapping and SNP marker identification for downy mildew and white rust resistance in spinach Downy mildew evaluation: 70 spinach cultivars were evaluated for disease reactions to downy mildew in two locations at the Salinas Valley in California and at Yuma in Arizona during the winter 2020-2021 season. The data of downy mildew illustrated a wide range in disease incidence form 0.0 to 100% and 30 spinach cultivars showed downy mildew resistance with no disease or <1% disease incidence. The 70 spinach cultivars were evaluated their reactions to downy mildew races and >10 spinach cultivars were resistant to each Pfs race, respectively (Dotun et al. 2020, 2021; Feng et al. 2021). Downy mildew resistance QTL/ gene mapping and genome-wide association study (GWAS): Several F2 populations segregating from Whale, Boeing, Califlay, Campania, Lazio, NIL1, NIL3, NIL6 crossed with Viroflay were phenotyped for resistance against Pfs 5 and Pfs 18. Two F2 populations (190 progenies plus two parents each) segregating from Whale and Lazio crossed with Viroflay have been phenotyped using Pfs 5 and Pfs 18 and genotyped using low-coverage whole genome resequencing (WGR) at TAMU Bioinformatics Center to generate high-density SNP markers for the F2 progenies. A F2 population with 192 individuals derived from Califlay x Viroflay were phenotyped using Pfs5. Genotyping will be performed using low-coverage WGR in TAMU Bioinformatics center. SNP markers will be identified for Pfs 5 resistance in Califlay (Olaoye 2021 MS Thesis; 2021b). . GWAS performed under greenhouse/growth chamber condition for resistance to Pfs 5 in 251 genotypes including 216 USDA spinach germplasm accessions and 35 commercial hybrids/cultivars; the major QTL/alleles was mapped near the previously mapped region on chr. 3; 7 out of 8 SNP markers were strongly associated with downy mildew resistance and the prediction accuracy (r-value) was 0.81 - 0.90 when 8 SNP markers were used (Olaoye 2021 MS Thesis; Olaoye, Shi, Correll et al 2021c; Olaoye et al 2020). GWAS and Genomic prediction (GP) for white rust resistance in USDA spinach germplasm: Around 400 USDA spinach accessions were evaluated for their white rust reactions in the Del Monte White Rust Nursery in Crystal City, Texas for four years during the winter seasons from 2015 to 2020. There were 23 accessions showed white rust resistance. Nine SNPs, located at chrs 2, 3, 4, and 6 were associated with white rust resistance. GP was estimated for white rust resistance in the panel. High genomic prediction accuracy were observed with r value >=0.82 when used 13,235 SNPs; r >=0.73 used 40 SNP marker set; and r >=0.59 in 9 SNP marker set estimated by Bayesian Lasso (BL) model (Shi et al. 2021). Another set of 322 USDA spinach accessions were screened for white rust resistance at both Rio Grande Valley and Wintergarden, TX during winter 2020-2021. Genotyping by whole genome resequencing (WGR) with 10 x genome size (~10 Gb short-read sequencing data each spinach line) has been done for this panel at BGI. II. Evaluation, QTL and association mapping and SNP marker identification for Fusarium wilt resistance in spinach Fusarium wilt resistance evaluation: 68 spinach commercial cultivars and 48 breeding lines from the University of Arkansas evaluated for resistance, AK17, AK6, and AK25 were partially resistant to Fos (Gyawali et al. 2021). Evaluation, GWAS and GP of Fusarium wilt resistance in wild spinach species S. turkestanica: 75 S. turkestanica accessions were obtained from The Centre for Genetic Resources in the Netherlands (CGN), Wageningen University and Research (WUR). The accessions were phenotyped for Fusarium wilt resistance and genotyped with genotyping-by-sequencing (GBS). The GWAS revealed a major QTL on chromosome 6 and minor QTLs on each of chromosomes 1 and 3 for Fusarium wilt resistance and 33 associated SNP markers were also identified. The prediction accuracy (r-value) was >0.6 based on six GP models. II. Introgression of downy mildew and white rust resistance into spinach lines with diverse leaf quality characteristics to satisfy market demand Crosses were made among cultivars with different downy mildew-resistant genes to combine their resistances. Progenies from 34 crosses, along with resistant and susceptible controls, were planted in fields at the USDA-ARS station in Salinas, CA. We have made steady progress in downy mildew resistance through the cycles of recurrent selection. For example, in 2019, ten populations had 0%, and another five populations had < 10% downy mildew incidences, as compared to the susceptible control ('Viroflay') with 98% disease incidence. That is compared to 2018, when only one population had 0% and another five populations had <10% downy mildew incidence. The 2019 populations are progenies of the plants selected from the 2018 populations. Of the 16 populations with data from both 2018 and 2019 seasons, 12 populations (75%) showed decreases of downy mildew incidences, 3 populations had a small increase, and only one population had a large increase in disease incidence. Six of the 16 populations dropped downy mildew incidences to 0%. These results show that the recurrent selection method was very effective to increase the downy mildew resistance in the spinach populations. If the downy mildew resistance is confirmed in future trials, these populations can be released to seed companies to produce seeds or develop new cultivars. For white rust, over 50 spinach lines were evaluated their white rust resistance in the field of Crystal City, TA and showed these lines are white rust resistant; and 30 crosses have been made between AR spinach lines with white rust resistance with commercial spinach cultivars with downy mildew resistance in order to release cultivars resistant to both diseases. Thirty advanced spinach breeding with white rust resistance were selected. 66 spinach lines have been released to Bowery Farming; 20 lines to 80 Acres Farms, and 30 lines to Clemson University for spinach production testing. IV. Construction of high density SNP consensus genetic maps of six chromosomes in spinach using whole genome resequencing Ten F2 populations were developed from Viroflay, a spinach cultivar with high susceptibility to all three diseases of downy mildew, white rust, and Fusarium wilt, crossed to ten other spinach lines including seven downy mildew resistant lines (Lazio, Whale, Boeing, Califlay, Campania, NIL1, and NIL3), two white rust resistant lines (F415 and F380), and one Fusarium wilt resistant line (AS101512F). So far, five F2 populations with a total of 960 F2 individuals were phenotyped and genotyped using low-coverage WGR in Texas A&M Bioinformatics Center. Over half million SNPs were identified in the seven F2 populations. The consensus genetic maps of the spinach six genomes has been analyzing and it is expected that the genetic maps will be constructed by the in the end of 2021 or early 2022. V. Extension Spinach field days for downy mildew disease: Jim Correll organized the Spinach Field Days on March 15, 2021 at Yuma, AZ; and at University of Massachusetts Amherst, UMass Extension on Jan 28, 2021 ( https://extension.arizona.edu/2021-downy-mildew-field-day; https://ag.umass.edu/vegetable/events/field-day-winter-greens-diseases-variety-trials). Spinach field day in Texas: The field day was organized by Larry Stein on February 25, 2021 at Tiro Tres Farms, Crystal City, TX with the presence of more than 50 producers and spinach industry representatives. Field days include fungicide trials against white rust and anthrachnose. In addition, results were presented including white rust disease evaluation trials on commercial and USDA accessions, Stemphylium evaluation, and commercial cultivar trials.

Publications

  • Type: Journal Articles Status: Published Year Published: 2021 Citation: 1. Awika, H.O., A.K. Mishra, H. Gill, J. DiPiazza, C.A. Avila*, and V. Joshi*. 2021a. Selection of Nitrogen Responsive Root Architectural Traits in Spinach Using Machine Learning and Genetic Correlations. Scientific Reports 11:9536 2. Awika, H.O., J. Solorzano, U.C. Rivera, A. Shi, J. Enciso, and C.A. Avila*. 2021b. Prediction modeling for yield and water-use efficiency in spinach using remote sensing via an unmanned aerial system. Smart Agriculture Technology 1 (2021) 100006. 3. Bhattarai, G., W. Yang, A. Shi*, C. Feng, B. Dhillon, J.C. Correll*, and B. Mou*. 2021a. Mapping and candidate gene identification of downy mildew race 16 resistance in spinach. BMC Genomics 22-478. 4. Bhattarai, G., A. Shi*, D.R. Kandel, N. Solis? -Gracia, J.A. da Silva, and C.A. Avila*. 2021b. Genomewide simple sequence repeats (SSR) markers discovered from whole-genome sequence comparisons of multiple spinach accessions. Scientific Reports, 11, Article number: 9999. 5. Gyawali, S., M.L. Derie, E.W. Gatch, D. Sharma-Poudyal, and L.J. du Toit. 2021a. Lessons from 10 years of stakeholder adoption of a soil bioassay for assessing the risk of spinach Fusarium wilt. Plant Pathology 70 (4):778-792. 6. Liu, B., L. Stein, K. Cochran, L.J. du Toit, C. Feng, and J.C. Correll. 2021. Three New Fungal Leaf Spot Diseases of Spinach in the United States and the Evaluation of Fungicide Efficacy for Disease Management. Plant Disease 105(2):316-323.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: 7. Awika, H.O., T.G. Marconi, R. Bedre, K.K. Mandadi, C.A. Avila*. 2020. Minor Alleles are Associated with White Rust Susceptibility in Spinach. Horticulture Research 6:129. 8. Bhattarai, G., A. Shi*, C. Feng, B. Dhillon, B. Mou*, J.C. Correll*. 2020a. Genome-wide association studies in multiple spinach breeding populations refine downy mildew race 13 resistance genes. Frontiers in Plant Science, doi:10.3389/fpls.2020.563187. 9. Bhattarai, G., C. Feng, B. Dhillon, A. Shi, M. Villarroel-Zeballos, J.C. Correll*. 2020b. Detached leaf inoculation assay for evaluating resistance to the spinach downy mildew pathogen. European Journal of Plant Pathology, 158:511520. 10. Kandel, S.L., A.M. Hulse-Kemp, K. Stoffel, S.T. Koike, A. Shi, B. Mou, A. Van Deynze*, and S.J. Klosterman*. 2020. Transcriptional analyses of resistant and susceptible spinach cultivars in response to the downy mildew pathogen, Peronospora effuse. Scientific Reports 10:6719 11. Liu, B., L. Stein, K. Cochran, L.J. du Toit, C. Feng, B. Dhillon, and J.C. Correll. 2020a. Characterization of Leaf Spot Pathogens from Several Spinach Production Areas in the United States. Plant Disease 104(7): 1994-2004.
  • Type: Journal Articles Status: Accepted Year Published: 2021 Citation: 12. Bhattarai, G., and A. Shi. 2021c. Research advances and prospects of spinach breeding, genetics, and genomics. Vegetable Research (accepted). 13. Gyawali, S., G. Bhattarai, A. Shi*, C. Kik, and L. du Toit*. 2021b. Early stages of allopatric speciation in Spinacia turkestanica and the domestication of cultivated spinach. Frontiers in Biology (accepted).
  • Type: Theses/Dissertations Status: Published Year Published: 2021 Citation: 14. Zia, B. 2021a. Genetic Resistance to the Downy Mildew Pathogen and Breeding towards Durable Disease Management in Spinach (PhD Dissertation at Shis lab), University of Arkansas. 15. Olaoye, D. 2021. Resistance Screening and Association Analysis of Downy Mildew Resistance in Spinach (MS Thesis at Shi and Corrells lab), University of Arkansas.
  • Type: Journal Articles Status: Under Review Year Published: 2021 Citation: 16. Awika, H.O., A.K Mishra, H. Gill, J. DiPiazza, C.A. Avila*, V. Joshi*. 2021c. Using predictive machine learning and genetic correlations to select root traits for yield of baby spinach grown in a hydroponic system under two nitrogen managements. In preparation for Scientific Reports. 17. Feng, C., K. Lamour, B.D.S, Dhillon, M.I. Villarroel-Zeballos, V.L. Castroagudin, B. Liu, B.H. Bluhm, A. Shi, A. Rojas, and J.C. Correll*. 2021. Genetic diversity of the spinach downy mildew pathogen based on hierarchical sampling (submitted to Phytopathology) (https://www.biorxiv.org/content/10.1101/2020.02.18.953661v1). 18. Olaoye, D., A. Shi*, J.C. Correll* et al. 2021b. Resistance Characterization to the Downy Mildew Pathogen in Spinach (Preparation for Plant Disease). 19. Olaoye, D., A. Shi*, J.C. Correll* et al. 2021c. Genome-wide association study and genomic prediction of resistance to downy mildew race 15 in spinach (preparation for Horticulture Research). 20. Shi, A.*, G. Bhattarai, H. Xiong, A. Carlos*, C. Feng, B. Liu, V. J. Joshi, L. Stein*, B. Mou*, L.J. du Toit*, J.C. Correll*. 2021. Genome-wide association study and genomic prediction of resistance to white rust in USDA spinach germplasm (submitted to Horticulture Research). 21. Zia, B., B. Dhillon, C. Feng, J.C. Correll*, and A. Shi*. 2021b. Gene expression profiling to identify genes associated with resistance to the downy mildew pathogen 13 Peronospora effusa in spinach (preparation for Frontiers in Genetics).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: 22. Bhattarai, G., and A. Shi. 2021d. Comparative Transcriptome and Proteome Analysis of Resistant and Susceptible Spinach in Response to Downy Mildew Pathogen. 2021 ASHS International Conference, August 5-9, Denver, Colorado. https://ashs.confex.com/ashs/2021/meetingapp.cgi/Paper/35991 23. Correll, J., D. Smilde, and A. K�nigs. 2021. Two New Races of Downy Mildew in Spinach, Pfs 18 and Pfs 19. https://vegetableswest.com/2021/04/19/two-new-races-of-downy-mildew-in-spinach/; http://cemonterey.ucdavis.edu/?blogpost=46392&blogasset=32041 24. Gyawali, S., G. Bhattarai, A. Shi, C. Kik, and L.J. du Toit. 2021c. Genetic Diversity and population Structure of Spinacia turkestanica, a Wild Progenitor of Cultivated Spinach, Spinacia oleracea. 2021 ASHS International Conference, August 5-9, Denver, Colorado. https://ashs.confex.com/ashs/2021/meetingapp.cgi/Paper/35994


Progress 09/01/19 to 08/31/20

Outputs
Target Audience:1. Seed company 2. Comsumer 3. Grower Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? A course Hort6033 "Molecular Plant Breeding (Genetic Techniques in Plant Breeding)" has been developed for training students and scientists in molecular breeding at University of Arkansas, Fayetteville and it has been opened the class in Fall 2017 and Fall 2019 and taught by Dr. Shi. Five postdoctoral research associates have been working on this project: one at Shi's lab, one at Correll's lab, one at Avila's lab, one at Mou's lab and one at du Toit's lab. Two PhD students and one MS student Research Assistant were hired and are working at both Shi's and Correll's labs. Dr. Carlos Avila was invited as a panelist in a workshop organized by the Vegetable Breeding interest group of the American Society for Horticultural Sciences (ASHS) during the annual meeting held on August 11th, 2020. Dr. Avila gave a presentation to attendees (online audience) about current efforts in his program to develop and utilize high-throughput phenotyping in vegetable breeding. How have the results been disseminated to communities of interest?New spinach breeding varieties/lines are available for companies through Material Transfer Agreements (MTAs). SNP markers associated with each of the three diseases, downy mildew, white rust, and Fusarium in spinach have been made available for both public and private sections to use and several manuscripts with the SNP markers have been written and will be published in 2020. PCR markers for three alleles of downy mildew resistance and SNP markers associated with the three disease resistance have been and will be published in refereed journals such as Euphytica, Frontiers in Plant Sciences, and BMC Genomics. What do you plan to do during the next reporting period to accomplish the goals? White rust resistance evaluation: Over 400 spinach genotypes from USDA-NPG system collection and developed University of Arkansas and Texas A&M AgriLife breeding programs will be evaluated for white rust resistance at Texas A&M AgriLife Research and Extension Center in Weslaco and Crystal City, TX during 2019-2020 winter. Fusarium wilt resistance evaluation: A draft manuscript on evaluation of spinach Fusarium wilt resistance reactions of 497 spinach genotypes, including 68 cultivars, 374 gene bank accessions, 48 breeding lines from the University Arkansas, and 75 wild species (S. turkestanica) is in internal review. The manuscript will be submitted to a journal this fall of 2020. GWAS of downy mildew, white rust and Fusarium wilt resistance: 480 spinach genotypes have been sequenced using whole genome resequencing (WGR) with 10 x spinach genome size (~10 Gb sequencing data each) will be done and over 10 million SNPs have been identified. The GWAS analysis will be conducted and completed to identify SNP markers associated with downy mildew, white rust and Fusarium wilt resistance in late 2020 and early 2021, respectively. QTL mapping of downy mildew resistance: The five F2 populations segregating from Boeing, Califlay, Campania, Lazio, and NIL6 crossed with Viroflay have been phenotyped and they are being genotyped in Texas A&M Bioinformatics Center using low-coverage whole genome resequencing. The downy mildew resistance region will be finely mapped, and tightly linked SNP markers will be developed by the end of 2020. QTL mapping of white rust resistance: Two F2-dereived F2BC1 segregating populations will be evaluated for white rust resistance and QTL mapping during the 2019-2020 winter. QTL mapping of Fusarium wilt resistance: Both phenotying and genotyping for Fusarium wilt resistance in the F2 population of Viroflay x AS10-1512F have been done. The QTL mapping data ara being analyzed, and SNP markers linked to Fusarium wilt resistance will be identified in the fall/winter of 2020. Candidate genes for downy mildew, white rust and Fusarium wilt resistance: RNAseq, isoSeq, and proteomics have been conducting for gene-expression study for resistance to the three disease pathogens. Combining GWAS, QTL mapping, and transcript filing, the candidate genes will be identified for resistance to each of the three diseases pathogen in early 2021. SNP consensus genetic maps of the spinach six genomes: We have started to do low-coverage whole genome resequencing in seven F2 populations with over 1300 plants and it is expected that the SNP consensus genetic maps in spinach will be constructed in early 2021. Selecting and developing downy mildew resistant lines: We will continue selecting and breeding new spinach lines for downy mildew resistance in both the USDA facility in Salinas, CA and University of Arkansas at Fayetteville, AR. Selecting and developing white rust resistant lines: We will continue selecting and breeding new spinach lines for white rust resistance at both the University of Arkansas at Fayetteville, AR and Texas A&M AgriLife Research and Extension Center in Weslaco, TX. QTL mapping for spinach biomass: A GWAS has been completed for mapping QTLs for spinach biomass in greenhouse trials. A draft manuscript has been developed on GWAS of spinach biomass of spinach and will be submitted to a journal this fall/winter 2020.

Impacts
What was accomplished under these goals? I. Genetic mapping and SNP marker identification for downy mildew and white rust resistance in spinach Downy mildew evaluation: (i) a total of 70 spinach cultivars were evaluated for disease reactions to downy mildew at Yuma in Arizona during the winter 2019-2020. The data of downy mildew illustrated the wide range in disease incidence with 0.0 to 61.7%. Forty-seven spinach cultivars had no disease or less than 1% disease incidence (Clark et al. 2020). (ii) The 70 spinach cultivars were also evaluated with Pfs isolate 01E (race 18) under greenhouse condition and 31 cultivars showed downy mildew resistance (Dotun et al. 2020). (iii) 300 spinach USDA association panel was evaluated for downy mildew disease response under field condition in the Texas Wintergarden area, TX. Downy mildew resistance gene mapping: (i) The downy mildew resistance gene alleles were mapped to chromosome (chr) 3 with a 0.5 M region for downy mildew pathogen Peronospora effusa race Pfs 13 in spinach hybrids T-Bird, Swan, Squirrel, and Tonga (Bhattarai et al. 2020a) and for Pfs 16 resistance in the population derived from Whale and Lazio (Bhattarai et al. 2020b). (ii) Four F2 populations segregating from Boeing, Califlay, Campania, and Lazio crossed with Viroflay are being genotyped to generate high-density SNP markers for the F2 progenies. Genome-wide association study for downy mildew resistance: Genome-wide association analysis has been performed using genotyping by sequencing (GBS) generated SNP marker, and the multi-year and multi-location downy mildew disease response data in 400 spinach germplasm lines (Bhattarai et al. 2019). White rust resistance evaluation: Around 300 spinach lines were evaluated at the Rio Grande Valley and Wintergarden during winter 2018-2019 and 2019-2020 seasons. White rust disease incidence and severity were performed at two time points during the season but USDA lines were planted in Weslaco, TX. Mild Downy mildew symptoms were observed at the beginning of the season. Unfortunately, symptoms did not develop to be able to score for resistance. Genome-wide association study (GWAS) for white rust resistance: (i) GWAS was conducted for white rust resistance in 356 USDA germplasm accession using 9,010 SNPs with high quality postulated from ddRADseq based on the Spov2 genome reference. Twenty-one SNPs were associated with white rust resistance with the LOD value >2.0 (2.19 to 4.68) using MLM model (Shi et al. 2020). (ii) Minor alleles were identified to be associated with white rust susceptibility in spinach (Awika et al. 2019a) and a new phenotyping was developed to do white rust phenotyping in the field (Awika et al. 2019b). II.Evaluation, QTL and association mapping and SNP marker identification for Fusarium wilt resistance in spinach 1. Fusarium wilt resistance evaluation: A total of 68 commercial cultivars was evaluated for Fusarium wilt resistance in spinach in a greenhouse. Bandicoot, Serpens, Galah, Sheep, Spoonbill, Kodiak, PV1452, Baboon, and Minkar showed very strong resistance to inoculum consisting of a mix of three isolates of F. oxysporum f. sp. spinaciae (Fos). 2. QTL mapping of Fusarium wilt resistance: A bi-parental spinach population derived from the susceptible cultivar Viroflay and the partially resistant line AS10-1512F was phenotyped for severity of Fusarium wilt. From this, 192 genotypes of Viroflay/AS10-1512F (including the parents) were sequenced at Texas A&M University, TX, using whole genome sequencing. 3. GWAS for Fusarium wilt resistance: The reactions of 351 USDA spinach accessions to a mixture of three Fos isolates (Fus058, Fus254, and Fus322) representing two pathogenicity groups of the fungus, were utilized for a GWAS of spinach Fusarium wilt resistance. In total, 46 resistance QTLs were discovered on six chromosomes, of which 11 QTL were detected in multiple evaluations of Fos resistance ratings. III.Introgression of downy mildew and white rust resistance into spinach lines with diverse leaf quality characteristics to satisfy market demand Progenies from 34 crosses, along with resistant and susceptible controls, were planted in a field at the USDA-ARS station in Salinas, CA on September 10, 2019. Ten populations had 0%, and another five populations had < 10% downy mildew incidences, as compared to the susceptible control ('Viroflay') with 98% disease incidence. The 2019 populations are progenies of the plants selected from the 2018 populations. Of the 16 populations, 12 populations (75%) showed decreases of downy mildew incidences, 3 populations had a small increase, and only one population had a large increase in disease incidence. Six of the 16 populations dropped downy mildew incidences to 0%. These results show that the recurrent selection method was very effective to increase the downy mildew resistance in the spinach populations. Resistant plants were selected from each of the 34 breeding populations and transplanted into our isolators for open-pollination. Seeds produced will be used for the next round of selection in the field. For white rust, 20 crosses have been made between AR spinach lines with white rust resistance with commercial spinach cultivars with downy mildew resistance in order to release cultivars resistant to both diseases. Ten advanced spinach breeding lines with white rust resistance were selected. Twenty new crosses between Arkansas white rust resistant, USDA white rust resistant, and susceptible lines with different leaf characteristics were made. In addition, five segregating F2 populations between the cross of resistant and susceptible white rust breeding lines were developed for cultivar development and marker validation. IV.Construction of high density SNP consensus genetic maps of six chromosomes in spinach using whole genome resequencing Ten F2 populations derived from Viroflay, a spinach cultivar with high susceptibility to all three diseases of downy mildew, white rust, and Fusarium wilt, crossed to 10 other spinach lines with resistance to downy mildew, white rust, and/or Fusarium wilt. Whole genome resequencing is been conducted for seven F2 populations (Viroflay x Lazio, Viroflay x Campania, Viroflay x Boeing, Viroflay x Califlay, Viroflay x NIL6, Viroflay x AR08-380, and Viroflay x AS10-1512F) with a total of over 1300 F2 individuals in 2020, and the SNP consensus genetic maps of the spinach six genomes will be constructed in early 2021. V. Extension Spinach field days for downy mildew disease: Dr. Jim Correll organized the multiple stakeholder Spinach Field Days in Yume, AZ in February 26, 2020 Extension and outreach for white rust: Dr. Carlos and Dr. Stein have built two new white rust screening plots (nursery) at the Rio Grande Valley planted and in Wintergarden area of TX planted during 2018-2019 and 2019-2020 seasons. The new white evaluation nursey allowed us to screen more spinach lines at multiple locations. Outreach included a spinach grower/industry meetings to discuss the various spinach white rust and other disease challenges being faced in the Wintergarden region of TX including Stemphylium leaf spot and Anthracnose. Spinach field day in Texas: A field day was organized by Dr. Stein on February 19th 2020 at Tiro Tres Farms near Crystal City with the presence of more than 50 producers and spinach industry representatives. Field day include fungicide trials against white rust and anthrachnose. In addition, commercial cultivars were demonstrated to attendees. Dr. Avila also gave a talk about spinach white rust evaluation to local producers and spinach industry representatives in the field day. Extension and outreach related to Fusarium wilt: Several presentations on spinach research were given at the Western Washington Seed Workshop and 75th Annual Meeting of the Puget Sound Seed Growers' Association (PSSGA) at the WSU Mount Vernon Northwestern Washington Research and Extension Center (NWREC) on Jan 10, 2020.

Publications

  • Type: Journal Articles Status: Published Year Published: 2020 Citation: 1. Bhattarai, G., A. Shi*, C. Feng, B. Dhillon, B. Mou*, J.C. Correll*. 2020a. Genome-wide association studies in multiple spinach breeding populations refine downy mildew race 13 resistance genes. Frontiers in Plant Science (Accepted). 2. Bhattarai, G., W. Yang, A. Shi*, C. Feng, B. Dhillon, J.C. Correll*, and B. Mou*. 2020b. High resolution mapping and candidate gene identification of downy mildew race 16 resistance in spinach. Submitted to BMC Genomics. 3. Bhattarai, G., C. Feng, B. Dhillon, A. Shi, M. Villarroel-Zeballos, J.C. Correll*. 2020c. Detached leaf inoculation assay for evaluating resistance to the spinach downy mildew pathogen. European Journal of Plant Pathology, Published: 11 August 2020 (https://doi.org/10.1007/s10658-020-02096-5). 4. Clark, K.J., C. Feng; B. Dhillon; S.L. Kandel; B. Poudel; B. Mou; S.J. Klosterman; J.C. Correll* 2020. Evaluation of spinach cultivars for downy mildew resistance in Yuma, AZ 2020. Plant Disease Management Reports14:V146. 5. Feng, C., K. Lamour, B.D.S, Dhillon, M.I. Villarroel-Zeballos, V.L. Castroagudin, B. Liu, B.H. Bluhm, A. Shi, A. Rojas, and J.C. Correll*. 2020. Genetic diversity of the spinach downy mildew pathogen based on hierarchical sampling (submitted to Phytopathology) (https://www.biorxiv.org/content/10.1101/2020.02.18.953661v1). 6. Kandel, S.L., A.M. Hulse-Kemp, K. Stoffel, S.T. Koike, A. Shi, B. Mou, A. Van Deynze*, and S.J. Klosterman1*. 2020. Transcriptional analyses of resistant and susceptible spinach cultivars in response to the downy mildew pathogen, Peronospora effuse. Scientific Reports 10:6719 | https://doi.org/10.1038/s41598-020-63668-3.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: 1. Awika, H.O., T.G. Marconi, R. Bedre, K.K. Mandadi, C.A. Avila*. 2019a. Minor alleles are associated with white rust (Albugo occidentalis) susceptibility in spinach (Spinacia oleracea). Nature Horticulture Research 6:129 (https://doi.org/10.1038/s41438-019-0214-7). 2. Awika, H, R. Bedre, J. Yeom, T.G. Marconi, J. Enciso, K.K. Mandadi, J. Jung, C.A. Avila*. 2019b. Developing growth-associated molecular markers via high-throughput phenotyping in spinach. The Plant Genome Journal 12(3):1-19 (http://doi.org/10.3835/plantgenome2019.03.0027). 3. Mou, B. 2019. USDA Red spinach. HortScience 54:2070-2072. https://doi.org/10.21273/HORTSCI14308-19 (Cover story).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: 1. 1. Ainong Shi, James C. Correll, Gehendra Bhattarai, Bo Liu, Chunda Feng, Henry O. Awika, Carlos A. Avila, and Beiquan Mou. 2020. Evaluation and Genome-Wide Association Study for White Rust Resistance in USDA Spinach Germplasm. 2020 ASHS Annual Conference. https://ashs.confex.com/ashs/2020/meetingapp.cgi/Paper/32849. 2. Avila Carlos. 2020. Wintergarden field day (Feb 2020). Dr. Avila presented results of white rust resistance evaluation to local producers and spinach industry representatives during field day on February 19th 2020 at Tiro Tres Farms near Crystal City, TX. 3. Batson, A., Gyawali, S., and du Toit, L. 2020. Evaluation of spinach and Beta vulgaris cultivars for differential susceptibility to two pathogenicity groups of Fusarium oxysporum f. sp. spinaciae. Phytopathology 110:in press. Abstract of poster presented at Plant Health 2020 Online, the Annual Meeting of American Phytopathological Society, 10-14 Aug. 2020. 4. Dotun Olaoye, Gehendra Bhattarai, Chunda Feng, Ainong Shi and Jim Correll. 2019. Evaluation of Incomplete Dominance in a Spinach Downy Mildew Resistance Locus. 2019 ASA-CSSA-SSSA International Annual Meeting | Nov. 10-13 | San Antonio, Texas. https://scisoc.confex.com/scisoc/2019am/meetingapp.cgi/Paper/122831 5. Dotun Olaoye, Gehendra Bhattarai, Chunda Feng, James C. Correll and Ainong Shi. 2020. Genome-Wide Association Study and Genomic Selection for Downy Mildew Resistance in Spinach. 2020 ASHS Annual Conference, August 9  13 ZOOM meetinghttps://ashs.confex.com/ashs/2020/meetingapp.cgi/Paper/33121 6. Gehendra Bhattarai, Ainong Shi, James C. Correll, Chunda Feng, and Beiquan Mou. 2020d. Field Evaluation and Genome-Wide Association Analysis of Downy Mildew Resistance in Spinach. 2020 ASHS Annual Conference, August 9  13 ZOOM meetinghttps://ashs.confex.com/ashs/2020/meetingapp.cgi/Paper/33056 7. Gehendra Bhattarai, Ainong Shi, James C. Correll, and Bindu Poudel. 2020e. Identification of Genomic Regions Associated with Bolting and Flowering Time in Spinach. 2020 ASHS Annual Conference, August 9  13 ZOOM meetinghttps://ashs.confex.com/ashs/2020/meetingapp.cgi/Paper/33055 8. Gehendra Bhattarai, Bo Liu, Ainong Shi, Chunda Feng and James C. Correll. 2020f. Genome-wide association of leaf spot (Stemphylium vesicarium) resistance in USDA spinach germplasm. 2020 ASHS Annual Conference, August 9  13 ZOOM meetinghttps://ashs.confex.com/ashs/2020/meetingapp.cgi/Paper/33054
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: 9. Gyawali, S., and L. du Toit. 2019. Spinach Fusarium wilt resistance assessment and mapping of QTLs associated with wilt resistance. Western Washington Seed Workshop and 75th Annual Meeting of the Puget Sound Seed Growers Association (PSSGA), Washington State University (WSU) Mount Vernon Northwestern Washington Research and Extension Center (NWREC), 10 January 2020. 10. Gyawali, S., M. Derie, and L. du Toit. 2020. Research updates on Spinach Fusarium wilt resistance and management. Western Washington Small Seed Advisory Committee meeting, WSU Mount Vernon Northwestern NWREC, 2 March 2020. 11. Henry O. Awika1, Jorge Solorzano, Uriel C Rivera, Ayrton Laredo, Juan Enciso, Carlos A. Avila.2020. Using RGB and multispectral sensors to assess growth rate and water use efficiency in spinach. 2020 ASHS Annual Conference, August 9  13 ZOOM meeting. https://ashs.confex.com/ashs/2020/meetingapp.cgi/Paper/32819 12. Avila, Carlos. High throughput phenotyping in Vegetable breeding. Vegetable Breeding Interest Group Workshop. 2020 ASHS Annual Conference, August 9  13 ZOOM meeting https://ashs.confex.com/ashs/2020/meetingapp.cgi/Paper/33980 13. Gehendra Bhattarai, Ainong Shi, James C Correll and Beiquan Mou. 2019. Mapping Resistance to Race of Downy Mildew in Multiple Spinach Populations. 2019 ASA-CSSA-SSSA International Annual Meeting | Nov. 10-13 | San Antonio, Texas. https://scisoc.confex.com/scisoc/2019am/meetingapp.cgi/Paper/122853 14. Jim Correll, Chunda Feng, Braham Dhillon. 2020. Update on downy mildew of spinach IWGP, Goude, Netherlands February 4, 2020 15. Mou, B. 2019. Spinach breeding. California Leafy Greens Research Program Mid-Year Meeting, October 8, 2019, Salinas, CA. 16. Mou, B. 2020. Spinach breeding. California Leafy Greens Research Program Year-end Meeting, March 17, 2020, Virtual.


Progress 09/01/18 to 08/31/19

Outputs
Target Audience:1. Seed company 2. Comsumer 3. Grower Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? A course Hort6033 "Molecular Plant Breeding (Genetic Techniques in Plant Breeding)" has been developed for training students and scientists in molecular breeding at University of Arkansas, Fayetteville and it has been opened the class in Fall 2017 and Fall 2019 and taught by Dr. Shi. Dr. Sanjaya Gyawali, the postdoc in Dr. Toit's lab organized a workshop and taught the population structure and genome wide association studies (GWAS) on 23-24 May 2019 at the WSU Mount Vernon NWREC, where there were ten participants and three observers, including graduate students and professional staff from WSU in the workshop. Dr. Gyawali participated a workshop as the main instructor to teach the population structure and genome wide association studies (GWAS) from 17-22 June 2019 at the International Center for Agricultural Research in Dry Areas (ICARDA), Rabat, Morocco, where there were nineteen participants, including graduate students (PhD and MS), and research scientists (pathologists, breeders, and gene bank managers) from India, Ghana, Rwanda, Tunisia, and Morocco. Five postdoctoral research associates have been working at this project: one at Shi's lab, one at Correll's lab, one at Avila's lab, one at Mou's lab and one at du Toit's lab. Two PhD Students and one MS student as the Research Assistant were hired and are working at both Shi's and Correll's labs. How have the results been disseminated to communities of interest?New spinach breeding varieties/lines are available for companies through Material Transfer Agreements (MTAs). SNP markers associated with each of the three diseases, downy mildew, white rust, and Fusarium in spinach have been made available for both public and private sections to use and several manuscripts with the SNP markers have been written and will be published in 2020. PCR markers for three alleles of downy mildew resistance have been published in Euphytica and Theoretical and Applied Genetics What do you plan to do during the next reporting period to accomplish the goals? Downy mildew resistance evaluation: four F2 populations with 1000 plants will be evaluated for downy mildew resistance in growth chambers at the University of Arkansas, Fayetteville, AR. White rust resistance evaluation: 300 spinach genotypes from USDA-NPG system collection and developed University of Arkansas and Texas A&M AgriLife breeding programs will be evaluated for white rust resistance at Texas A&M AgriLife Research and Extension Center in Weslaco and Crystal City, TX during 2019-2020 winter. Several F2 populations with more than 300 individuals will be evaluated with Fusarium wilt resistance. GWAS of downy mildew, white rust and Fusarium wilt resistance: 480 spinach genotypes have been sequenced using whole genome resequencing (WGR) with 10 x spinach genome size (~10 Gb sequencing data each) will be done by the end of 2019. The GWAS analysis will be conducted and completed to identify SNP markers associated with downy mildew, white rust and Fusarium wilt resistance in 2020, respectively. QTL mapping of downy mildew resistance: We will continuously evaluate 5-10 F2 segregating populations for downy mildew resistance and QTL mapping. QTL mapping of white rust resistance: We will evaluate 2 F2-dereived F2:3 or F2BC1 segregating populations for white rust resistance and QTL mapping. QTL mapping of Fusarium wilt resistance: We will evaluate the F2 population of Viroflay x AS10-1512F for Fusarium wilt resistance and genotyped using whole genome resequencing for QTL mapping. Candidate genes for downy mildew, white rust and Fusarium wilt resistance: RNAseq and isoSeq have been conducting for gene-expression study for resistance to the three disease pathogens. Combining GWAS, QTL mapping, and transcript filing, the candidate genes will be identified for resistance to each of the three diseases pathogen. SNP consensus genetic maps of the spinach six genomes: We have started to do whole genome resequencing with 10x genome size with about 10 Gb sequencing data each in F2 populations and it is expected that the SNP consensus genetic maps in spinach will be constructed in 2020. Selecting and developing downy mildew resistant lines: We will continue selecting and breeding new spinach lines for downy mildew resistance in both the USDA facility in Salinas, CA and University of Arkansas at Fayetteville, AR. Selecting and developing white rust resistant lines: We will continue selecting and breeding new spinach lines for white rust resistance at both the University of Arkansas at Fayetteville, AR and Texas A&M AgriLife Research and Extension Center in Weslaco, TX.

Impacts
What was accomplished under these goals? 1. Genetic mapping and SNP marker identification for downy mildew and white rust resistance in spinach Downy mildew field evaluation: A total of 70 spinach cultivars were evaluated for disease reactions to downy mildew in two locations at the Seminis Vegetable Seeds Research Station in San Juan Bautista in California and at Yuma in Arizona during the winter 2018-2019. The data of downy mildew illustrated the wide range in disease incidence (0.0 to 100%). Thirty spinach cultivars had no disease or less than 5% disease incidence. Downy mildew resistance gene mapping: (i) Phenotyping was done in the population segregating from cultivar Whale and Lazio with P. effusa race 16 in the growth chamber and dew chamber facility. The population was genotyped using genotyping by sequencing (GBS), and association analysis and identified six significant SNP markers. The downy mildew resistance RPF3 locus was mapped to a 0.57 Mb of chromosome (chr) 3 that include four disease resistance gene candidates (Spo12736, Spo12784, Spo12908, and Spo1282) within 2.69-11.28 kb of the peak SNP. (ii) The resistance locus from spinach population segregating from Swan, T-Bird, Squirrel, Tonga inoculated with P. effusa race 13, and to identify associated SNP markers and candidate genes. Association analysis was conducted using GBS markers and identified significant SNPs in 0.39, 0.98, and 1.2 Mb of chr 3. The associated SNPs were within 1-7 kb of the disease resistance genes Spo12719, Spo12905, and Spo12821. White rust resistance evaluation: A total of 240 spinach breeding lines were evaluated again for their white rust resistance at La Pryor, TX and 260 USDA germplasm accessions in Weslaco, TX during the winter 2018-2019. The disease incidence and severity were recorded for the 240 spinach breeding lines. However, no white rust disease was developed in Weslaco, so no data of white rust disease scale were observed for the 260 USDA germplasm accessions. Genome-wide association study (GWAS) for white rust resistance: GWAS was conducted for white rust resistance in 356 USDA germplasm accession using 9,010 SNPs postulated from GBS, three QTL regions on chromosome (chr) 2, one on chr 3, and one on chr 4 were identified to be associated with white rust resistance; and the associated SNP markers in each QTL region were also identified. Gene-expression for resistance to downy mildew pathogen (P. effuse): Transcriptome profile was studies in the downy mildew resistant and susceptible spinach cultivars, Solomon and Viroflay using RNAseq. Both up-regulated and downregulated host gene expression were detected resistance to downy mildew pathogen. 2. Evaluation, QTL and association mapping and SNP marker identification for Fusarium wilt resistance in spinach (1) Fusarium wilt resistance evaluation: A total of 499 spinach genotypes were phenotyped for resistance to Fusarium wilt of spinach in greenhouse trials completed in 2018-19. (2) QTL mapping of Fusarium wilt resistance: A bi-parental spinach population derived from the susceptible cultivar Viroflay and the resistant line AS10-1512F were phenotyped with Fusarium wilt resistance. The genotyping was on the way. (3) GWAS of Fusarium wilt resistance: So far, GWAS has been done in 333 spinach genotypes with 13,692 SNPs. The studies revealed 11 genomic regions/quantitative trait loci (QTL) for Fusarium wilt resistance. The R2 of these QTL ranged from 4.2 to 8.8%. 3. Introgression of downy mildew and white rust resistance into spinach lines with diverse leaf quality characteristics to satisfy market demand For downy mildew, progenies from 34 crosses, along with resistant and susceptible controls, were planted in a field at the USDA-ARS station in Salinas, CA for downy mildew evaluation. Downy mildew disease incidence and severity data were collected for these accessions and the breeding populations. One breeding population had 0%, three populations had < 2%, and five populations had < 10% downy mildew incidences, as compared to the susceptible control ('Viroflay') with 91% disease incidence. Resistant plants were selected from each of the 23 downy mildew-resistant populations and transplanted into our isolators for open-pollination. Seeds produced will be used for the next round of selection in the field. For white rust, 30 crosses have been made between AR spinach lines with white rust resistance with commercial spinach cultivars with downy mildew resistance in order to release cultivars resistant to both diseases. Ten advanced spinach breeding with white rust resistance were selected. Twenty new crosses between Arkansas white rust resistant, USDA white rust resistant, and susceptible lines with different leaf characteristics were made. In addition, five segregating F2 populations between the cross of resistant and susceptible white rust breeding lines was developed for cultivar development and marker validation. 4. Construction of high density SNP consensus genetic maps of six chromosomes in spinach using whole genome resequencing Eleven F2 populations have been developed; whole genome-resequencing have been conducting in 2019 and the SNP consensus genetic maps of the spinach six genomes will be constructed in 2020. 5. Extension Spinach field days for downy mildew disease: Dr, Jim Correll organized the multiple stakeholder Spinach Field Days held with approximately 150 attendees for each meeting. The Spinach Field Days were in Salinas, CA in October 9th, 2019 and in Yuma, AZ on February 20, 2019 (https://ucanr.edu/blogs/blogcore/postdetail.cfm?postnum=31421 and https://desertagsolutions.org/events/377-spinach-field-day). Extension and outreach for white rust: Dr. Carlos and Dr. Stein have built two new white rust screening plots (nursery) at the Rio Grande Valley planted on Nov 30th 2018 and Wintergarden planted Nov 15th 2019 and the new white evaluation nursey will provide us to screen more spinach lines in multiple locations. Outreach included a spinach grower/industry meeting to discuss the various spinach white rust challenges being faced in the Wintergarden region of TX. Extension and outreach for Fusarium wilt: Several talks were presented at the Western Washington Seed Workshop held at the Washington State University (WSU) Mount Vernon Northwestern Washington Research and Extension Center (NWREC) on 11 January 2019; in the WSU Mount Vernon NWREC Field Day on 11 July 2019; and the information was shared with ~125 participants, including growers, students, researchers, extension specialists, and the general public. Spinach extension and outreach activities in Dr. Larry Stein's lab: Larry Stein traveled to California and Washington State on July 7 to 11, 2019 to examine growing practices and seed production fields; (ii) worked with Peterson Brother's Nursery in San Antonio to prepare a leafy greens display for the HEB produce convention for their produce buyers; extension was instrumental in making this happen during an odd time of the year to try to grow leafy greens; and plants delivered 31 July 2019; (iii) held a series of 7 am breakfast meetings with producers to map out strategies for the upcoming growing season on July 22, August 6, and September 2, 16, and 25 in 2019; and (iv) planned a spinach field day in cooperation with Tiro Tres Farms and the Wintergarden Spinach Producers Board in the winter 2018-2019 and now have requested seed from the various seed companies and has planned to do a white rust screening for the various companies in the winter 2019-2020. Economic estimation: Dr. Hogan has been working on review trends and seasonality associated with fresh market spinach in 2018 and spinach varieties to be planted in year 2019.

Publications

  • Type: Journal Articles Status: Published Year Published: 2019 Citation: 1. Awika, H, R. Bedre, J. Yeom, T.G. Marconi, J. Enciso, K.K. Mandadi, J. Jung, C.A. Avila*. 2019. Developing Growth-Associated Molecular Markers Via High-Throughput Phenotyping in Spinach. The Plant Genome Journal 12(3):1-19 http://doi.org/10.3835/plantgenome2019.03.0027 (* Project PI, same in below articles and abstracts/presentations). 2. Awika, H.O., T.G. Marconi, R. Bedre, K.K. Mandadi, C.A. Avila*. 2019. Minor Alleles are Associated with White Rust (Albugo occidentalis) Susceptibility in Spinach (Spinacia oleracea)(Submitted to Nature Horticulture Research) 3. Bhattarai, G., C. Feng*, B. Dhillon, A. Shi*, M. Villarroel-Zeballos, J.C. Correll*. 2019. Evaluation of a detached leaf inoculation method to evaluate downy mildew disease reactions on an International set of spinach differential genotypes (submitted to Plant Disease). 4. Bhattarai, G., A. Shi*, J.C. Correll*. 2019. Mapping resistance to downy mildew race 16 in spinach population (Prepared for Theoretical and Applied Genetics). 5. Bhattarai, G., A. Shi*, J.C. Correll*. 2019. Mapping resistance to downy mildew race 13 in spinach breeding population (Prepared for BMC Genomics). 6. Correll, J. C.*, Feng, F.*, Matheron, M. E., Koike, S. T. 2019. Evaluation of spinach varieties for downy mildew resistance, Yuma, AZ, 2018. Plant Disease Management Reports (submitted). 7. Dhillon, B.D., C. Feng*, G. Bhattarai, B. Wodka, and J.C. Correll* 2019. Evaluation of spinach varieties for downy mildew resistance, San Juan Bautista, CA 2018. Plant Disease Management Reports 13:V017. 8. Feng, C.*, B.H. Bluhm, A. Shi*, J.C. Correll*. 2018. Molecular markers linked to three spinach downy mildew disease resistance loci. Euphytica 214: 174. https://doi.org/10.1007/s10681-018-2258-4. 9. Feng, C.*, K. Lamour, B.D.S, Dhillon, M.I. Villarroel-Zeballos, V.L. Castroagudin, B. Liu, B.H. Bluhm, A. Shi*, A. Rojas, and J.C. Correll*. 2019. Genetic diversities within and among spinach downy mildew isolates (submitted to Scientific Reports). 10. Feng, C.*, Lamour, K. H., Bluhm, B. H., Sharma, S. Shrestha, S., Dhillon, B. D. S., and Correll, J. C.*, Genome sequences resources of three races of Peronospora effusa: a resource for studying the evolution of the spinach downy mildew pathogen. Molecular Plant Molecular Interactions 31 (12):1230-1231. 11. Kandel, S.L., K.V. Subbarao, A. Shi*, B. Mou*, and S.J. Klosterman. 2019. Evaluation of biopesticides for managing downy mildew of spinach in organic production systems 2017 and 2018. Plant Disease Management Report 13: V171. 12. Kandel, S., B. Mou*, N. Shishkoff, A. Shi*, K. Subbarao, and S. Klosterman. 2019. Spinach downy mildew: Advances in our understanding of the disease cycle and prospects for disease management. Plant Disease 103: 791-803. https://doi.org/10.1094/PDIS-10-18-1720-FE. 13. Kandel, S.L., A.M. Hulse-Kemp, K. Stoffel, S.T. Koike, A. Shi*, B. Mou*, A. Van Deynze, and S.J. Klosterman1. 2019. Transcriptional analyses of resistant and susceptible spinach cultivars in response to the downy mildew pathogen, Peronospora effuse (Submitted to Scientific Reports). 14. Matheron, M. E., J.C. Correll*, M. Porchas, and C. Feng.* 2019. Evaluation of fungicides for management of downy mildew of spinach. Plant Disease Management Reports (submitted). 15. She, H., W. Qian, H. Zhang, Z. Liu, X. Wang, J. Wu, C. Feng*, J.C. Correll*, and Z. Xu. 2018. Fine mapping and candidate gene screening of the downy mildew resistance gene RPF1 in spinach. Theoretical and Applied Genetics 2018 Dec;131(12):2529-2541.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Abstracts/Presentations 1. Avila, C.A.* 2018. Texas A&M AgriLife Spinach Breeding Program: Selection tools for cultivar development. Texas A&M AgriLife Research and Extension Center. Uvalde, TX May 11th, 2018. Target audience: Wintergarden producers, extension specialists, and faculty members (*Project PI). 2. Avila, C.A.* D. Kandel, and H.O. Awika. 2019. Development of Molecular and Phenotyping Selection Tools for Spinach Breeding. American Society for Horticultural Sciences Annual Meeting, Las Vegas, NV July 21-25. 3. Awika, H., T.G. Marconi, R. Bedre, K.K. Mandadi and C.A. Avila*. 2019. White Rust Resistance in Spinach Is Multigenic and Non-Chromosome Specific. American Society for Horticultural Sciences Annual Meeting, Las Vegas, NV July 21-25. 4. Awika, H, T.G. Marconi, J. Enciso, J. Jung, and C.A. Avila*. 2018. Development of Molecular Markers Associated to Spinach Growth Parameters. American Society for Horticultural Sciences Annual Meeting, Washington D.C. July 31st to August, 3rd 2018. 5. Bhattarai, G., C, Feng*, B. Dhillon, A. Shi*, and J.C. Correll*. 2019. Evaluation of a Detached Leaf Inoculation Method to Screen for Resistance to Downy Mildew in Spinach. ASHS 2019 Annual Conference. July 21-25, Las Vegas Nevada. https://ashs.confex.com/ashs/2019/meetingapp.cgi/Paper/30872. 6. Bhattarai, G., A. Shi*, J.C. Correll*, and B. Mou*. 2019. Mapping of Resistance to Downy Mildew Race 16 in Spinach Cultivar Whale. ASHS 2019 Annual Conference. July 21-25, Las Vegas Nevada. https://ashs.confex.com/ashs/2019/meetingapp.cgi/Paper/30873. 7. Bhattarai, G., A. Shi*, J.C. Correll*, C. Feng*, B. Dhillon, J. Qin, and B. Mou*. 2019. Field Evaluation, Association Mapping, and QTL Analysis to Dissect Downy Mildew Resistance in Spinach. ASHS 2019 Annual Conference. July 21-25, Las Vegas Nevada. https://ashs.confex.com/ashs/2019/meetingapp.cgi/Paper/30874. 8. Correll, J.C.*, C. Feng*, D.D.S. Dhillon, A. Shi*, K.H. Lamour, B. Liu, G. Bhattarai, V. Castroagudin, and M. Villarroel-Zeballos. 2018. Spinach downy mildew. Mitigating a conundrum. Soilborne Oomycete International Conference. December 2018. 9. Correll, J. C.*, C. Feng*, B.D.S. Dhillon, A. Shi*, B. Liu, G. Bhattarai, and M. Villarroel-Zeballos. 2019. Economically Important Spinach Diseases: An Evolving Problem. Eucarpia Leafy Greens Meeting. Czech Republic June 22, 2019. 10. Dhillon, B., C. Feng*, M. Villarroel-Zeballos, V.L. Castroagudin, and J.C. Correll*. 2019. Primary inoculum, etiology, and oospore production of the spinach downy mildew pathogen, Peronospora effusa. Phytopathlogy 108. 11. Feng, C.*, K. Lamour, B. Dhillon, M.Villarroel-Zeballos, V.L. Castroagudin, B. Liu, B. Bluhm, A. Shi*, A. Rojas, and J. C. Correll*. 2019. Genetic diversity of the spinach downy mildew pathogen based on hierarchical sampling. Phytopathology 108. 12. Gyawali, S., L. du Toit*, J.C. Correll*, and A. Shi*. 2019. Genome wide association studies of Fusarium wilt resistance in spinach (Spinacia oleracea L.). Poster presented at the American Phytopathological Society (APS) Annual Meeting, Plant Health 2019, 3-7 August 2019, Cleveland, OH. Abstract. https://apsnet.confex.com/apsnet/2019/meetingapp.cgi/Paper/13443.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: 13. Gyawali, S., and L. du Toit*. 2019. Spinach Fusarium wilt resistance assessment and mapping of QTL associated with wilt resistance. Western Washington Seed Workshop held at the Washington State University (WSU) Mount Vernon Northwestern Washington Research and Extension Center (NWREC) on 11 January 2019. 14. Gyawali, S., and L. du Toit*. 2019. Progress of Fusarium wilt components of this spinach SCRI project in the WSU Mount Vernon NWREC Field Day on 11 July 2019. 15. Kandel, S.L., A. Hulse-Kemp, B. Mou*, A. Van Deynze, and S.J. Klosterman. 2019. Transcriptional analysis of spinach cultivars during resistant and susceptible interactions with the downy mildew pathogen, Peronospora effusa. American Phytopathological Society Annual Meeting, August 3-7, 2019, Cleveland, Ohio. Available: https://apsnet.confex.com/apsnet/2019/meetingapp.cgi/Paper/14429. 16. Mou, B.* 2018. Spinach breeding. California Leafy Greens Research Program Mid-Year Meeting, October 9, 2018, Salinas, CA. 17. Mou, B.* 2019. Spinach breeding. California Leafy Greens Research Program Year-end Meeting, March 19, 2019, Pismo Beach, CA. 18. Mou, B.* 2019. Spinach production and consumption in the United States. The EUCARPIA Leafy Vegetables International Conference, June 25, 2019, Palacky University in Olomouc, Czech Republic. 19. Mou, B.* 2019. Genetic variation and improvement of nutritional traits in lettuce and spinach. The EUCARPIA Leafy Vegetables International Conference, June 26, 2019, Palacky University in Olomouc, Czech Republic. 20. Qin, J., A. Shi,* J. Correll*, C.A. Avila*, C. Feng*, B. Liu, G. Bhattarai, B. Zia and W. Ravelombola. 2019. Genome-Wide Association Study and Genomic Selection for White Rust Resistance in Spinach. ASHS 2019 Annual Conference. July 21-25, Las Vegas Nevada. https://ashs.confex.com/ashs/2019/meetingapp.cgi/Paper/30001. 21. Qin, J., A. Shi*, J. Correll*, G. Bhattarai, B. Zia, and W. Ravelombola. 2019. Genome-wide study for white rust resistance in spinach. 2019 Plant & Animal Genomics XXVI on January 12-16, 2019 at San Diego, CA, USA. PE1112 at https://www.intlpag.org/2019/images/pdf/2019/PAGXXVII-abstracts-posters.pdf. 22. Shi, A.*, J. Correll*, C. Feng*, B. Mou*, C.A. Avila*, L.A. Stein*, R. Hogan*, L. du Toit*, J. Qin, G. Bhattarai, H. Awika, S. Gyawali, and S. Kandel. 2019. Progress at Developing Genetic and Molecular Resources to Improve Spinach Production and Management. ASHS 2019 Annual Conference. July 21-25, Las Vegas Nevada. (https://ashs.confex.com/ashs/2019/meetingapp.cgi/Paper/29998). 23. Smilde, D., and J.C. Correll*. 2019. A future-proof differential set for Peronospora effusa in spinach. International Eucarpia Meeting. June 24. Czech Republic. 24. Spawton, K.A., M.L. Derie, J.C. Correll*, L.A. Stein*, G. Olaya, R.N. Raid, G.V. Sandoya, T.L. Peever, and L.J. du Toit*. Characterization of Stemphylium spp. from spinach based on molecular data, host response, and azoxystrobin sensitivity. APS annual meeting Cleveland, OH August 3-7.


Progress 09/01/17 to 08/31/18

Outputs
Target Audience: Nothing Reported Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? A course Hort6033 "Genetic Techniques in Plant Breeding" has been developed for training students and scientists in molecular plant breeding at University of Arkansas, Fayetteville. Dr. Avila gave invited guess lecture at Hort404 Plant Breeding undergraduate course. Lecture include molecular breeding techniques to improve efficiency in vegetable crops. Approach and data generated in this project were discussed as examples in the lecture. Department of Horticultural Sciences, Texas A&M University, College Station, TX. April 19th, 2018. During the summer of 2018, Dr. Avila hired an undergraduate intern from Texas State Technical College, Harlingen, TX. A undergraduate was trained on several aspects of conventional and molecular spinach breeding. Five postdoctoral research associates were hired: one at Shi's lab, one at Correll's lab, one at Avila's lab, one at Mou's lab and one at du Toit's lab. Two PhD students were hired, one in each of Shi and Correll's labs. How have the results been disseminated to communities of interest?New spinach breeding varieties/lines are available for companies through Material Transfer Agreements (MTAs). SNP markers associated with white rust resistance in spinach have been made available for seed companies to use. PCR markers for three alleles of downy mildew resistance have been published in Euphytica and Theoretical and Applied Genetics What do you plan to do during the next reporting period to accomplish the goals? Downy mildew resistance evaluation: 400 spinach genotypes will be evaluated again for downy mildew resistance in two stations at Salinas, CA and Yuma, AZ during 2018-2019. We will also evaluate 400 spinach genotypes in growth chambers at the University of Arkansas, Fayetteville, AR. White rust resistance evaluation: 400 spinach genotypes from USDA-NPG system collection and 150 Texas A&M AgriLife breeding lines will be evaluated again for white rust resistance at Texas A&M AgriLife Research and Extension Center in Weslaco, TX during 2018-2019 winter. Approximately 500 more spinach lines will be screened for resistance to Fusarium wilt at the WSU Mount Vernon NWREC in Mount Vernon, WA. GWAS of downy mildew, white rust and Fusarium wilt resistance: 400 spinach genotypes will be sequenced using whole genome resequencing (WGR) and then GWAS analysis will be completed to identify SNP markers associated with downy mildew, white rust and Fusarium wilt resistance in 2019, respectively. QTL mapping of downy mildew resistance: We will evaluate 5-10 F2 segregating populations for downy mildew resistance and QTL mapping. Selecting and developing downy mildew resistant lines: We will continue selecting and breeding new spinach lines for downy mildew resistance in both the USDA facility in Salinas, CA and University of Arkansas at Fayetteville, AR. Selecting and developing white rust resistant lines: We will continue selecting and breeding new spinach lines for white rust resistance at both the University of Arkansas at Fayetteville, AR and Texas A&M AgriLife Research and Extension Center in Weslaco, TX.

Impacts
What was accomplished under these goals? 1. Genetic mapping and SNP marker identification for downy mildew and white rust resistance in spinach Downy mildew field evaluation: Seventy spinach lines were evaluated for downy mildew resistance at the University of Arizona, Yuma Valley Agricultural Center in January to February 2018 and 22 spinach lines showed resistance to downy mildew with disease severity (DS) less than 1% (Correll et al. 2018). A total of 409 spinach genotypes including USDA spinach germplasm, commercial hybrids and varieties and Arkansas lines were evaluated for downy mildew resistance in the USDA downy mildew selection nursery at Salinas, CA and Yuma, AZ with two replicates per line during the winter of 2017-18. Nineteen spinach germplasm lines showed lower disease severity levels less than 5% (Bhattarai et al. 2018a). Downy mildew greenhouse/growth evaluation: Over 300 spinach genotypes were evaluated for downy mildew disease incidence and severity to several Pfs races in growth chamber assays (Feng et al. 2018). Downy mildew resistance inheritance: Nine F2 segregating populations were evaluated for downy mildew resistance. We are evaluating 100-150 seeds from each of the F2 populations to determine the inheritance and map the resistance loci. Molecular markers for downy mildew resistance: Thirteen, two and eight molecular markers have been developed for three loci, RPF1, RPF2 and RPF3, of downy mildew resistance, respectively. One marker was found to be linked to both RPF2 and RPF3 loci, and four markers were linked to all three loci, indicating that these three resistance loci are closely linked (Feng et al. 2018). White rust evaluation: A total of 440 spinach germplasm genotypes were evaluated for resistance to white rust in a white rust nursey at Crystal City, TX and at Texas A&M AgriLife Research and Extension Center in Weslaco, TX during the 2017-18 winter. Of these lines, 52 accessions exhibited resistance to white rust. Genome-wide association study (GWAS) and genome-selection (GS) for white rust resistance: GWAS was conducted for white rust resistance; 20 SNP markers were strongly associated with white rust resistance; 3 SNP markers were validated in companies' spinach lines; and 8 SNP markers can be used as a set for genomic selection with a correlation coefficient (r) = 0.68 between the predicted breeding value and the observed white rust scale in the 162 lines in a validation set when another 250 spinach lines were used as the training set. SSR discovery: Genome-wide SSRs have been discovered and a total of 79,347 SSR loci with minimum numbers of repeats of 6, 5, 4, 4, and 4 were identified, respectively (Bhattarai et al. 2018b). Spinach genetic diversity: A total of 480 spinach genotypes were sequenced using genotype by sequencing (GBS), 343 of which were used to do genetic diversity and population structure analysis in spinach. The results showed that genetic background in improved commercial F1 hybrids and in Arkansas cultivars/lines had different structured populations from the USDA germplasm. In addition, the genetic diversity and population structures were associated with geographic origin. Germplasm from the US Arkansas breeding program had a unique genetic background. These data could provide genetic diversity information and the molecular markers for selecting parents in spinach breeding programs (Shi et al. 2017). 2. Evaluation, QTL and association mapping and SNP marker identification for Fusarium wilt resistance in spinach Progress was made towards developing a growth room facility for completing spinach Fusarium wilt resistance screening trials with controlled photoperiod and temperature at the WSU Mount Vernon NWREC to continue screening spinach germplasm year-round since the long daylength in this region from late spring through early fall does not enable screening spinach in a vegetative stage of growth in the greenhouse. By screening plants in the vegetative state, we can avoid confounding symptoms of Verticillium wilt with those of Fusarium wilt. Fusarium wilt soil bioassay trials were conducted from 2014-2018 to assess risk for >150 spinach seed growers' fields for this disease. The severity of Fusarium wilt was evaluated for 100 spinach genotypes at three soil inoculation levels. The results showed that there was a wide range in susceptibility to Fusarium wilt, and 39 entries had a less severe mean Fusarium wilt index and a lower AUDPC rating than the partially resistant inbred control line. Seed of a total of 514 spinach genotypes have been received at the WSU Mount Vernon NWREC from various spinach germplasm collections, which will comprise the spinach association mapping panel. Fusarium wilt screening is resuming in October 2018 in the greenhouse at this location, as well as in the new growth room completed in September 2018. 3. Introgression of downy mildew and white rust resistance into spinach lines with diverse leaf quality characteristics to satisfy market demand For downy mildew, crosses were made among 15 cultivars with different downy mildew-resistant genes to combine their resistances. Progenies from over 30 crosses were developed and their resistance to downy mildew was evaluated in a field, greenhouse and growth chamber for further selection and crosses. For white rust, 30 crosses have been made between AR spinach lines with white rust resistance with commercial spinach cultivars with downy mildew resistance in order to release cultivars resistant to both diseases. Thirty-two crosses between Arkansas white rust resistant, USDA white rust resistant, and susceptible lines with different leaf characteristics were made. In addition, a segregating F1-2 population between the cross of resistant and susceptible white rust breeding lines was developed for cultivar development and marker validation. The F1, F1-2 lines will be evaluated for resistance at Wintergarden and Weslaco Texas locations during 2018-2019 Winter season. 4. Construction of high density SNP consensus genetic maps of six chromosomes in spinach using whole genome resequencing Eleven F2 populations have been developed; whole genome-resequencing will be conducted in 2019 and the SNP consensus genetic maps of the spinach six genomes will be constructed in 2020. 5. Extension A spinach variety trial was conducted in the Texas Wintergarden area consisting of 84 varieties to screen for tolerance to white rust, downy mildew, Stemphylium leaf spot, and anthracnose. Spinach field days: Mulitple stakeholder Spinach Field Days were held with approximately 100-150 attendees for each meeting. The Spinach Field Days were in Salinas, CA in October 2017 and 2018 and in Yuma, AZ in February 2017 and 2018. In addition, the University of Arkansas organized and hosted the International Spinach Conference in Murcia, Spain in February 2018 - Spinach portal meeting website Outreach included a spinach grower/industry meeting to discuss the various spinach white rust challenges being faced in the Wintergarden region of TX. Dr. Stein held 6 early morning (7:00 am) grower meetings to discuss disease control as well as other management practices. Dr. Avila gave a presentation to producers and industry representatives about Texas A&M breeding program efforts on cultivar development as part of the annual Texas A&M AgriLife Research Station at Uvalde, TX (Wintergarden region of Texas) field day. Presentations on spinach Fusarium wilt were made at the Puget Sound Seed Growers' Annual Meeting in Mount Vernon, WA in Jan. 2018, at the Internat. Spinach Conf. in Spain in Feb. 2018, and at the WSU Mount Vernon NWREC Field Day in July 2018.

Publications

  • Type: Journal Articles Status: Published Year Published: 2018 Citation: 1. Correll, J.C., C. Feng, M.E. Matheron, and M. Porchas, and S.T. Koike. 2017. Evaluation of spinach varieties for downy mildew resistance. Plant Disease Management Reports 11:V108. 2. Correll, J.C., Feng, F., Matheron, M.E., Koike, S. T. 2018. Evaluation of spinach varieties for downy mildew resistance, Monterey County, CA, 2018. Plant Disease Management Reports (submitted). 3. du Toit, L.J., Derie, M.L., and Holmes, B.J. 2018. Evaluation of natamycin seed treatments for Stemphylium, Verticillium, and other fungi on spinach seed, 2017. Plant Disease Management Reports 12:ST003. 4. du Toit, L.J., Derie, M.L., Holmes, B.J., and Batson, A. 2018. Evaluation of natamycin seed treatments for Stemphylium botryosum and other necrotrophic fungi on spinach seed, 2017. Plant Disease Management Reports 12:V050. 5. du Toit, L.J., Derie, M.L., Holmes, B.J., and Correll, J.C. 2018. Evaluation of seed treatments for Colletotrichum dematium, Stemphylium botryosum, and Verticillium dahliae on spinach seed, 2017. Plant Disease Management Reports 12:V051. 6. Feng, F., C. K. Saito, B. Liu, A. Manley, K. Kammeijer, S.J. Mauzey, S. Koike, and J.C. Correll. 2018a. New races and novel strains of the spinach downy mildew pathogen Peronospora effusa. Plant Disease 102:613-618. https://doi.org/10.1094/PDIS-05-17-0781-RE. 7. Feng, C., B.H. Bluhm, A. Shi, and J.C. Correll. 2018b. Molecular markers linked to three spinach downy mildew disease resistance loci. Euphytica (in press). 8. Feng, C., K.H. Lamour, B.H. Bluhm, S. Sharma, S. Shrestha, B.D.S. Dhillon, and J.C. Correll. 2018c. Genome sequences of three races of Peronospora effusa: a resource for studying the evolution of the spinach downy mildew pathogen. Molecular Plant Molecular Interactions https://doi.org/10.1094/MPMI-04-18-0085-A. 9. Matheron, M. E., J.C. Correll, M. Porchas, C. Feng. 2017. Assessment of fungicides for managing downy mildew of spinach, 2017. Plant Disease Management Reports 11:V108. 10. She, H., Qian , W., Zhang , H., Liu, Z., Wang, X., Wu, J., Feng, C., Correll, J. C., and Xu Z. 2018. Fine mapping and candidate gene screening of the downy mildew resistance gene RPF1 in spinach. Theoretical and Applied Genetics (in press). 11. Shi, A., J. Qin, B. Mou, J. Correll, Y. Weng, D. Brenner, C. Feng, D. Motes, W. Yang, L. Dong, and G. Bhattarai, and W. Ravelombola. 2017. Genetic diversity and population structure analysis of spinach by single-nucleotide polymorphisms identified through genotyping-by-sequencing. PLOS ONE, published: November 30, 2017, https://doi.org/10.1371/journal.pone.0188745.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Abstracts/Presentations 12. Batson, A.M., Peever, T.L., and du Toit, L.J. 2018. Determining the genetic basis of pathogenicity of Fusarium oxysporum f. sp. spinaciae on spinach. Internat. Spinach Conf., 14-16 Feb. 2018, Murcia, Spain. https://spinach.uark.edu/spain-presentations/ 13. Batson, A.M., Peever, T.L., and du Toit, L.J. 2018. The Secreted in Xylem gene profile of the spinach Fusarium wilt pathogen. Internat. Congress Plant Pathology, 29 Jul.-5 Aug. 2018, Boston, MA. 14. Deep, B., S. Dhillon, C. Feng, A. Shi, Q. Pan, and J. Correll. 2018 Spinach genome sequence overview including NIL1 and candidate resistance genes. The 2018 International Spinach Conference, 02/14-02/15, 2018 in Murcia, Spain. 15. du Toit, L.J., and Correll, J.C. 2018. Spinach seed production in the Pacific Northwest USA. Invited presentation, Internat, Spinach Conf, 14-16 Feb. 2018, Murcia, Spain. https://spinach.uark.edu/spain-presentations/ 16. du Toit, L.J., and Correll, J.C. 2018. Case studies of the complexity of seedborne and seed transmitted fungi affecting regional and global seed trade. Guest speaker, joint symposium of American Phytopathological Society (APS) and Societ� Italiana di Patologia Vegetale (SIPaV), 24th National Congress of SIPaV, 5-7 Sep. 2018, Ancona, Italy. 17. du Toit, L.J., and Derie, M.L. 2018. Evaluation of natamycin seed treatments for Stemphylium botroyosum and other necrotrophic fungi on spinach seed. Internat. Spinach Conf., 14-16 Feb. 2018, Murcia, Spain. https://spinach.uark.edu/spain-presentations/ 18. Correll, J., C. Feng, and A. Shi. 2018. White rust: beyond borders. The 2018 International Spinach Conference, 02/14-02/15, 2018 in Murcia, Spain. 19. Correll, J., and C. Feng. 2018. Overview of downy mildew disease resistance and race diversity. International Spinach Conference, Murcia, Spain. February 14. 20. Dhillon, B., C. Feng, A. Shi, Q. Pan, J.C. Correll. Genome sequencing of spinach Near Isogenic Line 1 and candidate resistance genes. International Spinach Conference, Murcia, Spain. February 14. 21. Feng, C. and J.C. Correll. 2018. PurGrow: a novel methodology for cleaning seed and managing diseases. International Spinach Conference, Murcia, Spain. February 14. 22. Feng, C., J. Correll, and B. Bluhm. 2017. Characterization and marker development for three resistance loci to the spinach downy mildew pathogen. Phytopathology 107. 23. Feng, C., B. Liu, B. Dhillon, M. Villarroel-Zeballos, B. Bluhm, A. Shi, J. Correll. 2018. Molecular markers for spinach sex determination gene. The 2018 International Spinach Conference, 02/14-02/15, 2018 in Murcia, Spain. 24. Bhattarai, G., B. Zia, W. Zhou, C. Feng, J. Qin, W. Ravelombola, Y. Weng, J. Correll, A. Shi, and B. Mou. 2018a. Field phenotyping and genome wide association analysis for downy mildew resistance in USDA spinach germplasm. 2018 ASHS Annual Conference on July 30-August 3, Washington, DC. https://ashs.confex.com/ashs/2018/meetingapp.cgi/Paper/28214. 25. Bhattarai, G., B. Zia, W. Zhou, J. Qin, W. Ravelombola, Y. Weng, C. Feng, J. Correll, A. Shi, and B. Mou. 2018b. Development of Genome-wide Simple Sequence Repeat (SSR) Markers in Spinach. 2018 ASHS Annual Conference on July 30-August 3, Washington, DC. https://ashs.confex.com/ashs/2018/meetingapp.cgi/Paper/28558.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: 26. Lamour, K., K. Shrestha, B. Liu, C. Feng, and J.C. Correll. 2018. Whole genome variation in 2016 field populations of spinach downy mildew. International Spinach Conference, Murcia, Spain. February 14. 27. Liu, B., C. Feng, and J. C. Correll. 2018. Evaluation of oospores on spinach seed. International Spinach Conference, Murcia, Spain. February 14. 28. Mou, B. 2018. Spinach breeding at USDA-ARS, Salinas, CA. Year-end Meeting of the California Leafy Greens Research Program, Pismo Beach, CA, March 27, 2018. 29. Mou, B. 2017a. Spinach breeding at USDA-ARS, Salinas, CA. Mid-year Meeting of the California Leafy Greens Research Program, Salinas, CA, October 10, 2017. 30. Mou, B. 2017b. Spinach Breeding at USDA-ARS, Salinas, CA, presented to about 150 spinach growers, producers, shippers, processors, researchers, breeders, and other leafy vegetable industry personnel attending the California Leafy Greens Research Program (CLGRP) annual meeting, Pismo Beach, CA, 14 March. 31. Mou, B. 2017c. Spinach Breeding at USDA-ARS, Salinas, CA, presented to about 40 CLGRP Board members, spinach growers, producers, processors, researchers, and breeders attending the California Leafy Greens Research Program mid-year meeting, Salinas, CA, 10 October. 32. Shi, A. 2018. Genome-wide association study and genomic selection in spinach. Guest talk on February 23, 2018 at ABI, Arkansas State University, Jonesboro, AR. 33. Shi, A., J. Qin, Y. Weng, J. Correll, C. Feng, G. Bhattarai, W. Ravelombola, B. Zia, W. Zhou, and B. Mou. 2018a. Genetic diversity, genome-wide association study and genomic selection in spinach. The 2018 International Spinach Conference, 02/14-02/15, 2018 in Murcia, Spain.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: 34. Shi, A., J. Qin, Y. Weng, G. Bhattarai, W. Ravelombola, B. Zia, W. Zhou, J. Correll, and B. Mou. 2018b. Genetic diversity and genome-wide association study in spinach. 2018 SR-ASHS conference on February 2-4, Jacksonville, FL. 35. Shi, A., J. Qin, B. Mou, and J. Correll. 2018. Phenotypic and genetic diversity of spinach USDA germplasm accessions. 2018 Plant & Animal Genomics XXVI on January 13-17, 2018 at San Diego, CA, USA. 36. Shi, A., J. Qin , J. Correll, W. Zhou, G. Bhattarai, B. Zia, W. Ravelombola, Y. Weng, C. Feng, B. Liu , C. Avila, and B. Mou. Enhance Spinach Development through Molecular Breeding. 2018 ASHS Annual Conference on July 30-August 3, Washington, DC. https://ashs.confex.com/ashs/2018/meetingapp.cgi/Paper/28869. 37. Shi, A., J. Correll, C. Feng, B. Mou, C. Avila, L. du Toit, L. Stein, R. Hogan, J. Qin, W. Zhou, G. Bhattarai, B. Zia, W. Ravelombola, Y. Weng, B. Liu, S. Gyawali, and S. Kandel. 2018. Developing Genetic and Molecular Resources to Improve Spinach Production and Management. 2018 ASHS Annual Conference on July 30-August 3, Washington, DC. https://ashs.confex.com/ashs/2018/meetingapp.cgi/Paper/28249. 38. Shi, A., J. Qin, J. Correll, W. Zhou, G. Bhattarai, B. Zia, W. Ravelombola, Y. Weng, C. Feng, B. Liu, and C. Avila. 2018. Genome-wide Association Study and Genomic Selection for White Rust in Spinach. 2018 ASHS Annual Conference on July 30-August 3, Washington, DC. https://ashs.confex.com/ashs/2018/meetingapp.cgi/Paper/28248. 39. Shyam, L.K., B. Mou, S. Kunjeti, K. Subbarao, S. Klosterman. 2018. Downy mildew of Spinach: Oospore production, viability, and incidence on seed. International Spinach Conference, Murcia, Spain, February 14-15, 2018. 40. Villarroel-Zeballos, M., B. Dhillon, C. Feng, and J.C. Correll. 2018. Tissue culture approaches for spinach research on disease resistance. International Spinach Conference, Murcia, Spain. February 14. 41. Zia, B., G. Bhattarai, C, Feng, W. Zhou, J. Qin, M.I. Villarroel-Zeballos, Y. Weng, W. Ravelombola, Jim Correll, A. Shi, and B. Mou. 2018. Evaluation and Association Analysis of Downy Mildew Resistance in USDA Spinach Germplasm (submitted to 2018 ASHS Annual Conference on July 30-August 3, Washington, DC. https://ashs.confex.com/ashs/2018/meetingapp.cgi/Paper/28047. 42. Stein, L.A. 2018. Development of a spinach white rust management strategy in Texas. International Spinach Conference. Murcia, Spain February 14-15 43. Avila, C.A., Juan Enciso, Jinha Jung, Thiago Marconi, and Henry Awika. 2018. Combining high-throughput genotyping and phenotyping to improve spinach breeding efficiency. International Spinach Conference. Murcia, Spain February 14-15 44. Avila, C.A., J Enciso, J Jung, J Kurpis, and TG. Marconi. 2017. Development of a high throughput phenotyping (HTP) system for Spinach breeding. American Society for Horticultural Sciences Annual Meeting, Waikoloa, HI Sept 19-22 45. Avila, C.A., V. Joshi, K. Cochran, D. Leskovar, K. Mandadi. 2017. Improving Spinach Productivity by Developing Cultivars Adapted for Conventional and Organic production in Texas. Texas A&M Vegetable Working Group meeting, College Station, TX October 2017 46. Awika, H., T. Marconi, J. Enciso, J. Jung, and C.A. Avila. 2018. Development of Molecular Markers Associated to Spinach Growth Parameters. 2018 ASHS Annual Conference on July 30-August 3, Washington, DC. 47. Avila, C.A. 2018. Texas A&M AgriLife Spinach Breeding Program: Selection tools for cultivar development. Texas A&M AgriLife Research and Extension Center. Uvalde, TX May 11th, 2018.