DEVELOPING STRATEGIES TO IDENTIFY USEFUL GENES IN PEANUT AND BREEDING HIGH YIELDING PEANUT VARIETIES AND GERMPLASM WITH BIOTIC AND ABIOTIC STRESS TOLERANCE/RESISTANCE

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: COMPLETE
• Funding Source: HATCH
• Reporting Frequency: Annual
• Accession No.: 1002705
• Project Start Date: Mar 30, 2014
• Project End Date: Jan 31, 2019
• Program Code: [(N/A)]- (N/A)

Recipient Organization
AUBURN UNIVERSITY
108 M. WHITE SMITH HALL
AUBURN,AL 36849

Performing Department
Crop, Soil and Environmental Sciences

Non Technical Summary
Summary: New peanut cultivars play a major role in improving in peanut production and peanut quality for shellers, manufactories, and consumers. The three major factors that result in economic losses for peanut farmers and industry are leaf-spot diseases, drought stress, and aflatoxin contamination. Objectives of this research are to develop new peanut cultivars with improved yields and biotic and abiotic stress tolerance/resistance. These goals will be achieved through conventional breeding and molecular marker-assisted selection. Thus genome-wide molecular marker approaches and association mapping strategy will be applied to identify molecular markers directly linked to leaf-spot resistance and drought tolerance, so they can be incorporated as tools within breeding programs. The expected impact of this project is to improve yields and profits from peanut in USA.

Animal Health Component

50%

Research Effort Categories

Basic

50%

Applied

50%

Developmental

(N/A)

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
201	1830	1080	25%
202	1830	1081	25%
212	1830	1081	25%
204	1830	1081	25%

Knowledge Area
212 - Pathogens and Nematodes Affecting Plants; 204 - Plant Product Quality and Utility (Preharvest); 202 - Plant Genetic Resources; 201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1830 - Peanut;

Field Of Science
1081 - Breeding; 1080 - Genetics;

Keywords

peanut genetics

peanut breeding

drought tolerance

disease resistance.

Goals / Objectives
Objective 1: Identify key components of the drought response regulation system in peanuts through transcriptome.Objective 2: Develop and release high yielding peanut cultivars with biotic and abiotic stress tolerance for the United States using conventional breeding and marker-assisted methods.

Project Methods
Drought treatment and sampling. Peanut genotypes with different response to drought will be evaluated. These are C76-16, a breeding line that was identified as drought tolerant (Holbrook et al., 2007); Georgia Green, a released variety that showed moderate tolerance; and AP-3, a variety that is susceptible to drought. Peanuts will be planted with treatments distributed in a randomized block design in (5.5 m X 12.2 m) environmental controlled rainout shelters.The treatments will be: full irrigation and drought. Leaf samples will be collected once a week for four consecutive weeks during the main flowering stage that is 40 to 80 days after planting (DAP). The first sampling will be done at the initial stage, another three samplings as the drought progresses, and one final sampling during recovery after resuming irrigation. Fully expanded leaves (second nodal) from randomly selected plants, with two plants per row and 3 row-replicates per treatments will be assayed. Fresh leaves will be collected and immediately frozen in liquid nitrogen for RNA extraction. Leaves (third nodal) from the same main stem will be collected to determine relative water content (RWC), specific leaf area (SLA)and leaf density moisture content. These determinations will be done on the day of collection to associate relative degrees of drought stress. Total RNA isolation will be performed using previously reported methods with minor modifications. RNA-seq libraries will be generated using ScriptSeq v2 for transcriptome sequencing. Isolation of Small RNAs and library construction will be performed using TruSeq Small RNA Sample Prep Kit (Illumina, San Diego, CA). Transcriptome libraries will be sequenced using Roche 454 configured for long-reads and small RNA libraries will be sequenced on Illumina sequencer at the Genomics and Bioinformatics Research Unit in USDA, MS. Contigs or consensus sequences will be searched against nucleotide (BLASTn) and protein (BLASTx) NCBI databases (Altschul et al., 1990) and identification of gene function determination by Blast2GO (www.blast2go.com/b2glaunch/start-blast2go). To identify conserved small RNAs, sRNA consensus sequences will be query against precursor and mature miRNA and sRNA public database (www.mirbase.org, release 19 August 2012) which contains 21,264 sequences from 193 species. Since the peanut genome has not been sequenced, novel small RNAs, sequences will be queried against both newly sequenced transcriptomes and existing transcriptomes in public databases to identify gene targets.Discover alleles that contribute to leaf-spot resistance in Arachis germplasm. The initial gene pool for identifying a core collection with highly diverse germplasm in leaf-spot resistance will include 192 accessions from plant introductions (PIs), recombinant inbreed lines (RILs) of two mapping populations, advanced breeding lines, and released cultivars. This material will be used as a genetically diverse panel for marker-trait association analysis. We propose to phenotype and genotype the 192 accessions to identify a core collection for leaf-spot resistance as a resource in Arachis germplasm. These 192 (PI) genotypes will be planted using a complete block design with three replicates in Headland, AL in 2013. To increase disease pressure, non leaf-spot- fungicide treated control, and monthly (four total applications) program will be included in addition to the standard twice-monthly fungicide program as a positive control. Plant will be rated using the Florida leaf-spot scale during flowering, two weeks before harvest, and at harvest time (Chiteka et al., 1988). Leaf tissue of each genotype will be collected for genomic DNA isolation and fingerprinting. Through the work of Dr. Arias and Puppala, simple sequence repeat (SSR)-enriched libraries have been generated from genomic DNA of Valencia peanuts. The libraries were sequenced using Roche 454 Jr. and 900 primer sets were designed. Sequences containing potential SSRs were processed with BLAST2GO (http://www.blast2go.org); those returning hits on pathogen or stress response genes were included in the first set of primers that will be used in fingerprinting. Currently, 288 primers are ready for fingerprinting of leaf-spot resistant and susceptible varieties of peanut in search of polymorphisms. Additional primer sets will be used as needed.Genotypic and phenotypic data will be employed for analysis. Cluster analysis based on phenotypic data will be performed using average linkage and complete linkage algorithms in SAS. For genotypic data, cluster analysis and principal coordinate analysis will be done using FREETREE. STRUCTURE and EIGENSTRAT will also be used to group the accessions and estimate the population structure. The information will be used to select a subpopulation and form a core collection with highly diverse germplasm in leaf-spot resistance. We estimate that about 96 accessions will become part of the leaf-spot resistance core collection. We will mine candidate genes in search for allele variation in the diverse association panel. A wide range of genes can contribute to fungal resistance; we will first focus on potential disease-resistant genes identified in peanuts, . To phenotype the estimated 96 lines in the core collection, plants will be tested by inoculation of different strains of Cercospora arachidicola and Cercosporidium personatum both in greenhouse and field. Four seeds of each accession will be planted in 3-gallon pots using a completely randomized design with three replicates in a greenhouse at the National Peanut Lab., Dawson, GA. Linear mixed models will be used to correct false positives due to population structure in the association mapping of quantitative traits. Potential bias due to population structure or genetic relatedness will be corrected at the time of the analysis.

Progress 03/30/14 to 01/31/19

Outputs
Target Audience:Genetictists, breeders, plant pathologists, students, science community, farmer groups and peanut related commodity groups. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Trained five graduate students during the peroid of this program. One graduate student is going to finsh by this summer in 2020. How have the results been disseminated to communities of interest?Throught publication, conference, farmer show, and field day. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? 1.Cultivated peanut (Arachis hypogaea) is one of the most widely grown food legumes in the world being valued for its high protein and unsaturated oil contents. Drought stress is one of the major constraints that limits peanut production. To identify key components of the drought response regulation system in peanuts through transcriptome, we used four genotypes (drought tolerant: C76-16 and 587; drought susceptible: Tifrunner and 506) and examined used in a rainout shelter for drought stress. Whole-transcriptome sequencing analysis identified 7,780 genes differentially expressed in Tifrunner and 9,767 in 506. Of the 7,780 genes in Tifrunner, 5,310 genes were up-regulated and 2,470 were down-regulated. For the drought tolerant genotypes, 12,348 DEGs were identified in AU-587, including 7,172 up-regulated genes and 5,176 down-regulated genes. In C76-16, a total of 13,005 DEGs were identified with 7,718 up-regulated genes and 5,287 down-regulated genes. A total of 2,457 DEGs were shared by all four genotypes. Functional analysis of the shared DEGs identified a total of 139 enriched gene ontology (GO) terms consisting of 86 biological processes, and 53 molecular function, and defense response, reproductive process and signaling pathways were significantly enriched. Total of 43 significantly enriched Kyoto encyclopedia of genes and genomes (KEGG) pathways were also identified, and the most enriched pathways are those process involved in metabolic pathways, biosynthesis of secondary metabolites, plant circadian rhythm, phenylpropanoid biosynthesis, starch and sucrose metabolism, etc. This research expands our current understanding of the mechanisms that facilitate peanut drought tolerance and shed light on breeding advanced peanut lines to combat drought stress. 2. In 2017 we released 'AU-NPL 17', a new release of runner-type peanut cultivar t is high-yielding, tomato spot wilted virus (TSWV) resistant, leaf spots tolerant, high grade, and superior shelling characteristics. It has a prostrate growth habit with a main stem. AU-NPL 17 has high oleic fatty acid content and good flavor. Seeds of AU-NPL 17 are pink testa seed coats. AU-NPL 17 flowers approximately 35 days after planting and is medium maturity of 140 days in the Southeastern growing region. It is large-seeded cultivar.We have produced 200,000 pounds of 'AU-NPL 17', a new released peanut variety, as certified seeds in 2019.A new advanced breeding line 'AU14-34' is currently under production for breeder seeds and it will be released in 2021. it is a virgina-type peanut with high oleic, high yielding and strong resistance to tomoto spotted wilt virus, leaf spots and white mold.

Publications

• Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Hui Zhang, Ming Li Wang, Robert Schaefer, Phat Dang, Tao Jiang, and Charles Chen. 2019. GWAS and Coexpression Network Reveal Ionomic Variation in Cultivated Peanut. American Peanut Research and Education Society Proceedings. Auburn, AL. July 9-11, 2019.
• Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Phat M. Dang*, and Charles Y. Chen, 2019. Evaluation of peanut breeding lines to identify differential expressed genes involved in leaf spot resistance. American Peanut Research and Education Society Proceedings. Auburn, AL. July 9-11, 2019.
• Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: J. Patel, T.Jiang, M.L. Wang, L.L.Dean, P.M. Dang, M. Lamb, Y. Chu, J.P. Clevenger, P. Ozias-Akins, C.C.Holbrook, and C.Y. Chen 2019.Genome-Wide Association study of pod and seed quality traits in peanut. American Peanut Research and Education Society Proceedings. Auburn, AL. July 9-11, 2019.
• Type: Theses/Dissertations Status: Submitted Year Published: 2019 Citation: F.E. KUMRAL. Genome Wide Association Study (GWAS) on Root-Knot Nematode Resistance in Cultivated Peanut. MS Theses. Auburn University, June, 2019
• Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Hui Zhang, Ming Li Wang, Phat Dang, Tao Jiang, and Charles Chen 2019.Identification of potential QTLs and genes associated with seed composition traits in peanut (Arachis hypogaea) using GWAS and RNA-seq analysis. ASA-CSSA-SSSA International Annual Meeting San Antonio, Texas, November 10-13. 2019.
• Type: Theses/Dissertations Status: Submitted Year Published: 2019 Citation: Xu Wang. Integration of physiological and molecular approaches for selecting peanut genotypes with superior drought tolerant and nitrogen fixation traits. Theses. Auburn University, September, 2019

Progress 10/01/18 to 01/31/19

Outputs
Target Audience:Genetictists, breeders, plant pathologists, students, science community, farmer groups and peanut related commodity groups. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Trained two graduate students with completion of M.S. degree in 2019. Training one visiting scholar. Seven graduate students are currently training in the program. How have the results been disseminated to communities of interest?Throught publication, conference, farmer show, and field day. What do you plan to do during the next reporting period to accomplish the goals?A new advanced breeding line 'AU14-34' is currently under production for breeder seeds and it will be released in 2021. it is a virgina-type peanut with high oleic, high yielding and strong resistance to tomoto spotted wilt virus, leaf spots and white mold.

Impacts
What was accomplished under these goals? We have produced 200,000 pounds of 'AU-NPL 17', a new released peanut variety, as certified seeds in 2019.

Publications

• Type: Journal Articles Status: Published Year Published: 2019 Citation: Hui Zhang, Ming Li Wang, Robert Schaefer, Phat Dang, Tao Jiang, and Charles Chen. 2019. GWAS and Coexpression Network Reveal Ionomic Variation in Cultivated Peanut. J. Agric. Food Chem. 67, 12026-12036. DOI: https://pubs.acs.org/doi/pdf/10.1021/acs.jafc.9b04939
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Li Li, Xinlei Yang, Shunli Cui, Guojun Mu, Mingyu Hou, Meijing He, Hui Zhang, Lifeng Liu, and Charles Y Chen. 2019. Construction of High Density Genetic Map and Mapping Quantitative Trait Loci for Growth Habit Related Traits of Peanut (Arachis hypogaea L.). Frontiers in Plant Science: DOI: 10.3389/fpls.2019.00745.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Mei Yuan, Jun Zhu, Limin Gong, Liangqiong He, Crystal Lee, Suoyi Han, Charles Chen, and Guohao He. 2019. Mutagenesis of FAD2 genes in peanut with CRISPR/Cas9 based gene editing. BMC Biotechnology 19:24. https://doi.org/10.1186/s12896-019-0516-8.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Phat M Dang, Marshall C Lamb, Kira L Bowen, and Charles Y Chen. 2019. Identification of expressed R-genes associated with leaf spot diseases in cultivated peanut. Molecular Biology Reports (2019) 46:225239.

Progress 10/01/17 to 09/30/18

Outputs
Target Audience:Genetictists, breeders, plant pathologists, students, science community, farmer groups and peanut related commodity groups. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Trained one graduate student with completion of M.S. degree in 2018. Training one visiting scholar. Seven graduate students are currently training in the program. How have the results been disseminated to communities of interest?Throught publication, conference, farmer show, and field day. What do you plan to do during the next reporting period to accomplish the goals?Identified key components of the drought response regulation elements in peanuts through transcriptome will be validated by RT-PCR in 2019. Two new promising advanced breeding lines 'AU16-28' and 'AU18-21' will be under farm trial and produce fundation seeds for release in 2019. Performance testing for boths lines was begun in the F5:7 generation for three consecutive years (2016, 2017, 2018) at multiple locations of Dawson, GA; Headland, AL; Fairhope, AL. The results showed that they are a unique from other commercial runner-type peanut cultivars in having a high yield, high TSMK, good seed size, high oleic, medium maturity with the same maturity as Georgia Green.

Impacts
What was accomplished under these goals? GO enrichment analysis was performed on the 2,344 identified DEGs to predict processes and functions over-represented in the DEGs that identified in drought resistant genotypes. A total of 6,219 GO terms were assigned to the 2,344 DEGs. Among the 6,219 GO terms, a total of 139 GO terms were significantly enriched in drought resistant genotypes. The most significantly enriched GO term was cellular protein modification process. Particularly, a cluster of GO terms relate to defense response, such as responses to heat and abiotic stimulus were identified in the DEGs in drought resistant genotypes. Regulation of cellular process, metabolism, and transcription were also enriched. A new runner type peanut cultivar 'AU-NPL 17" was under seed production for registered seeds and in 2019 certified seeds will be produced for peanut farmers for 2020 growing season.

Publications

• Type: Journal Articles Status: Published Year Published: 2018 Citation: . Zifan Zhao, Yu-Chien Tseng, Ze Peng, Yolanda Lopez, Charles Y. Chen, Barry L. Tillman, Phat Dang, and Jianping Wang. 2018. Refining a major QTL controlling spotted wilt disease resistance in cultivated peanut (Arachis hypogaea L.) and evaluating its contribution to the resistance variations in peanut germplasm. BMC Genetics (2018): 19:17. https://doi.org/10.1186/s12863-018-0601-3.
• Type: Journal Articles Status: Published Year Published: 2018 Citation: R. Kandel, C.Y. Chen, C.R. Grau, A.E. Dorrance, J.Q. Liu, Y. Wang, and D. Wang. 2018. Soybean Resistance to White Mold: Evaluation of Soybean Germplasm under Different Conditions and Validation of QTL. Frontiers in Plant Science.
• Type: Journal Articles Status: Published Year Published: 2018 Citation: Wang M.L. C.Y. Chen, Brandon Tonnis, David Pinnow, Jerry Davis, Yong-Qiang Charles An, and Phat Dang. 2018. Changes of Seed Weight, Fatty Acid Composition, and Oil and Protein Contents from Different Peanut FAD2 Genotypes at Different Seed Developmental and Maturation Stages. J. Agric. Food Chem. DOI: 10.1021/acs.jafc.8b01238.
• Type: Journal Articles Status: Published Year Published: 2018 Citation: Jing Li, Yueyi Tanga, Alana L. Jacobson, Phat M. Dang, Xiao Li, Ming Li Wang, Austin Hagan, Charles Y. Chen, 2018. Population structure and association mapping to detect QTL controlling tomato spotted wilt virus resistance in cultivated peanuts, The Crop Journal 2018 https://doi.org/10.1016/j.cj.2018.04.001

Progress 10/01/16 to 09/30/17

Outputs
Target Audience:Genetictists, breeders, plant pathologists, students, science community,farmer groups and peanut related commodity groups. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Trained one graduate student with completion of M.S. degree in 2017. Training one visiting scholar. Five graduate students are currently training in the program. How have the results been disseminated to communities of interest?Throught publication, conference, farmer show, and field day. What do you plan to do during the next reporting period to accomplish the goals?With the objective of Identifying key components of the drought response regulation system in peanuts through transcriptome, we have phenotyped a RIL population of a cross between 'C76-16' X 'Tifrunner' to identify drought resistant genotypes in relations to symbiotic nitrogen fixation capacity with rhizobium colonization. The RIL line 'AU-587' was identified as the most drought tolerance and RNAseq data was generated and will be used for furtheranalysisfor elucidating drought response regulation system in peanut in 2018.

Impacts
What was accomplished under these goals? Peanut breeding program resulted in the development of a new runner-type peanut cultivar 'AU-NPL 17'. It is high-yielding, tomato spot wilted virus (TSWV) resistant, leaf spots tolerant, high grade, and superior shelling characteristics. It has a prostrate growth habit with a main stem. AU-NPL 17 has high oleic fatty acid content and good flavor. In 2017, Alabama Crop Improvement Association produced 90,000 lbs of foundation seeds available for registered seed production in 2018. We estimated 2.4 million lbs of registered seeds in 2018. By 2020, about 50% Alabama peanut producers (~200) having 100,000 acres would like to adopt the latest variety. Due to high oleic trait of 'AU-NPL 17', with $50 per ton higher premium alone, the producers will have $100 per acre increase in revenue or total of $10 million increase in Alabama every year. 'AU-NPL 17' also has a strong disease resistant package so farmers can reduce the number of times of fungicide application while maintaining yield. We estimated another $50 per acre saving from reduction of fungicide application or total of $5.0 million saving in the state.

Publications

• Type: Journal Articles Status: Published Year Published: 2017 Citation: Leamy, L.J., H. Zhang, C. Li, C.Y. Chen*, and B.H. Song*. 2017. A genome-wide association study of seed composition traits in wild soybean (Glycine soja). BMC Genomics.18:18. DOI 10.1186/s12864-016-33974.
• Type: Books Status: Published Year Published: 2017 Citation: Grey, T.L., C.Y. Chen, Russell Nuti, W.S. Monfort and G. Cutts. 2017. Characterization of genotype by planting date effects on runner-type peanut seed germination and vigor response to temperature. in Advance in Seed Biology. http://dx.doi.org/10.5772/intechopen.70584.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Sorensen, R.B., R.C. Nuti, C.C. Holbrook, and C.Y. Chen.2017. Peanut peg strength and associated pod yield and loss by cultivar. Peanut Science. 44:77-82.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Chen, Zhongyu, Lianxing Gao, C.Y. Chen, and C.L. Butts. 2017. Analysis on technology status and development of peanut harvest mechanization of china and the United States. Transactions of the Chinese Society for Agricultural Mechinery. 48:1-21. Doi:10.6041/j.issn.1000-1298.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Davis, J.P., Leek, J.M., Sweigart, D.S., Dang, P., Butts, C.L., Sorensen, R.B., Chen, C.Y. and Lamb, M.C. 2017. Measurements of Oleic Acid among Individual Kernels Harvested from Test Plots of Purified Runner and Spanish High Oleic Seed. Peanut Science. 44(2): 134-142. https://doi.org/10.3146/PS16-21.1.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Lamb, M.C., Sorensen, R.B., Butts, C.L., Dang, P.M., Chen, C.Y., Arias, R.S. 2017. Chemical Interruption of Late Season Flowering to Improve Harvested Peanut Maturity. Peanut Science. 44(1): 60-65. https://doi.org/10.3146/PS16-2.1.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Gao Lianxing, Zhongyu Chen, C.Y. Chen and C.L. Butts. 2017. Development course of peanut harvest mechanization technology of the United States and enlightenment to China. Transactions of the Chinese Society for Agricultural Mechinery. 33(12):1-9. Doi:10.11975/j.issn.1002-6819.2017.12.0001.
• Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Tao Jiang, Lisa Dean, Yueyi Tang, Phat Dang, Ming Li Wang, Guohao He, Marshall Lamb, C. Corley Holbrook, Peggy Ozias-Akins, Charles Chen. 2017. Association Mapping of SSR Markers to Sweet, Bitter and Roasted Peanut Sensory Attributes in Cultivated Peanut. 2017 ASA-CSSA-SSSA Annual Meeting, October 22  25, 2017. Tampa, FL.
• Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Hui Zhang, Nathan Hall, Leslie R Goertzen, Charles Chen, Eric Peatman, J. Scott McElroy. 2017. Constructing Eleusine Transcriptome References for Determination African Finger Millet (Eleusine coracana) Parentage. 2017 ASA-CSSA-SSSA Annual Meeting, October 22  25, 2017. Tampa, FL.
• Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: C. Corley Holbrook, Peggy Ozias-Akins, Ye Chu, Thomas George Isleib, Scott A. Jackson5, Albert K. Culbreath, Tim Brenneman, Charles Chen, Chris Butts, Marshall Lamb, Thomas R. Sinclair, Barry L. Tillman, Mark D. Burow, Craig Kvien, Josh Clevenger, Baozhu Guo.2017. Phenotyping and Genotyping of Ril Populations of Peanut for Gene Discovery and Marker Development. 2017 ASA-CSSA-SSSA Annual Meeting, October 22  25, 2017. Tampa, FL.
• Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: X. WANG, Y. FENG and C. CHEN, P. DANG and M. LAMB, C. HOLBROOK, P. OZIAS-AKINS and Y. CHU, T.G. ISLEIB, 2017. Genotypic variability in symbiotic nitrogen fixation and carbon isotope discrimination among peanut genotypes under drought stress. 2017 ASA-CSSA-SSSA Annual Meeting, October 22  25, 2017. Tampa, FL.
• Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Grey, T.L., C.Y. Chen, and Russell Nuti. 2017. Characterization of genotype by planting date effects on runner-type peanut seed germination and vigor response to temperature. 2017 American Peanut Research and Education Society Proceedings. Albuquerque, NM. 10-13 July 2017.
• Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Dang, P.M., M.C. Lamb, and C.Y. Chen. 2017. Differential Expression of R-genes to Associate leaf spot resistance in cultivated peanut. 2017 American Peanut Research and Education Society Proceedings. Albuquerque, NM. 10-13 July 2017.
• Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Charles Chen*, Kris Balkcom, Austin Hagan, Phat Dang, Marshall Lamb, Ming Li Wang, 2017. Characteristics of a newly released runner-type peanut cultivar AU-NPL 17. 2017 American Peanut Research and Education Society Proceedings. Albuquerque, NM. 10-13 July 2017.
• Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Mei Yuan, Jun Zhu, Crystal Lee, Guohao He, Liangqiong He, Suoyi Han, Charles Chen, and Phat Dang 2017. Mutagenesis of FAD2 genes in peanut with CRISPR/Cas9. 2017 American Peanut Research and Education Society Proceedings. Albuquerque, NM. 10-13 July 2017.
• Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Corley Holbrook, Peggy Ozias-Akins, Ye Chu, Thomas G. Isleib, Josh Clevenger, Carolina Chavarro, Scott Jackson, Albert Culbreath, Tim Brenneman, Renjie Cui, Charles Chen, Christopher Butts1, Marshall Lamb, Tom Sinclair, Barry Tillman, Mark Burow, C. K. Kvien, and Baozhu Guo. 2017. Phenotyping and genotyping of RIL populations for gene discovery and marker development. The 9th International Conference of the Peanut Research Community on Advances in Arachis through Genomics and Biotechnology (AAGB) in Cordoba, Argentina, March. 9-11, 2017.
• Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: L Dean, T Jiang, YY Tang, PM Dang, ML Wang, GH He, MC Lamb, CC Holbrook, P. Ozias-Akins, and CY Chen. 2017. Association mapping of SSR markers to sweet, bitter and roasted peanut sensory attributes in cultivated peanut. The 9th International Conference of the Peanut Research Community on Advances in Arachis through Genomics and Biotechnology (AAGB) in Cordoba, Argentina,  March. 5-7, 2017.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: Wang, M.L., M.A. Grusak, C.Y. Chen, B. Tonnis, N.A. Barkley, S. Evans, D. Pinnow, J. Davis, C.C. Holbrook, and G.A. Pederson. 2016. Seed protein percentage and mineral concentration variability and their correlation with other seed quality traits in the U.S. peanut mini-core collection. Peanut Science. doi:10.3146/PS15-15.1.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: Meng, S., X. Yang, P.M. Dang, S. Cui, G. Mu, L. Liu, and C.Y Chen. 2016. Evaluation of genetic diversity with Insertion-Deletion marker and marker-trait association analysis in cultivated peanut (Arachis hypogaea L.). Genetics and Molecular Research. Doi: http://dx.doi.org/10.4238/gmr.15028207.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: Leamy, L.J., C.R. Lee, I. Mujacic, Q. Song, R.L. Nelson, Y. Luo, C.Y. Chen, E. Peregrine, and B.H. Song. 2016. Environmental adaption in wild soybean (Glycine soja) across their native geographic range in northeast Asia. Ecology and Evolution. Doi:10.1002/ece3.2351.

Progress 10/01/15 to 09/30/16

Outputs
Target Audience:Genetictists, breeders, plant pathologists, students, science community and farmer groups. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Training one graduate student and one visiting scholar. How have the results been disseminated to communities of interest?Throught publication, conference and field day. What do you plan to do during the next reporting period to accomplish the goals?One cultivarwithhigh-yielding, Tomato spot wilted virus (TSWV)-resistant, and leaf spot tolerance, high grade, and superior shelling characters will be released in 2017.

Impacts
What was accomplished under these goals? One hundred eighteen genotypes of the U.S. peanut mini-core germplasm collection were used for screening for TSWV resistance by mechanical inoculation and ELISA assay. One hundred and thirty-three SSR markers were applied for genotyping the panel of 104 genotypes. Four genotypes, PI356004, PI493880, PI355271, and PI496401, were identified as resistant to TSWV based on the data from mechanical inoculation, ELISA, and field evaluation. Four subpopulations were classified by population structure analysis, and corresponded to botanical types to a certain extent. Association mapping analysis indicated that the five markers, pPGPseq5D5, GM1135, GM1991, TC23C08, and TC24C06, were consistently associated with visual symptoms by four models, Q model, PCA model, Q+K model, and PCA+K model. These identified markers accounted for 36.4% of the phenotypic variance for TSWV resistance. Moreover, pPGPseq5D5 and GM1991 were both associated with visual symptoms and ELISA resulting in a high R2. These highly resistant genotypes along with their associated markers could be used for development of TSWV-resistant cultivars in a peanut breeding program.

Publications

• Type: Journal Articles Status: Published Year Published: 2015 Citation: Liu, L. P. Dang, and C.Y. Chen*. 2015. Development and utilization of InDel markers to identify peanut (Arachis hypogaea) disease resistance. Frontiers in Plant Science. 6:988. doi: 10.3389/fpls.2015.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: Wang, M.L., M.A. Grusak, C.Y. Chen, B. Tonnis, N.A. Barkley, S. Evans, D. Pinnow, J. Davis, C.C. Holbrook, and G.A. Pederson. 2016. Seed protein percentage and mineral concentration variability and their correlation with other seed quality traits in the U.S. peanut mini-core collection. Peanut Science. doi:10.3146/PS15-15.1.
• Type: Theses/Dissertations Status: Published Year Published: 2015 Citation: Joshua W. Carter. 2015. Middle-Season Drought Tolerance in a RIL Population of Cultivated Peanut. M.S. Thesis. Auburn University.

Progress 10/01/14 to 09/30/15

Outputs
Target Audience:Geneticists, breeders, plant pathologists and science community, students, and farmers. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Training one graduate student and one visiting scholar. How have the results been disseminated to communities of interest?throught publication, conference and field day. What do you plan to do during the next reporting period to accomplish the goals?keep developing cultivars that are resistant to leaf spot and TSWV diseases.

Impacts
What was accomplished under these goals? A total of 192 genotypes including the US mini-core collection, elite germplasm, and primary co-ancients were planted in the Wiregrass Experiment Station for phenotyping for leaf spot resistance in 2014 and 2015. The PI 576614, PI 576634, PI 371521, and PI 268868 were identified as new sources of leaf spot resistance, which have been used in peanut breeding program. We have successfully developed 48 InDel markers based on EST sequence data of disease gene family and applied those markers to genotype the association mapping population. Five InDels were identified to be significantly correlated to tomato spotted wilt virus (TSWV) infection and leaf spot (Liu, Dang and Chen, 2015). The diverse association mapping panel of 134 accessions from six botanical varieties was genotyped with 200 SSR markers. Among 200 tested SSR markers, 133 markers showed polymorphism in the panel and used for association analysis for leaf spot resistance. The results showed that six effective markers were associated with LLS resistance in Arachis germplasm by both GLM (general linear model) and MLM (mixed linear model) analysis. "Ah3" was consistently detected in multiple years and can explain about 10% of phenotypical variation so it could be considered as a major QTL underlying LLS resistance in Arachis germplasm. The results demonstrated that the leaf spot resistances in peanuts are controlled by multiple genes with many with minor effects and a few with major effects.

Publications

• Type: Journal Articles Status: Published Year Published: 2015 Citation: Lifeng Liu, Phat Dang, and Charles Chen*. 2015. Development and Utilization of InDel Markers to Identify Peanut (Arachis hypogaea) Disease Resistance. Frontiers in Plant Science. 6:988. doi: 10.3389/fpls.2015.00988.
• Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Y. Tang, C. Chen*, P. Dang; A. Hagan, K. Bowen, and G. He. Association mapping of SSR markers to leaf spot and TSWV resistances in cultivated peanut. 2015. The 8th International Conference of the Peanut Research Community on Advances in Arachis through Genomics and Biotechnology (AAGB) in Brisbane, Australia,  Nov. 5-7, 2015.
• Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Y. Tang, C. Chen*, P. Dang; A. Hagan, K. Bowen, and G. He. 2015. Association Mapping of SSR Markers to Leaf Spot Disease Resistance in Cultivated Peanut. 2015 American Peanut Research and Education Society Proceedings. 14-16 July 2015, Charleston, SC.
• Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: C. Chen*, M. Wang, L. Dean, N. Barkley, A. Hagan, P. Dang, C. Holbrook, C. Butts, M. Lamb, and T. Sanders. 2015. Genetic Variation in the US Peanut Mini-Core Collection for Agronomy, Seed Chemistry, and Nutrient Quality Traits in Peanut. 2015 ASA-CSSA-SSSA Annual Meeting, November 15  18, 2015. Minneapolis, MN.

Progress 03/30/14 to 09/30/14

Outputs
Target Audience: Nothing Reported Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Nothing Reported How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? AAES does not require reporting for less than one year. These six months will be reported in the first full year report.

Publications