Progress 10/01/17 to 09/30/18
Outputs
Target Audience:Target audience is Oregon processed vegetable growers and processors, along with national and international seed companies that have snap bean breeding programs. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?One undergraduate stuident obtained experience in establishing and evaluating a disease resistance trial. How have the results been disseminated to communities of interest?Results have been reported at the National Sclerotinia Initiative annual meeting and at the W3150 meeting.We have also repored on resluts ot the Willamette Valley Vegetable Growers meeting and to the Oregon Processed Vegetable Commission. What do you plan to do during the next reporting period to accomplish the goals?NAM population is being genotyped, after which we can conduct a QTL analysis. We are also evaluating lines from the RI populations for suitability for release as snap bean cultivars.
Impacts
What was accomplished under these goals?
A nested association mapping (NAM) population for evaluating P. coccineus-derived white mold resistance involves the cross of the introgression line WM904-20-3 with five parents. The panel evaluated in 2018 consisted of four populations (Cornell 501/WMG904-20-3, n = 56; NY6020-4/WMG904-20-3, n = 69; M0070/WMG904-20-3, n = 60 and WMG904-20-3/A195, n = 62). These populations were evaluated in the field for resistance to white mold. Two populations in particular (Cornell 501/WMG904-20-3 and WMG904-20-3/A195 had greater than 50% of the lines with a DSI of nine or less. Genotyping of the NAM panel is underway. A fifth population (WMG904-20-3/G122) has been phenotyped and genotyped, and a preliminary QTL analysis identified two QTL - one on Pv07 and the other on Pv08 - conferring resistance. The Unidor/OSU5630 RI population consisting of 184 F4:7 lines was screened in the field at the OSU Vegetable Research Farm near Corvallis, OR for resistance to white mold. The population exhibited a normally distributed reaction to white mold, with 19 lines showing a disease severity index (DSI) of 6 or less (DSI is the geometric mean of incidence and severity and ranges from 0 - 30 where 0 is highly resistant). A QTL analysis of the population revealed two SNPs associated with various resistance traits. One SNP on Pv02 was associated with reduced incidence, severity and disease severity index, while a second SNP on Pv03 was associated with increased incidence and DSI, implying that the resistant allele originates from 5630. This population was previously screened in 2017 for resistance using the seedling straw test in the greenhouse, and a single QTL on Pv03 was discovered at a different location from the 2018 field QTL. The Unidor seedling straw test QTL is within 0. 7 Mb of putative WM 3.4 identified in GWAS of the SnAP, while the Unidor Pv02 field QTL overlaps with the putative WM 2.4 QTL also identified by GWAS of the SnAP. This population has excellent architecture which may contribute to avoidance in the field. Snap beans show a higher level of susceptibility to white mold compared to dry bean but partial resistance can be found and this group is a potential source of resistance QTL not present in dry bean. Supporting this assertion, we conducted a structure analysis of snap bean and compared these to dry bean to associate snap beans to dry bean race structure (Wallace et al., 2018). Overall, we found eight gene pools of snap bean, some of which represent distinct assemblage of genes compared to dry bean. This research helps inform future approaches to mining the snap bean gene pool for useful resistance genes.
Publications
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2018
Citation:
Arkwazee, H.A., 2018. Quantitative trait loci and genome wide association study for resistance to white mold in common (snap) bean. Ph.D. Dissertation, Oregon State University. http://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/pc289q25h
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Wallace, L., H. Arkwazee, K. Vining and J.R. Myers. 2018. Genetic diversity within snap beans and their relation to dry beans. Genes 9(587); doi:10.3390/genes9120587. http://www.mdpi.com/2073-4425/9/12/587/htm.
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Progress 10/01/16 to 09/30/17
Outputs
Target Audience:Target audience is Oregon processed vegetable growers and processors, along with national and international seed companies that have snap bean breeding programs. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?One Ph.D. graduate student completed his dissertation research under this project. How have the results been disseminated to communities of interest?Results have been reported at the National Sclerotinia Initiative annual meeting and at the Bean Improvement Cooperative meeting. What do you plan to do during the next reporting period to accomplish the goals?The WM904-20-3 and Unidor recombinant inbred populations are being grown in the field for evaluation of white mold reaction. This constitutes the second year of evaluation for the former population and the first year for the latter population. These populations have been genotyped and will be ready for analysis at the end of the growing season.
Impacts
What was accomplished under these goals?
Breeding for White Mold Resistance: The project contains four parts: 1) QTL mapping of G122/WM904-20-3 recombinant inbred (RI) population, 2) conduct QTL mapping of A195/OSU6137 RI population. 3) screen of a 'Unidor/OSU5630 RI population for white mold reaction and 4) a genome wide association mapping study (GWAS) conducted using the Bean CAP Snap Bean Diversity Panel (SBDP) (n = 146) and the Snap bean Association Panel (SnAP) (n = 376), 1) Quantitative trait loci (QTL) analysis was conducted on the G122/WMG904-20-3, recombinant inbred population (n=82 with both parents), to detect QTL associated with partial resistance to white mold. The population was evaluated for white mold in the field for two consecutive years and in the greenhouse using the seedling straw test. Using composite interval mapping (CIM) and interval mapping (IM), we detected two significant QTL that were associated with partial resistance to white mold. The QTL that was detected by CIM was located on Pv08 and explained 18.8% of the variation for the field and greenhouse tests; while the QTL that was detected by IM was located on Pv07 which accounted for 19.1% of the phenotypic variation for both field and greenhouse tests. A few lines were more resistant than both parents for the field and greenhouse tests, including B8346/6-59, B8346/6-79, B8346/6-76 and B8346/6-39. 2) Quantitative trait loci (QTL) analysis conducted on the A195/OSU6137 RI population (n=116) detected new QTL associated with partial resistance to white mold. The population was evaluated for white mold in the field for two consecutive years and in the greenhouse using the seedling straw test. CIM detected seven significant QTL that were associated with partial resistance to white mold. Three QTL located on Pv01, Pv03 and Pv09 and accounting for 17.5, 21.3 and 21.8% of the variation respectively, were identified in the field test. Four significant QTL on Pv01, Pv05, Pv07 and Pv09 were detected by the seedling straw test which explained 13.7, 14.7, 13.7 and 13.4% of the disease reaction, respectively. 3) Unidor/OSU5630, RI population (n=190 plus both parents) was screened for white mold reaction in the greenhouse using the seedling straw test. The population was genotyped using the Illumina 6000 SNP BARCbean6K_3 Beadchip. Out of 5,398 bead types, 1,296 SNPs were polymorphic and were used to construct the linkage map. Multiple QTL mapping (MQM) was used to implement QTL analysis. One significant QTL was detected on Pv03. The QTL was located at the proximal end between 1.07 and 2.57Mb with LOD score 3.11. The QTL explained 7.2% of the variation with additive effect of -0.31. 4) A genome wide association study (GWAS) was conducted to detect markers significantly associated with white mold resistance in two panels of snap bean cultivars: BeanCAP SBDP (Coordinated Agriculture Project Snap Bean Diversity Panel) (n= 138) and the Snap Bean Association Panel (SnAP) consists of 376 cultivars and breeding lines. The BeanCAP SBDP was evaluated for white mold reaction in the field in summer 2012 and 2013, while the SnAP was screened in greenhouse only using the seedling straw test method in 2016. The population was genotyped using genotyping by sequencing (GBS) for which 40,023 SNPs were generated. GWAS was analyzed using FarmCPU. One-hundred forty-six significant SNPs that were associated with white mold were detected on all (11) common bean chromosomes. Twenty significant SNPs were detected by the seedling straw test while 126 significant SNPs were detected in one or both years of field testing; 51 SNPs in 2012 and 75 SNPs in 2013. The significant SNPs (146) grouped into 39 regions distributed across all chromosomes. The regions overlapped with 13 previously identified QTL (WM1.1, WM2.2, WM3.1, WM3.3, WM5.5, WM6.1, WM6.2, WM7.1, WM7.4, WM7.5, WM8.1, WM8.3 and WM9.3) that have been found in bi-parental populations. Also, the associations in the present study overlapped with 13 significant markers that were associated with white mold detected by GWAS in a dry bean panel. 'NY6020-5' and 'Unidor' were the most outstanding snap bean cultivars in the field tests for both years while 'Homestyle' and 'Top Crop' were the most resistant snap bean cultivars in the straw test.
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Arkwazee, H., J. Hart, T. Porch, P. Griffiths, J. Davis and J.R. Myers. 2018. Genome wide association study (GWAS) for white mold resistance in snap bean. Annu. Rept. Bean Improv. Coop. 61:85-86.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Myers, J.R., J. Davis, H. Arkwazee, L. Wallace, R. Lee S. Mafi Moghaddam and P. McClean 2018. Why wax beans lack carotenoids. Annu. Rept. Bean Improv. Coop. 61:29-30.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Myers, J., H. Arkwazee, J. Davis, P. Miklas, J. Hart, and P. McClean. 2018. GWAS and QTL mapping of white mold resistance in common bean. National Sclerotinia Initiative Meetings, 17-18 Jan., Bloomington, MN.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2017
Citation:
Myers, J.R. A. Huster, L. Wallace and C. Hagerty. 2017. Genome Wide Association Study (GWAS) of Fusarium solani Resistance using the Bean CAP Snap Bean Diversity Panel. 7th International Legume Root Disease (ILRD) Workshop. 11/1/17.
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Progress 10/30/15 to 09/30/16
Outputs
Target Audience:Target audience is Oregon processed vegetable growers and processors, along with national and international seed companies that have snap bean breeding programs. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?One graduate student has developed expertise in evaluating disease resistance, and conducting linkage mapping, QTL analysis, and GWAS. How have the results been disseminated to communities of interest?Information has been disseminated to local growers and processors through field days conducted during the growning season and at the annual growers meeting during the winter. Information has been communicated to peers at the Bean Improvement Cooperative biennial meetings and at the W1350 regional project. What do you plan to do during the next reporting period to accomplish the goals?WM904-20-3 NAM population needs to be genotyped and GWAS conducted. We plan to conduct a meta analysis of GWAS populations to validate QTLs that have been indentifed associated with resistance to white mold. An additional set of Unidor crosses need to be phenotyped and genotyped for white mold resistance for construction of a NAM population with Unidor as the common parent.
Impacts
What was accomplished under these goals?
Breeding for White Mold Resistance: A nested association mapping (NAM) population with the common parent WM904-20-3 crossed to four different lines was screened for white mold resistance in the field. Populations were grown in a replicated trial at the Vegetable Research Farm. Normal cultural practices were used except beginning at flowering, plots were irrigated by solid set sprinklers for ½ hour in evenings to increase leaf wetness period and create conditions more favorable for disease development. Data on incidence (%) and severity (1 - 9 scale, 1 = no disease) was recorded. A disease severity index (DSI) was calculated based on the geometric mean of incidence and severity.WM904-20-3 combinesthe best common bean traits with white mold resistance introgressed from the Phaseolus coccineus accession PI 255956. The other parents in these populations also carry partial resistance to white mold. The populations were screened for white mold reaction at OSU Vegetable Research Farm. Incidence and severity were measured as parameters of disease in three replicates arranged in a randomized complete block design. The analysis of variance showed highly significant difference among families although all parents within the populations had some degree of partial resistance to white mold. Also highly significant differences were observed among the replications probably due to the large size of the population. Population distributions were skewed towards resistance for all crosses as would be expected for resistant x resistant combinations. WMG904-20-3 had the lowest incidence, severity and disease severity index compared with all others parents and the resistant check, G122 The next step is genotyping the NAM population to conduct GWAS. The DNA has been isolated at OSU/Center for Genome Research and Biocomputing. Also the NAM population should be screened to white mold reaction in the greenhouse using straw test and field for second year. A genome wide association mapping study (GWAS) was conducted using the Bean CAP Snap Bean Diversity Panel (SBDP) (n = 146) and the Snap bean Association Panel (SnAP) (n = 376). The objectives of the present study were: 1) to verify previously reported QTLs detected in other populations and studies, 2) to detect novel QTLs associated with white mold resistance and 3) to identify new sources of resistance to this disease in common bean, with particular emphasis on snap bean. The SBDP was phenotyped for white mold reaction in the field in 2012 and 2013, while the SnAP was screened for white mold reaction in 2016 greenhouse only using the seedling straw test. The population was genotyped using genotyping by sequencing (GBS) for which 40,023 SNPs were generated. GWAS was analyzed using the R package FarmCPU. One-hundred forty-six significant SNPs associated with white mold reaction were detected on all 11 common bean chromosomes. Twenty significant SNPs were detected by the seedling straw test while 126 significant SNPs were detected in one or both years. The 146 significant SNPs could be grouped into 39 regions distributed across all chromosomes. The regions overlapped with 13 previously identified QTLs (WM1.1, WM2.2, WM3.1, WM3.3, WM5.5, WM6.1, WM6.2, WM7.1, WM7.4, WM7.5, WM8.1, WM8.3 and WM9.3) identified in bi-parental populations. In addition, the associations found in the present study overlapped with 13 significant markers that were associated with white mold resistance detected by GWAS in a dry bean panel. Twenty-five associations were unique to this study. NY6020-5 and Unidor were the most outstanding snap bean cultivars in the field tests for both years while Homestyle and Top Crop were the most resistant snap beam cultivars in straw test. In a preliminary trial to investigate the resistance carried by Unidor, the population Unidor/OSU5630 (n=190, F4:5) was phenotyped using seedling straw test in 2016 and genotyped in 2017 using Illumina iSelect 6K SNPchip. A linkage map of 1,296 SNPs was constructed using Joinmap 4.1. Quantitative trait loci analysis was conducted implementing multiple QTL mapping (MQM) using MapQTL6. One significant QTL (LOD = 3.11) associated with white mold resistance was detected on Pv03 at 15.1 cM (Fig. 6). The QTL was located at about 1.07 to 2.57Mb on the physical map. The QTL explained 7.2% of the phenotypic variation with additive effect of -0.31.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Vasconcellos, R.C.C., O.B. Oraguzie, A. Soler, H. Arkwazee, J.R. Myers, J.J. Ferreira, Q. Song, P. McClean, P.N. Miklas. 2017. Meta-QTL for resistance to white mold in common bean. PLoS ONE 12(2): e0171685. doi:10.1371/journal.pone.0171685
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Feng, X., P. Guzm�n, J.R. Myers and A.V. Karasev. 2017. Resistance to bean common mosaic necrosis virus conferred by the bc-1 gene affects systemic spread of the virus in common bean. Phytopathology 107:893-900. https://doi.org/10.1094/PHYTO-01-17-0013-R.
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Feng X., J.R. Myers, and A.V. Karasev. 2015. A bean common mosaic virus isolate exhibits a novel pathogenicity profile in common bean, overcoming the bc-3 resistance allele coding for the mutated eIF4E translation initiation factor. Phytopathology 105:1487-1495.
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Hagerty, Christina H. Aphonso Cuesta-Marcos, Perry Cregan, Q. Song, Phillip McClean, Steven Noffsinger and James R. Myers. 2015. Mapping Fusarium solani and Aphanomyces euteiches root rot resistance and root architecture quantitative trait loci in common bean (Phaseolus vulgaris). Crop Science 55:1969-1977. (DOI: 10.2135/cropsci2014.11.0805).
- Type:
Other
Status:
Published
Year Published:
2017
Citation:
Arkwazee, H. and Myers, J.R., 2017. Seedling straw test: A rapid and resource-efficient method for evaluating white mold resistance. Annu. Rept. Bean Improv. Coop. 60:39-40.
- Type:
Other
Status:
Published
Year Published:
2017
Citation:
Arkwazee, H., J. Davis and J.R. Myers 2017. Comparison of the conventional and seedling straw tests for quantifying white mold resistance. Ann. Rep. Bean Impr. Coop. 60:41-42.
- Type:
Book Chapters
Status:
Awaiting Publication
Year Published:
2018
Citation:
Myers, James R. and Ken Kmiecik. Economic and Academic Significance of Common Bean. 2017. Marcelino P�rez de la Vega, Marta Santalla, and Fr�d�ric Marsolais (Eds.) The Common Bean (Phaseolus vulgaris L.) Genome. Springer DOI 10.1007/978-3-319-63526-2.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2017
Citation:
Haidar Arkwazee, John P. Hart and James Myers. 2017. Association Mapping to Identify QTL conferring White Mold Resistance in the Snap Bean Association Panel (SnAP). National Sclerotinia Initiative Meetings, 18-20 Jan., Bloomington, MN. (https://www.ars.usda.gov/ARSUserFiles/30000000/WhiteMoldResearch/2017meeting/2017%20Program.pdf)
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2017
Citation:
Haidar Arkwazee and James Myers. 2017. Characterizing a New Common Bean Recombinant Inbred Population (Unidor/OSU5630) for White Mold Resistance. National Sclerotinia Initiative Meetings, 18-20 Jan., Bloomington, MN. (https://www.ars.usda.gov/ARSUserFiles/30000000/WhiteMoldResearch/2017meeting/2017%20Program.pdf)
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