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United States Department of Agriculture

Agricultural Research Service

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Research Project: Identification of Qtl for White Mold Resistance in Mesoamerican Beans

Location: Sunflower Research

2013 Annual Report


1a.Objectives (from AD-416):
The long term goals of this project are to develop pinto beans with enhanced levels of resistance to white mold.


1b.Approach (from AD-416):
The project is to phenotype a pinto bean RIL population for reaction to white mold over a multi-year period in field trials and greenhouse. The RIL population will be grown and evaluated in a 4-replicate white mold field nursery. The nursery, located at the Montcalm Research Farm in Entrican, Michigan, is naturally infested with high levels of Sclerotinia sclerotiorum, and is irrigated during and after flowering to further encourage disease development. The RILs will be planted in two row plots and will be flanked by two rows of a highly susceptible variety that serves as a spreader of the disease to further promote uniform white mold development. Resistance to white mold will be evaluated, along with yield under disease pressure, architecture, and agronomic desirability. Additionally, the RILs will be evaluated in the greenhouse for genetic resistance to white mold using the straw and oxalate tests. The QTL study will be to genotype the individual lines in the mapping populations and develop a molecular linkage map. The individual RILs of each population will be genotyped using available SSR, TRAP and SRAP markers. Upon completion of this genotyping step, mapping software will be employed to develop a linkage map for each population. Once a linkage map is obtained, QTL analysis software will be used to determine the location of QTL for white mold resistance in the mapping population, and the parent from which each QTL originated. In order to validate the potential of resistance QTL identified in this study a MAS study based on the same resistance QTL will be conducted under severe white mold pressure in a second pinto population during the final growing season. We will investigate the role of specific defense genes in conferring resistance to white mold in pinto bean and explore synteny of Phaseolus QTL with other legumes.


3.Progress Report:

This project was initiated on July 1, 2010, research is ongoing, and the overall objective is to identify resistance genes important in plant defense responses of dry beans to Sclerotinia.

QTLs controlling disease incidence in the field and greenhouse and yield were identified in two 94-entry pinto bean RIL populations (AP630 and AP647) generated from crosses between AN-37 and P02630 and AN-37 and P02647 pinto bean breeding lines respectively. Heritability estimates in AP630 were low for traits like lodging (0.23), days to maturity (0.21), plant canopy height (0.25) and field disease incidence (0.23), whereas traits like yield, seed weight and the straw test had moderately high heritability estimates of 0.53, 0.74 and 0.46 respectively. Higher heritability estimates for seed weight (0.88), days to flowering (0.74) and maturity (0.72) were observed in the AP647 population suggesting relatively more genetic control of these traits than yield (0.58), disease incidence (0.49) or lodging (0.46); respectively. The two populations were also screened with the BARCBean6K 3 Beadchip consisting of a total of 5,398 bead-types. Genotyping resulted in an average hybridization rate of 45% for the AP630 and 44% for AP647 population. A final total of 1024 SNP markers were polymorphic and were mapped in AP630 and 1016 markers were polymorphic and were mapped in the AP647 population.

The final map assembly of the AP630 population resulted in 11 linkage groups corresponding to the 11 chromosomes of P. vulgaris. The average marker distance was estimated at 1.2 cM however there were regions of both high and low recombination on some linkage groups. The maximum distance between adjacent markers was approximately 22 cM on Pv04. The integrated map of AP630 covered a total of 1183 cM. The total map distance for AP647 was 953 cM represented on 11 linkage groups corresponding to 11 bean chromosomes with an average marker distance of 1.0 cM. Both high and low recombination regions were observed in AP647 and the maximum distance between two loci was 45 cM on Pv01.

Eight traits namely yield, white mold disease incidence, 100 seed weight, days to flowering, days to maturity, plant height, lodging, and greenhouse disease severity (straw test) were analyzed through the multiple QTL model. Thirty six QTL were identified in AP630 in different years for seven traits (white mold disease incidence, seed yield, days to flowering, days to maturity, 100 seed weight, lodging and the straw test) and these QTL were located on 10 chromosomes. LOD scores ranged from the threshold of 2.5 to 10.5.

Fourteen QTL spread across 10 chromosomes were identified in AP647 in different years associated with seed yield, the greenhouse straw test, 100 seed weight, and number of days to maturity, number of days to flowering and plant canopy height. LOD scores ranged from 2.5 to 6.9 for these traits. Six new QTL for yield were identified on Pv01, Pv02, Pv03, Pv05 and Pv09 explaining 11 to 30% of total variation. Seven new QTL for white mold were identified on Pv01, Pv04, Pv07 and Pv08 and two were validated on Pv02 and Pv03 accounting for 19 to 41% of phenotypic variation.


Last Modified: 12/28/2014
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