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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Soybean Genomics & Improvement Laboratory » Research » Publications at this Location » Publication #325231

Title: Joint linkage QTL mapping for yield and agronomic traits in a composite map of three common bean RIL populations

item HOYOS-VILLEGAS, V - Michigan State University
item Song, Qijian
item WRIGHT, EVAN - Michigan State University
item BEEBE, STEPHEN - International Center For Tropical Agriculture (CIAT)
item KELLY, JAMES - Michigan State University

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/6/2016
Publication Date: 5/14/2016
Citation: Hoyos-Villegas, V., Song, Q., Wright, E.M., Beebe, S.E., Kelly, J.D. 2016. Joint linkage QTL mapping for yield and agronomic traits in a composite map of three common bean RIL populations. Crop Science. 56(5):2546-2563.

Interpretive Summary: An estimated 60% of common bean production is affected by drought. This issue is of particular importance for small red beans, as it is grown in many drought-prone environments of sub-Saharan Africa. In this study, multiple populations were created by crossing drought tolerant breeding lines with a susceptible cultivar in small red beans, and the objective was to identify genes associated with drought resistance and other traits under rainfed and water-sufficient conditions. A total of 14 gene regions associated with drought tolerance and high yield-related traits were identified on six chromosomes. The study confirmed previously reported regions on five chromosomes and identified a new one. The findings will increase the efficiency of common bean breeding programs through marker-assisted selection and help breeders select for cultivars with improved yield and drought resistance in their breeding programs.

Technical Abstract: Bean production is challenged by many limitations with drought being among the top causes of crop failure worldwide. An estimated 60% of common bean production is affected by drought. In this study, we constructed three small red-seeded bean RIL populations (S48M, S94M and S95M) with a common parent (Merlot) and performed joint interval mapping analysis as a small nested association mapping (NAM) population for agronomic traits and performance under rainfed conditions in Michigan. The objective was to identify novel sources of improved performance and genomic regions associated with desirable traits under rainfed and water-sufficient conditions in small red bean breeding materials adapted to temperate zones. A composite linkage map was constructed using single nucleotide polymorphism (SNP) markers from the three populations and resulted in an improved version of the individual linkage maps, shown by a greater genome span covered in the composite map (909 cM). A number of QTL of different size effects were identified for seed yield (R2=15.4 to 30.7%), seed size (R2=16.4 to 20.2%), days to flowering (R2=12.4 to 36.1%), days to maturity (R2=16.2%), lodging score (R2=10.3 to 12.9%) and canopy height (R2=17%). Our study confirmed previously reported QTL on five chromosomes and identified a new QTL for canopy height on chromosome Pv10. The use of a composite map and QTL analysis under a NAM population structure increased our ability to detect small effect QTL that were segregating in at least two of the populations, but would not have been detected using individual linkage maps due in part to insufficient power associated with small population sizes.