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ARS Home » Midwest Area » East Lansing, Michigan » Sugarbeet and Bean Research » Research » Publications at this Location » Publication #395955
Research Project: Utilizing Genetic Diversity within Phaseolus vulgaris to Develop Dry Beans with Enhanced Functional Properties

Location: Sugarbeet and Bean Research

Title: Combination of meta-analysis of QTL and GWAS to uncover the genetic architecture of seed yield and seed yield components in common bean

Author
item IZQUIERDO, PAULO - Michigan State University
item KELLY, JAMES - Michigan State University
item BEEBE, STEVE - Alliance Of Bioversity International And The International Center For Tropical Agriculture (CIAT)
item Cichy, Karen

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/1/2023
Publication Date: 4/21/2023
Citation: Izquierdo, P., Kelly, J.D., Beebe, S., Cichy, K.A. 2023. Combination of meta-analysis of QTL and GWAS to uncover the genetic architecture of seed yield and seed yield components in common bean. The Plant Genome. 16(2). Article e20328. https://doi.org/10.1002/tpg2.20328.
DOI: https://doi.org/10.1002/tpg2.20328

Interpretive Summary: Like most grain legumes, seed yield is a universally important trait in dry bean breeding programs and a major factor of varietal adoption and success. Genetic characterization of seed yield in dry beans has been studied in numerous populations and in various temperate and tropical bean growing regions of the world. This study presents the compilation of 20 plus years of genetic results for seed yield and components consisting of 743 genomic data points from 21 independent studies to identify which regions of the bean genome most contribute to increasing seed yields. In total 58 key genomic regions associated with seed yield were identified, 51 of which were important in drought stress as well as non-drought conditions, and 14 of which were similar to seed yield related regions in other legume crops including soybean and pea. The integration of genomic region and comparative genomics used in this study will be applicable to breeding for increased yields.

Technical Abstract: Increasing seed yield in common bean will help to improve food security and reduce malnutrition globally due to the high nutritional quality of this crop. However, the complex genetic architecture and prevalent genotype by environment interactions for seed yield makes increasing genetic gains challenging. The aim of this study was to identify the most consistent genomic regions related with seed yield components in common bean reported in the last 20 years. A meta-analysis of QTL for seed yield components (MQTL-YC) was performed for 394 QTL reported in 21 independent studies under sufficient water and drought conditions. In total, 58 MQTL-YC over different genetic backgrounds and environments were identified, reducing three-fold on average the confidence interval (CI) compared with the CI for the initial QTL. Furthermore, 40 MQTL-YC identified were co-located with 210 SNP peak positions reported on GWAS, guiding the identification of candidate genes. Comparative genomics among of these MQTL-YC with MQTL-YC reported in soybean and pea allowed the identification of 14 orthologous MQTL-YC shared across species. The integration of MQTL-YC, GWAS and comparative genomics used in this study will be useful to refine and uncover the most consistent genomic regions related with seed yield components for their use in plant breeding.