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

Combination of meta‐analysis of QTL and GWAS to uncover the genetic architecture of seed yield and seed yield components in common bean
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DOI：
10.1002/tpg2.20328
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发表时间：
2023-04
期刊：
The Plant Genome
影响因子：
--
通讯作者：
P. Izquierdo;J. Kelly;S. Beebe;K. Cichy
P. Izquierdo;J. Kelly;S. Beebe;K. Cichy
中科院分区：
其他
文献类型：
--
作者：
P. Izquierdo;J. Kelly;S. Beebe;K. Cichy

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提高菜豆种子产量有助于改善粮食安全，并减少全球营养不良，因为这种作物的营养品质很高。然而，种子产量的复杂遗传结构和普遍的基因型与环境的相互作用使得增加遗传增益具有挑战性。本研究的目的是确定最一致的基因组区域与种子产量的组成部分和物候在过去的20年报告。在充足水分和干旱条件下，对21项独立研究中报告的394个种子产量构成因素和物候的数量性状位点（QTL）（MQTL-YC）进行了Meta分析。总共鉴定了58个不同遗传背景和环境的MQL-YC，与初始QTL的置信区间（CI）相比，平均降低了三倍。此外，通过全基因组关联（GWAS）报告的40个MQTL-YC与210个SNP峰位置共定位，指导候选基因的鉴定。这些MQL-YC与大豆和豌豆中报道的MQL-YC之间的比较基因组学允许鉴定跨物种共享的14个正向QTL-YC。本研究中使用的MQTL-YC、GWAS和比较基因组学的整合有助于发现和细化与种子产量组分相关的最一致的基因组区域，以用于植物育种。
Increasing seed yield in common bean could 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 and phenology reported in the last 20 years in common bean. A meta‐analysis of quantitative trait locus (QTL) for seed yield components and phenology (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 threefold 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 via genome‐wide association (GWAS), guiding the identification of candidate genes. Comparative genomics among 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 is useful to uncover and refine the most consistent genomic regions related with seed yield components for their use in plant breeding.