Cao Yongce, Jia Shihao, Chen Liuxing, Zeng Shunan, Zhao Tuanjie, Karikari Benjamin
Shaanxi Key Laboratory of Chinese Jujube, College of Life Science, Yan'an University, Yan'an, Shaanxi, 716000 China.
Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, National Center for Soybean Improvement, National Key Laboratory for Crop Genetics and Germplasm Enhancement, Soybean Research Institute of Nanjing Agricultural University, Nanjing, 210095 Jiangsu China.
Mol Breed. 2022 Jun 28;42(7):38. doi: 10.1007/s11032-022-01310-y. eCollection 2022 Jul.
The hundred-seed weight (HSW) is an important yield component and one of the principal breeding traits in soybean. More than 250 quantitative trait loci (QTL) for soybean HSW have been identified. However, most of them have a large genomic region or are environmentally sensitive, which provide limited information for improving the phenotype in marker-assisted selection (MAS) and identifying the candidate genes. Here, we utilized 281 soybean accessions with 58,112 single nucleotide polymorphisms (SNPs) to dissect the genetic basis of HSW in across years in the northern Shaanxi province of China through one single-locus (SL) and three multi-locus (ML) genome-wide association study (GWAS) models. As a result, one hundred and fifty-four SNPs were detected to be significantly associated with HSW in at least one environment via SL-GWAS model, and 27 of these 154 SNPs were detected in all (three) environments and located within 7 linkage disequilibrium (LD) block regions with the distance of each block ranged from 40 to 610 Kb. A total of 15 quantitative trait nucleotides (QTNs) were identified by three ML-GWAS models. Combined with the results of different GWAS models, the 7 LD block regions associated with HSW detected by SL-GWAS model could be verified directly or indirectly by the results of ML-GWAS models. Eleven candidate genes underlying the stable loci that may regulate seed weight in soybean were predicted. The significantly associated SNPs and the stable loci as well as predicted candidate genes may be of great importance for marker-assisted breeding, polymerization breeding, and gene discovery for HSW in soybean.
The online version contains supplementary material available at 10.1007/s11032-022-01310-y.
百粒重（HSW）是大豆重要的产量构成因素之一，也是大豆主要的育种性状。目前已鉴定出250多个与大豆百粒重相关的数量性状位点（QTL）。然而，其中大多数位点的基因组区域较大或对环境敏感，这为标记辅助选择（MAS）中改善表型和鉴定候选基因提供的信息有限。在此，我们利用281份大豆种质材料和58112个单核苷酸多态性（SNP），通过单基因座（SL）和三个多基因座（ML）全基因组关联研究（GWAS）模型，剖析中国陕西省北部多年种植条件下大豆百粒重的遗传基础。结果表明，通过SL-GWAS模型在至少一种环境中检测到154个与百粒重显著相关的SNP，其中27个SNP在所有（三种）环境中均被检测到，并位于7个连锁不平衡（LD）块区域内，每个块的距离在40至610 Kb之间。通过三个ML-GWAS模型共鉴定出15个数量性状核苷酸（QTN）。结合不同GWAS模型的结果，SL-GWAS模型检测到的与百粒重相关的7个LD块区域可通过ML-GWAS模型的结果直接或间接得到验证。预测了11个可能调控大豆种子重量的稳定位点的候选基因。这些显著相关的SNP、稳定位点以及预测的候选基因对于大豆百粒重的标记辅助育种、聚合育种和基因发现可能具有重要意义。
在线版本包含可在10.1007/s11032-022-01310-y获取的补充材料。
