Singh Sahadev, Gaurav Shailendra Singh, Vasistha Neeraj Kumar, Kumar Uttam, Joshi Arun Kumar, Mishra Vinod Kumar, Chand Ramesh, Gupta Pushpendra Kumar
Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India.
Department of Genetics-Plant Breeding and Biotechnology, Dr Khem Singh Gill, Akal College of Agriculture, Eternal University, Sirmaur, India.
Front Plant Sci. 2023 Jan 18;13:1036064. doi: 10.3389/fpls.2022.1036064. eCollection 2022.
Genetic architecture of resistance to spot blotch in wheat was examined using a Genome-Wide Association Study (GWAS) involving an association panel comprising 303 diverse genotypes. The association panel was evaluated at two different locations in India including Banaras Hindu University (BHU), Varanasi (Uttar Pradesh), and Borlaug Institute for South Asia (BISA), Pusa, Samastipur (Bihar) for two consecutive years (2017-2018 and 2018-2019), thus making four environments (E1, BHU 2017-18; E2, BHU 2018-19; E3, PUSA, 2017-18; E4, PUSA, 2018-19). The panel was genotyped for 12,196 SNPs based on DArT-seq (outsourced to DArT Ltd by CIMMYT); these SNPs included 5,400 SNPs, which could not be assigned to individual chromosomes and were therefore, described as unassigned by the vendor. Phenotypic data was recorded on the following three disease-related traits: (i) Area Under Disease Progress Curve (AUDPC), (ii) Incubation Period (IP), and (iii) Lesion Number (LN). GWAS was conducted using each of five different models, which included two single-locus models (CMLM and SUPER) and three multi-locus models (MLMM, FarmCPU, and BLINK). This exercise gave 306 MTAs, but only 89 MTAs (33 for AUDPC, 30 for IP and 26 for LN) including a solitary MTA detected using all the five models and 88 identified using four of the five models (barring SUPER) were considered to be important. These were used for further analysis, which included identification of candidate genes (CGs) and their annotation. A majority of these MTAs were novel. Only 70 of the 89 MTAs were assigned to individual chromosomes; the remaining 19 MTAs belonged to unassigned SNPs, for which chromosomes were not known. Seven MTAs were selected on the basis of minimum P value, number of models, number of environments and location on chromosomes with respect to QTLs reported earlier. These 7 MTAs, which included five main effect MTAs and two for epistatic interactions, were considered to be important for marker-assisted selection (MAS). The present study thus improved our understanding of the genetics of resistance against spot blotch in wheat and provided seven MTAs, which may be used for MAS after due validation.
利用全基因组关联研究（GWAS）对小麦抗叶斑病的遗传结构进行了研究，该研究涉及一个由303个不同基因型组成的关联群体。该关联群体在印度的两个不同地点进行了评估，包括瓦拉纳西的贝拿勒斯印度教大学（BHU）（北方邦）和比哈尔邦萨马斯蒂布尔的博洛格南亚研究所（BISA），连续两年（2017 - 2018年和2018 - 2019年），从而形成了四个环境（E1，BHU 2017 - 18；E2，BHU 2018 - 19；E3，PUSA 2017 - 18；E4，PUSA 2018 - 19）。基于DArT - seq对该群体进行了12,196个单核苷酸多态性（SNP）的基因分型（由国际玉米小麦改良中心外包给DArT有限公司）；这些SNP包括5,400个无法定位到单个染色体上的SNP，因此供应商将其描述为未定位。记录了以下三个与病害相关性状的表型数据：（i）病害进展曲线下面积（AUDPC），（ii）潜育期（IP），以及（iii）病斑数（LN）。使用五种不同模型中的每一种进行GWAS，其中包括两个单基因座模型（CMLM和SUPER）和三个多基因座模型（MLMM、FarmCPU和BLINK）。该研究共得到306个显著关联位点（MTA），但仅89个MTA（AUDPC相关33个、IP相关30个和LN相关26个）被认为是重要的，其中包括一个使用所有五个模型检测到的单独MTA以及88个使用五个模型中的四个（不包括SUPER）鉴定出的MTA。这些被用于进一步分析，包括鉴定候选基因（CG）及其注释。这些MTA中的大多数是新发现的。89个MTA中只有70个被定位到单个染色体上；其余19个MTA属于未定位的SNP，其所在染色体未知。根据最小P值、模型数量、环境数量以及相对于先前报道位点在染色体上的位置，选择了7个MTA。这7个MTA包括5个主效MTA和2个上位性互作MTA，被认为对标记辅助选择（MAS）很重要。本研究因此增进了我们对小麦抗叶斑病遗传机制的理解，并提供了7个MTA，经过适当验证后可用于MAS。
