Devate Narayana Bhat, Krishna Hari, Parmeshwarappa Sunil Kumar V, Manjunath Karthik Kumar, Chauhan Divya, Singh Shweta, Singh Jang Bahadur, Kumar Monu, Patil Ravindra, Khan Hanif, Jain Neelu, Singh Gyanendra Pratap, Singh Pradeep Kumar
Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India.
Division of Genetics and Plant Breeding, ICAR-Indian Agricultural Research Institute, Gauria Karma, India.
Front Plant Sci. 2022 Aug 16;13:943033. doi: 10.3389/fpls.2022.943033. eCollection 2022.
Identification of marker trait association is a prerequisite for marker-assisted breeding. To find markers linked with traits under heat and drought stress in bread wheat ( L.), we performed a genome-wide association study (GWAS). GWAS mapping panel used in this study consists of advanced breeding lines from the IARI stress breeding programme produced by pairwise and complex crosses. Phenotyping was done at multi locations namely New Delhi, Karnal, Indore, Jharkhand and Pune with augmented-RCBD design under different moisture and heat stress regimes, namely timely sown irrigated (IR), timely sown restricted irrigated (RI) and late sown (LS) conditions. Yield and its component traits, ., Days to Heading (DH), Days to Maturity (DM), Normalized Difference Vegetation Index (NDVI), Chlorophyll Content (SPAD), Canopy temperature (CT), Plant Height (PH), Thousand grain weight (TGW), Grain weight per spike (GWPS), Plot Yield (PLTY) and Biomass (BMS) were phenotyped. Analysis of variance and descriptive statistics revealed significant differences among the studied traits. Genotyping was done using the 35k SNP Wheat Breeder's Genotyping Array. Population structure and diversity analysis using filtered 10,546 markers revealed two subpopulations with sufficient diversity. A large whole genome LD block size of 7.15 MB was obtained at half LD decay value. Genome-wide association search identified 57 unique markers associated with various traits across the locations. Twenty-three markers were identified to be stable, among them nine pleiotropic markers were also identified. search of the identified markers against the IWGSC ref genome revealed the presence of a majority of the SNPs at or near the gene coding region. These SNPs can be used for marker-assisted transfer of genes/QTLs after validation to develop climate-resilient cultivars.
鉴定标记性状关联是标记辅助育种的前提条件。为了找到与面包小麦（L.）在高温和干旱胁迫下的性状相关的标记，我们进行了全基因组关联研究（GWAS）。本研究中使用的GWAS作图群体由印度农业研究机构（IARI）胁迫育种计划通过成对杂交和复合杂交产生的先进育种系组成。在新德里、卡纳尔、印多尔、贾坎德邦和浦那等多个地点进行表型分析，采用增广随机区组设计，设置不同的水分和热胁迫条件，即适时播种灌溉（IR）、适时播种限制灌溉（RI）和晚播（LS）条件。对产量及其构成性状，如抽穗天数（DH）、成熟天数（DM）、归一化植被指数（NDVI）、叶绿素含量（SPAD）、冠层温度（CT）、株高（PH）、千粒重（TGW）、每穗粒重（GWPS）、小区产量（PLTY）和生物量（BMS）进行了表型分析。方差分析和描述性统计显示所研究的性状之间存在显著差异。使用35k SNP小麦育种家基因分型芯片进行基因分型。利用筛选出的10546个标记进行群体结构和多样性分析，发现了两个具有足够多样性的亚群。在半LD衰减值时获得了7.15 MB的大的全基因组LD块大小。全基因组关联搜索确定了57个与各地不同性状相关的独特标记。鉴定出23个稳定标记，其中还鉴定出9个多效性标记。将鉴定出的标记与国际小麦基因组测序联盟（IWGSC）参考基因组进行比对，发现大多数SNP位于基因编码区或其附近。这些SNP经验证后可用于标记辅助的基因/QTL转移，以培育适应气候变化的品种。
