Genome-wide association mapping and genomic prediction of water deficit stress tolerance indices in spring bread wheat

IF 1 Q4 GENETICS & HEREDITY Gene Reports Pub Date : 2024-10-02 DOI:10.1016/j.genrep.2024.102054

Ahmad MajidiMehr , Mohammad Hadi Pahlavani , Zakaria El Gataa , Reza Amiri-Fahliani

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Abstract

Genome-wide association mapping (GWAM) is crucial for identifying the genetic architecture of quantitative traits, such as drought tolerance indices in bread wheat. This study aims to identify Marker-Trait Associations (MTAs) and genes related to drought tolerance indices in wheat. Seven drought tolerance indices were calculated based on grain weight per spike under field drought stress (FDS) and field non-stress (FNS) conditions. These indices included mean productivity (MP), geometric mean productivity (GMP), relative drought index (RDI), stress tolerance index (STI), tolerance index (TOL), stress susceptibility index (SSI), and yield stability index (YSI). Genotyping of the samples was performed using single nucleotide polymorphism (SNP) markers. A total of 96 MTAs were identified for the studied indices and conditions FNS and FDS in this experiment, with a threshold of -log10p ≥ 3.0. These included FNS, FDS, GMP, MP, STI, SSI, RDI, and YSI, with 15, 11, 16, 16, 20, 6, 6, and 6 MTAs, respectively. The MTAs identified for the drought tolerance indices GMP, MP, and STI were located on chromosomes 2 A, 3B, and 6 A, respectively. Moreover, this study identified four genes related to the indices, namely “TraesCS2B02G000100,” “TraesCS3A02G000100,” “TraesCS2B02G000200,” and “TraesCS4B02G000100”. These genes play a crucial role in drought tolerance and can be utilized for marker-assisted selection to enhance drought tolerance wheat genotypes.

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全基因组关联图谱和春季面包小麦耐缺水胁迫指数的基因组预测

全基因组关联图谱（GWAM）对于确定面包小麦耐旱指数等数量性状的遗传结构至关重要。本研究旨在鉴定与小麦耐旱指数相关的标记-性状关联（MTAs）和基因。在田间干旱胁迫（FDS）和田间非胁迫（FNS）条件下，根据每穗粒重计算了七个抗旱指数。这些指数包括平均生产力（MP）、几何平均生产力（GMP）、相对干旱指数（RDI）、胁迫耐受指数（STI）、耐受指数（TOL）、胁迫易感指数（SSI）和产量稳定指数（YSI）。利用单核苷酸多态性（SNP）标记对样本进行了基因分型。在本实验中，针对所研究的指数和条件 FNS 和 FDS 共鉴定出 96 个 MTA，阈值为 -log10p≥3.0。其中包括 FNS、FDS、GMP、MP、STI、SSI、RDI 和 YSI，分别有 15、11、16、16、20、6、6 和 6 个 MTA。耐旱指数 GMP、MP 和 STI 的 MTA 分别位于染色体 2 A、3B 和 6 A 上。此外，本研究还发现了与这些指数相关的四个基因，即 "TraesCS2B02G000100"、"TraesCS3A02G000100"、"TraesCS2B02G000200 "和 "TraesCS4B02G000100"。这些基因在抗旱性中起着至关重要的作用，可用于标记辅助选择，以提高小麦基因型的抗旱性。

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来源期刊

Gene Reports Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

3.30

自引率

7.70%

发文量

246

审稿时长

49 days

期刊介绍： Gene Reports publishes papers that focus on the regulation, expression, function and evolution of genes in all biological contexts, including all prokaryotic and eukaryotic organisms, as well as viruses. Gene Reports strives to be a very diverse journal and topics in all fields will be considered for publication. Although not limited to the following, some general topics include: DNA Organization, Replication & Evolution -Focus on genomic DNA (chromosomal organization, comparative genomics, DNA replication, DNA repair, mobile DNA, mitochondrial DNA, chloroplast DNA). Expression & Function - Focus on functional RNAs (microRNAs, tRNAs, rRNAs, mRNA splicing, alternative polyadenylation) Regulation - Focus on processes that mediate gene-read out (epigenetics, chromatin, histone code, transcription, translation, protein degradation). Cell Signaling - Focus on mechanisms that control information flow into the nucleus to control gene expression (kinase and phosphatase pathways controlled by extra-cellular ligands, Wnt, Notch, TGFbeta/BMPs, FGFs, IGFs etc.) Profiling of gene expression and genetic variation - Focus on high throughput approaches (e.g., DeepSeq, ChIP-Seq, Affymetrix microarrays, proteomics) that define gene regulatory circuitry, molecular pathways and protein/protein networks. Genetics - Focus on development in model organisms (e.g., mouse, frog, fruit fly, worm), human genetic variation, population genetics, as well as agricultural and veterinary genetics. Molecular Pathology & Regenerative Medicine - Focus on the deregulation of molecular processes in human diseases and mechanisms supporting regeneration of tissues through pluripotent or multipotent stem cells.