Haplotype analysis of key genes governing grain yield and quality traits across 3K RG panel reveals scope for the development of tailor-made rice with enhanced genetic gains
Haplotype analysis of key genes governing grain yield and quality traits across 3K RG panel reveals scope for the development of tailor-made rice with enhanced genetic gains
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DOI：
10.1111/pbi.13087
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发表时间：
2019-08-01
影响因子：
13.8
通讯作者：
Kumar, Arvind
中科院分区：
文献类型：
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作者：
Abbai, Ragavendran;Singh, Vikas Kumar;Kumar, Arvind
尽管在水稻中已经报道了控制各种主要性状的几种基因，但用于开发理想品种的优良单倍型组合仍然难以捉摸。在这项研究中，对影响谷物产量（87 个基因）和谷物品质（33 个基因）的 120 个先前功能表征的基因进行单倍型分析，揭示了 3K 水稻基因组 (RG) 组中的显着变异。对于选定的基因，使用现有数据集和共表达网络进行元表达分析提供了系统级别的见解。此外，我们对这 120 个基因进行了基于候选基因的关联研究，并鉴定了 21 个控制 10 个谷物产量和品质性状的强相关基因。我们在对 3K RG panel 的子集进行表型分析时报告了优越的单倍型，SD1-H8 在 3K RG panel 中的单倍型频率 (HF) 为 30.13%，MOC1-H9 (HF: 23.08%)、IPA1-H14 (HF: 6.64%)、DEP3-H2 (HF: 5.59%)、DEP1-H2 (HF: HF: 37.53%)、SP1-H3 (HF: 5.05%)、LAX1-H5 (HF: 1.56%)、LP-H13 (3.64%)、OSH1-H4 (5.52%)、PHD1-H14 (HF: 15.21%)、AGO7-H15 (HF: 3.33%)、ROC5-H2 (31.42%)、RSR1-H8 (HF: 4.20%) 和 OsNAS3-H2 (HF: 1.00%)。对于抽穗期，Ghd7-H8 (HF: 3.08%)、TOB1-H10 (HF: 4.60%) 开花较早，Ghd7-H14 (HF: 42.60%)、TRX1-H9 (HF: 27.97%)、OsVIL3-H14 (HF: 1.72%) 开花时间中等，而 Ghd7-H6 (HF: 1.65%)、SNB-H9(HF:9.35%)开花较晚。 GS5-H4 (HF: 65.84%) 为细粒，GS5-H5 (HF: 29.00%)、GW2-H2 (HF: 4.13%) 为中等细粒，GS5-H9 (HF: 2.15%) 为粗粒。此外，单倍型分析解释了所选巨型品种优越性的可能遗传基础。总体而言，这项研究表明，通过基于单倍型的育种，有可能开发出具有目标基因的优质单倍型组合的下一代定制水稻，以满足未来食品和营养需求。
Though several genes governing various major traits have been reported in rice, their superior haplotype combinations for developing ideal variety remains elusive. In this study, haplotype analysis of 120 previously functionally characterized genes, influencing grain yield (87 genes) and grain quality (33 genes) revealed significant variations in the 3K rice genome (RG) panel. For selected genes, meta-expression analysis using already available datasets along with co-expression network provided insights at systems level. Also, we conducted candidate gene based association study for the 120 genes and identified 21 strongly associated genes governing 10-grain yield and quality traits. We report superior haplotypes upon phenotyping the subset of 3K RG panel, SD1-H8 with haplotype frequency (HF) of 30.13% in 3K RG panel, MOC1-H9 (HF: 23.08%), IPA1-H14 (HF: 6.64%), DEP3-H2 (HF: 5.59%), DEP1-H2 (HF: 37.53%), SP1-H3 (HF: 5.05%), LAX1-H5 (HF: 1.56%), LP-H13 (3.64%), OSH1-H4 (5.52%), PHD1-H14 (HF: 15.21%), AGO7-H15 (HF: 3.33%), ROC5-H2 (31.42%), RSR1-H8 (HF: 4.20%) and OsNAS3-H2 (HF: 1.00%). For heading date, Ghd7-H8 (HF: 3.08%), TOB1-H10 (HF: 4.60%) flowered early, Ghd7-H14 (HF: 42.60%), TRX1-H9 (HF: 27.97%), OsVIL3-H14 (HF: 1.72%) for medium duration flowering, while Ghd7-H6 (HF: 1.65%), SNB-H9 (HF: 9.35%) were late flowering. GS5-H4 (HF: 65.84%) attributed slender, GS5-H5 (HF: 29.00%), GW2-H2 (HF: 4.13%) were medium slender and GS5-H9 (HF: 2.15%) for bold grains. Furthermore, haplotype analysis explained possible genetic basis for superiority of selected mega-varieties. Overall, this study suggests the possibility for developing next-generation tailor-made rice with superior haplotype combinations of target genes suiting future food and nutritional demands via haplotype-based breeding.