Genetic dissection of yield-related traits via genome-wide association analysis across multiple environments in wild soybean (Glycine soja Sieb. and Zucc.)
Genetic dissection of yield-related traits via genome-wide association analysis across multiple environments in wild soybean (Glycine soja Sieb. and Zucc.)
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通过野生大豆（Glycine soja Sieb. 和 Zucc.）跨多种环境的全基因组关联分析对产量相关性状进行遗传剖析
DOI：
10.1007/s00425-019-03329-6
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发表时间：
2020-01-06
期刊：
影响因子：
4.3
通讯作者：
Kan, Guizhen
中科院分区：
文献类型：
--
作者：
Hu, Dezhou;Zhang, Huairen;Kan, Guizhen
在不同环境下的野生大豆群体中，共有41个SNPs与5个产量相关性状显著相关，候选基因GsCID1与粒重相关。这些结果可能有助于栽培大豆的改良。与作物相关的野生物种为作物改良提供了新的遗传多样性来源。野生大豆(Glyine soja Sieb.)和Zucc.)是栽培大豆[Glyine max(L.)[MERR.]可作为产量改良的重要遗传资源。在这项研究中，利用基因组关联研究，在113份野生大豆种质中的96份具有114,090个单核苷酸多态(等位基因频率≤0.05)，在多个环境中鉴定了与5个产量相关性状相关的SNPs。共有41个SNPs与两个或两个以上环境中的性状显著相关(显著阈值P≤为8.76×10-6)，其中29个、7个、3个和2个SNP分别检测到百粒重(Sw)、成熟期(MT)、单株籽粒产量(SY)和开花时间(FT)。对大豆W05参考基因组进行BLAST搜索，根据这41个有意义的SNPs确定了20个候选基因。一个候选基因GsCID1(Glysoja.04g010563)含有两个重要的SNPs-AX-93713187和AX-93713188，前者具有非同义突变，后者具有同义突变。GsCID1在基于公共信息资源的种子发育过程中高度表达。该基因的多态与Sw相关。我们开发了GsCID1的衍生切割扩增多态序列(DCAPS)标记，该标记与Sw高度相关，并被证实是一个功能标记。综上所述，所揭示的SNPs/基因有助于了解野生大豆产量相关性状的遗传结构，可作为潜在的外来资源用于提高栽培大豆产量。
A total of 41 SNPs were identified as significantly associated with five yield-related traits in wild soybean populations across multiple environments, and the candidate gene GsCID1 was found to be associated with seed weight. These results may facilitate improvements in cultivated soybean. Crop-related wild species contain new sources of genetic diversity for crop improvement. Wild soybean (Glycine soja Sieb. and Zucc.) is the progenitor of cultivated soybean [Glycine max (L.) Merr.] and can be used as an essential genetic resource for yield improvements. In this research, using genome-wide association study (GWAS) in 96 out of 113 wild soybean accessions with 114,090 single nucleotide polymorphisms (SNPs) (with minor allele frequencies ≤ 0.05), SNPs associated with five yield-related traits were identified across multiple environments. In total, 41 SNPs were significantly associated with the traits in two or more environments (significance threshold P ≤ 8.76 × 10-6), with 29, 7, 3, and 2 SNPs detected for 100-seed weight (SW), maturity time (MT), seed yield per plant (SY) and flowering time (FT), respectively. BLAST search against the Glycine soja W05 reference genome was performed, 20 candidate genes were identified based on these 41 significant SNPs. One candidate gene, GsCID1 (Glysoja.04g010563), harbored two significant SNPs-AX-93713187, with a non-synonymous mutation, and AX-93713188, with a synonymous mutation. GsCID1 was highly expressed during seed development based on public information resources. The polymorphisms in this gene were associated with SW. We developed a derived cleaved amplified polymorphic sequence (dCAPS) marker for GsCID1 that was highly associated with SW and was validated as a functional marker. In summary, the revealed SNPs/genes are useful for understanding the genetic architecture of yield-related traits in wild soybean, which could be used as a potential exotic resource to improve cultivated soybean yields.