Genic and nongenic contributions to natural variation of quantitative traits in maize.
Genic and nongenic contributions to natural variation of quantitative traits in maize.
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DOI：
10.1101/gr.140277.112
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发表时间：
2012-12
期刊：
影响因子：
7
通讯作者：
Yu J
中科院分区：
文献类型：
--
作者：
Li X;Zhu C;Yeh CT;Wu W;Takacs EM;Petsch KA;Tian F;Bai G;Buckler ES;Muehlbauer GJ;Timmermans MC;Scanlon MJ;Schnable PS;Yu J
许多具有重要经济意义的作物的复杂基因组对了解许多数量性状的遗传控制提出了巨大的挑战，这些性状在作物生产、适应和进化中具有重要意义。基因组技术的进步需要与战略性基因设计和新观点相结合，以开辟新的领域。作为对个体基因靶向研究的补充，从数量性状的基因组扫描中发现的性状相关snp （TASs）的基因组分布的全球评估可以提供对遗传结构的见解，并有助于未来研究的设计。在这里，我们报告了不同基因组区域对玉米数量性状变异的相对贡献的第一个系统制表。我们发现TASs富集于非基因区域，特别是基因上游的5kb窗口内，这突出了多态性调节基因表达在形成自然变异中的重要性。与这些发现一致的是，玉米数量性状中44%-59%的表型变异由TASs共同解释，平均而言，79%的解释变异可归因于位于基因或基因上游5kb内的TASs，这些基因仅占基因组的13%。我们的研究结果表明，在具有复杂基因组的物种中，高效、经济的全基因组关联研究（GWAS）可以专注于基因和启动子区域。
The complex genomes of many economically important crops present tremendous challenges to understand the genetic control of many quantitative traits with great importance in crop production, adaptation, and evolution. Advances in genomic technology need to be integrated with strategic genetic design and novel perspectives to break new ground. Complementary to individual-gene–targeted research, which remains challenging, a global assessment of the genomic distribution of trait-associated SNPs (TASs) discovered from genome scans of quantitative traits can provide insights into the genetic architecture and contribute to the design of future studies. Here we report the first systematic tabulation of the relative contribution of different genomic regions to quantitative trait variation in maize. We found that TASs were enriched in the nongenic regions, particularly within a 5-kb window upstream of genes, which highlights the importance of polymorphisms regulating gene expression in shaping the natural variation. Consistent with these findings, TASs collectively explained 44%–59% of the total phenotypic variation across maize quantitative traits, and on average, 79% of the explained variation could be attributed to TASs located in genes or within 5 kb upstream of genes, which together comprise only 13% of the genome. Our findings suggest that efficient, cost-effective genome-wide association studies (GWAS) in species with complex genomes can focus on genic and promoter regions.
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影响因子：
12.3
作者：
Cirulli ET;Singh A;Shianna KV;Ge D;Smith JP;Maia JM;Heinzen EL;Goedert JJ;Goldstein DB;Center for HIV/AIDS Vaccine Immunology (CHAVI)
通讯作者：
Center for HIV/AIDS Vaccine Immunology (CHAVI)
影响因子：
48
作者：
Cloonan, Nicole;Forrest, Alistair R. R.;Grimmond, Sean M.
通讯作者：
Grimmond, Sean M.
影响因子：
56.9
作者：
Buckler, Edward S.;Holland, James B.;McMullen, Michael D.
通讯作者：
McMullen, Michael D.
稀有变体会产生整个基因组的关联。
影响因子：
9.8
作者：
Dickson SP;Wang K;Krantz I;Hakonarson H;Goldstein DB
通讯作者：
Goldstein DB
通过454转录组测序发现SNP。
影响因子：
7.2
作者：
Barbazuk, W Brad;Emrich, Scott J;Chen, Hsin D;Li, Li;Schnable, Patrick S
通讯作者：
Schnable, Patrick S