Genome-wide association study identifies candidate genes that affect plant height in Chinese elite maize (Zea mays L.) inbred lines.
Genome-wide association study identifies candidate genes that affect plant height in Chinese elite maize (Zea mays L.) inbred lines.
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全基因组关联研究鉴定了影响中国优良玉米 (Zea mays L.) 自交系株高的候选基因
DOI：
10.1371/journal.pone.0029229
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发表时间：
2011
期刊：
影响因子：
3.7
通讯作者：
Li X
中科院分区：
文献类型：
--
作者：
Weng J;Xie C;Hao Z;Wang J;Liu C;Li M;Zhang D;Bai L;Zhang S;Li X
背景通过引入矮秆植物以提高抗倒伏能力，结合早熟，可以提高许多作物的收获指数。自交系沈5003是我国玉米育种中广泛使用的矮秆性状的重要供体。此外，在多个玉米双亲群体中，已在bin 5.05-5.06中鉴定了一个控制株高的主要数量性状位点（QTL）。随着玉米全基因组序列公开的进展，本研究旨在利用全基因组关联分析（genome wide association studies，GWAS）技术对中国玉米自交系中影响株高的候选基因进行鉴定。方法和发现使用超过55，000个均匀间隔的SNP对总共284个玉米自交系进行基因分型，通过严格的质量控制从其中筛选出一组41，101个SNP用于进一步的数据分析。利用TASSEL软件实现的混合线性模型（MLM）控制群体结构，我们对株高进行了全基因组关联研究（GWAS）。共鉴定出204个SNPs（P≤0.0001）和105个含有编码区的基因组位点。含有与赤霉素（GA），生长素，和表观遗传途径相关的基因的四个位点可能参与自然变异，导致优良玉米自交系的矮化表型。其中，在6个沈5003衍生系中还发现了位于第5染色体上的一个矮秆有利等位基因（SNP PZE-105115518）。结论我们的研究中缺失了大量先前鉴定的矮秆基因，这一事实凸显了含有SNP PZE-105115518的基因与株高持续显着相关性的发现（P = 8.91e-10）及其在Shen 5003渐渗系中的证实。 本研究结果表明，在我国玉米育种模式中，选择了在玉米生产中发挥重要作用的特异等位基因。
Background The harvest index for many crops can be improved through introduction of dwarf stature to increase lodging resistance, combined with early maturity. The inbred line Shen5003 has been widely used in maize breeding in China as a key donor line for the dwarf trait. Also, one major quantitative trait locus (QTL) controlling plant height has been identified in bin 5.05–5.06, across several maize bi-parental populations. With the progress of publicly available maize genome sequence, the objective of this work was to identify the candidate genes that affect plant height among Chinese maize inbred lines with genome wide association studies (GWAS). Methods and Findings A total of 284 maize inbred lines were genotyped using over 55,000 evenly spaced SNPs, from which a set of 41,101 SNPs were filtered with stringent quality control for further data analysis. With the population structure controlled in a mixed linear model (MLM) implemented with the software TASSEL, we carried out a genome-wide association study (GWAS) for plant height. A total of 204 SNPs (P≤0.0001) and 105 genomic loci harboring coding regions were identified. Four loci containing genes associated with gibberellin (GA), auxin, and epigenetic pathways may be involved in natural variation that led to a dwarf phenotype in elite maize inbred lines. Among them, a favorable allele for dwarfing on chromosome 5 (SNP PZE-105115518) was also identified in six Shen5003 derivatives. Conclusions The fact that a large number of previously identified dwarf genes are missing from our study highlights the discovery of the consistently significant association of the gene harboring the SNP PZE-105115518 with plant height (P = 8.91e-10) and its confirmation in the Shen5003 introgression lines. Results from this study suggest that, in the maize breeding schema in China, specific alleles were selected, that have played important roles in maize production.