Institute of Crop Science, Chinese Academy of Agricultural Sciences, The National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, China.
PLoS One. 2011;6(12):e29229. doi: 10.1371/journal.pone.0029229. Epub 2011 Dec 28.
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).
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.
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.
通过引入矮化株型来提高抗倒伏能力，并结合早熟性，可以提高许多作物的收获指数。自交系 Shen5003 作为矮化性状的关键供体系，已在中国玉米育种中广泛应用。此外，在几个玉米双亲群体中，已在 bin 5.05-5.06 上鉴定到一个控制株高的主要数量性状位点（QTL）。随着玉米基因组序列的公开进展，本工作的目的是通过全基因组关联研究（GWAS）鉴定中国玉米自交系中影响株高的候选基因。
共对 284 个玉米自交系进行了基因组分型，使用了超过 55000 个均匀分布的 SNPs，其中一组 41101 个 SNPs 通过严格的质量控制进行了过滤，以便进一步进行数据分析。通过软件 TASSEL 中的混合线性模型（MLM）控制群体结构，我们对株高进行了全基因组关联研究（GWAS）。共鉴定到 204 个 SNP（P≤0.0001）和 105 个含有编码区的基因组位点。包含与赤霉素（GA）、生长素和表观遗传途径相关基因的 4 个位点可能参与了导致优良玉米自交系矮化表型的自然变异。其中，在六个 Shen5003 衍生系中也鉴定到位于第 5 号染色体上与矮化相关的有利等位基因（SNP PZE-105115518）。
我们的研究中缺少大量先前鉴定的矮化基因，这一事实突出了 SNP PZE-105115518 所包含基因与株高的一致性显著关联（P=8.91e-10）及其在 Shen5003 导入系中的确认。本研究结果表明，在中国的玉米育种方案中，选择了特定的等位基因，这些等位基因在玉米生产中发挥了重要作用。
