Population genomic and genome-wide association studies of agroclimatic traits in sorghum
Population genomic and genome-wide association studies of agroclimatic traits in sorghum
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DOI：
10.1073/pnas.1215985110
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发表时间：
2013-01-08
影响因子：
11.1
通讯作者：
Kresovich, Stephen
中科院分区：
文献类型：
--
作者：
Morris, Geoffrey P.;Ramu, Punna;Kresovich, Stephen
高粱是发展中国家半干旱地区人民的主食，加快高粱作物改良是确保气候变化背景下全球粮食安全的关键。为了促进高粱的基因发现和分子育种，我们在全球971份适应不同农业气候条件的种质中鉴定了265，000个单核苷酸多态性（SNP）。使用这个全基因组SNP图谱，我们已经确定了人口结构的地理起源和形态类型，并确定了古代作物扩散到非洲和亚洲不同农业气候区的模式。为了更好地了解高粱多样化的基因组模式，我们量化了整个基因组的核苷酸多样性，连锁不平衡和重组率的变化。在地方品种的核苷酸多样性分析，我们发现周围的淀粉代谢基因的选择性扫描的证据，而在地方品种衍生的渐渗系，我们发现渐渗周围已知的高度和成熟度位点。为了确定其他位点的主要农业气候性状的变化，我们进行了全基因组关联研究（GWAS）的株高组成部分和花序结构。GWAS定位了几个经典的株高基因座，花序构型的候选基因。最后，我们跟踪携带等位基因的多个单倍型的独立传播身材矮小或长花序分支。高粱SNP变异的全基因组图谱为通过标记辅助育种和基因组选择进行作物改良提供了基础。
Accelerating crop improvement in sorghum, a staple food for people in semiarid regions across the developing world, is key to ensuring global food security in the context of climate change. To facilitate gene discovery and molecular breeding in sorghum, we have characterized similar to 265,000 single nucleotide polymorphisms (SNPs) in 971 worldwide accessions that have adapted to diverse agroclimatic conditions. Using this genome-wide SNP map, we have characterized population structure with respect to geographic origin and morphological type and identified patterns of ancient crop diffusion to diverse agroclimatic regions across Africa and Asia. To better understand the genomic patterns of diversification in sorghum, we quantified variation in nucleotide diversity, linkage disequilibrium, and recombination rates across the genome. Analyzing nucleotide diversity in landraces, we find evidence of selective sweeps around starch metabolism genes, whereas in landrace-derived introgression lines, we find introgressions around known height and maturity loci. To identify additional loci underlying variation in major agroclimatic traits, we performed genome-wide association studies (GWAS) on plant height components and inflorescence architecture. GWAS maps several classical loci for plant height, candidate genes for inflorescence architecture. Finally, we trace the independent spread of multiple haplotypes carrying alleles for short stature or long inflorescence branches. This genome-wide map of SNP variation in sorghum provides a basis for crop improvement through marker-assisted breeding and genomic selection.