人口农业气候特征的高粱基因组和全基因组关联研究

来源：仪方生物 www.yeslab.com

高梁是位于半干旱的发展中国家的主食，加速改进高粱类谷物的质量是解决应对气候变化所引发的食品安全的关键。为研究高粱基因发现和分子育种的便利，通过世界各地的971个高粱品种的基因研究，发现265,000个单核苷酸多态性位点（SNPs）。利用这些全基因组SNP图谱，研究者描述了地理起源的群体结构、形态特征，并确认出祖先谷物向多样性农业气候的亚非地区扩散的模式。为更好地理解高粱基因组多样化，研究者量化了单核苷酸变异、连锁不平衡、基因组间的重组率。通过分析地方品种的核苷酸多样性，研究组发现淀粉代谢基因的选择性扫描的证据，籍此在地方品种衍生的渗入系中的位于发现已知高度和成熟的位点附近。为了鉴定主要农业气候特征之上的额外特征位点，研究者展开了全基因组关联研究（GWAS）研究植物高度组分和花序架构。全基因组关联分析（GWAS）谱绘了一些植物高度、花序候选基因的经典位点。最后，研究者追踪携带短小或长花序分支的多个单倍体独立传播。此基因组水平的高粱SNP变异图谱通过遗传标记育种和基因组选择为改善谷物提供了基础。

Population genomic and genome-wide association studies of agroclimatic traits in sorghum

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 ∼265,000 single nucleotide polymorphisms (SNPs) in 971 worldwide accessions that have adapted to diverse agroclimatic conditions. Using this genome-wide SNPmap, 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.