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

这篇高粱的重测序文章于2013年发表在PANS上。

材料:选自世界各地的971份高粱品种(Of these accessions, 238 are landrace-derived sorghum conversion lines, in which alleles for short stature and early maturity were introgressed into tropical landraces to facilitate the use of tropical germplasm in temperate breeding programs. The remainder consists of wild/weedy relatives or elite lines and breeding materials, many of which have unknown geographic origin and/or mixed ancestry)。

方法:重测序(简化测序,Genomic DNAs were digested individually with ApeKI (recognition site: GjCWCG), and 96- or 384-plex GBS libraries were constructed (Dataset S2) (17). DNA sequencing was performed either on the Illumina Genome Analyzer IIx or HiSeq2000;BWA比对,TASSEL 3.0 GBS pipeline call SNP)

Population Genetic Analysis:ADMIXTURE program;进化树和杂合率计算用ape package in R

GWAS was carried out in Genomic Association and Prediction Integrated Tool。

结果主要分为三部分

第一部分:对这971株高粱进行了进化树分析和群体结构分析,结果显示高粱的群体结构与高粱形态和地域起源都有关,揭示了祖先高粱扩散至非洲和亚洲不同气候区域的模式。


图1.高粱种质起源和遗传关系

2. 选择压力分析

•为了研究高粱驯化与分化的基因选择信号,对全基因组进行了核苷酸多样性检测(π, θ)、Tajima’D检验、杂合率(He)计算。

•全基因组扫描显示很多区域呈现低杂合率(Mb级别的),表明高粱基因组的很多区域潜在受到了进化选择。在之前鉴定到的6个与淀粉代谢相关的驯化候选基因中,两个位于这些低杂合率区域,分别是bt2和o2(图2 A)。

•在携带早熟和矮小等位基因的高粱导入系(conversion lines)中,也同样观察到几个杂合率降低的区域,这些区域与已知的株高相关基因(Dw2, Dw3, Dw1)和成熟相关基因(Ma1)共定位(图2 B)。


图2 全基因组SNP变异图谱

3. GWAS分析筛选农业性状相关基因

•然后作者利用全基因组关联分析(GWAS)的方法筛选与株高和花序结构相关的基因。

•结果:

1)定位到三个株高相关已知基因:dw1, dw2, dw3(图3)

2)定位到多个花序结构相关基因,这些基因与玉米、水稻、拟南芥的花调控因子同源,包括GDD1,APO1等。



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