不同光周期条件下谷子株高的全基因组关联分析

doi:10.7668/hbnxb.201750856

摘要/Abstract

摘要： 为揭示控制株高的遗传机理，为开展理想株型标记辅助选择育种奠定基础，在海南、洛阳、吉林3个不同种植区光周期条件下调查了98份谷子材料的株高，并对98份谷子材料进行基因组重测序，开展单核苷酸多态性（SNP）位点标记与株高的全基因组关联分析。结果表明：不同光周期条件下谷子株高的变异在58.5~169.3 cm，广义遗传力为0.501，且随着日照时间的延长，谷子株高呈递增的趋势。基因组重测序获得了4 482 208个高质量的SNP位点，主成分分析将98份谷子材料分为3个亚群，连锁不平衡（LD）分析发现谷子基因组LD衰减距离为47.5 kb。全基因组关联分析获得10 703个与株高关联的SNP位点（P<0.000 1），这些位点多在海南种植区短日照条件下检测到，且集中于1号染色体上，只有1号染色体上3个关联SNP位点（SNP_13861443、SNP_14872616、SNP_18601830）能在海南、洛阳2个种植区光周期条件下稳定检测到，说明谷子1号染色体存在海南、洛阳种植区短日照和中日照条件下控制株高的数量性状位点（QTL）。在关联SNP位点候选区域发现3个候选基因，推定为成蛋白的基因（LOC_101783280）在外显子区检测到一个SNP位点（SNP_14876527），推测该基因可能为控制谷子株高的主要候选基因。

关键词: 谷子, 光周期, 重测序, 株高, 全基因组关联分析

Abstract: In order to reveal the genetic mechanism controlling plant height, provide foundation for marker-assisted selection of ideal-plant type in foxtail millet, 98 foxtail millet materials were selected to investigate plant height in Hainan, Luoyang and Jilin, three different planting regions corresponding to three different photoperiod conditions, and further genome resequencing was performed for the 98 foxtail millet materials to carry out genome-wide association between SNPs and plant height. The results showed that the variation range of plant height was from 58.5 cm to 169.3 cm among different photoperiod conditions, the broad-sensed heritability was 0.501. With the prolonging of day length, plant height of foxtail millet gave an incremental trend. 4 482 208 high-quality SNP loci were obtained by resequencing, 98 foxtail millet materials were divided into three subgroups by principal component analysis. LD analysis showed that the genome LD decline distance of foxtail millet was 47.5 kb. Genome-wide association analysis obtained 10 703 SNPs associated with plant height(P<0.000 1), most of which were detected in Hainan planting region(short-daylength condition)and centralized on Chr.1. Only three associated SNPs(SNP_13861443, SNP_14872616, SNP_18601830)on Chr.1 could be stably detected in two planting regions(Luoyang and Hainan, which represented two different photoperiod environments), indicating that Chr.1 harbored QTLs controlling plant height of foxtail millet in Hainan(short-day)and Luoyang(moderate-day)planting regions. Three candidate genes were found in regions around associated SNPs, only the putative Formin protein gene(LOC_101783280) gave a mutation site in exon region(SNP_14876527), which indicated that the Formin protein gene might be the main candidate gene controlling plant height.

Key words: Foxtail millet, Photoperiod, Resequencing, Plant height, Genome-wide association analysis

中图分类号:

S565.03

贾小平, 张博, 全建章, 李剑峰, 王永芳, 袁玺垒. 不同光周期条件下谷子株高的全基因组关联分析[J]. 华北农学报, 2019, 34(4): 16-23. doi: 10.7668/hbnxb.201750856.

JIA Xiaoping, ZHANG Bo, QUAN Jianzhang, LI Jianfeng, WANG Yongfang, YUAN Xilei. Genome-wide Association Analysis of Plant Height in Foxtail Millet under Different Photoperiod Conditions[J]. ACTA AGRICULTURAE BOREALI-SINICA, 2019, 34(4): 16-23. doi: 10.7668/hbnxb.201750856.

http://www.hbnxb.net/CN/Y2019/V34/I4/16

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