Genome-wide Association Analysis of Plant Height in Foxtail Millet under Different Photoperiod Conditions

doi:10.7668/hbnxb.201750856

Abstract

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

CLC Number:

S565.03

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.

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