Genome-wide association analysis of lodging resistance of millet in Luoyang and Jilin ecological regions

doi:10.3969/j.issn.1004-1524.2018.12.01

›› 2018, Vol. 30 ›› Issue (12): 1981-1991.DOI: 10.3969/j.issn.1004-1524.2018.12.01

• Crop Science • Previous Articles Next Articles

Genome-wide association analysis of lodging resistance of millet in Luoyang and Jilin ecological regions

JIA Xiaoping¹, ZHANG Bo¹, QUAN Jianzhang², WANG Yongfang², DONG Zhiping², YUAN Xilei¹, LI Jianfeng¹

1. College of Agriculture, Henan University of Science and Technology, Luoyang 471023, China;
2. Institute of Millet, Hebei Academy of Agriculture and Forestry Sciences/National Millet Improvement Center, Shijiazhuang 050035, China

Received:2018-02-04 Online:2018-12-25 Published:2018-12-28

Abstract

Abstract: Lodging is an important factor affecting the yield and quality of millet. In order to uncover the genetic mechanism of lodging resistance in foxtail millet, 98 foxtail millet cultivars were selected to investigate lodging rate in Luoyang and Jilin, further re-sequencing was performed for the association analysis between SNPs and lodging resistance. The results showed that lodging rate of 98 foxtail millet cultivars gave same distribution law in Luoyang and Jilin: number of cultivars without lodging>number of cultivars with fewer lodging>number of cultivars with quite a few lodging. 4 482 208 SNP markers were developed by re-sequencing and the 98 foxtail millet cultivars were divided into three groups by population structure analysis. LD analysis found that linkage disequilibrium decline distance of foxtail millet genome was 47.5 kb. 764 and 24 SNP sites associated with lodging resistance were detected in Luoyang and Jilin respectively by genome-wide association analysis. A candidate gene coding LRR receptor-like serine/threonine-protein kinase (LOC101776261) on Chr6 was detected both in Luoyang and Jilin. Furthermore, some wall-associated receptor kinase genes(LOC105914550,LOC101786429,LOC105913474,LOC101766879) that were function-related but lied in different loci were detected on Chr6 and Chr8 in Luoyang and Jilin. Some genes such as cytochrome P450 protein, UDP-glycosyltransferase and kinesin protein were detected on different chromosomes in Luoyang and Jilin. All of candidate genes above may be related to lodging resistance of foxtail millet. Lodging resistance was a complicated quantitative character that controlled by multiple genes in foxtail millet and the protein kinase genes may play important role in lodging resistance of foxtail millet.

Key words: millet, genome-wide association analysis, SNP, lodging

CLC Number:

S515

JIA Xiaoping, ZHANG Bo, QUAN Jianzhang, WANG Yongfang, DONG Zhiping, YUAN Xilei, LI Jianfeng. Genome-wide association analysis of lodging resistance of millet in Luoyang and Jilin ecological regions[J]. , 2018, 30(12): 1981-1991.

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Genome-wide association analysis of lodging resistance of millet in Luoyang and Jilin ecological regions

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