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Identification of molecular markers for starch content in barley (Hordeum vulgare L.) by genome-wide association studies based on bulked samples

Published online by Cambridge University Press:  16 July 2020

Yinghu Zhang
Jiangsu Coastal Area Institute of Agricultural Sciences, Kai fang North Avenue 9, Yancheng City, Jiangsu Province224002, People's Republic of China
Haiye Luan
Jiangsu Coastal Area Institute of Agricultural Sciences, Kai fang North Avenue 9, Yancheng City, Jiangsu Province224002, People's Republic of China
Hui Zang
Jiangsu Coastal Area Institute of Agricultural Sciences, Kai fang North Avenue 9, Yancheng City, Jiangsu Province224002, People's Republic of China
Hongyan Yang
Jiangsu Coastal Area Institute of Agricultural Sciences, Kai fang North Avenue 9, Yancheng City, Jiangsu Province224002, People's Republic of China
Xiao Xu
Jiangsu Coastal Area Institute of Agricultural Sciences, Kai fang North Avenue 9, Yancheng City, Jiangsu Province224002, People's Republic of China
He Chen
Jiangsu Coastal Area Institute of Agricultural Sciences, Kai fang North Avenue 9, Yancheng City, Jiangsu Province224002, People's Republic of China
Hailong Qiao*
Jiangsu Coastal Area Institute of Agricultural Sciences, Kai fang North Avenue 9, Yancheng City, Jiangsu Province224002, People's Republic of China
Huiquan Shen*
Jiangsu Coastal Area Institute of Agricultural Sciences, Kai fang North Avenue 9, Yancheng City, Jiangsu Province224002, People's Republic of China
*Corresponding authors. E-mail:,
*Corresponding authors. E-mail:,


Starch content is an important trait in barley. To evaluate the genetic diversity and identify molecular markers of starch content in barley, 40 cultivated barley genotypes collected from different regions, including genotypes whose starch content is at either the high or low end of the spectrum (15), were used in this study. All the genotypes were re-sequenced by the double-digest-restriction associated DNA sequencing method, and a total of 299,103 single-nucleotide polymorphism (SNP) markers were obtained. The genotypes were divided into four sub-populations based on FASTSTRUCTURE, principal component analysis and neighbour-joining tree analysis. All four sub-populations had a high linkage disequilibrium, especially group 3, whose members were recently bred for malting in the Jiangsu coastal area. The starch content of the barley lines was evaluated during three growing seasons (2014–2017), and the average values of starch content across the three growing seasons at the low and high ends were 51.5 and 55.0%, respectively. The starch content was affected by population structure, the barley in group 2 had a low starch content, while the barley in group 4 had a high starch content. Twenty-six SNP markers were identified as being significantly associated with starch content (P ⩽ 0.001) based on the average values across the three growing seasons using the mixed linear model method. These SNP markers were located on chromosomes 1H and 4H, and were considered loci of qSC1-1 and qSC4-1, respectively. The major identified QTLs for starch content are helpful for further research on carbohydrates and for barley breeding.

Research Article
Copyright © NIAB 2020

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