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Journal of Integrative Agriculture  2019, Vol. 18 Issue (11): 2446-2456    DOI: 10.1016/S2095-3119(19)62631-6
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Genome-wide association study for starch content and constitution in sorghum (Sorghum bicolor (L.) Moench)
CHEN Bing-ru1, 3, WANG Chun-yu2, WANG Ping2, ZHU Zhen-xing2, XU Ning3, SHI Gui-shan3, YU Miao3, WANG Nai3, LI Ji-hong3, HOU Jia-ming3, LI Shu-jie3, ZHOU Yu-fei1, GAO Shi-jie3, LU Xiao-chun2, HUANG Rui-dong1 
1 College of Agronomy, Shenyang Agricultural University, Shenyang 110866, P.R.China
2 Molecular Improvement of Agricultural Crops Lab, Liaoning Academy of Agricultural Sciences, Shenyang 110161, P.R.China
3 Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, P.R.China
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Abstract  Starch is the most important component in endosperm of sorghum grain.  Usually, two types of starch are present: amylose (AM) and amylopectin (AP).  The levels of AM and AP contents play a significant role in the appearance, structure, and quality of sorghum grains and in marketing applications.  In the present study, a panel of 634 sorghum (Sorghum bicolor (L.) Moench) accessions were evaluated for starch, AM, and AP contents of grain, which included a mini core collection of 242 accessions from the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) in India, and 252 landraces and 140 cultivars from China.  The average starch content was 67.64% and the average AM and AP contents were 20.19 and 79.81%, respectively.  We developed a total of 260 000 high-confidence single nucleotide polymorphism (SNP) markers in the panel of 634 accessions of S. bicolor using specific locus amplified fragment sequencing (SLAF-seq).  We performed genome-wide association studies (GWAS) of starch, AM, and AM/AP of grain and SNP markers based on a mixed linear model (MLM).  In total, 70 significant association signals were detected for starch, AM, and AM/AP ratio of grain with P<4.452×10–7, of which 10 SNPs were identified with significant starch, 51 SNPs were associated with AM, and nine SNPs were associated with the AM/AP ratio.  The Gene Ontology (GO) analysis identified 12 candidate genes at five QTLs associated with starch metabolism within the 200-kb intervals, located on chromosomes 1, 5, 6, and 9.  Of these genes, Sobic.006G036500.1 encodes peptidyl-prolyl cis-trans-isomerase CYP38 responsible for hexose monophosphate shunt (HMS) and Sobic.009G071800 encodes 6-phospho-fructokinase (PFK), which is involved in the embden-meyerhof pathway (EMP).  Kompetitive allele specific PCR (KASP) markers were developed to validate the GWAS results.  The C allele is correlated with a high starch content, while the T allele is linked with a low level of starch content, and provides reliable haplotypes for MAS in sorghum quality improvement.
Keywords:  sorghum               genome-wide association mapping (GWAS)              starch content              amylose (AM)              candidate genes              KASP  
Received: 20 June 2018   Accepted:
Fund: This work was supported by the earmarked fund for China Agriculture Research System (CARS-06).
Corresponding Authors:  Correspondence HUANG Rui-dong, E-mail:; LU Xiao-chun, Tel: +86-24-31021083, E-mail:   
About author:  CHEN Bing-ru, Tel: +86-434-6283190, E-mail: chenbingru1979;

Cite this article: 

CHEN Bing-ru, WANG Chun-yu, WANG Ping, ZHU Zhen-xing, XU Ning, SHI Gui-shan, YU Miao, WANG Nai, LI Ji-hong, HOU Jia-ming, LI Shu-jie, ZHOU Yu-fei, GAO Shi-jie, LU Xiao-chun, HUANG Rui. 2019. Genome-wide association study for starch content and constitution in sorghum (Sorghum bicolor (L.) Moench). Journal of Integrative Agriculture, 18(11): 2446-2456.

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