Genome-wide association study reveals that different pathways contribute to grain quality variation in sorghum (Sorghum bicolor)

doi:10.1186/s12864-020-6538-8

CORC > 植物研究所 > 中国科学院植物研究所 > 中科院北方资源植物重点实验室

	Genome-wide association study reveals that different pathways contribute to grain quality variation in sorghum (Sorghum bicolor)
	Kimani, Wilson ; Zhang, Li-Min ; Wu, Xiao-Yuan ; Hao, Huai-Qing ; Jing, Hai-Chun
刊名	BMC GENOMICS
	2020
卷号	21 期号:1
关键词	Sorghum Grain quality Genome-wide association study Amino acids Starch Tannins
ISSN号	1471-2164
DOI	10.1186/s12864-020-6538-8
文献子类	Article
英文摘要	Background In sorghum (Sorghum bicolor), one paramount breeding objective is to increase grain quality. The nutritional quality and end use value of sorghum grains are primarily influenced by the proportions of tannins, starch and proteins, but the genetic basis of these grain quality traits remains largely unknown. This study aimed to dissect the natural variation of sorghum grain quality traits and identify the underpinning genetic loci by genome-wide association study. Results Levels of starch, tannins and 17 amino acids were quantified in 196 diverse sorghum inbred lines, and 44 traits based on known metabolic pathways and biochemical interactions amongst the 17 amino acids calculated. A Genome-wide association study (GWAS) with 3,512,517 SNPs from re-sequencing data identified 14, 15 and 711 significant SNPs which represented 14, 14, 492 genetic loci associated with levels of tannins, starch and amino acids in sorghum grains, respectively. Amongst these significant SNPs, two SNPs were associated with tannin content on chromosome 4 and colocalized with three previously identified loci for Tannin1, and orthologs of Zm1 and TT16 genes. One SNP associated with starch content colocalized with sucrose phosphate synthase gene. Furthermore, homologues of opaque1 and opaque2 genes associated with amino acid content were identified. Using the KEGG pathway database, six and three candidate genes of tannins and starch were mapped into 12 and 3 metabolism pathways, respectively. Thirty-four candidate genes were mapped into 16 biosynthetic and catabolic pathways of amino acids. We finally reconstructed the biosynthetic pathways for aspartate and branched-chain amino acids based on 15 candidate genes identified in this study. Conclusion Promising candidate genes associated with grain quality traits have been identified in the present study. Some of them colocalized with previously identified genetic regions, but novel candidate genes involved in various metabolic pathways which influence grain quality traits have been dissected. Our study acts as an entry point for further validation studies to elucidate the complex mechanisms controlling grain quality traits such as tannins, starch and amino acids in sorghum.
学科主题	Biotechnology & Applied Microbiology ; Genetics & Heredity
出版地	LONDON
WOS关键词	MAIZE KERNEL COMPOSITION ; SEED COAT DEVELOPMENT ; ARABIDOPSIS ; ENCODES ; PROTEIN ; GENE ; IDENTIFICATION ; DIGESTIBILITY ; INTEGRATION ; EXPRESSION
WOS研究方向	Biotechnology & Applied Microbiology ; Genetics & Heredity
语种	英语
出版者	BMC
WOS记录号	WOS:000513540400006
资助机构	National Key R&D Program of China [2018YFD1000701, 2018YFD1000700] ; Ministry of Science and Technology of the People's Republic of ChinaMinistry of Science and Technology, China [2015BAD15B03] ; Science and Technology Service Network Initiative Project of Chinese Academy of Sciences [KFJ-FP-201809, KFJ-STS-ZDTP-056] ; National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [31461143023] ; SinoAfrica Joint Research Center, Chinese Academy of Sciences [SAJC201603] ; CAS-TWASChinese Academy of Sciences
内容类型	期刊论文
源URL	[http://ir.ibcas.ac.cn/handle/2S10CLM1/21910]
专题	中科院北方资源植物重点实验室
作者单位	1.Chinese Acad Sci, Inst Bot, Engn Lab Grass Based Livestock Husb, Beijing 100093, Peoples R China 2.Hao, Huai-Qing 3.Chinese Acad Sci, Inst Bot, Key Lab Plant Resources, Beijing 100093, Peoples R China 4.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 5.[Kimani, Wilson 6.Zhang, Li-Min 7.Wu, Xiao-Yuan
推荐引用方式 GB/T 7714	Kimani, Wilson,Zhang, Li-Min,Wu, Xiao-Yuan,et al. Genome-wide association study reveals that different pathways contribute to grain quality variation in sorghum (Sorghum bicolor)[J]. BMC GENOMICS,2020,21(1).
APA	Kimani, Wilson,Zhang, Li-Min,Wu, Xiao-Yuan,Hao, Huai-Qing,&Jing, Hai-Chun.(2020).Genome-wide association study reveals that different pathways contribute to grain quality variation in sorghum (Sorghum bicolor).BMC GENOMICS,21(1).
MLA	Kimani, Wilson,et al."Genome-wide association study reveals that different pathways contribute to grain quality variation in sorghum (Sorghum bicolor)".BMC GENOMICS 21.1(2020).