Extensive variation within the pan-genome of cultivated and wild sorghum

doi:10.1038/s41477-021-00925-x

	Extensive variation within the pan-genome of cultivated and wild sorghum
	Tao, Yongfu ; Luo, Hong 1; Xu, Jiabao 2; Cruickshank, Alan 3; Zhao, Xianrong ; Teng, Fei 2; Hathorn, Adrian ; Wu, Xiaoyuan 1; Liu, Yuanming 1,4; Shatte, Tracey 3; Jordan, David ; Jing, Haichun1,4 ; Mace, Emma 3
	2021
发表期刊	NATURE PLANTS
ISSN	2055-026X
卷号	7 期号:6 页码:766-773
摘要	Sorghum is a drought-tolerant staple crop for half a billion people in Africa and Asia, an important source of animal feed throughout the world and a biofuel feedstock of growing importance. Cultivated sorghum and its inter-fertile wild relatives constitute the primary gene pool for sorghum. Understanding and characterizing the diversity within this valuable resource is fundamental for its effective utilization in crop improvement. Here, we report analysis of a sorghum pan-genome to explore genetic diversity within the sorghum primary gene pool. We assembled 13 genomes representing cultivated sorghum and its wild relatives, and integrated them with 3 other published genomes to generate a pan-genome of 44,079 gene families with 222.6 Mb of new sequence identified. The pan-genome displays substantial gene-content variation, with 64% of gene families showing presence/absence variation among genomes. Comparisons between core genes and dispensable genes suggest that dispensable genes are important for sorghum adaptation. Extensive genetic variation was uncovered within the pan-genome, and the distribution of these variations was influenced by variation of recombination rate and transposable element content across the genome. We identified presence/absence variants that were under selection during sorghum domestication and improvement, and demonstrated that such variation had important phenotypic outcomes that could contribute to crop improvement. The constructed sorghum pan-genome represents an important resource for sorghum improvement and gene discovery. A sorghum pan-genome generated from 16 genomes representing cultivated and wild sorghum shows extensive variation, with 64% of the gene families exhibiting presence/absence variations, some of which confer phenotypic outcomes and contribute to domestication and improvement.
学科领域	Plant Sciences
DOI	10.1038/s41477-021-00925-x
收录类别	SCI
语种	英语
WOS关键词	GENE PREDICTION ; DOMESTICATION ; DIVERSITY ; EVOLUTION ; MODEL
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
WOS记录号	WOS:000652425600001
出版者	NATURE PORTFOLIO
文献子类	Article
出版地	BERLIN
EISSN	2055-0278
资助机构	Government of Norway ; Australian Research Council through the Centre of Excellence for Translational Photosynthesis [CE1401000015] ; National Key R&D Program of China [2019YFD1002701, 2018YFD1000701] ; Strategic Priority Research Program of Chinese Academy of Sciences [XDA26050101]
作者邮箱	david.jordan@uq.edu.au ; hcjing@ibcas.ac.cn ; emma.mace@uq.edu.au
引用统计	被引频次：74[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/26586
专题	中科院北方资源植物重点实验室
作者单位	1.Univ Queensland, Hermitage Res Facil, Queensland Alliance Agr & Food Innovat QAAFI, Warwick, Qld, Australia 2.Chinese Acad Sci, Inst Bot, Key Lab Plant Resources, Beijing, Peoples R China 3.BGI Shenzhen, BGI Genom, Shenzhen, Peoples R China 4.Agrisci Queensland, Dept Agr & Fisheries DAF, Hermitage Res Facil, Warwick, Qld, Australia 5.Univ Chinese Acad Sci, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Tao, Yongfu,Luo, Hong,Xu, Jiabao,et al. Extensive variation within the pan-genome of cultivated and wild sorghum[J]. NATURE PLANTS,2021,7(6):766-773.
APA	Tao, Yongfu.,Luo, Hong.,Xu, Jiabao.,Cruickshank, Alan.,Zhao, Xianrong.,...&Mace, Emma.(2021).Extensive variation within the pan-genome of cultivated and wild sorghum.NATURE PLANTS,7(6),766-773.
MLA	Tao, Yongfu,et al."Extensive variation within the pan-genome of cultivated and wild sorghum".NATURE PLANTS 7.6(2021):766-773.

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