Early Domestication History of Asian Rice Revealed by Mutations and Genome-Wide Analysis of Gene Genealogies

doi:10.1186/s12284-022-00556-6

	Early Domestication History of Asian Rice Revealed by Mutations and Genome-Wide Analysis of Gene Genealogies
	Lu, Yingqing1 ; Xu, Yunzhang 1,2; Li, Nan 1
	2022
发表期刊	RICE
ISSN	1939-8425
卷号	15 期号:1
摘要	Background: Asian rice (Oryza sativa L.) has been a model plant but its cultivation history is inadequately understood, and its origin still under debate. Several enigmas remain, including how this annual crop shifted its growth habit from its perennial ancestor, O. rufipogon, why genetic divergence between indica and japonica appears older than the history of human domestication, and why some domestication genes do not show signals of introgression between subgroups. Addressing these issues may benefit both basic research and rice breeding. Results: Gene genealogy-based mutation (GGM) analysis shows that history of Asian rice is divided into two phases (Phase I and II) of about equal lengths. Mutations occurred earlier than the partition of indica and japonica to Os genome mark Phase-I period. We diagnosed 91 such mutations among 101 genes sampled across 12 chromosomes of Asian rice and its wild relatives. Positive selection, detected more at 5' regions than at coding regions of some of the genes, involved 22 loci (e.g., An-1, SH4, Rc, Hd3a, GL3.2, OsMYB3, OsDFR, and OsMYB15), which affected traits from easy harvesting, grain color, flowering time, productivity, to likely taste and tolerance. Phase-I mutations of OsMYB3, OsHd3a and OsDFR were experimentally tested and all caused enhanced functions of the genes in vivo. Phase-II period features separate cultivations, lineage-specific selection, and expanded domestication to more genes. Further genomic analysis, along with phenotypic comparisons, indicates that O. sativa is hybrid progeny of O. rufipogon and O. nivara, inherited slightly more genes of O. rufipogon. Congruently, modern alleles of the sampled genes are approximately 6% ancient, 38% uni-specific, 40% bi-specific (mixed), and 15% new after accumulating significant mutations. Results of sequencing surveys across modern cultivars/landraces indicate locus-specific usages of various alleles while confirming the associated mutations. Conclusions: Asian rice was initially domesticated as one crop and later separate selection mediated by human resulted in its major subgroups. This history and the hybrid origin well explain previous puzzles. Positive selection, particularly in 5' regions, was the major force underlying trait domestication. Locus-specific domestication can be characterized and the result may facilitate breeders in developing better rice varieties in future.
关键词	5 ' Genealogy Coding genealogy Early mutations Positive selection New alleles Domestication genes Domesticated traits Gene type Hybrid origin Asian rice
学科领域	Agronomy
DOI	10.1186/s12284-022-00556-6
收录类别	SCI
语种	英语
WOS关键词	QUANTITATIVE TRAIT LOCUS ; LOOP-HELIX PROTEIN ; ORYZA-SATIVA ; TRANSCRIPTION FACTOR ; CULTIVATED RICE ; GRAIN-SIZE ; PHOTOPERIOD SENSITIVITY ; SHIKIMATE PATHWAY ; FLOWERING TIME ; WILD-RICE
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
WOS记录号	WOS:000755872700001
出版者	SPRINGER
文献子类	Article
出版地	NEW YORK
EISSN	1939-8433
资助机构	National Natural Science Foundation of China [91331116] ; Chinese Academy of Sciences [XDA08020204] ; State Key Laboratory of Systematic Botany and Evolution
作者邮箱	yqlu@ibcas.ac.cn
作品OA属性	gold, Green Published
引用统计	被引频次：6[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/2S10CLM1/28820
专题	系统与进化植物学国家重点实验室
作者单位	1.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, 20 Nan Xin Cun, Beijing 100093, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 3.Qinghai Univ, Coll Agr & Anim Husb, Xining 810016, Peoples R China
推荐引用方式 GB/T 7714	Lu, Yingqing,Xu, Yunzhang,Li, Nan. Early Domestication History of Asian Rice Revealed by Mutations and Genome-Wide Analysis of Gene Genealogies[J]. RICE,2022,15(1).
APA	Lu, Yingqing,Xu, Yunzhang,&Li, Nan.(2022).Early Domestication History of Asian Rice Revealed by Mutations and Genome-Wide Analysis of Gene Genealogies.RICE,15(1).
MLA	Lu, Yingqing,et al."Early Domestication History of Asian Rice Revealed by Mutations and Genome-Wide Analysis of Gene Genealogies".RICE 15.1(2022).

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