Nucleotide Diversity and Molecular Evolution of the ALK Gene in Cultivated Rice and its Wild Relatives

doi:10.1007/s11105-016-0975-1

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	Nucleotide Diversity and Molecular Evolution of the ALK Gene in Cultivated Rice and its Wild Relatives
	Xing, Yongzhong 4,5; Han, Yuepeng 2,3; Zhou, Ying 2; Zheng, Hongyu 1,2; Wei, Guochao 1,2; Zhou, Hui 1,2; Han, Yanni 1,2; Bai, Xufeng 4,5
刊名	PLANT MOLECULAR BIOLOGY REPORTER
	2016-10-01
卷号	34 期号:5 页码:923-930
关键词	Rice Gelatinization temperature ALK Single nucleotide polymorphism Balancing selection
ISSN号	0735-9640
DOI	10.1007/s11105-016-0975-1
英文摘要	Gelatinization temperature (GT), an important parameter for rice cooking quality, is mainly regulated by the ALK gene encoding starch synthase IIa. Here, we reported the nucleotide diversity of the ALK gene in 122 cultivated accessions and 199 wild rice accessions that were collected around the Pearl River Basin in China. A total of 93 single nucleotide ploymorphisms (SNPs) were identified, with an average of one SNP per 40 bp. Tajima D statistics revealed that the DNA sequences covering the last exon have probably evolved under balancing selection. Based on two functional SNPs (an A to G substitution at 4198 bp and a GC to TT dinucleotide substitution at 4330/4331 bp), three haplotypes, G/GC, G/TT, and A/GC, were identified in both wild and cultivated accessions, with the G/GC haplotype being predominant. Interestingly, the A/GC haplotype was exclusively found in the wild accessions from Guangdong province, while the G/TT haplotype was only present in the wild accessions from Jiangxi province and Hainan Island. This suggests that the G/TT and A/GC variants may have arisen independently and undergone balancing selection on separate haplotypes in multiple populations. Our result supports earlier hypothesis that cultivated rice was independently domesticated from multiple domestication events in China. Our study aids in the understanding of the domestication process that led to the improvement of rice grain quality.
资助项目	CAS Strategic Priority Research Program[XDA05130403] ; Overseas Construction Plan for Science and Education Base, China-Africa Center for Research and Education, Chinese Academy of Sciences[SAJC201327]
WOS研究方向	Biochemistry & Molecular Biology ; Plant Sciences
语种	英语
出版者	SPRINGER
WOS记录号	WOS:000383149500005
内容类型	期刊论文
源URL	[http://202.127.146.157/handle/2RYDP1HH/26]
专题	中国科学院武汉植物园
通讯作者	Han, Yuepeng
作者单位	1.Chinese Acad Sci, Grad Univ, 19A Yuquanlu, Beijing 100049, Peoples R China 2.Chinese Acad Sci, Key Lab Plant Germplasm Enhancement & Specialty A, Wuhan Bot Garden, Wuhan 430074, Peoples R China 3.Chinese Acad Sci, Sino African Joint Res Ctr, Wuhan 430074, Peoples R China 4.Huazhong Agr Univ, Natl Ctr Plant Gene Res Wuhan, Wuhan 430070, Peoples R China 5.Huazhong Agr Univ, Natl Key Lab Crop Genet Improvement, Wuhan 430070, Peoples R China
推荐引用方式 GB/T 7714	Xing, Yongzhong,Han, Yuepeng,Zhou, Ying,et al. Nucleotide Diversity and Molecular Evolution of the ALK Gene in Cultivated Rice and its Wild Relatives[J]. PLANT MOLECULAR BIOLOGY REPORTER,2016,34(5):923-930.
APA	Xing, Yongzhong.,Han, Yuepeng.,Zhou, Ying.,Zheng, Hongyu.,Wei, Guochao.,...&Bai, Xufeng.(2016).Nucleotide Diversity and Molecular Evolution of the ALK Gene in Cultivated Rice and its Wild Relatives.PLANT MOLECULAR BIOLOGY REPORTER,34(5),923-930.
MLA	Xing, Yongzhong,et al."Nucleotide Diversity and Molecular Evolution of the ALK Gene in Cultivated Rice and its Wild Relatives".PLANT MOLECULAR BIOLOGY REPORTER 34.5(2016):923-930.