Characterization and utilization of microsatellites in the Coffea canephora genome to assess genetic association between wild species in Kenya and cultivated coffee

doi:10.1007/s11295-016-1014-y

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	Characterization and utilization of microsatellites in the Coffea canephora genome to assess genetic association between wild species in Kenya and cultivated coffee
	Ogutu, Collins 1,3,4; Han, Yuepeng 3,4; Nyende, Aggrey 2; Owiti, Albert 1,3,4; Deng, Xianbao 3; Ma, Baiquan 1,3; Wang, Xiaoyang 5; Huang, Lifang 5; Wang, Lu 3; Yan, Lin 5
刊名	TREE GENETICS & GENOMES
	2016-06-01
卷号	12 期号:3 页码:9
关键词	Coffee SSR Genetic diversity Population structure Wild species
ISSN号	1614-2942
DOI	10.1007/s11295-016-1014-y
英文摘要	Coffee is an important beverage crop in the world and has a significant contribution to Kenya's economy. Here, we analyzed the genome-wide distribution of microsatellites in the Coffea canephora genome. A total of 159,041 SSRs were identified, with an overall density of 308 SSRs per Mb. Tetra-nucleotide repeats are the most abundant, accounting for 32 % of the total SSRs. AT-rich motifs are dominant across all SSR repeat units, while GC-rich motifs were generally rare. A set of 100 SSRs was selected to amplify 96 coffee accessions, including 10 wild accessions collected from Mt. Marsabit (Kenya). Of these SSRs, 33 % generated clear polymorphic bands among all tested accessions, with an average of 3.9 alleles per SSR locus. Wild coffee species from Mt. Marsabit showed a close genetic similarity with cultivated accessions in Kenya, suggesting that the wild species in Mt. Marsabit played an important role in the domestication of cultivated coffee in Kenya. Significantly low pairwise genetic divergence was observed between cultivated and wild accessions in Kenya, suggesting a relatively narrow level of genetic basis among coffee germplasm in Kenya. In addition, cultivated and wild coffee accessions in Kenya show a great divergence from those in other countries. Our results not only provide molecular tools for genetic studies in coffee but are also helpful for conservation and coffee breeding programs in Kenya.
资助项目	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	Forestry ; Genetics & Heredity ; Agriculture
语种	英语
出版者	SPRINGER HEIDELBERG
WOS记录号	WOS:000377392000014
内容类型	期刊论文
源URL	[http://202.127.146.157/handle/2RYDP1HH/66]
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.Jomo Kenyatta Univ Agr & Technol, Biotechnol Res Inst, Nairobi 6200000200, Kenya 3.Chinese Acad Sci, Key Lab Plant Germplasm Enhancement & Specialty A, Wuhan Bot Garden, Wuhan 430074, Peoples R China 4.Chinese Acad Sci, Sinoafrican Joint Res Ctr, Wuhan 430074, Peoples R China 5.Chinese Acad Trop Agr Sci, Spice & Beverage Res Inst, Wanning 571533, Hainan, Peoples R China
推荐引用方式 GB/T 7714	Ogutu, Collins,Han, Yuepeng,Nyende, Aggrey,et al. Characterization and utilization of microsatellites in the Coffea canephora genome to assess genetic association between wild species in Kenya and cultivated coffee[J]. TREE GENETICS & GENOMES,2016,12(3):9.
APA	Ogutu, Collins.,Han, Yuepeng.,Nyende, Aggrey.,Owiti, Albert.,Deng, Xianbao.,...&Fang, Ting.(2016).Characterization and utilization of microsatellites in the Coffea canephora genome to assess genetic association between wild species in Kenya and cultivated coffee.TREE GENETICS & GENOMES,12(3),9.
MLA	Ogutu, Collins,et al."Characterization and utilization of microsatellites in the Coffea canephora genome to assess genetic association between wild species in Kenya and cultivated coffee".TREE GENETICS & GENOMES 12.3(2016):9.