Genetic Diversity and Linkage Disequilibrium in Chinese Bread Wheat (Triticum aestivum L.) Revealed by SSR Markers

doi:10.1371/journal.pone.0017279

	Genetic Diversity and Linkage Disequilibrium in Chinese Bread Wheat (Triticum aestivum L.) Revealed by SSR Markers
	Hao, Chenyang; Wang, Lanfen; Ge, Hongmei; Dong, Yuchen; Zhang, Xueyong
刊名	PLOS ONE
	2011
卷号	6 期号:2 页码:-
ISSN号	1932-6203
DOI	10.1371/journal.pone.0017279
通讯作者	Hao, Chenyang
英文摘要	Two hundred and fifty bread wheat lines, mainly Chinese mini core accessions, were assayed for polymorphism and linkage disequilibrium (LD) based on 512 whole-genome microsatellite loci representing a mean marker density of 5.1 cM. A total of 6,724 alleles ranging from 1 to 49 per locus were identified in all collections. The mean PIC value was 0.650, ranging from 0 to 0.965. Population structure and principal coordinate analysis revealed that landraces and modern varieties were two relatively independent genetic sub-groups. Landraces had a higher allelic diversity than modern varieties with respect to both genomes and chromosomes in terms of total number of alleles and allelic richness. 3,833 (57.0%) and 2,788 (41.5%) rare alleles with frequencies of <5% were found in the landrace and modern variety gene pools, respectively, indicating greater numbers of rare variants, or likely new alleles, in landraces. Analysis of molecular variance (AMOVA) showed that A genome had the largest genetic differentiation and D genome the lowest. In contrast to genetic diversity, modern varieties displayed a wider average LD decay across the whole genome for locus pairs with r(2)>0.05 (P<0.001) than the landraces. Mean LD decay distance for the landraces at the whole genome level was <5 cM, while a higher LD decay distance of 5-10 cM in modern varieties. LD decay distances were also somewhat different for each of the 21 chromosomes, being higher for most of the chromosomes in modern varieties (<5 similar to 25 cM) compared to landraces (<5 similar to 15 cM), presumably indicating the influences of domestication and breeding. This study facilitates predicting the marker density required to effectively associate genotypes with traits in Chinese wheat genetic resources.
学科主题	Multidisciplinary Sciences ; MULTIDISCIPLINARY SCIENCES
语种	英语
出版者	PUBLIC LIBRARY SCIENCE
WOS记录号	WOS:000287482800043
内容类型	期刊论文
源URL	[http://111.203.20.206/handle/2HMLN22E/5343]
专题	作物科学研究所_分子生物学系
作者单位	Chinese Acad Agr Sci, Inst Crop Sci, Key Lab Crop Germplasm Resources & Utilizat, Minist Agr,Natl Key Facil Crop Gene Resources & G, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Hao, Chenyang,Wang, Lanfen,Ge, Hongmei,et al. Genetic Diversity and Linkage Disequilibrium in Chinese Bread Wheat (Triticum aestivum L.) Revealed by SSR Markers[J]. PLOS ONE,2011,6(2):-.
APA	Hao, Chenyang,Wang, Lanfen,Ge, Hongmei,Dong, Yuchen,&Zhang, Xueyong.(2011).Genetic Diversity and Linkage Disequilibrium in Chinese Bread Wheat (Triticum aestivum L.) Revealed by SSR Markers.PLOS ONE,6(2),-.
MLA	Hao, Chenyang,et al."Genetic Diversity and Linkage Disequilibrium in Chinese Bread Wheat (Triticum aestivum L.) Revealed by SSR Markers".PLOS ONE 6.2(2011):-.