Dataset Information

Natural positive selection and north-south genetic diversity in East Asia.

ABSTRACT: Recent reports have identified a north-south cline in genetic variation in East and South-East Asia, but these studies have not formally explored the basis of these clinical differences. Understanding the origins of these variations may provide valuable insights in tracking down the functional variants in genomic regions identified by genetic association studies. Here we investigate the genetic basis of these differences with genome-wide data from the HapMap, the Human Genome Diversity Project and the Singapore Genome Variation Project. We implemented four bioinformatic measures to discover genomic regions that are considerably differentiated either between two Han Chinese populations in the north and south of China, or across 22 populations in East and South-East Asia. These measures prioritized genomic stretches with: (i) regional differences in the allelic spectrum for SNPs common to the two Han Chinese populations; (ii) differential evidence of positive selection between the two populations as quantified by integrated haplotype score (iHS) and cross-population extended haplotype homozygosity (XP-EHH); (iii) significant correlation between allele frequencies and geographical latitudes of the 22 populations. We also explored the extent of linkage disequilibrium variations in these regions, which is important in combining genetic association studies from North and South Chinese. Two of the regions that emerged are found in HLA class I and II, suggesting that the HLA imputation panel from the HapMap may not be directly applicable to every Chinese sample. This has important implications to autoimmune studies that plan to impute the classical HLA alleles to fine map the SNP association signals.

SUBMITTER: Suo C

PROVIDER: S-EPMC3234507 | biostudies-literature | 2012 Jan

REPOSITORIES: biostudies-literature

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Natural positive selection and north-south genetic diversity in East Asia.

Suo Chen C Xu Haiyan H Khor Chiea-Chuen CC Ong Rick Th RT Sim Xueling X Chen Jieming J Tay Wan-Ting WT Sim Kar-Seng KS Zeng Yi-Xin YX Zhang Xuejun X Liu Jianjun J Tai E-Shyong ES Wong Tien-Yin TY Chia Kee-Seng KS Teo Yik-Ying YY

European journal of human genetics : EJHG 20110727 1

Recent reports have identified a north-south cline in genetic variation in East and South-East Asia, but these studies have not formally explored the basis of these clinical differences. Understanding the origins of these variations may provide valuable insights in tracking down the functional variants in genomic regions identified by genetic association studies. Here we investigate the genetic basis of these differences with genome-wide data from the HapMap, the Human Genome Diversity Project a ...[more]

PMID: 21792231

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Project description:Background and aimsBesides bananas belonging to the AAA triploid Mutika subgroup, which predominates in the Great Lakes countries, other AAA triploids as well as edible AA diploids, locally of considerable cultural weight, are cultivated in East Africa and in the nearby Indian Ocean islands as far as Madagascar. All these varieties call for the genetic identification and characterization of their interrelations on account of their regional socio-economic significance and their potential for banana breeding strategies.MethodsAn extensive sampling of all traditional bananas in East Africa and near Indian Ocean islands was genotyped with simple sequence repeat (SSR) markers, with particular emphasis on the diploid forms and on the bananas of the Indian Ocean islands, which remain poorly characterized.Key resultsAll the edible AA varieties studied here are genetically homogeneous, constituting a unique subgroup, here called 'Mchare', despite high phenotypic variation and adaptions to highly diverse ecological zones. At triploid level, and besides the well-known AAA Mutika subgroup, at least two other genetically related AAA subgroups specific to this region are identified. Neither of these East African AAA genotypes can be derived directly from the local AA Mchare diploids. However, it is demonstrated that the East African diploids and triploids together belong to the same genetic complex. The geographical distribution of their wild acuminata relatives allowed identification of the original area of this complex in a restricted part of island South-East Asia. The inferred origin leads to consideration of the history of banana introduction in Africa. Linked to biological features, documentation on the embedding of bananas in founding legends and myths and convincing linguistic elements were informative regarding the period and the peoples who introduced these Asian plants into Africa. The results point to the role of Austronesian-speaking peoples who colonized the Indian Ocean islands, particularly Madagascar, and reached the East African coasts.ConclusionsUnderstanding of the relations between the components of this complex and identifying their Asian wild relatives and related cultivars will be a valuable asset in breeding programmes and will boost the genetic improvement of East African bananas, but also of other globally important subgroups, in particular the AAA Cavendish.

Dataset Information

Natural positive selection and north-south genetic diversity in East Asia.

Publications

Natural positive selection and north-south genetic diversity in East Asia.

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