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ISSR Analysis of Genetic Diversity and Structure of Plum Varieties Cultivated in Southern China.

ABSTRACT: Plums (Prunus spp.) are important deciduous fruit crops in the world. China is a major producer of P. salicina Lindl., but the genetic relationship of Chinese plums in key production regions remain unclear. In this study, 14 University of British Columbia (UBC) inter simple sequence repeats (ISSR) primers were used to analyze 33 plum varieties cultivated in Fujian Province to determine their genetic diversity and population structure. A total of 146 bands were generated, of which 130 were polymorphic. Mean percentage of polymorphic bands was 89.04%, Shannon's information index value was 0.38, and the Nei's genetic index value was 0.24. Using unrooted trees (Neighbor-Joining method), 33 varieties were classified into four groups. Split graph separated them into two major groups, each with two subgroups. The two phylogenetic trees indicate that environmental or natural selection pressure is an important factor influencing their genetic relationship. Analysis of population structure revealed that they have frequent genetic exchanges among closed subpopulations; thus, genetic variation mainly occurs within the population. Additionally, based on the phylogenetic analysis and unique morphological characteristics of fruits, we propose that the Chinese landrace Nai could contribute significantly to development of the famous variety Wickson.

SUBMITTER: Wu W

PROVIDER: S-EPMC6466324 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature

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ISSR Analysis of Genetic Diversity and Structure of Plum Varieties Cultivated in Southern China.

Wu Weifeng W Chen Faxing F Yeh Kaiwun K Chen Jianjun J

Biology 20181221 1

Plums (<i>Prunus</i> spp.) are important deciduous fruit crops in the world. China is a major producer of <i>P. salicina</i> Lindl., but the genetic relationship of Chinese plums in key production regions remain unclear. In this study, 14 University of British Columbia (UBC) inter simple sequence repeats (ISSR) primers were used to analyze 33 plum varieties cultivated in Fujian Province to determine their genetic diversity and population structure. A total of 146 bands were generated, of which 1 ...[more]

PMID: 30577627

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Project description:BackgroundThe tomato (Solanum lycopersium L.) is the most widely grown vegetable in the world. It was domesticated in Latin America and Italy and Spain are considered secondary centers of diversification. This food crop has experienced severe genetic bottlenecks and modern breeding activities have been characterized by trait introgression from wild species and divergence in different market classes.ResultsWith the aim to examine patterns of polymorphism, characterize population structure and identify putative loci under positive selection, we genotyped 214 tomato accessions (which include cultivated landraces, commercial varieties and wild relatives) using a custom-made Illumina SNP-panel. Most of the 175 successfully scored SNP loci were found to be polymorphic. Population structure analysis and estimates of genetic differentiation indicated that landraces constitute distinct sub-populations. Furthermore, contemporary varieties could be separated in groups (processing, fresh and cherry) that are consistent with the recent breeding aimed at market-class specialization. In addition, at the 95% confidence level, we identified 30, 34 and 37 loci under positive selection between landraces and each of the groups of commercial variety (cherry, processing and fresh market, respectively). Their number and genomic locations imply the presence of some extended regions with high genetic variation between landraces and contemporary varieties.ConclusionsOur work provides knowledge concerning the level and distribution of genetic variation within cultivated tomato landraces and increases our understanding of the genetic subdivision of contemporary varieties. The data indicate that adaptation and selection have led to a genomic signature in cultivated landraces and that the subpopulation structure of contemporary varieties is shaped by directed breeding and largely of recent origin. The genomic characterization presented here is an essential step towards a future exploitation of the available tomato genetic resources in research and breeding programs.

Dataset Information

ISSR Analysis of Genetic Diversity and Structure of Plum Varieties Cultivated in Southern China.

Publications

ISSR Analysis of Genetic Diversity and Structure of Plum Varieties Cultivated in Southern China.

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