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Whole-genome resequencing of 472 Vitis accessions for grapevine diversity and demographic history analyses.

ABSTRACT: Understanding the Vitis species at the genomic level is important for cultivar improvement of grapevine. Here we report whole-genome genetic variation at single-base resolution of 472 Vitis accessions, which cover 48 out of 60 extant Vitis species from a wide geographic distribution. The variation helps to identify a recent dramatic expansion and contraction of effective population size in the domesticated grapevines and that cultivars from the pan-Black Sea region have a unique demographic history in comparison to the other domesticated cultivars. We also find selective sweeps for berry edibility and stress resistance improvement. Furthermore, we find associations between candidate genes and important agronomic traits, such as berry shape and aromatic compounds. These results demonstrate resource value of the resequencing data for illuminating the evolutionary biology of Vitis species and providing targets for grapevine genetic improvement.

SUBMITTER: Liang Z

PROVIDER: S-EPMC6416300 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

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Whole-genome resequencing of 472 Vitis accessions for grapevine diversity and demographic history analyses.

Liang Zhenchang Z Duan Shengchang S Sheng Jun J Zhu Shusheng S Ni Xuemei X Shao Jianhui J Liu Chonghuai C Nick Peter P Du Fei F Fan Peige P Mao Ruzhi R Zhu Yifan Y Deng Weiping W Yang Min M Huang Huichuan H Liu Yixiang Y Ding Yiqing Y Liu Xianju X Jiang Jianfu J Zhu Youyong Y Li Shaohua S He Xiahong X Chen Wei W Dong Yang Y

Nature communications 20190313 1

Understanding the Vitis species at the genomic level is important for cultivar improvement of grapevine. Here we report whole-genome genetic variation at single-base resolution of 472 Vitis accessions, which cover 48 out of 60 extant Vitis species from a wide geographic distribution. The variation helps to identify a recent dramatic expansion and contraction of effective population size in the domesticated grapevines and that cultivars from the pan-Black Sea region have a unique demographic hist ...[more]

PMID: 30867414

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Project description:BackgroundThe mountainous region between the Caucasus and China is considered to be the center of domestication for grapevine. Despite the importance of Central Asia in the history of grape growing, information about the extent and distribution of grape genetic variation in this region is limited in comparison to wild and cultivated grapevines from around the Mediterranean basin. The principal goal of this work was to survey the genetic diversity and relationships among wild and cultivated grape germplasm from the Caucasus, Central Asia, and the Mediterranean basin collectively to understand gene flow, possible domestication events and adaptive introgression.ResultsA total of 1378 wild and cultivated grapevines collected around the Mediterranean basin and from Central Asia were tested with a set of 20 nuclear SSR markers. Genetic data were analyzed (Cluster analysis, Principal Coordinate Analysis and STRUCTURE) to identify groups, and the results were validated by Nei's genetic distance, pairwise FST analysis and assignment tests. All of these analyses identified three genetic groups: G1, wild accessions from Croatia, France, Italy and Spain; G2, wild accessions from Armenia, Azerbaijan and Georgia; and G3, cultivars from Spain, France, Italy, Georgia, Iran, Pakistan and Turkmenistan, which included a small group of wild accessions from Georgia and Croatia. Wild accessions from Georgia clustered with cultivated grape from the same area (proles pontica), but also with Western Europe (proles occidentalis), supporting Georgia as the ancient center of grapevine domestication. In addition, cluster analysis indicated that Western European wild grapes grouped with cultivated grapes from the same area, suggesting that the cultivated proles occidentalis contributed more to the early development of wine grapes than the wild vines from Eastern Europe.ConclusionsThe analysis of genetic relationships among the tested genotypes provided evidence of genetic relationships between wild and cultivated accessions in the Mediterranean basin and Central Asia. The genetic structure indicated a considerable amount of gene flow, which limited the differentiation between the two subspecies. The results also indicated that grapes with mixed ancestry occur in the regions where wild grapevines were domesticated.

Project description:IntroductionWhole-genome resequencing technology covers almost all nucleotide variations in the genome, which makes it possible to carry out conservation genomics research on endangered species at the whole-genome level.MethodsIn this study, based on the whole-genome resequencing data of 101 critically endangered Artocarpus nanchuanensis individuals, we evaluated the genetic diversity and population structure, inferred the demographic history and genetic load, predicted the potential distributions in the past, present and future, and classified conservation units to propose targeted suggestions for the conservation of this critically endangered species.ResultsWhole-genome resequencing for A. nanchuanensis generated approximately 2 Tb of data. Based on abundant mutation sites (25,312,571 single nucleotide polymorphisms sites), we revealed that the average genetic diversity (nucleotide diversity, π) of different populations of A. nanchuanensis was relatively low compared with other trees that have been studied. And we also revealed that the NHZ and QJT populations harboured unique genetic backgrounds and were significantly separated from the other five populations. In addition, positive genetic selective signals, significantly enriched in biological processes related to terpene synthesis, were identified in the NHZ population. The analysis of demographic history of A. nanchuanensis revealed the existence of three genetic bottleneck events. Moreover, abundant genetic loads (48.56% protein-coding genes) were identified in Artocarpus nanchuanensis, especially in genes related to early development and immune function of plants. The predication analysis of suitable habitat areas indicated that the past suitable habitat areas shifted from the north to the south due to global temperature decline. However, in the future, the actual distribution area of A. nanchuanensis will still maintain high suitability.DiscussionBased on total analyses, we divided the populations of A. nanchuanensis into four conservation units and proposed a number of practical management suggestions for each conservation unit. Overall, our study provides meaningful guidance for the protection of A. nanchuanensis and important insight into conservation genomics research.

Project description:BackgroundVietnam possesses a vast diversity of rice landraces due to its geographical situation, latitudinal range, and a variety of ecosystems. This genetic diversity constitutes a highly valuable resource at a time when the highest rice production areas in the low-lying Mekong and Red River Deltas are enduring increasing threats from climate changes, particularly in rainfall and temperature patterns.ResultsWe analysed 672 Vietnamese rice genomes, 616 newly sequenced, that encompass the range of rice varieties grown in the diverse ecosystems found throughout Vietnam. We described four Japonica and five Indica subpopulations within Vietnam likely adapted to the region of origin. We compared the population structure and genetic diversity of these Vietnamese rice genomes to the 3000 genomes of Asian cultivated rice. The named Indica-5 (I5) subpopulation was expanded in Vietnam and contained lowland Indica accessions, which had very low shared ancestry with accessions from any other subpopulation and were previously overlooked as admixtures. We scored phenotypic measurements for nineteen traits and identified 453 unique genotype-phenotype significant associations comprising twenty-one QTLs (quantitative trait loci). The strongest associations were observed for grain size traits, while weaker associations were observed for a range of characteristics, including panicle length, heading date and leaf width.ConclusionsWe showed how the rice diversity within Vietnam relates to the wider Asian rice diversity by using a number of approaches to provide a clear picture of the novel diversity present within Vietnam, mainly around the Indica-5 subpopulation. Our results highlight differences in genome composition and trait associations among traditional Vietnamese rice accessions, which are likely the product of adaption to multiple environmental conditions and regional preferences in a very diverse country. Our results highlighted traits and their associated genomic regions that are a potential source of novel loci and alleles to breed a new generation of low input sustainable and climate resilient rice.

Dataset Information

Whole-genome resequencing of 472 Vitis accessions for grapevine diversity and demographic history analyses.

Publications

Whole-genome resequencing of 472 Vitis accessions for grapevine diversity and demographic history analyses.

Similar Datasets

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