Dataset Information

An integrated peach genome structural variation map uncovers genes associated with fruit traits.

ABSTRACT:

Background

Genome structural variations (SVs) have been associated with key traits in a wide range of agronomically important species; however, SV profiles of peach and their functional impacts remain largely unexplored.

Results

Here, we present an integrated map of 202,273 SVs from 336 peach genomes. A substantial number of SVs have been selected during peach domestication and improvement, which together affect 2268 genes. Genome-wide association studies of 26 agronomic traits using these SVs identify a number of candidate causal variants. A 9-bp insertion in Prupe.4G186800, which encodes a NAC transcription factor, is shown to be associated with early fruit maturity, and a 487-bp deletion in the promoter of PpMYB10.1 is associated with flesh color around the stone. In addition, a 1.67 Mb inversion is highly associated with fruit shape, and a gene adjacent to the inversion breakpoint, PpOFP1, regulates flat shape formation.

Conclusions

The integrated peach SV map and the identified candidate genes and variants represent valuable resources for future genomic research and breeding in peach.

SUBMITTER: Guo J

PROVIDER: S-EPMC7539501 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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Publications

An integrated peach genome structural variation map uncovers genes associated with fruit traits.

Guo Jian J Cao Ke K Deng Cecilia C Li Yong Y Zhu Gengrui G Fang Weichao W Chen Changwen C Wang Xinwei X Wu Jinlong J Guan Liping L Wu Shan S Guo Wenwu W Yao Jia-Long JL Fei Zhangjun Z Wang Lirong L

Genome biology 20201006 1

<h4>Background</h4>Genome structural variations (SVs) have been associated with key traits in a wide range of agronomically important species; however, SV profiles of peach and their functional impacts remain largely unexplored.<h4>Results</h4>Here, we present an integrated map of 202,273 SVs from 336 peach genomes. A substantial number of SVs have been selected during peach domestication and improvement, which together affect 2268 genes. Genome-wide association studies of 26 agronomic traits us ...[more]

PMID: 33023652

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Project description:BackgroundPeach (Prunus persica (L.) Batsch) is a major temperate fruit crop with an intense breeding activity. Breeding is facilitated by knowledge of the inheritance of the key traits that are often of a quantitative nature. QTLs have traditionally been studied using the phenotype of a single progeny (usually a full-sib progeny) and the correlation with a set of markers covering its genome. This approach has allowed the identification of various genes and QTLs but is limited by the small numbers of individuals used and by the narrow transect of the variability analyzed. In this article we propose the use of a multi-progeny mapping strategy that used pedigree information and Bayesian approaches that supports a more precise and complete survey of the available genetic variability.ResultsSeven key agronomic characters (data from 1 to 3 years) were analyzed in 18 progenies from crosses between occidental commercial genotypes and various exotic lines including accessions of other Prunus species. A total of 1467 plants from these progenies were genotyped with a 9 k SNP array. Forty-seven QTLs were identified, 22 coinciding with major genes and QTLs that have been consistently found in the same populations when studied individually and 25 were new. A substantial part of the QTLs observed (47%) would not have been detected in crosses between only commercial materials, showing the high value of exotic lines as a source of novel alleles for the commercial gene pool. Our strategy also provided estimations on the narrow sense heritability of each character, and the estimation of the QTL genotypes of each parent for the different QTLs and their breeding value.ConclusionsThe integrated strategy used provides a broader and more accurate picture of the variability available for peach breeding with the identification of many new QTLs, information on the sources of the alleles of interest and the breeding values of the potential donors of such valuable alleles. These results are first-hand information for breeders and a step forward towards the implementation of DNA-informed strategies to facilitate selection of new cultivars with improved productivity and quality.

Dataset Information

An integrated peach genome structural variation map uncovers genes associated with fruit traits.

Background

Results

Conclusions

Publications

An integrated peach genome structural variation map uncovers genes associated with fruit traits.

Similar Datasets

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