Dataset Information

A High-Quality Melon Genome Assembly Provides Insights into Genetic Basis of Fruit Trait Improvement.

ABSTRACT: Accurate reference genomes have become indispensable tools for characterization of genetic and functional variations. Here we generated a high-quality assembly of the melon Payzawat using a combination of short-read sequencing, single-molecule real-time sequencing, Hi-C, and a high-density genetic map. The final 12 chromosome-level scaffolds cover ?94.13% of the estimated genome (398.57 Mb). Compared with the published DHL92 genome, our assembly exhibits a 157-fold increase in contig length and remarkable improvements in the assembly of centromeres and telomeres. Six genes within STHQF12.4 on pseudochromosome 12, identified from whole-genome comparison between Payzawat and DHL92, may explain a considerable proportion of the skin thickness. In addition, our population study showed that melon domesticated at multiple times from whole-genome perspective and melons in China are introduced from different routes. Selective sweeps underlying the genes related to desirable traits, haplotypes of alleles associated with agronomic traits, and the variants from resequencing data enable efficient breeding.

SUBMITTER: Zhang H

PROVIDER: S-EPMC6864349 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

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A High-Quality Melon Genome Assembly Provides Insights into Genetic Basis of Fruit Trait Improvement.

Zhang Hong H Li Xuming X Yu Haiyan H Zhang Yongbing Y Li Meihua M Wang Haojie H Wang Dengming D Wang Huaisong H Fu Qiushi Q Liu Min M Ji Changmian C Ma Liming L Tang Juan J Li Song S Miao Jianshun J Zheng Hongkun H Yi Hongping H

iScience 20191031

Accurate reference genomes have become indispensable tools for characterization of genetic and functional variations. Here we generated a high-quality assembly of the melon Payzawat using a combination of short-read sequencing, single-molecule real-time sequencing, Hi-C, and a high-density genetic map. The final 12 chromosome-level scaffolds cover ∼94.13% of the estimated genome (398.57 Mb). Compared with the published DHL92 genome, our assembly exhibits a 157-fold increase in contig length and ...[more]

PMID: 31739171

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Project description:IntroductionAvocado (Persea americana) is a highly nutritious fruit gaining worldwide popularity. However, its cultivation is currently reliant on a limited number of cultivars with restricted genetic diversity. This study aims to investigate the genetic diversity and population structure of avocado germplasm and identify genetic loci associated with key fruit quality traits that influence customer preference.MethodsA diversity panel of 110 avocado accessions was analyzed using 4,706 high-quality single nucleotide polymorphisms (SNPs). Genetic diversity and population structure were analyzed using pairwise FST, AMOVA, admixture analysis, and phylogenetic analysis. Genome-wide association studies (GWAS) were conducted targeting nine fruit quality traits using two models: General Linear Model (GLM) with Principal Component Analysis (PCA) and Mixed Linear Model (MLM) with PCA and kinship (PCA + K).ResultsThe analysis revealed three distinct populations corresponding to the three avocado ecotypes: Guatemalan, West Indian, and Mexican. Phylogenetic analysis indicated a closer relationship between the Guatemalan and West Indian races compared to the Mexican race in our Florida germplasm collection. GWAS led to identification of 12 markers within 11 genomic regions significantly associated with fruit quality traits such as fruit color, shape, taste, and skin texture. These markers explained between 14.84% to 43.96% of the phenotypic variance, with an average of 24.63%. Annotation of these genomic regions unveiled candidate genes potentially responsible for controlling these traits.DiscussionThe findings enhance our understanding of genetic diversity and population structure in avocado germplasm. The identified genetic loci provide valuable insights into the genetic basis of fruit quality traits, aiding breeding programs in developing improved avocado cultivars. Marker-assisted selection can accelerate the development of new varieties, promoting a more diverse and resilient avocado market.

Dataset Information

A High-Quality Melon Genome Assembly Provides Insights into Genetic Basis of Fruit Trait Improvement.

Publications

A High-Quality Melon Genome Assembly Provides Insights into Genetic Basis of Fruit Trait Improvement.

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