Genetic diversity and population structure of core watermelon (Citrullus lanatus) genotypes using DArTseq-based SNPs

Xingping Yang, Runsheng Ren, Rumiana Ray, Jinhua Xu, Pingfang Li, Man Zhang, Guang Liu, Xiefeng Yao

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

Watermelon [Citrullus lanatus (Thunb.) Matsum. Nakai var. lanatus] is an economically important vegetable belonging to the Cucurbitaceae family. Genotypes that exhibit agronomically important traits are selected for the development of elite cultivars. Understanding the genetic diversity and the genotype population structure based on molecular markers at the genome level can speed up the utilization of diverse genetic resources for varietal improvement. In the present study, we carried out an analysis of genetic diversity based on 3882 SNP markers across 37 core watermelon genotypes, including the most widely used watermelon varieties and wild watermelon. Based on the SNP genotyping data of the 37 watermelon genotypes screened, gene diversity and polymorphism information content values across chromosomes varied between 0.03-0.5 and 0.02-0.38, with averages of 0.14 and 0.13, respectively. The two wild watermelon genotypes were distinct from cultivated varieties and the remaining 35 cultivated genotypes were differentiated into three major clusters: 20 genotypes were grouped in cluster I; 11 genotypes were grouped in cluster II; three advanced breeding lines of yellow fruit flesh and genotype SW043 were grouped in cluster III. The results from neighbour-joining dendrogram, principal coordinate analysis and STRUCTURE analysis approaches were consistent, and the grouping of genotypes was generally in agreement with their origins. Here we reveal the genetic relationships among the core watermelon genotypes maintained at the Jiangsu Academy of Agricultural Sciences, China. The molecular and phenotypic characterization of the existing core watermelon genotypes, together with specific agronomic characteristics, can be utilized by researchers and breeders for future watermelon improvement.
Original languageEnglish
Pages (from-to)226-233
Number of pages8
JournalPlant Genetic Resources
Volume14
Issue number3
DOIs
Publication statusPublished - 2016
Externally publishedYes

Fingerprint

Citrullus
Citrullus lanatus
watermelons
Single Nucleotide Polymorphism
population structure
Genotype
genetic variation
genotype
Population
Cucurbitaceae
China
cultivars
breeding lines
genetic resources
agronomic traits
Vegetables
genotyping
genetic relationships
Breeding

Cite this

Yang, Xingping ; Ren, Runsheng ; Ray, Rumiana ; Xu, Jinhua ; Li, Pingfang ; Zhang, Man ; Liu, Guang ; Yao, Xiefeng. / Genetic diversity and population structure of core watermelon (Citrullus lanatus) genotypes using DArTseq-based SNPs. In: Plant Genetic Resources. 2016 ; Vol. 14, No. 3. pp. 226-233.
@article{149bf19fad044a43864ee8965b461a8d,
title = "Genetic diversity and population structure of core watermelon (Citrullus lanatus) genotypes using DArTseq-based SNPs",
abstract = "Watermelon [Citrullus lanatus (Thunb.) Matsum. Nakai var. lanatus] is an economically important vegetable belonging to the Cucurbitaceae family. Genotypes that exhibit agronomically important traits are selected for the development of elite cultivars. Understanding the genetic diversity and the genotype population structure based on molecular markers at the genome level can speed up the utilization of diverse genetic resources for varietal improvement. In the present study, we carried out an analysis of genetic diversity based on 3882 SNP markers across 37 core watermelon genotypes, including the most widely used watermelon varieties and wild watermelon. Based on the SNP genotyping data of the 37 watermelon genotypes screened, gene diversity and polymorphism information content values across chromosomes varied between 0.03-0.5 and 0.02-0.38, with averages of 0.14 and 0.13, respectively. The two wild watermelon genotypes were distinct from cultivated varieties and the remaining 35 cultivated genotypes were differentiated into three major clusters: 20 genotypes were grouped in cluster I; 11 genotypes were grouped in cluster II; three advanced breeding lines of yellow fruit flesh and genotype SW043 were grouped in cluster III. The results from neighbour-joining dendrogram, principal coordinate analysis and STRUCTURE analysis approaches were consistent, and the grouping of genotypes was generally in agreement with their origins. Here we reveal the genetic relationships among the core watermelon genotypes maintained at the Jiangsu Academy of Agricultural Sciences, China. The molecular and phenotypic characterization of the existing core watermelon genotypes, together with specific agronomic characteristics, can be utilized by researchers and breeders for future watermelon improvement.",
author = "Xingping Yang and Runsheng Ren and Rumiana Ray and Jinhua Xu and Pingfang Li and Man Zhang and Guang Liu and Xiefeng Yao",
year = "2016",
doi = "10.1017/S1479262115000659",
language = "English",
volume = "14",
pages = "226--233",
journal = "Plant Genetic Resources: Characterisation and Utilisation",
issn = "0952-3863",
publisher = "Cambridge University Press",
number = "3",

}

Genetic diversity and population structure of core watermelon (Citrullus lanatus) genotypes using DArTseq-based SNPs. / Yang, Xingping; Ren, Runsheng; Ray, Rumiana; Xu, Jinhua; Li, Pingfang; Zhang, Man; Liu, Guang; Yao, Xiefeng.

In: Plant Genetic Resources, Vol. 14, No. 3, 2016, p. 226-233.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Genetic diversity and population structure of core watermelon (Citrullus lanatus) genotypes using DArTseq-based SNPs

AU - Yang, Xingping

AU - Ren, Runsheng

AU - Ray, Rumiana

AU - Xu, Jinhua

AU - Li, Pingfang

AU - Zhang, Man

AU - Liu, Guang

AU - Yao, Xiefeng

PY - 2016

Y1 - 2016

N2 - Watermelon [Citrullus lanatus (Thunb.) Matsum. Nakai var. lanatus] is an economically important vegetable belonging to the Cucurbitaceae family. Genotypes that exhibit agronomically important traits are selected for the development of elite cultivars. Understanding the genetic diversity and the genotype population structure based on molecular markers at the genome level can speed up the utilization of diverse genetic resources for varietal improvement. In the present study, we carried out an analysis of genetic diversity based on 3882 SNP markers across 37 core watermelon genotypes, including the most widely used watermelon varieties and wild watermelon. Based on the SNP genotyping data of the 37 watermelon genotypes screened, gene diversity and polymorphism information content values across chromosomes varied between 0.03-0.5 and 0.02-0.38, with averages of 0.14 and 0.13, respectively. The two wild watermelon genotypes were distinct from cultivated varieties and the remaining 35 cultivated genotypes were differentiated into three major clusters: 20 genotypes were grouped in cluster I; 11 genotypes were grouped in cluster II; three advanced breeding lines of yellow fruit flesh and genotype SW043 were grouped in cluster III. The results from neighbour-joining dendrogram, principal coordinate analysis and STRUCTURE analysis approaches were consistent, and the grouping of genotypes was generally in agreement with their origins. Here we reveal the genetic relationships among the core watermelon genotypes maintained at the Jiangsu Academy of Agricultural Sciences, China. The molecular and phenotypic characterization of the existing core watermelon genotypes, together with specific agronomic characteristics, can be utilized by researchers and breeders for future watermelon improvement.

AB - Watermelon [Citrullus lanatus (Thunb.) Matsum. Nakai var. lanatus] is an economically important vegetable belonging to the Cucurbitaceae family. Genotypes that exhibit agronomically important traits are selected for the development of elite cultivars. Understanding the genetic diversity and the genotype population structure based on molecular markers at the genome level can speed up the utilization of diverse genetic resources for varietal improvement. In the present study, we carried out an analysis of genetic diversity based on 3882 SNP markers across 37 core watermelon genotypes, including the most widely used watermelon varieties and wild watermelon. Based on the SNP genotyping data of the 37 watermelon genotypes screened, gene diversity and polymorphism information content values across chromosomes varied between 0.03-0.5 and 0.02-0.38, with averages of 0.14 and 0.13, respectively. The two wild watermelon genotypes were distinct from cultivated varieties and the remaining 35 cultivated genotypes were differentiated into three major clusters: 20 genotypes were grouped in cluster I; 11 genotypes were grouped in cluster II; three advanced breeding lines of yellow fruit flesh and genotype SW043 were grouped in cluster III. The results from neighbour-joining dendrogram, principal coordinate analysis and STRUCTURE analysis approaches were consistent, and the grouping of genotypes was generally in agreement with their origins. Here we reveal the genetic relationships among the core watermelon genotypes maintained at the Jiangsu Academy of Agricultural Sciences, China. The molecular and phenotypic characterization of the existing core watermelon genotypes, together with specific agronomic characteristics, can be utilized by researchers and breeders for future watermelon improvement.

U2 - 10.1017/S1479262115000659

DO - 10.1017/S1479262115000659

M3 - Article

VL - 14

SP - 226

EP - 233

JO - Plant Genetic Resources: Characterisation and Utilisation

JF - Plant Genetic Resources: Characterisation and Utilisation

SN - 0952-3863

IS - 3

ER -