Major Quantitative Trait Loci and Putative Candidate Genes for Powdery Mildew Resistance and Fruit-Related Traits Revealed by an Intraspecific Genetic Map for Watermelon (Citrullus lanatus var. lanatus)

PLoS One. 2015 Dec 23;10(12):e0145665. doi: 10.1371/journal.pone.0145665. eCollection 2015.

Abstract

An intraspecific genetic map for watermelon was constructed using an F2 population derived from 'Arka Manik' × 'TS34' and transcript sequence variants and quantitative trait loci (QTL) for resistance to powdery mildew (PMR), seed size (SS), and fruit shape (FS) were analyzed. The map consists of 14 linkage groups (LGs) defined by 174 cleaved amplified polymorphic sequences (CAPS), 2 derived-cleaved amplified polymorphic sequence markers, 20 sequence-characterized amplified regions, and 8 expressed sequence tag-simple sequence repeat markers spanning 1,404.3 cM, with a mean marker interval of 6.9 cM and an average of 14.6 markers per LG. Genetic inheritance and QTL analyses indicated that each of the PMR, SS, and FS traits is controlled by an incompletely dominant effect of major QTLs designated as pmr2.1, ss2.1, and fsi3.1, respectively. The pmr2.1, detected on chromosome 2 (Chr02), explained 80.0% of the phenotypic variation (LOD = 30.76). This QTL was flanked by two CAPS markers, wsb2-24 (4.00 cM) and wsb2-39 (13.97 cM). The ss2.1, located close to pmr2.1 and CAPS marker wsb2-13 (1.00 cM) on Chr02, explained 92.3% of the phenotypic variation (LOD = 68.78). The fsi3.1, detected on Chr03, explained 79.7% of the phenotypic variation (LOD = 31.37) and was flanked by two CAPS, wsb3-24 (1.91 cM) and wsb3-9 (7.00 cM). Candidate gene-based CAPS markers were developed from the disease resistance and fruit shape gene homologs located on Chr.02 and Chr03 and were mapped on the intraspecific map. Colocalization of these markers with the major QTLs indicated that watermelon orthologs of a nucleotide-binding site-leucine-rich repeat class gene containing an RPW8 domain and a member of SUN containing the IQ67 domain are candidate genes for pmr2.1 and fsi3.1, respectively. The results presented herein provide useful information for marker-assisted breeding and gene cloning for PMR and fruit-related traits.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromosome Mapping / methods*
  • Chromosomes, Plant / genetics
  • Citrullus / genetics*
  • Citrullus / growth & development
  • Disease Resistance / genetics*
  • Disease Resistance / immunology
  • Fruit / genetics*
  • Genetic Linkage
  • Genome, Plant
  • Phenotype
  • Plant Proteins / genetics*
  • Quantitative Trait Loci*

Substances

  • Plant Proteins

Grants and funding

This research was fully funded by the Ministry of Agriculture, Food and Rural Affairs (MAFRA), Korea, by a grant (710001-07-5) from the Vegetable Breeding Research Center. Further, this research was supported by the Golden Seed Project (213002-04-1-SBR20), MAFRA, the Ministry of Oceans and Fisheries (MOF), Rural Development Administration (RDA), and Korea Forest Service (KFS). The funders provided in the form of salaries for authors (KHK, JHH, and DYH), but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the "author contributions" section. A commercial affiliation, "Partner Seed" (affiliated author: Yongjae Kim) did not provide financial support, but played a role in the study design and data collection by field evaluation of the F2 population. Phenotyping of the F2 population was conducted by Yongjae Kim (the owner of "Partner Seed") at the breeding field owned by Partner Seed Company which collaborated for this study.