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.
Highlights
Watermelon is a fruit crop of the family Cucurbitaceae that is known to originate from Africa and is found in the temperate regions of Africa, central Asia, and the Mediterranean [1,2,3]
Non-orthologous genomic regions contain genes homologous to resistance gene analog (RGA)-like nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes, and several quantitative trait loci (QTL) for Powdery mildew resistance (PMR) have been identified and used for map-based cloning of PMR genes [21,22]. These findings indicate that QTLs for PMR in watermelon may be under genetic control of NBS-LRR class resistance genes (R genes)(s)
Primer pairs for 455 cleaved amplified polymorphic sequences (CAPS) and 11 dCAPS were designed based on single nucleotide polymorphisms (SNPs), while those for 56 Sequence characterized amplified region (SCAR) were generated based on indels
Summary
Watermelon is a fruit crop of the family Cucurbitaceae that is known to originate from Africa and is found in the temperate regions of Africa, central Asia, and the Mediterranean [1,2,3]. Watermelon has 11 gametic chromosomes (2n = 2x = 22) and a genome size of approximately 425 Mb [4,5] It belongs the xerophytic genus Citrullus Schrad. Several molecular markers have been developed for watermelon via genetic map construction. Lanatus, construction of early genetic maps was based on interspecific crosses between C. lanatus var. NGS of the entire genome and transcriptome facilitated the discovery of a large set of sequence variants such as single nucleotide polymorphisms (SNPs), and enabled the construction of high-resolution intraspecific genetic maps [13] and quantitative trait loci (QTL) analysis [14] in watermelon. Despite the progress in genomics, publicly available molecular markers for disease resistance and important horticultural traits [14] are very limited when compared to other crop species for which a reference genome sequence is available
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