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)

Kim, Kwang-Hwan; Hwang, Jang Yeon; Han, Dong-Yeup; Park, Minkyu; Kim, Seungill; Choi, Doil; Kim, Yong-Jae; Lee, Gung Pyo; Kim, Suntae; Park, Young-Hoon

doi:10.1371/journal.pone.0145665

Cited by 46 publications

(50 citation statements)

References 40 publications

(65 reference statements)

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“…In addition to Arabidopsis , NBS-LRR proteins have been found in powdery mildew resistance-associated regions in watermelon, a relative of Cucurbita spp. in the Cucurbitaceae family [71–74]. In addition to the putative NBS-LRR locus, numerous other candidates exist in the interval.…”

Section: Resultsmentioning

confidence: 99%

Cultivar-Based Introgression Mapping Reveals Wild Species-Derived Pm-0, the Major Powdery Mildew Resistance Locus in Squash

Holdsworth

LaPlant

Bell³

et al. 2016

PLoS ONE

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Powdery mildew is a major fungal disease on squash and pumpkin (Cucurbita spp.) in the US and throughout the world. Genetic resistance to the disease is not known to occur naturally within Cucurbita pepo and only infrequently in Cucurbita moschata, but has been achieved in both species through the introgression of a major resistance gene from the wild species Cucurbita okeechobeensis subsp. martinezii. At present, this gene, Pm-0, is used extensively in breeding, and is found in nearly all powdery mildew-resistant C. pepo and C. moschata commercial cultivars. In this study, we mapped C. okeechobeensis subsp. martinezii-derived single nucleotide polymorphism (SNP) alleles in a set of taxonomically and morphologically diverse and resistant C. pepo and C. moschata cultivars bred at Cornell University that, by common possession of Pm-0, form a shared-trait introgression panel. High marker density was achieved using genotyping-by-sequencing, which yielded over 50,000 de novo SNP markers in each of the three Cucurbita species genotyped. A single 516.4 kb wild-derived introgression was present in all of the resistant cultivars and absent in a diverse set of heirlooms that predated the Pm-0 introgression. The contribution of this interval to powdery mildew resistance was confirmed by association mapping in a C. pepo cultivar panel that included the Cornell lines, heirlooms, and 68 additional C. pepo cultivars and with an independent F2 population derived from C. okeechobeensis subsp. martinezii x C. moschata. The interval was refined to a final candidate interval of 76.4 kb and CAPS markers were developed inside this interval to facilitate marker-assisted selection.

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Section: Resultsmentioning

confidence: 99%

Cultivar-Based Introgression Mapping Reveals Wild Species-Derived Pm-0, the Major Powdery Mildew Resistance Locus in Squash

Holdsworth

LaPlant

Bell³

et al. 2016

PLoS ONE

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“…Recently, Kim et al . () identified a major QTL ( pmr2 . 1 ) for resistance to powdery mildew race 1W on chromosome 2 that explained 80.0% of the phenotypic variation.…”

Section: Discussionmentioning

confidence: 99%

“…In the United States, two distinct powdery mildew races, 1W and 2W, are known for watermelon, and several cultivars and wild species highly resistant to these races have been identified (Davis et al, 2007;Tetteh et al, 2010). Recently, Kim et al (2015) identified a major QTL (pmr2.1) for resistance to powdery mildew race 1W on chromosome 2 that explained 80.0% of the phenotypic variation. In the present study, GWAS analysis identified a major peak associated with powdery mildew race 2W resistance also on chromosome 2 (~29.2-31.0 Mb) overlapping with QTL pmr2.1, and additional SNPs on chromosomes 3, 6, 8, 9 and 10 associated with race 2W resistance (Figure 4b and Table S12).…”

Section: Discussionmentioning

confidence: 99%

Genome of ‘Charleston Gray’, the principal American watermelon cultivar, and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection

Wang

Reddy

et al. 2019

Plant Biotechnology Journal

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Summary Years of selection for desirable fruit quality traits in dessert watermelon (Citrullus lanatus) has resulted in a narrow genetic base in modern cultivars. Development of novel genomic and genetic resources offers great potential to expand genetic diversity and improve important traits in watermelon. Here, we report a high‐quality genome sequence of watermelon cultivar ‘Charleston Gray’, a principal American dessert watermelon, to complement the existing reference genome from ‘97103’, an East Asian cultivar. Comparative analyses between genomes of ‘Charleston Gray’ and ‘97103’ revealed genomic variants that may underlie phenotypic differences between the two cultivars. We then genotyped 1365 watermelon plant introduction (PI) lines maintained at the U.S. National Plant Germplasm System using genotyping‐by‐sequencing (GBS). These PI lines were collected throughout the world and belong to three Citrullus species, C. lanatus, C. mucosospermus and C. amarus. Approximately 25 000 high‐quality single nucleotide polymorphisms (SNPs) were derived from the GBS data using the ‘Charleston Gray’ genome as the reference. Population genomic analyses using these SNPs discovered a close relationship between C. lanatus and C. mucosospermus and identified four major groups in these two species correlated to their geographic locations. Citrullus amarus was found to have a distinct genetic makeup compared to C. lanatus and C. mucosospermus. The SNPs also enabled identification of genomic regions associated with important fruit quality and disease resistance traits through genome‐wide association studies. The high‐quality ‘Charleston Gray’ genome and the genotyping data of this large collection of watermelon accessions provide valuable resources for facilitating watermelon research, breeding and improvement.

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“…For fruit shape, two CAPS markers SUN -Cla011257 and wsb3 -24 reported by Kim et al (2015c) were examined ( Table 1).…”

Section: Marker Genotyping For Fruit -Related Traitsmentioning

confidence: 99%

“…Based on bulked segregant analysis (BSA), Kim et al (2015b) demonstrated that a sequence characterized amplified region (SCAR) marker (wsb6 -11) is tightly linked to the stripe pattern observed in the JT cultivar, which is useful for discriminating this cultivar from CT and non -striped rind types. By constructing an intraspecific genetic map and performing quantitative trait locus (QTL) analysis, Kim et al (2015c) identified two cleaved amplified polymorphic sequence (CAPS) markers, SUN -Cla011257 and wsb3 -24, for fruit shape. For fruit flesh color, Bang et al (2007) developed a CAPS (Lcyb) and a SCAR (Clcyb.600) marker from the Lycopene βcyclase (Lcyb)gene, distinguishing red and canary yellow -fleshed fruit.…”

Section: Introductionmentioning

confidence: 99%

Evaluation of DNA Markers for Fruit-related Traits and Genetic Relationships Based on Simple Sequence Repeat in Watermelon Accessions

Jin,

Park,

Choi

et al. 2017

HST

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Modern watermelon cultivars (Citrullus lanatus [Thunb.] Matsum.& Nakai var. lanatus) have fruits with diverse phenotypes, including fruit shape, rind patterns, and flesh color. Molecular markers enable efficient selection of plants harboring desirable phenotypes. In the present study, publicly available DNA markers tightly linked to fruit shape, rind stripe pattern, and flesh color were evaluated using 85 watermelon accessions with diverse fruit phenotypes. For fruit shape, the dCAPS SUN-Cla011257 marker revealed an 81% of marker-trait match for accessions with elongated or round fruits. For rind stripe pattern, the SCAR wsb6-11marker was effective for selecting Jubilee-type rind pattern from other rind patterns. For flesh color, the Clcyb.600 and Lcyb markers derived from a mutation in the Lycopene βcyclase (Lcyb) gene, were effective at selecting red or yellow flesh. Forty-eight accessions possessing diverse fruit-related traits were selected as a reference array and their genetic relationships assessed using 16 SSR markers. At a coefficient of 0.11, the 48 accessions grouped into two major clades: Clade I and Clade II. Clade I subdivided further into subclades I-1 and I-2 at a coefficient of 0.39. All accessions with colored flesh were classified into Clade I, whereas those with white-flesh were classified into Clade II. Differences in fruit traits between subclades I-1 and I-2 were observed for rind pattern and fruit color; a majority of the accessions with Crimson-type striped or non-striped rind were grouped together in subclade I-1, while most accessions in subclade I-2 had a Jubilee-type rind stripe pattern. These results imply that reference array watermelon accessions possess distinguishable genetic structure based on rind stripe pattern. However, no significant grouping pattern was observed based on other fruit-related traits.

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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)

Cited by 46 publications

References 40 publications

Cultivar-Based Introgression Mapping Reveals Wild Species-Derived Pm-0, the Major Powdery Mildew Resistance Locus in Squash

Cultivar-Based Introgression Mapping Reveals Wild Species-Derived Pm-0, the Major Powdery Mildew Resistance Locus in Squash

Genome of ‘Charleston Gray’, the principal American watermelon cultivar, and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection

Evaluation of DNA Markers for Fruit-related Traits and Genetic Relationships Based on Simple Sequence Repeat in Watermelon Accessions

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