An Extended Genetic Linkage Map for Watermelon Based on a Testcross and a BC&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;F&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; Population

Levi, Amnon; Wechter, Patrick; Massey, Laura; Carter, Louisa; Hopkins, D. L.

doi:10.4236/ajps.2011.22012

Cited by 35 publications

(20 citation statements)

References 22 publications

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“…In grapevine (Vitis vinifera), Barba et al (2014) allowed up to 10% missing data in GBS-derived SNPs for genetic map construction. The genetic map obtained in this study was significantly longer (3,955.2 cM) than that obtained in previous watermelon mapping studies (Hashizume et al, 2003;Hawkins et al, 2001;Levi et al, 2002Levi et al, , 2006Levi et al, , 2011Ren et al, 2012Ren et al, , 2014Sandlin et al, 2012). Massive elongation of the genetic maps often occurs when working with SNP data generated through GBS due to high levels of genotyping errors that tend to over-estimate the number of double cross-over events (Barba et al, 2014;Spindel et al, 2013).…”

Section: Genotyping By Sequencing and Snp Analysiscontrasting

confidence: 58%

“…However, none of these EST markers mapped closely to RAPD marker (OP01/700) previously described by Xu et al (1999) in PI 296341-FR. The inability to find useful marker-trait associations in PI 296341-FR in earlier studies was probably due to low genome coverage and high segregation distortion of marker alleles in this PI (Levi et al, 2011). The narrow genetic diversity among cultivated watermelon has previously hindered genetic mapping studies in elite by elite biparental populations due to low genetic diversity.…”

Section: Introductionmentioning

confidence: 98%

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Genotyping by sequencing for SNP discovery and genetic mapping of resistance to race 1 of Fusarium oxysporum in watermelon

Meru

McGregor

2016

Scientia Horticulturae

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a b s t r a c t Management of fusarium wilt caused by Fusarium oxysporum f. sp. niveum (Fon) (E.F. Sm.) W.C. Snyder & H.N. Han. in watermelon [Citrullus lanatus (Thunb.) Matsum.& Nakai] is largely dependent on cultivation of resistant cultivars. Application of marker-assisted selection (MAS) in conventional breeding programs can accelerate the release of new watermelon cultivars resistant to fusarium wilt. Towards developing tools for MAS, physical (1024 SNPs) and genetic (389 SNPs) maps were developed in the current study for an F 2 population (n = 89; Calhoun Gray x Sugar Baby) segregating for resistance against Fon race 1 using the genotyping by sequencing platform. A modified tray-dip method was established for high-throughput phenotyping of the segregating F 3 population. A major quantitative trait locus (QTL) accounting for up to 38.4% of the phenotypic variation in the F 3 population was identified on chromosome 1 on both the physical and genetic maps in a region previously associated with Fon race 1 resistance. This resistance locus was consistently detected over five different time points and three different phenotypic screens, showing the reliability of the screening method in discriminating susceptible and resistant genotypes. Eight resistance genes were found within the confidence interval of the identified QTL. SNPs close to this QTL may be exploited in MAS for fusarium wilt resistance in breeding programs. This study confirms the resistance locus on chromosome 1 and demonstrates the use of a physical map for QTL detection in watermelon. The SNPs reported here will be useful for future genetic studies in watermelon.

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Section: Genotyping By Sequencing and Snp Analysiscontrasting

confidence: 58%

Section: Introductionmentioning

confidence: 98%

Genotyping by sequencing for SNP discovery and genetic mapping of resistance to race 1 of Fusarium oxysporum in watermelon

Meru

McGregor

2016

Scientia Horticulturae

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“…Due to the adoption of unique primers, SRAP markers are more reproducible and less complex. Levi et al (2011) developed a genetic linkage map for watermelon consisting of numerous SRAP markers (the second most prevalent markers after RAPDs), strongly verifying high polymorphism.…”

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confidence: 90%

Comparative analysis of genetic diversity among Chinese watermelon germplasmsusing SSR and SRAP markers, and implications for future genetic improvement

Wang¹,

Li²,

Hu³

et al. 2015

Turk J Agric For

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The genetic diversity of watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] in China, the world's largest producer of watermelon fruits, has not been examined. Two molecular markers, sequence-related amplified polymorphism (SRAP) and simple sequence repeat (SSR), were used to investigate the genetic variation and genetic relationship among 54 Chinese watermelon accessions, as well as 7 accessions from Africa, the United States, and Japan. SRAP assay generated 312 bands, of which 163 were polymorphic, while SSR assay detected 101 alleles with 87 polymorphic alleles and 114 genotypes. A comparative analysis of the diversity index, effective multiplex ratio, and marker index of the 2 markers showed higher efficiency of SRAP markers in watermelon germplasm fingerprinting. The Mantel test resulted in a high correlation between SRAP and SSR data with a value of γ = 0.863, revealing a good fit between the 2 marker systems. Genetic diversity among the accession set was estimated by a construction of dendrograms using SRAP, SSR, or SRAP-SSR combined data. There was clear consistency between the 3 dendrograms on the positioning of most accessions. The study demonstrated that most Chinese cultivated germplasms (CCGs) were clustered independently of their geographical distribution and horticultural classification, and had a narrow genetic base; most CCGs and foreign cultivars had a high genetic closeness and showed similar lineages; and the 4 wild accessions were the most genetically diverse, followed by the small-fruited accessions from northern China and edible-seeded accessions. We concluded that CCGs lacked genetic variation, and we offer a means of introducing new genetic diversity into the watermelon germplasm pool in China, which is essential to maximizing productivity in watermelon.

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“…Analysis of SRAP data has frequently been employed for the construction of linkage maps (LM; Lin et al, 2003, 2009; Yeboah et al, 2007; Levi et al, 2011;D. Guo et al, 2012) and identification of quantitative trait loci (QTL; Chen et al, 2007; Yuan et al, 2008; Zhang et al, 2009).…”

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confidence: 99%

Sequence‐related amplified polymorphism (SRAP) markers: A potential resource for studies in plant molecular biology¹

2014

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In the past few decades, many investigations in the field of plant biology have employed selectively neutral, multilocus, dominant markers such as inter-simple sequence repeat (ISSR), random-amplified polymorphic DNA (RAPD), and amplified fragment length polymorphism (AFLP) to address hypotheses at lower taxonomic levels. More recently, sequence-related amplified polymorphism (SRAP) markers have been developed, which are used to amplify coding regions of DNA with primers targeting open reading frames. These markers have proven to be robust and highly variable, on par with AFLP, and are attained through a significantly less technically demanding process. SRAP markers have been used primarily for agronomic and horticultural purposes, developing quantitative trait loci in advanced hybrids and assessing genetic diversity of large germplasm collections. Here, we suggest that SRAP markers should be employed for research addressing hypotheses in plant systematics, biogeography, conservation, ecology, and beyond. We provide an overview of the SRAP literature to date, review descriptive statistics of SRAP markers in a subset of 171 publications, and present relevant case studies to demonstrate the applicability of SRAP markers to the diverse field of plant biology. Results of these selected works indicate that SRAP markers have the potential to enhance the current suite of molecular tools in a diversity of fields by providing an easy-to-use, highly variable marker with inherent biological significance.

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An Extended Genetic Linkage Map for Watermelon Based on a Testcross and a BC<sub>2</sub>F<sub>2</sub> Population

Abstract: ABSTRACT

Cited by 35 publications

References 22 publications

Genotyping by sequencing for SNP discovery and genetic mapping of resistance to race 1 of Fusarium oxysporum in watermelon

Genotyping by sequencing for SNP discovery and genetic mapping of resistance to race 1 of Fusarium oxysporum in watermelon

Comparative analysis of genetic diversity among Chinese watermelon germplasmsusing SSR and SRAP markers, and implications for future genetic improvement

Sequence‐related amplified polymorphism (SRAP) markers: A potential resource for studies in plant molecular biology¹

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An Extended Genetic Linkage Map for Watermelon Based on a Testcross and a BC&lt;sub&gt;2&lt;/sub&gt;F&lt;sub&gt;2&lt;/sub&gt; Population

Abstract: ABSTRACT

Cited by 35 publications

References 22 publications

Genotyping by sequencing for SNP discovery and genetic mapping of resistance to race 1 of Fusarium oxysporum in watermelon

Genotyping by sequencing for SNP discovery and genetic mapping of resistance to race 1 of Fusarium oxysporum in watermelon

Comparative analysis of genetic diversity among Chinese watermelon germplasmsusing SSR and SRAP markers, and implications for future genetic improvement

Sequence‐related amplified polymorphism (SRAP) markers: A potential resource for studies in plant molecular biology1

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An Extended Genetic Linkage Map for Watermelon Based on a Testcross and a BC<sub>2</sub>F<sub>2</sub> Population

Sequence‐related amplified polymorphism (SRAP) markers: A potential resource for studies in plant molecular biology¹