QTL mapping for melon ( Cucumis melo L.) fruit traits by assembling and utilization of novel SNPs based CAPS markers

Amanullah, Sikandar; Liu, Shi; Gao, Peng; Zhang, Zhu; Fan, Chao; Luan, Feishi

doi:10.1016/j.scienta.2018.02.041

Cited by 31 publications

(20 citation statements)

References 43 publications

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“…CAPS MARKER VERIFICATION USING PCR. The PCR amplification was performed in a 20-mL mixture using the touchdown PCR system (Amanullah et al, 2018). The mixture contained 2 mL of template of gDNA, 0.4 mL Taq endonuclease, 1 mL each of forward and reverse primer, 2 mL Taq buffer, 0.6 mL dNTPs, and 13 mL nuclease-free water.…”

Section: Methodsmentioning

confidence: 99%

Fine Mapping of Cla015407 Controlling Plant Height in Watermelon

Zhang¹,

Li²,

Amanullah³

et al. 2021

J. Amer. Soc. Hort. Sci.

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The plant compact and dwarf growth habit is an important agronomic trait when breeding watermelon (Citrullus lanatus) cultivars because of their reduced vine length, high-density planting, and better land utilization; however, the genetic basis of the dwarf growth habit is not well-known. In this study, the plant population of six generations, P1, P2, F1, F2, BC1P1, and BC1P2, were studied. A genetic segregation analysis demonstrated that dwarfism is mainly controlled by a single recessive Cldw gene. Furthermore, whole-genome sequencing of two distinct watermelon cultivars, W1-1 (P1) and 812 (P2), was performed and preliminarily mapped through a bulked segregant analysis of F2 individuals that revealed the Cldw gene locus on chromosome 9. Two candidate genes, Cla015407 and Cla015408, were discovered at the delimited region of 43.2 kb by fine mapping, and gene annotation exposed that the Cla015407 gene encodes gibberellic acid 3β-hydroxylase protein. In addition, a comparative analysis of gene sequence and cultivars sequences across the reference genome of watermelon revealed the splice site mutation in the intron region of the Cldw gene in dwarf-type cultivar 812. The quantitative real-time polymerase chain reaction exhibited a significantly higher expression of the Cla015407 gene in cultivar W1-1 compared with 812. There was no significant difference in the vine length of both cultivars after gibberellic acid treatment. In brief, our fine mapping demonstrated that Cla015407 is a candidate gene controlling dwarfism of watermelon plants.

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Section: Methodsmentioning

confidence: 99%

Fine Mapping of Cla015407 Controlling Plant Height in Watermelon

Zhang¹,

Li²,

Amanullah³

et al. 2021

J. Amer. Soc. Hort. Sci.

Self Cite

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“…The melon draft genome was recently released [17], which helped characterize genes related to melon domestication or selection, and many quantitative trait loci have been reported [18][19][20][21]. To understand the evolution of the melon genomic structure, a genomewide association study (GWAS) was also performed [10,[22][23][24].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide SNP Markers for Genotypic and Phenotypic Differentiation of Melon (Cucumis melo L.) Varieties Using Genotyping-by-Sequencing

Hyun

Raveendar

Lee

et al. 2021

IJMS

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Melon (Cucumis melo L.) is an economically important horticultural crop with abundant morphological and genetic variability. Complex genetic variations exist even among melon varieties and remain unclear to date. Therefore, unraveling the genetic variability among the three different melon varieties, muskmelon (C. melo subsp. melo), makuwa (C. melo L. var. makuwa), and cantaloupes (C. melo subsp. melo var. cantalupensis), could provide a basis for evolutionary research. In this study, we attempted a systematic approach with genotyping-by-sequencing (GBS)-derived single nucleotide polymorphisms (SNPs) to reveal the genetic structure and diversity, haplotype differences, and marker-based varieties differentiation. A total of 6406 GBS-derived SNPs were selected for the diversity analysis, in which the muskmelon varieties showed higher heterozygote SNPs. Linkage disequilibrium (LD) decay varied significantly among the three melon varieties, in which more rapid LD decay was observed in muskmelon (r2 = 0.25) varieties. The Bayesian phylogenetic tree provided the intraspecific relationships among the three melon varieties that formed, as expected, individual clusters exhibiting the greatest genetic distance based on the posterior probability. The haplotype analysis also supported the phylogeny result by generating three major networks for 48 haplotypes. Further investigation for varieties discrimination allowed us to detect a total of 52 SNP markers that discriminated muskmelon from makuwa varieties, of which two SNPs were converted into cleaved amplified polymorphic sequence markers for practical use. In addition to these markers, the genome-wide association study identified two SNPs located in the genes on chromosome 6, which were significantly associated with the phenotypic traits of melon seed. This study demonstrated that a systematic approach using GBS-derived SNPs could serve to efficiently classify and manage the melon varieties in the genebank.

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“…SSR-PCR reaction system, amplification program, and gel electrophoresis of PCR products were as previously described ( Zhu et al, 2016 ). CAPS amplification, enzyme digestion, and agarose gel electrophoresis of enzyme-digested products were same as the report of Amanullah et al (2018) .…”

Section: Methodsmentioning

confidence: 99%

Dissecting the Genetic Architecture of Melon Chilling Tolerance at the Seedling Stage by Association Mapping and Identification of the Elite Alleles

et al. 2018

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Low temperature is an important abiotic stress that negatively affects morphological growth and fruit development in melon (Cucumis melo L.). Chilling stress at the seedling stage causes seedling injury and poor stand establishment, prolonging vegetative growth and delaying fruit harvest. In this study, association mapping was performed for chilling tolerance at the seedling stage on an expanded melon core collection containing 212 diverse accessions by 272 SSRs and 27 CAPSs. Chilling tolerance of the melon seedlings was evaluated by calculating the chilling injury index (CII) in 2016 and 2017. Genetic diversity analysis of the whole accession panel presented two main groups, which corresponded to the two subspecies of C. melo, melo, and agrestis. Both the subspecies were sensitive to chilling but with agrestis being more tolerant. Genome-wide association study (GWAS) was conducted, respectively, on the whole panel and the two subspecies, totally detecting 51 loci that contributed to 74 marker-trait associations. Of these associations, 35 were detected in the whole panel, 21 in melo, and 18 in agrestis. About half of the associations identified in the two subspecies were also observed in the whole panel, and seven associations were shared by both the subspecies. CMCT505_Chr.1 was repeatedly detected in different populations with high phenotypic contribution and could be a key locus controlling chilling tolerance in C. melo. Nine loci were selected for evaluation of the phenotypic effects related to their alleles, which identified 11 elite alleles contributing to seedling chilling tolerance. Four such alleles existed in both the subspecies and six in either of the two subspecies. Analysis of 20 parental combinations for their allelic status and phenotypic values showed that the elite alleles collectively contributed to enhancement of the chilling tolerance. Tagging the loci responsible for chilling tolerance may simultaneously favor dissecting the complex adaptability traits and elevate the efficiency to improve chilling tolerance using marker-assisted selection in melon.

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QTL mapping for melon ( Cucumis melo L.) fruit traits by assembling and utilization of novel SNPs based CAPS markers

Cited by 31 publications

References 43 publications

Fine Mapping of Cla015407 Controlling Plant Height in Watermelon

Fine Mapping of Cla015407 Controlling Plant Height in Watermelon

Genome-Wide SNP Markers for Genotypic and Phenotypic Differentiation of Melon (Cucumis melo L.) Varieties Using Genotyping-by-Sequencing

Dissecting the Genetic Architecture of Melon Chilling Tolerance at the Seedling Stage by Association Mapping and Identification of the Elite Alleles

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