Genetic diversity in Vietnamese melon landraces revealed by the analyses of morphological traits and nuclear and cytoplasmic molecular markers

Nhi, Phan Thị Phương; Akashi, Yukari; Hang, Tran Thi Minh; Tanaka, Katsunori; Aierken, Yasheng; Yamamoto, Tatsuya; Nishida, Hidetaka; Long, Chunlin; Kato, Kenji

doi:10.1270/jsbbs.60.255

Cited by 21 publications

(30 citation statements)

References 25 publications

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“…A total of 24 melon accessions were selected based on RAPD profile from previous studies for screening polymorphism of RAPD-STS markers [5,6]. The polymorphic RAPD-STS markers were used to genotype of 41 melon accessions [6].…”

Section: Dna Materialsmentioning

confidence: 99%

“…RAPD reactions were performed and analyzed following the method described by Nhi et al [6]. The bright and highly reproducible products of 16 RAPD markers were excised from agarose gel and purified by QIAquick PCR purification kit (QIAGEN, USA).…”

Section: Cloning and Sequencing Of Rapd-generated Dna Fragmentsmentioning

confidence: 99%

“…To confirm the accuracy and stability of new RAPD-STS markers (A20, A22, A31, A57, B15, B71, B99 and C00), 41 melon accessions were genotyped and compared with RAPD profile [6]. All markers produced clear and reproducible polymorphic fragments in the 41 accessions, except for C00.…”

Section: Validation Of Rapd-sts Markersmentioning

confidence: 99%

“…Abundant of molecular markers are applicable to reveal the variation within melon accessions, including restriction fragment length polymorphisms (RFLP) [4], random amplified polymorphic DNA (RAPD) [5,6], simple sequence repeats (SSR) [7] and single nucleotide polymorphisms (SNP) [8]. PCR-based markers, especially RAPD and SSR, have received much attention; however, RAPD markers are dominant markers and incapable to detect heterozygote, and also difficult to reproduce RAPD profile between different laboratories due to their lack D DAVID PUBLISHING Development of RAPD-Derived STS Markers for Genetic Diversity Assessment in Melon (Cucumis melo L.) 450 of specificity.…”

Section: Introductionmentioning

confidence: 99%

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Development of RAPD-Derived STS Markers for Genetic Diversity Assessment in Melon (Cucumis melo L.)

Dung¹,

Thuy²,

Tanaka³

et al. 2015

JAST-A

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Random amplified polymorphic DNA (RAPD) has been used widely in diversity studies, including population structure and phylogenetics at all taxonomic levels. However, there is a problem in stability and repeatability of RAPD in some cases. Therefore, conversion of RAPD markers into new type of PCR-based marker to overcome low levels of repeatability of RAPD marker is needed. The aim of this study was to develop sequence-tagged site (STS) markers by designing specific primers based on RAPD marker sequences to provide the potential markers for analyzing genetic diversity of melon germplasm. Eight RAPD-STS markers were successfully converted from RAPD markers and have two polymorphism types: A20 and B99 showed different sizes of fragment; A22, A31, A57, B15, B71 and C00 showed presence/absence polymorphism in melon germsplasm. The applicability of new RAPD-STS markers has been demonstrated by comparing genotype analysis of 41 melon accessions using RAPD and RAPD-STS markers. Both of RAPD markers and RAPD-STS markers divided them into two major clusters. However, the RAPD-STS markers were more polymorphic than RAPD markers (polymorphic index content (PIC) values were 0.346 and 0.274, respectively). Mantel's test showed significant correlation (r = 0.896, P < 0.01) between RAPD-STS dendrogram and RAPD dendrogram. Furthermore, RAPD-STS markers could give more information in population structure and identify admixture individuals by using STRUCTURE software. Eight RAPD-STS markers developed in this study are useful for genetic diversity analysis and population studies in melon.

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Section: Dna Materialsmentioning

confidence: 99%

Section: Cloning and Sequencing Of Rapd-generated Dna Fragmentsmentioning

confidence: 99%

Section: Validation Of Rapd-sts Markersmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Development of RAPD-Derived STS Markers for Genetic Diversity Assessment in Melon (Cucumis melo L.)

Dung¹,

Thuy²,

Tanaka³

et al. 2015

JAST-A

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“…Several researchers have used successfully a variety of DNA markers to characterize the genetic diversity of melons such as isozymes (Staub et al, 1997;Akashi et al, 2002), restriction fragment length polymorphism (RFLPs) (Zheng et al, 1999), random amplification of polymorphic DNAs (RAPDs) (Garcia et al, 1998;Stepansky et al, 1999;Mliki et al, 2001;Lo´pez-Sese et al, 2003;Staub et al, 2004;Sensoy et al, 2007;Tanaka et al, 2007, Nhi et al, 2010Soltani et al, 2010), amplified fragment length polymorphism (AFLPs) (Garcia-Mas et al, 2000, Yashiro et al, 2005, intersimple sequence repeat (ISSR) and simple-sequence repeat (SSR) (Katzir et al, 1996;Staub et al, 2000;Danin-Poleg et al, 2001;Lo´pez-Sese´ et al, 2002;Monforte et al, 2003;Nakata et al, 2005;Tzitzikas et al, 2009;Raghami et al, 2014;Trimech et al, 2015) using diverse germplasm from different locations worldwide. Of all classes of DNA based marker, SSR markers represented by the repeats of 1-6 nucleotide-long DNA motifs arranged in tandem, have been considered one of the most powerful Mendelian markers (Jarne and Lagoda, 1996) because of their high reproducibility, codominance inheritance, multi-allelic character, and extensive genome coverage (Powell et al, 1996).…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity among muskmelon (Cucumis melo L.) germplasm in Bangladesh as revealed by microsatellite markers

Molla¹,

Ahmed²,

Rahman³

et al. 2017

Afr. J. Agric. Res.

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Information about genetic variation has become more critical and deciding factor for any breeding and improvement effort,is difficult inefficient and inaccurate when based on morphological traits only. Therefore, this investigation was conducted using nine microsatellite DNA markers to evaluate genetic variation among 96 muskmelon germplasm in Bangladesh. All nine microsatellite markers were polymorphic. Lower values detected in observed than expected heterozygosity for all loci, indicating homozygous condition in the sample population. A total number of 28 alleles were generated by the nine primers across 96 germplasm. The locus TJ10 showed the highest number of alleles (5), whereas CMGA104, CMCT44, CMAG59, CMTA134a and J27 were generated lowest (3) number of alleles. Allele size ranged between 98 bp (CMCT44) to 198 (CMCTT144). The Polymorphism Information Content (PIC) values ranged from 0.117 to 0.770for the locus CMCTN86and TJ10, repectively. Values of genetic differentiation (Fst) and gene flow (Nm) ranged from 0.535 to 1.000 with an average of 0.776 and from 0.000 to 0.218 with a mean value of 0.072, respectively. Broad genetic base was found among the muskmelon germplasm used in this study. The average pair-wise Nei's genetic distance value was 0.605. The highest genetic dissimilarity coefficient (GD=2.300) was between the germplasm AHM-241 and IAH-102, whereas germplasm IAH-251 and IAH-259 comprised lowest genetic diversity (GD=0.000). In the UPGMA dendrogram, among 96 germplasm of muskmelon 84 grouped in cluster "I" and other 12 in cluster "II".

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SNP genotyping in melons: genetic variation, population structure, and linkage disequilibrium

et al. 2013

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Novel sequencing technologies were recently used to generate sequences from multiple melon (Cucumis melo L.) genotypes, enabling the in silico identification of large single nucleotide polymorphism (SNP) collections. In order to optimize the use of these markers, SNP validation and large-scale genotyping are necessary. In this paper, we present the first validated design for a genotyping array with 768 SNPs that are evenly distributed throughout the melon genome. This customized Illumina GoldenGate assay was used to genotype a collection of 74 accessions, representing most of the botanical groups of the species. Of the assayed loci, 91 % were successfully genotyped. The array provided a large number of polymorphic SNPs within and across accessions. This set of SNPs detected high levels of variation in accessions from this crop's center of origin as well as from several other areas of melon diversification. Allele distribution throughout the genome revealed regions that distinguished between the two main groups of cultivated accessions (inodorus and cantalupensis). Population structure analysis showed a subdivision into five subpopulations, reflecting the history of the crop. A considerably low level of LD was detected, which decayed rapidly within a few kilobases. Our results show that the GoldenGate assay can be used successfully for high-throughput SNP genotyping in melon. Since many of the genotyped accessions are currently being used as the parents of breeding populations in various programs, this set of mapped markers could be used for future mapping and breeding efforts.

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Genetic diversity in Vietnamese melon landraces revealed by the analyses of morphological traits and nuclear and cytoplasmic molecular markers

Cited by 21 publications

References 25 publications

Development of RAPD-Derived STS Markers for Genetic Diversity Assessment in Melon (Cucumis melo L.)

Development of RAPD-Derived STS Markers for Genetic Diversity Assessment in Melon (Cucumis melo L.)

Genetic diversity among muskmelon (Cucumis melo L.) germplasm in Bangladesh as revealed by microsatellite markers

SNP genotyping in melons: genetic variation, population structure, and linkage disequilibrium

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