Development of Simple Sequence Repeat Markers from De Novo Assembled Transcriptomes of Pumpkins

Kong, Qiusheng; Liu, Yong; Xie, Jin; Bie, Zhilong

doi:10.1007/s11105-019-01189-8

Cited by 11 publications

(6 citation statements)

References 35 publications

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“…Molecular markers, especially DNA markers, are an effective tool to explore genetic variations in crop species. Of these markers, simple sequence repeats (SSRs) have been commonly used for DNA fingerprinting and genetic diversity assessment due to advantages such as codominant and multi-allelic natures [11][12][13][14][15][16][17] . However, SSR markers are not suitable for high-throughput genotyping with a large number of markers.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide SNP discovery and core marker sets for assessment of genetic variations in cultivated pumpkin (Cucurbita spp.)

et al. 2020

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Three pumpkin species Cucurbita maxima, C. moschata, and C. pepo are commonly cultivated worldwide. To identify genome-wide SNPs in these cultivated pumpkin species, we collected 48 F 1 cultivars consisting of 40 intraspecific hybrids (15 C. maxima, 18 C. moschata, and 7 C. pepo) and 8 interspecific hybrids (C. maxima x C. moschata). Genotyping by sequencing identified a total of 37,869 confident SNPs in this collection. These SNPs were filtered to generate a subset of 400 SNPs based on polymorphism and genome distribution. Of the 400 SNPs, 288 were used to genotype an additional 188 accessions (94 F 1 cultivars, 50 breeding lines, and 44 landraces) with a SNP array-based platform. Reliable polymorphisms were observed in 224 SNPs (78.0%) and were used to assess genetic variations between and within the four predefined populations in 223 cultivated pumpkin accessions. Both principal component analysis and UPGMA clustering found four major clusters representing three pumpkin species and interspecific hybrids. This genetic differentiation was supported by pairwise F st and Nei's genetic distance. The interspecific hybrids showed a higher level of genetic diversity relative to the other three populations. Of the 224 SNPs, five subsets of 192, 96, 48, 24, and 12 markers were evaluated for variety identification. The 192, 96, and 48 marker sets identified 204 (91.5%), 190 (85.2%), and 141 (63.2%) of the 223 accessions, respectively, while other subsets showed <25% of variety identification rates. These SNP markers provide a molecular tool with many applications for genetics and breeding in cultivated pumpkin.

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Section: Introductionmentioning

confidence: 99%

Genome-wide SNP discovery and core marker sets for assessment of genetic variations in cultivated pumpkin (Cucurbita spp.)

et al. 2020

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“…The Illumina short read-length platforms produce higher coverage and lower sequencing cost per nucleotide compared with long read-length platforms and have been used for de novo transcriptome assembly along with the advances in read sequencing technology and computational tools. In several crops, including sugarcane [37], peanut [35], sainfoin [58], alfalfa [59], carrot [60], radish [61], sweet potato [62], and pumpkin [63], sequence variations (SNPs, InDels, and SSRs) have been discovered using the Illumina platform for DNA marker development. In oat, the number of available molecular markers for genetic studies and other purposes is insufficient.…”

Section: Discussionmentioning

confidence: 99%

“…Incorrect assemble of reads can also lead to PCR amplification failures. Primers can also cause size differences in PCR products due to the presence or absence of repeats, InDels, and/or introns in the template DNA [63]. In this study, two markers, OH-6-1 and SH-20-1, which showed polymorphisms based on differences in band size in the oat cultivars, were used as InDel markers without restriction enzymes applied (Figure 5c).…”

Section: Discussionmentioning

confidence: 99%

De Novo Transcriptome Assembly and SNP Discovery for the Development of dCAPS Markers in Oat

et al. 2022

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Cultivated oat (Avena sativa L.) is an important cereal crop that has captured interest worldwide due to its nutritional properties and associated health benefits. Despite this interest, oat has lagged behind other cereal crops in genome studies and the development of DNA markers due to its large and complex genome. RNA-Seq technology has been widely used for transcriptome analysis, functional gene study, and DNA marker development. In this study, we performed the transcriptome sequencing of 10 oat varieties at the seedling stage using the Illumina platform for the development of DNA markers. In total, 31,187,392~41,304,176 trimmed reads (an average of 34,322,925) were generated from 10 oat varieties. All of the trimmed reads of these varieties were assembled and generated, yielding a total of 128,244 assembled unigenes with an average length of 1071.7 bp and N50 of 1752 bp. According to gene ontology (GO) analysis, 30.7% of unigenes were assigned to the “catalytic activity” of the parent term in the molecular function category. Of the 1273 dCAPS markers developed using 491 genotype-specific SNPs, 30 markers exhibiting polymorphism in 28 oat varieties were finally selected. The transcriptome data of oat varieties could be used for functional studies about the seedling stage of oat and information about sequence variations in DNA marker development. These 30 dCAPS markers will be utilized for oat genetic analysis, cultivar identification, and breeders’ rights protection.

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“…High-density genetic map is an e cient tool to dissect the genetic architecture of interested traits. In the past, traditional molecular makers, such as SSR, were used to construct genetic map (Kong et al 2020). Due to the limited number of available makers, resolution of the genetic map constructed using the traditional markers is usually very low, which hampers the subsequent cloning of the targeted genes.…”

Section: Introductionmentioning

confidence: 99%

QTL mapping for pumpkin fruit traits using a GBS-based high-density genetic map

et al. 2022

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Pumpkin is a popular vegetable crop and exhibits a broad diversity in fruit shape and size. Fruit-related traits are the decisive factors determining consumer acceptance and market value of pumpkin cultivar. As a result, deciphering the genetic basis of fruitrelated traits is of great importance for pumpkin breeding. To address this problem, a F2 population was generated by two Cucurbita moschata inbred lines with contrasting fruit shapes and genotyping by sequencing approach were used to construct a high-density genetic map and localize the QTLs underlying the fruit-related traits in this study. The results showed that a highquality genetic map was constructed for pumpkin, which comprised of 2413 bins and spanned a total length of 2252.10 cM with an average genetic distance of 0.94 cM. A total of 30 signi cant QTLs with moderate or small effects were identi ed for 7 fruitrelated traits, including fruit length, fruit diameter, fruit shape index, fruit weight, fruit esh thickness, seed cavity size, and total soluble solids content. Co-locations were observed between the QTLs underlying different traits, demonstrating that pleiotropic effect plays an important role in genetic control of fruit-related traits. The identi ed QTLs provide valuable information for further ne mapping of the related genes and pumpkin breeding programs with the aim of improving fruit quality.

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Development of Simple Sequence Repeat Markers from De Novo Assembled Transcriptomes of Pumpkins

Cited by 11 publications

References 35 publications

Genome-wide SNP discovery and core marker sets for assessment of genetic variations in cultivated pumpkin (Cucurbita spp.)

Genome-wide SNP discovery and core marker sets for assessment of genetic variations in cultivated pumpkin (Cucurbita spp.)

De Novo Transcriptome Assembly and SNP Discovery for the Development of dCAPS Markers in Oat

QTL mapping for pumpkin fruit traits using a GBS-based high-density genetic map

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