Genome diversity and gene haplotypes in the grapevine (Vitis vinifera L.), as revealed by single nucleotide polymorphisms

Salmaso, Marzia; Faes, Giorgia; Segala, C.; Stefanini, M.; Salakhutdinov, Ilkhom; Zyprian, Eva; Toepfer, Reinhard; Grando, S.; Velasco, Riccardo

doi:10.1007/s11032-004-0261-z

Cited by 77 publications

(43 citation statements)

References 34 publications

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“…Although, probabilistically, the expected proportion between transitions and transversions is 1:2, a bias towards transitions is frequently observed, probably as a consequence of greater purifying selection against transversions (Keller et al 2007) that may vary for different organisms (Strandberg and Salter 2004). The transition/transversion ratio observed here (1.77) is similar to that observed in grape (1.56 by Salmaso et al 2004 and1.46 by Lijavetzky et al 2007) and potato (1.5 by Simko et al 2006) and higher than that observed in apple (1.27 by Micheletti et al 2011). The number of polymorphic sites in polymorphic loci (including SNPs and indels) varied from one to six, with an average of 2.3 (Table 4).…”

Section: Sequence Variabilitysupporting

confidence: 87%

A first insight into peach [Prunus persica (L.) Batsch] SNP variability

Aranzana

Illa

Howad

et al. 2012

Tree Genetics & Genomes

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Three factors may have reduced the diversity at both individual gene and whole genome levels in cultivated peach: its self-compatible mating system, the narrow genetic basis of most commercial cultivars, and the recent strong selection towards agronomically interesting traits. Previous diversity analyses with markers such as simple sequence repeats (SSRs) have revealed low levels of genetic variability. Here, we sequenced 23 genome-wide distributed DNA fragments in 47 occidental peach varieties, also observing reduced variability levels. On average, there was one single nucleotide polymorphism (SNP) every 598 bp and one indel every 4,189 bp. As expected, variability was higher in noncoding than in coding regions (one SNP every 390 noncoding bp versus one in 1,850 bp in coding DNA). In general, SNPs were observed at relatively high frequency, mean minor allele frequency00.225, meaning that a large proportion of the SNPs discovered by sequencing similar germplasm will be useful for other purposes, such as association mapping. The average heterozygosity of the varieties was 0.28, with a low correlation between SSR and SNP heterozygosity. The whole sequence of two candidate genes, a pectate lyase 1 candidate for fruit firmness (CGPAA2668) and a sucrose synthase 1 candidate for sugar content (CGPPB6189), in the 47 varieties revealed that they both may have suffered a process of balancing selection.

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Section: Sequence Variabilitysupporting

confidence: 87%

A first insight into peach [Prunus persica (L.) Batsch] SNP variability

Aranzana

Illa

Howad

et al. 2012

Tree Genetics & Genomes

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“…Thus, haplotypes were inferred using PHASE v.2.1.1 [32,33] that included in DnaSP v5. A similar situation was experienced with grapevine [34] and cassava [35]. Haplotype based gene diversity (Hd) was estimated for each polymorphic gene fragment using DnaSP v5.…”

Section: Data Analysesmentioning

confidence: 99%

Nucleotide Diversities and Genetic Relationship in the Three Japanese Pine Species; Pinus thunbergii, Pinus densiflora, and Pinus luchuensis

Suharyanto

Shiraishi

2011

Diversity

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Abstract:The nucleotide diversities and genetic relationship in the three Japanese pine species, P. thunbergii, P. densiflora, and P. luchuensis, were measured using low-copy anchor loci in Pinaceae. The average nucleotide diversity among these three Japanese pines revealed that P. thunbergii was the highest (6.05 × 10 −3 ), followed by P. densiflora (5.27 × 10 −3 ) and P. luchuensis (5.02 × 10 −3 ). In comparison to other conifer species, it was concluded that the pines possessed an intermediate level of nucleotide diversity. The Heat shock protein (HSP) gene in P. thunbergii, Phenylalanine tRNA synthetase, RuBP carboxylase, and Disease resistance response protein 206 genes in P. densiflora were significantly deviated from standard neutral models. Some of these genes were related to stress or pathogen/defense response. As the samples used in this study were collected from natural populations that showed specific characteristics of being resistant to pine wilt nematode, it was hypothesized that the initial selection was an important factor in discriminating the deviation from neutrality models. Phylogenetic reconstruction revealed that the three Japanese pines were split into two lineages corresponding to P. densiflora and P. thunbergii-P. luchuensis. The latter lineage was differentiated further into two clades; P. thunbergii and P. luchuensis. The result concludes that the three Japanese pines are closely related and P. thunbergii is genetically closer to P. luchuensis, than P. densiflora. OPEN ACCESSDiversity 2011, 3 122

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“…SNPs can be found in large numbers and are more prevalent in the genome, therefore increasing the probability of finding SNP markers near the locus of interest. Currently, there is great interest in genome-wide studies, such as gene mapping (Wang et al, 1998;Yang et al, 2004), evolution (Cargill et al, 1999;Stoneking, 2001;Primmer et al, 2002) and genetic variation assessment (Salmaso et al, 2004;Shamay et al, 2006). SNPs can be the best choice for markers in the studies mentioned.…”

Section: Introductionmentioning

confidence: 99%

“…SNPs can be the best choice for markers in the studies mentioned. The utilization of SNPs in fruit tree genetic assessment is quite recent (Salmaso et al, 2004). The availability of expressed sequence tag (EST) data has made it feasible to discover putative SNPs in silico prior to experimental verification.…”

Section: Introductionmentioning

confidence: 99%

Characterization of SNPs in strawberry cultivars in China

Han²,

Li³

et al. 2013

Genet. Mol. Res.

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ABSTRACT. Single nucleotide polymorphisms (SNPs) occur at high frequencies in both plant and animal genomes and can provide broad genome coverage and reliable estimates of genetic relationships. The availability of expressed sequence tag (EST) data has made it feasible to discover SNPs. DNA analysis is crucial in genetic studies not only for strawberry breeding programs but also for characterization of hybrids and species. We cloned 96 EST sequences, and 116 SNPs were discovered by comparing 16 strawberry cultivars grown in the region of Nanjing, China. Sequence alignment of 6 group sequences derived from 16 sample cultivars yielded 116 SNPs, within a total genomic sequence length of 1755 bp. The SNPs were discovered with a mean frequency of one SNP per 15 bp. These SNPs were comprised of 57% transitions, 32.7% transversions, 8.6% InDels, and 1.7% others, based on which a phylogenetic tree was constructed. Among the 116 SNPs, 75% were located within the open reading frame (ORF), while 25% were located outside the ORF. All 16 cultivars scattered well in the dendrogram derived from the SNP data, demonstrating that SNPs can be a powerful tool for cultivar identification and genetic diversity analysis in strawberries.

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Genome diversity and gene haplotypes in the grapevine (Vitis vinifera L.), as revealed by single nucleotide polymorphisms

Cited by 77 publications

References 34 publications

A first insight into peach [Prunus persica (L.) Batsch] SNP variability

A first insight into peach [Prunus persica (L.) Batsch] SNP variability

Nucleotide Diversities and Genetic Relationship in the Three Japanese Pine Species; Pinus thunbergii, Pinus densiflora, and Pinus luchuensis

Characterization of SNPs in strawberry cultivars in China

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