A novel high-density grapevine (Vitis vinifera L.) integrated linkage map using GBS in a half-diallel population

Tello, Javier; Roux, Catherine; Chouiki, Hajar; Laucou, Valérie; Sarah, Gautier; Weber, Audrey; Santoni, Sylvain; Flutre, Timothée; Pons, Thierry; This, Patrice; Péros, Jean‐Pierre; Doligez, Agnès

doi:10.1007/s00122-019-03351-y

Cited by 37 publications

(35 citation statements)

References 94 publications

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“…In this study, we used the GBS method (Baird et al, 2008;Elshire et al, 2011) to simultaneously discover new SNP markers and genotype individual samples from two Lepidium species (L. campestre and L. heterophyllum) as well as an F 2 mapping population of interspecific hybrid between genotypes of the two species. SNP markers discovered through GBS has previously been successfully used for the construction of high-density genetic linkage mapping in various plant species including barley and wheat (Poland et al, 2012), Aethionema arabicum (Nguyen et al, 2019), Avena species (Latta et al, 2019), and grapevine (Tello et al, 2019). The eight linkage groups constructed in this study correspond to the eight haploid chromosome number previously reported for both L. campestre and L. heterophyllum (Rice et al, 2015).…”

Section: Discussionsupporting

confidence: 56%

High-Density Genetic Linkage Mapping of Lepidium Based on Genotyping-by-Sequencing SNPs and Segregating Contig Tag Haplotypes

et al. 2020

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Lepidium campestre has been targeted for domestication as future oilseed and catch crop. Three hundred eighty plants comprising genotypes of L. campestre, Lepidium heterophyllum, and their interspecific F 2 mapping population were genotyped using genotyping by sequencing (GBS), and the generated polymorphic markers were used for the construction of high-density genetic linkage map. TASSEL-GBS, a reference genome-based pipeline, was used for this analysis using a draft L. campestre whole genome sequence. The analysis resulted in 120,438 biallelic single-nucleotide polymorphisms (SNPs) with minor allele frequency (MAF) above 0.01. The construction of genetic linkage map was conducted using MSTMap based on phased SNPs segregating in 1:2:1 ratio for the F 2 individuals, followed by genetic mapping of segregating contig tag haplotypes as dominant markers against the linkage map. The final linkage map consisted of eight linkage groups (LGs) containing 2,330 SNP markers and spanned 881 Kosambi cM. Contigs (10,302) were genetically mapped to the eight LGs, which were assembled into pseudomolecules that covered a total of ∼120.6 Mbp. The final size of the pseudomolecules ranged from 9.4 Mbp (LG-4) to 20.4 Mpb (LG-7). The following major correspondence between the eight Lepidium LGs (LG-1 to LG-8) and the five Arabidopsis thaliana (At) chromosomes (Atx-1-Atx-5) was revealed through comparative genomics analysis: LG-1&2_Atx-1, LG-3_Atx-2&3, LG-4_Atx-2, LG-5_Atx-2&Atx-3, LG-6_Atx-4&5, LG-7_Atx-4, and LG-8_Atx-5. This analysis revealed that at least 66% of the sequences of the LGs showed high collinearity with At chromosomes. The sequence identity between the corresponding regions of the LGs and At chromosomes ranged from 80.6% (LG-6) to 86.4% (LG-8) with overall mean of 82.9%. The map positions on Lepidium LGs of the homologs of 24 genes that regulate various traits in A. thaliana were also identified. The eight LGs revealed in this study confirm the previously reported (1) haploid chromosome number of eight in L. campestre and L. heterophyllum and (2) chromosomal fusion, translocation, and inversion events

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Section: Discussionsupporting

confidence: 56%

High-Density Genetic Linkage Mapping of Lepidium Based on Genotyping-by-Sequencing SNPs and Segregating Contig Tag Haplotypes

et al. 2020

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“…A (high-density) genetic map is essential for QTL mapping [21]. In the past ten years, a number of grape genetic maps have been constructed based on different mapping populations [20,[22][23][24][25][26][27][28][29][30][31][32][33]. Numerous QTLs for important economic traits, including resistance to downy mildew [10,16,22,[34][35][36][37][38], powdery mildew [34,36,[39][40][41], anthracnose [24], root-knot nematodes [42], and grape phylloxera [43,44], as well as flower sex [45,46], berry color [46,47], seedlessness [48], berry weight [18,32], soluble solid content [32], acidity [20], and muscat flavor [49], have been identified.…”

Section: Introductionmentioning

confidence: 99%

“…Next-generation sequencing is a high-throughput, low-cost technology that has been used to identify a large number of SNPs for high-density genetic map construction in various crops, such as soybean [57], cotton [58], and pear [59]. In recent years, several genetic maps for grapevine have been constructed on the basis of high-throughput sequencing technology; these maps have increased marker density and have led to the identification of some new QTLs [10,24,28,33,46]. Nearly all of the genetic maps were constructed using reduced representation methods, such as restriction site-associated DNA sequencing and genotyping-by-sequencing, which are relatively cheap as they sample only a fraction of the genome, but they also produce incomplete data [60].…”

Section: Introductionmentioning

confidence: 99%

Construction of a High-Density Genetic Map and Mapping of Firmness in Grapes (Vitis vinifera L.) Based on Whole-Genome Resequencing

Jiang

Fan

Zhang

et al. 2020

IJMS

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Berry firmness is one of the most important quality traits in table grapes. The underlying molecular and genetic mechanisms for berry firmness remain unclear. We constructed a high-density genetic map based on whole-genome resequencing to identify loci associated with berry firmness. The genetic map had 19 linkage groups, including 1662 bin markers (26,039 SNPs), covering 1463.38 cM, and the average inter-marker distance was 0.88 cM. An analysis of berry firmness in the F1 population and both parents for three consecutive years revealed continuous variability in F1, with a distribution close to the normal distribution. Based on the genetic map and phenotypic data, three potentially significant quantitative trait loci (QTLs) related to berry firmness were identified by composite interval mapping. The contribution rate of each QTL ranged from 21.5% to 28.6%. We identified four candidate genes associated with grape firmness, which are related to endoglucanase, abscisic acid (ABA), and transcription factors. A qRT-PCR analysis revealed that the expression of abscisic-aldehyde oxidase-like gene (VIT_18s0041g02410) and endoglucanase 3 gene (VIT_18s0089g00210) in Muscat Hamburg was higher than in Crimson Seedless at the veraison stage, which was consistent with that of parent berry firmness. These results confirmed that VIT_18s0041g02410 and VIT_18s0089g00210 are candidate genes associated with berry firmness.

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“…But majority of the genetic maps consist a limited number of markers with large map spacing and low resolution, thus are not able to provide precise and complete information about the numbers and locations of QTLs controlling the traits [30]. With the rapid development of the next generation sequencing (NGS) technology, genotyping through sequencing becomes the most direct and powerful method for the large-scale detection of SNP,which are considered as the markers of best choice for high-density genetic map construction [31][32]. At present, several high density genetic maps have been constructed using NGS technologies, and some new QTLs have been successfully identified in grapevine [7,11,[33][34].…”

Section: Introductionmentioning

confidence: 99%

Novel stable QTLs identification for berry quality traits based on high-density genetic linkage map construction in table grape

Wang

Yan

Sun

et al. 2020

Preprint

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Backgroud: Aroma, berry firmness and berry shape are three main quality traits in table grape production, and also the important target traits in grapevine breeding. However, limited information about their genetic determinants leads to low accuracy and efficiency of quality breeding in grapevine. Mapping and isolation of quantitative trait locus (QTLs) based on the construction of genetic linkage map is a powerful approach to decipher the genetic determinants of complex quantitative traits in grape.Results: In the present work, a final integrated map consisted of 6,436 SLAF markers on 19 linkage groups (LGs) spanning 3,365.41 cM in genome size with an average distance of 0.52 cM between adjacent markers was generated using the specific length amplified fragment sequencing (SLAF-seq) technique. Total 16 significant QTLs were identified on six linkage groups based on phenotypic data of Muscat flavor, berry firmness and berry shape among the hybrids analyzed over three consecutive years from 2016 to 2018. Notably, new QTLs for berry firmness and berry shape were found on LG 8 respectively for the first time, which had the strongest and most stable effects over 2-3 years. Based on biological function and expression profiles of candidate genes in the major QTL regions, 3 genes (VIT_08s0007g00440, VIT_08s0040g02740 and VIT_08s0040g02350) related to berry firmness and 3 genes (VIT_08s0032g01110, VIT_08s0032g01150 and VIT_08s0105g00200) linked to berry shape were highlighted. Overexpression of VIT_08s0032g01110 in transgenic Arabidopsis plants caused the change of pod shape.Conclusions: A new high-density genetic map with total 6634 markers was constructed with SLAF-seq technique, and thus enabled the detection of narrow interval QTLs for relevant traits in grapevine. VIT_08s0007g00440, VIT_08s0040g02740 and VIT_08s0040g02350 were found to be related to berry firmness, and VIT_08s0032g01110, VIT_08s0032g01150 and VIT_08s0105g00200 were linked to berry shape.

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A novel high-density grapevine (Vitis vinifera L.) integrated linkage map using GBS in a half-diallel population

Cited by 37 publications

References 94 publications

High-Density Genetic Linkage Mapping of Lepidium Based on Genotyping-by-Sequencing SNPs and Segregating Contig Tag Haplotypes

High-Density Genetic Linkage Mapping of Lepidium Based on Genotyping-by-Sequencing SNPs and Segregating Contig Tag Haplotypes

Construction of a High-Density Genetic Map and Mapping of Firmness in Grapes (Vitis vinifera L.) Based on Whole-Genome Resequencing

Novel stable QTLs identification for berry quality traits based on high-density genetic linkage map construction in table grape

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