High-density linkage maps and loci for berry color and flower sex in muscadine grape (Vitis rotundifolia)

Lewter, Jennifer A.; Worthington, Margaret; Clark, John R.; Varanasi, Aruna; Nelson, L. D.; Owens, Christopher L.; Conner, Patrick J.; Gunawan, Gunawati

doi:10.1007/s00122-019-03302-7

Cited by 31 publications

(69 citation statements)

References 51 publications

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“…vinifera is hermaphroditic 32 . The region around 5Mbp on chromosome 2 has been identified in several linkage mapping and population genetic studies, and the boundary of the sex locus and the sex determining genes were proposed but are still under debate [32][33][34][35][36] . Here, we used the sex locus to assess the performance of our rhAmpSeq markers in genetic mapping.…”

Section: Resultsmentioning

confidence: 99%

Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus

et al. 2020

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Transferable DNA markers are essential for breeding and genetics. Grapevine (Vitis) breeders utilize disease resistance alleles from congeneric species~20 million years divergent, but existing Vitis marker platforms have cross-species transfer rates as low as 2%. Here, we apply a marker strategy targeting the inferred Vitis core genome. Incorporating seven linkedread de novo assemblies and three existing assemblies, the Vitis collinear core genome is estimated to converge at 39.8 Mb (8.67% of the genome). Adding shotgun genome sequences from 40 accessions enables identification of conserved core PCR primer binding sites flanking polymorphic haplotypes with high information content. From these target regions, we develop 2,000 rhAmpSeq markers as a PCR multiplex and validate the panel in four biparental populations spanning the diversity of the Vitis genus, showing transferability increases to 91.9%. This marker development strategy should be widely applicable for genetic studies in many taxa, particularly those~20 million years divergent.

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Section: Resultsmentioning

confidence: 99%

Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus

et al. 2020

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“…The advent of NGS-based methods provides good opportunities for SNP markers development. Several high density genetic maps for grapevine have been constructed with NGS techniques [7,11,[33][34][40][41]. In the present work, a high-density genetic map for 'Moldova' × 'Ruidu Xiangyu' was constructed with SLAF-seq technique.…”

Section: Genetic Mapmentioning

confidence: 99%

“…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]. There is no doubt that these high-density maps improve the efficiency and accuracy of QTL mapping, which can be used more effectively in breeding programs.…”

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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“…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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High-density linkage maps and loci for berry color and flower sex in muscadine grape (Vitis rotundifolia)

Cited by 31 publications

References 51 publications

Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus

Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus

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

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

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