Genetic structure and first genome‐wide insights into the adaptation of a wild relative of grapevine, Vitis berlandieri

In grafted plants, such as grapevine, increasing the diversity of rootstocks available to growers is an ideal strategy for helping plants to adapt to climate change. The rootstocks used for grapevine are hybrids of various American Vitis, including V. berlandieri. The rootstocks currently use in vin...

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Published inEvolutionary applications Vol. 16; no. 6; pp. 1184 - 1200
Main Authors Blois, Louis, de Miguel, Marina, Bert, Pierre‐François, Girollet, Nabil, Ollat, Nathalie, Rubio, Bernadette, Segura, Vincent, Voss‐Fels, Kai P., Schmid, Joachim, Marguerit, Elisa
Format Journal Article
LanguageEnglish
Published England John Wiley & Sons, Inc 01.06.2023
Blackwell
John Wiley and Sons Inc
Wiley
Subjects
Adaptation
Association analysis
Barley
Climate change
Fertilization
Genetic diversity
Genetic structure
Genetics
Genomes
genome‐wide association
genotyping by sequencing
grapevine
Hybrids
Life Sciences
long reads
Mutation
Original
Plants genetics
Population
population genetics
Quantitative genetics
Quantitative trait loci
rootstock
Rootstocks
Sampling
Seeds
Single-nucleotide polymorphism
Vitis berlandieri
Whole genome sequencing
United States > US
Texas
Edwards Plateau
genotyping by sequencing
population genetics
long reads
grapevine
rootstock
whole‐genome sequencing
genome‐wide association
grapevinelong reads
genome-wide association
whole-genome sequencing
Online AccessGet full text

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Abstract In grafted plants, such as grapevine, increasing the diversity of rootstocks available to growers is an ideal strategy for helping plants to adapt to climate change. The rootstocks used for grapevine are hybrids of various American Vitis, including V. berlandieri. The rootstocks currently use in vineyards are derived from breeding programs involving very small numbers of parental individuals. We investigated the structure of a natural population of V. berlandieri and the association of genetic diversity with environmental variables. In this study, we collected seeds from 78 wild V. berlandieri plants in Texas after open fertilization. We genotyped 286 individuals to describe the structure of the population, and environmental information collected at the sampling site made it possible to perform genome–environment association analysis (GEA). De novo long‐read whole‐genome sequencing was performed on V. berlandieri and a STRUCTURE analysis was performed. We identified and filtered 104,378 SNPs. We found that there were two subpopulations associated with differences in elevation, temperature, and rainfall between sampling sites. GEA identified three QTL for elevation and 15 QTL for PCA coordinates based on environmental parameter variability. This original study is the first GEA study to be performed on a population of grapevines sampled in natural conditions. Our results shed new light on rootstock genetics and could open up possibilities for introducing greater diversity into genetic improvement programs for grapevine rootstocks.
AbstractList In grafted plants, such as grapevine, increasing the diversity of rootstocks available to growers is an ideal strategy for helping plants to adapt to climate change. The rootstocks used for grapevine are hybrids of various American Vitis, including V. berlandieri. The rootstocks currently use in vineyards are derived from breeding programs involving very small numbers of parental individuals. We investigated the structure of a natural population of V. berlandieri and the association of genetic diversity with environmental variables. In this study, we collected seeds from 78 wild V. berlandieri plants in Texas after open fertilization. We genotyped 286 individuals to describe the structure of the population, and environmental information collected at the sampling site made it possible to perform genome-environment association analysis (GEA). De novo long-read whole-genome sequencing was performed on V. berlandieri and a STRUCTURE analysis was performed. We identified and filtered 104,378 SNPs. We found that there were two subpopulations associated with differences in elevation, temperature, and rainfall between sampling sites. GEA identified three QTL for elevation and 15 QTL for PCA coordinates based on environmental parameter variability. This original study is the first GEA study to be performed on a population of grapevines sampled in natural conditions. Our results shed new light on rootstock genetics and could open up possibilities for introducing greater diversity into genetic improvement programs for grapevine rootstocks.In grafted plants, such as grapevine, increasing the diversity of rootstocks available to growers is an ideal strategy for helping plants to adapt to climate change. The rootstocks used for grapevine are hybrids of various American Vitis, including V. berlandieri. The rootstocks currently use in vineyards are derived from breeding programs involving very small numbers of parental individuals. We investigated the structure of a natural population of V. berlandieri and the association of genetic diversity with environmental variables. In this study, we collected seeds from 78 wild V. berlandieri plants in Texas after open fertilization. We genotyped 286 individuals to describe the structure of the population, and environmental information collected at the sampling site made it possible to perform genome-environment association analysis (GEA). De novo long-read whole-genome sequencing was performed on V. berlandieri and a STRUCTURE analysis was performed. We identified and filtered 104,378 SNPs. We found that there were two subpopulations associated with differences in elevation, temperature, and rainfall between sampling sites. GEA identified three QTL for elevation and 15 QTL for PCA coordinates based on environmental parameter variability. This original study is the first GEA study to be performed on a population of grapevines sampled in natural conditions. Our results shed new light on rootstock genetics and could open up possibilities for introducing greater diversity into genetic improvement programs for grapevine rootstocks.
In grafted plants, such as grapevine, increasing the diversity of rootstocks available to growers is an ideal strategy for helping plants to adapt to climate change. The rootstocks used for grapevine are hybrids of various American Vitis, including V. berlandieri. The rootstocks currently use in vineyards are derived from breeding programs involving very small numbers of parental individuals. We investigated the structure of a natural population of V. berlandieri and the association of genetic diversity with environmental variables. In this study, we collected seeds from 78 wild V. berlandieri plants in Texas after open fertilization. We genotyped 286 individuals to describe the structure of the population, and environmental information collected at the sampling site made it possible to perform genome–environment association analysis (GEA). De novo long-read whole-genome sequencing was performed on V. berlandieri and a STRUCTURE analysis was performed. We identified and filtered 104,378 SNPs. We found that there were two subpopulations associated with differences in elevation, temperature, and rainfall between sampling sites. GEA identified three QTL for elevation and 15 QTL for PCA coordinates based on environmental parameter variability. This original study is the first GEA study to be performed on a population of grapevines sampled in natural conditions. Our results shed new light on rootstock genetics and could open up possibilities for introducing greater diversity into genetic improvement programs for grapevine rootstocks.
In grafted plants, such as grapevine, increasing the diversity of rootstocks available to growers is an ideal strategy for helping plants to adapt to climate change. The rootstocks used for grapevine are hybrids of various American Vitis , including V .  berlandieri . The rootstocks currently use in vineyards are derived from breeding programs involving very small numbers of parental individuals. We investigated the structure of a natural population of V .  berlandieri and the association of genetic diversity with environmental variables. In this study, we collected seeds from 78 wild V .  berlandieri plants in Texas after open fertilization. We genotyped 286 individuals to describe the structure of the population, and environmental information collected at the sampling site made it possible to perform genome–environment association analysis (GEA). De novo long‐read whole‐genome sequencing was performed on V .  berlandieri and a STRUCTURE analysis was performed. We identified and filtered 104,378 SNPs. We found that there were two subpopulations associated with differences in elevation, temperature, and rainfall between sampling sites. GEA identified three QTL for elevation and 15 QTL for PCA coordinates based on environmental parameter variability. This original study is the first GEA study to be performed on a population of grapevines sampled in natural conditions. Our results shed new light on rootstock genetics and could open up possibilities for introducing greater diversity into genetic improvement programs for grapevine rootstocks.
In grafted plants, such as grapevine, increasing the diversity of rootstocks available to growers is an ideal strategy for helping plants to adapt to climate change. The rootstocks used for grapevine are hybrids of various American , including .  . The rootstocks currently use in vineyards are derived from breeding programs involving very small numbers of parental individuals. We investigated the structure of a natural population of .  and the association of genetic diversity with environmental variables. In this study, we collected seeds from 78 wild .  plants in Texas after open fertilization. We genotyped 286 individuals to describe the structure of the population, and environmental information collected at the sampling site made it possible to perform genome-environment association analysis (GEA). De novo .  and a STRUCTURE analysis was performed. We identified and filtered 104,378 SNPs. We found that there were two subpopulations associated with differences in elevation, temperature, and rainfall between sampling sites. GEA identified three QTL for elevation and 15 QTL for PCA coordinates based on environmental parameter variability. This original study is the first GEA study to be performed on a population of grapevines sampled in natural conditions. Our results shed new light on rootstock genetics and could open up possibilities for introducing greater diversity into genetic improvement programs for grapevine rootstocks.
Abstract In grafted plants, such as grapevine, increasing the diversity of rootstocks available to growers is an ideal strategy for helping plants to adapt to climate change. The rootstocks used for grapevine are hybrids of various American Vitis, including V. berlandieri. The rootstocks currently use in vineyards are derived from breeding programs involving very small numbers of parental individuals. We investigated the structure of a natural population of V. berlandieri and the association of genetic diversity with environmental variables. In this study, we collected seeds from 78 wild V. berlandieri plants in Texas after open fertilization. We genotyped 286 individuals to describe the structure of the population, and environmental information collected at the sampling site made it possible to perform genome–environment association analysis (GEA). De novo long‐read whole‐genome sequencing was performed on V. berlandieri and a STRUCTURE analysis was performed. We identified and filtered 104,378 SNPs. We found that there were two subpopulations associated with differences in elevation, temperature, and rainfall between sampling sites. GEA identified three QTL for elevation and 15 QTL for PCA coordinates based on environmental parameter variability. This original study is the first GEA study to be performed on a population of grapevines sampled in natural conditions. Our results shed new light on rootstock genetics and could open up possibilities for introducing greater diversity into genetic improvement programs for grapevine rootstocks.
Author Blois, Louis
Segura, Vincent
de Miguel, Marina
Girollet, Nabil
Schmid, Joachim
Ollat, Nathalie
Rubio, Bernadette
Voss‐Fels, Kai P.
Marguerit, Elisa
Bert, Pierre‐François
AuthorAffiliation 2 Department of Grapevine Breeding Geisenheim University Geisenheim Germany
3 AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier France
1 EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV Villenave d'Ornon France
AuthorAffiliation_xml – name: 3 AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier France
– name: 2 Department of Grapevine Breeding Geisenheim University Geisenheim Germany
– name: 1 EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV Villenave d'Ornon France
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  orcidid: 0000-0001-8392-5639
  surname: Blois
  fullname: Blois, Louis
  email: louis.blois@inrae.fr
  organization: Geisenheim University
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  orcidid: 0000-0001-6398-2660
  surname: de Miguel
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  organization: EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV
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  surname: Girollet
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  surname: Rubio
  fullname: Rubio, Bernadette
  organization: EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV
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  surname: Segura
  fullname: Segura, Vincent
  organization: AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro
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  givenname: Kai P.
  surname: Voss‐Fels
  fullname: Voss‐Fels, Kai P.
  organization: Geisenheim University
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  givenname: Joachim
  surname: Schmid
  fullname: Schmid, Joachim
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  surname: Marguerit
  fullname: Marguerit, Elisa
  organization: EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV
BackLink https://www.ncbi.nlm.nih.gov/pubmed/37360024$$D View this record in MEDLINE/PubMed
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2023 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.
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Issue 6
Keywords genotyping by sequencing
population genetics
long reads
grapevine
rootstock
whole‐genome sequencing
genome‐wide association
grapevinelong reads
genome-wide association
whole-genome sequencing
Language English
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PublicationDate June 2023
PublicationDateYYYYMMDD 2023-06-01
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  year: 2023
  text: June 2023
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PublicationTitle Evolutionary applications
PublicationTitleAlternate Evol Appl
PublicationYear 2023
Publisher John Wiley & Sons, Inc
Blackwell
John Wiley and Sons Inc
Wiley
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Snippet In grafted plants, such as grapevine, increasing the diversity of rootstocks available to growers is an ideal strategy for helping plants to adapt to climate...
Abstract In grafted plants, such as grapevine, increasing the diversity of rootstocks available to growers is an ideal strategy for helping plants to adapt to...
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pubmed
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Open Access Repository
Aggregation Database
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Publisher
StartPage 1184
SubjectTerms Adaptation
Association analysis
Barley
Climate change
Fertilization
Genetic diversity
Genetic structure
Genetics
Genomes
genome‐wide association
genotyping by sequencing
grapevine
Hybrids
Life Sciences
long reads
Mutation
Original
Plants genetics
Population
population genetics
Quantitative genetics
Quantitative trait loci
rootstock
Rootstocks
Sampling
Seeds
Single-nucleotide polymorphism
Vitis berlandieri
Whole genome sequencing
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Title Genetic structure and first genome‐wide insights into the adaptation of a wild relative of grapevine, Vitis berlandieri
URI https://onlinelibrary.wiley.com/doi/abs/10.1111%2Feva.13566
https://www.ncbi.nlm.nih.gov/pubmed/37360024
https://www.proquest.com/docview/2828291379
https://www.proquest.com/docview/2830219916
https://hal.inrae.fr/hal-04221476
https://pubmed.ncbi.nlm.nih.gov/PMC10286229
https://doaj.org/article/644052431c404d7c9ecb9c1a489d9255
Volume 16
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