Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus.
Identifieur interne : 000102 ( Main/Corpus ); précédent : 000101; suivant : 000103Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus.
Auteurs : Cheng Zou ; Avinash Karn ; Bruce Reisch ; Allen Nguyen ; Yongming Sun ; Yun Bao ; Michael S. Campbell ; Deanna Church ; Stephen Williams ; Xia Xu ; Craig A. Ledbetter ; Sagar Patel ; Anne Fennell ; Jeffrey C. Glaubitz ; Matthew Clark ; Doreen Ware ; Jason P. Londo ; Qi Sun ; Lance Cadle-DavidsonSource :
- Nature communications [ 2041-1723 ] ; 2020.
English descriptors
- KwdEn :
- Alleles (MeSH), Chromosome Mapping (methods), DNA, Plant (genetics), DNA, Plant (isolation & purification), Genetic Markers (genetics), Genome, Plant (MeSH), Genotyping Techniques (methods), Haplotypes (MeSH), High-Throughput Nucleotide Sequencing (MeSH), Microsatellite Repeats (genetics), Phylogeny (MeSH), Plant Breeding (MeSH), Polymorphism, Single Nucleotide (MeSH), Sequence Analysis, DNA (methods), Vitis (genetics).
- MESH :
- chemical , genetics : DNA, Plant, Genetic Markers.
- chemical , isolation & purification : DNA, Plant.
- genetics : Microsatellite Repeats, Vitis.
- methods : Chromosome Mapping, Genotyping Techniques, Sequence Analysis, DNA.
- Alleles, Genome, Plant, Haplotypes, High-Throughput Nucleotide Sequencing, Phylogeny, Plant Breeding, Polymorphism, Single Nucleotide.
Abstract
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 linked-read 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.
DOI: 10.1038/s41467-019-14280-1
PubMed: 31964885
PubMed Central: PMC6972940
Links to Exploration step
pubmed:31964885Le document en format XML
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<sourceDesc><biblStruct><analytic><title xml:lang="en">Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus.</title>
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<author><name sortKey="Xu, Xia" sort="Xu, Xia" uniqKey="Xu X" first="Xia" last="Xu">Xia Xu</name>
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</affiliation>
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<author><name sortKey="Ledbetter, Craig A" sort="Ledbetter, Craig A" uniqKey="Ledbetter C" first="Craig A" last="Ledbetter">Craig A. Ledbetter</name>
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<affiliation><nlm:affiliation>Agronomy, Horticulture and Plant Science Department, South Dakota State University, Brookings, SD, 57007, USA.</nlm:affiliation>
</affiliation>
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</affiliation>
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</affiliation>
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</affiliation>
</author>
<author><name sortKey="Sun, Qi" sort="Sun, Qi" uniqKey="Sun Q" first="Qi" last="Sun">Qi Sun</name>
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<term>Chromosome Mapping (methods)</term>
<term>DNA, Plant (genetics)</term>
<term>DNA, Plant (isolation & purification)</term>
<term>Genetic Markers (genetics)</term>
<term>Genome, Plant (MeSH)</term>
<term>Genotyping Techniques (methods)</term>
<term>Haplotypes (MeSH)</term>
<term>High-Throughput Nucleotide Sequencing (MeSH)</term>
<term>Microsatellite Repeats (genetics)</term>
<term>Phylogeny (MeSH)</term>
<term>Plant Breeding (MeSH)</term>
<term>Polymorphism, Single Nucleotide (MeSH)</term>
<term>Sequence Analysis, DNA (methods)</term>
<term>Vitis (genetics)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Plant</term>
<term>Genetic Markers</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="isolation & purification" xml:lang="en"><term>DNA, Plant</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Microsatellite Repeats</term>
<term>Vitis</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Chromosome Mapping</term>
<term>Genotyping Techniques</term>
<term>Sequence Analysis, DNA</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Alleles</term>
<term>Genome, Plant</term>
<term>Haplotypes</term>
<term>High-Throughput Nucleotide Sequencing</term>
<term>Phylogeny</term>
<term>Plant Breeding</term>
<term>Polymorphism, Single Nucleotide</term>
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<front><div type="abstract" xml:lang="en">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 linked-read 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.</div>
</front>
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<Day>21</Day>
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<Title>Nature communications</Title>
<ISOAbbreviation>Nat Commun</ISOAbbreviation>
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<ArticleTitle>Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus.</ArticleTitle>
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<Abstract><AbstractText>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 linked-read 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.</AbstractText>
</Abstract>
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