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Use of Targeted Amplicon Sequencing in Peanut to Generate Allele Information on Allotetraploid Sub-Genomes

The use of molecular markers in plant breeding has become a routine practice, but the cost per accession can be a hindrance to the routine use of Quantitative Trait Loci (QTL) identification in breeding programs. In this study, we demonstrate the use of targeted re-sequencing as a proof of concept o...

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Autores principales: Kulkarni, Roshan, Chopra, Ratan, Chagoya, Jennifer, Simpson, Charles E., Baring, Michael R., Hillhouse, Andrew, Puppala, Naveen, Chamberlin, Kelly, Burow, Mark D.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7650781/
https://www.ncbi.nlm.nih.gov/pubmed/33080972
http://dx.doi.org/10.3390/genes11101220
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author Kulkarni, Roshan
Chopra, Ratan
Chagoya, Jennifer
Simpson, Charles E.
Baring, Michael R.
Hillhouse, Andrew
Puppala, Naveen
Chamberlin, Kelly
Burow, Mark D.
author_facet Kulkarni, Roshan
Chopra, Ratan
Chagoya, Jennifer
Simpson, Charles E.
Baring, Michael R.
Hillhouse, Andrew
Puppala, Naveen
Chamberlin, Kelly
Burow, Mark D.
author_sort Kulkarni, Roshan
collection PubMed
description The use of molecular markers in plant breeding has become a routine practice, but the cost per accession can be a hindrance to the routine use of Quantitative Trait Loci (QTL) identification in breeding programs. In this study, we demonstrate the use of targeted re-sequencing as a proof of concept of a cost-effective approach to retrieve highly informative allele information, as well as develop a bioinformatics strategy to capture the genome-specific information of a polyploid species. SNPs were identified from alignment of raw transcriptome reads (2 × 50 bp) to a synthetic tetraploid genome using BWA followed by a GATK pipeline. Regions containing high polymorphic SNPs in both A genome and B genomes were selected as targets for the resequencing study. Targets were amplified using multiplex PCR followed by sequencing on an Illumina HiSeq. Eighty-one percent of the SNP calls in diploids and 68% of the SNP calls in tetraploids were confirmed. These results were also confirmed by KASP validation. Based on this study, we find that targeted resequencing technologies have potential for obtaining maximum allele information in allopolyploids at reduced cost.
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spelling pubmed-76507812020-11-10 Use of Targeted Amplicon Sequencing in Peanut to Generate Allele Information on Allotetraploid Sub-Genomes Kulkarni, Roshan Chopra, Ratan Chagoya, Jennifer Simpson, Charles E. Baring, Michael R. Hillhouse, Andrew Puppala, Naveen Chamberlin, Kelly Burow, Mark D. Genes (Basel) Article The use of molecular markers in plant breeding has become a routine practice, but the cost per accession can be a hindrance to the routine use of Quantitative Trait Loci (QTL) identification in breeding programs. In this study, we demonstrate the use of targeted re-sequencing as a proof of concept of a cost-effective approach to retrieve highly informative allele information, as well as develop a bioinformatics strategy to capture the genome-specific information of a polyploid species. SNPs were identified from alignment of raw transcriptome reads (2 × 50 bp) to a synthetic tetraploid genome using BWA followed by a GATK pipeline. Regions containing high polymorphic SNPs in both A genome and B genomes were selected as targets for the resequencing study. Targets were amplified using multiplex PCR followed by sequencing on an Illumina HiSeq. Eighty-one percent of the SNP calls in diploids and 68% of the SNP calls in tetraploids were confirmed. These results were also confirmed by KASP validation. Based on this study, we find that targeted resequencing technologies have potential for obtaining maximum allele information in allopolyploids at reduced cost. MDPI 2020-10-18 /pmc/articles/PMC7650781/ /pubmed/33080972 http://dx.doi.org/10.3390/genes11101220 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Kulkarni, Roshan
Chopra, Ratan
Chagoya, Jennifer
Simpson, Charles E.
Baring, Michael R.
Hillhouse, Andrew
Puppala, Naveen
Chamberlin, Kelly
Burow, Mark D.
Use of Targeted Amplicon Sequencing in Peanut to Generate Allele Information on Allotetraploid Sub-Genomes
title Use of Targeted Amplicon Sequencing in Peanut to Generate Allele Information on Allotetraploid Sub-Genomes
title_full Use of Targeted Amplicon Sequencing in Peanut to Generate Allele Information on Allotetraploid Sub-Genomes
title_fullStr Use of Targeted Amplicon Sequencing in Peanut to Generate Allele Information on Allotetraploid Sub-Genomes
title_full_unstemmed Use of Targeted Amplicon Sequencing in Peanut to Generate Allele Information on Allotetraploid Sub-Genomes
title_short Use of Targeted Amplicon Sequencing in Peanut to Generate Allele Information on Allotetraploid Sub-Genomes
title_sort use of targeted amplicon sequencing in peanut to generate allele information on allotetraploid sub-genomes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7650781/
https://www.ncbi.nlm.nih.gov/pubmed/33080972
http://dx.doi.org/10.3390/genes11101220
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