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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...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2020
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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. |
format | Online Article Text |
id | pubmed-7650781 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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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