Use of Targeted Amplicon Sequencing in Peanut to Generate Allele Information on Allotetraploid Sub-Genomes
| Autor: | Naveen Puppala, Andrew Hillhouse, K. D. Chamberlin, Michael R. Baring, Roshan Kulkarni, Jennifer Chagoya, Charles E. Simpson, Mark D. Burow, Ratan Chopra |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
0106 biological sciences
0301 basic medicine Arachis lcsh:QH426-470 Quantitative Trait Loci Single-nucleotide polymorphism Computational biology Biology Quantitative trait locus 01 natural sciences Genome Polymorphism Single Nucleotide Chromosomes Plant Article Transcriptome 03 medical and health sciences Polyploid tetraploids Multiplex polymerase chain reaction Genetics SNP Allele Genetics (clinical) Alleles allopolyploid Computational Biology High-Throughput Nucleotide Sequencing food and beverages targeted resequencing heterozygous SNP calls Tetraploidy Plant Breeding lcsh:Genetics 030104 developmental biology Genome Plant 010606 plant biology & botany |
| Zdroj: | Genes, Vol 11, Iss 1220, p 1220 (2020) Genes Volume 11 Issue 10 |
| ISSN: | 2073-4425 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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