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Open AccessArticle

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

1
Department of Plant and Soil Sciences, Texas Tech University, Lubbock, TX 79409, USA
2
Plant Stress and Germplasm Development Unit, United States Department of Agriculture-Agricultural Research Service, Lubbock, TX 79415, USA
3
Texas A&M AgriLife Research and Extension Center, Lubbock, TX 79403, USA
4
Texas A&M AgriLife Research and Extension Center, Stephenville, TX 76401, USA
5
Texas A&M AgriLife Research, College Station, TX 77843, USA
6
Department of Veterinary Medicine and Biomedical Sciences, Texas A & M University, College Station, TX 77843, USA
7
Agricultural Sciences Center, New Mexico State University, Clovis, NM 88101, USA
8
USDA-ARS, Wheat, Peanut and other Field Crops Research, Stillwater, OK 74075, USA
*
Author to whom correspondence should be addressed.
This work was done in partial fulfillment of the work for the M.S. degree.
Genes 2020, 11(10), 1220; https://doi.org/10.3390/genes11101220
Received: 8 September 2020 / Revised: 9 October 2020 / Accepted: 14 October 2020 / Published: 18 October 2020
(This article belongs to the Special Issue Food Legume Genomics)
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. View Full-Text
Keywords: targeted resequencing; allopolyploid; heterozygous SNP calls; tetraploids targeted resequencing; allopolyploid; heterozygous SNP calls; tetraploids
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MDPI and ACS Style

Kulkarni, R.; Chopra, R.; Chagoya, J.; Simpson, C.E.; Baring, M.R.; Hillhouse, A.; Puppala, N.; Chamberlin, K.; Burow, M.D. Use of Targeted Amplicon Sequencing in Peanut to Generate Allele Information on Allotetraploid Sub-Genomes. Genes 2020, 11, 1220.

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