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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| Format: | Article |
| Language: | English |
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MDPI AG
2020-10-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/11/10/1220 |
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| author | Roshan Kulkarni Ratan Chopra Jennifer Chagoya Charles E. Simpson Michael R. Baring Andrew Hillhouse Naveen Puppala Kelly Chamberlin Mark D. Burow |
| author_facet | Roshan Kulkarni Ratan Chopra Jennifer Chagoya Charles E. Simpson Michael R. Baring Andrew Hillhouse Naveen Puppala Kelly Chamberlin Mark D. Burow |
| author_sort | Roshan Kulkarni |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-10T15:32:38Z |
| format | Article |
| id | doaj.art-93bdf987e60148d1a5ded6d44db0350c |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T15:32:38Z |
| publishDate | 2020-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-93bdf987e60148d1a5ded6d44db0350c2023-11-20T17:33:19ZengMDPI AGGenes2073-44252020-10-011110122010.3390/genes11101220Use of Targeted Amplicon Sequencing in Peanut to Generate Allele Information on Allotetraploid Sub-GenomesRoshan Kulkarni0Ratan Chopra1Jennifer Chagoya2Charles E. Simpson3Michael R. Baring4Andrew Hillhouse5Naveen Puppala6Kelly Chamberlin7Mark D. Burow8Department of Plant and Soil Sciences, Texas Tech University, Lubbock, TX 79409, USAPlant Stress and Germplasm Development Unit, United States Department of Agriculture-Agricultural Research Service, Lubbock, TX 79415, USATexas A&M AgriLife Research and Extension Center, Lubbock, TX 79403, USATexas A&M AgriLife Research and Extension Center, Stephenville, TX 76401, USATexas A&M AgriLife Research, College Station, TX 77843, USADepartment of Veterinary Medicine and Biomedical Sciences, Texas A & M University, College Station, TX 77843, USAAgricultural Sciences Center, New Mexico State University, Clovis, NM 88101, USAUSDA-ARS, Wheat, Peanut and other Field Crops Research, Stillwater, OK 74075, USADepartment of Plant and Soil Sciences, Texas Tech University, Lubbock, TX 79409, USAThe 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.https://www.mdpi.com/2073-4425/11/10/1220targeted resequencingallopolyploidheterozygous SNP callstetraploids |
| spellingShingle | Roshan Kulkarni Ratan Chopra Jennifer Chagoya Charles E. Simpson Michael R. Baring Andrew Hillhouse Naveen Puppala Kelly Chamberlin Mark D. Burow Use of Targeted Amplicon Sequencing in Peanut to Generate Allele Information on Allotetraploid Sub-Genomes Genes targeted resequencing allopolyploid heterozygous SNP calls tetraploids |
| 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 | targeted resequencing allopolyploid heterozygous SNP calls tetraploids |
| url | https://www.mdpi.com/2073-4425/11/10/1220 |
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