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Single Nucleotide Polymorphism Identification in Polyploids： A Review, Example, and Recommendations

Molecular Plant 2015年第6期8卷 831-846页

作者： josh clevenger Carolina Chavarro Stephanie A. Pearl Peggy Ozias-Akins Scott A. Jackson Center for AppLied Genetic Technologies University of Georgia Athens GA 30602 USA Institute of Plant Breeding Genetics & Genomics University of Georgia Tifton GA 31793 USA These authors contributed equally to this article.

Understanding the relationship between genotype and phenotype is a major biological question and being able to predict phenotypes based on molecular genotypes is integral to molecular breeding. Whole- genome duplications have shaped the history of all flowering plants and present challenges to elucidating the relationship between genotype and phenotype, especially in neopolyploid species. Although single nucleotide polymorphisms （SNPs） have become popular tools for genetic mapping, discovery and appli- cation of SNPs in polyploids has been difficult. Here, we summarize common experimental approaches to SNP calling, highlighting recent polyploid successes. To examine the impact of software choice on these analyses, we called SNPs among five peanut genotypes using different alignment programs （BWA-mem and Bowtie 2） and variant callers （SAMtools, GATK, and Freebayes）. Alignments produced by Bowtie 2 and BWA-mem and analyzed in SAMtools shared 24.5% concordant SNPs, and SAMtools, GATK, and Freebayes shared 1.4% concordant SNPs. A subsequent analysis of simulated Brassica napus chromosome 1A and 1C genotypes demonstrated that, of the three software programs, SAMtools performed with the highest sensitivity and specificity on Bowtie 2 alignments. These results, however, are likely to vary among species, and we therefore propose a series of best practices for SNP calling in polyploids.

关键词： genomics homeolog next-generation sequencing (NGS) peanut polyptoid single nucleotide poly-morphism (SNP)

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Genome-wide SNP Genotyping Resolves Signatures of Selection and Tetrasomic Recombination in Peanut

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Molecular Plant 2017年第2期10卷 309-322页

作者： josh clevenger Ye Chu Carolina Chavarro Gaurav Agarwal David J. Bertioli Soraya C.M. LeaI-Bertioli Manish K. Pandey Justin Vaughn Brian Abernathy Noelle A. Barkley Ran Hovav Mark Burow Spurthi N. Nayak Annapurna Chitikineni Thomas G. Isleib C. Corley Holbrook Scott A. Jackson Rajeev K. Varshney Peggy Ozias-Akins Department of Horticulture and Institute of Plant Breeding Genetics & Genomics The University of Georgia 2356 Rainwater Road Tifton GA 31793 USA Center for Applied Genetic Technologies and Institute of Plant Breeding Genetics & Genomics The University of Georgia Athens GA 30602 USA International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Hyderabad 502324 India University of Brasilia Institute of Biological Sciences Campus Darcy Ribeiro 70910-900 Brasilia DF Brazil Embrapa Genetic Resources and Biotechnology 70770-917 Brasflia DF Brazil eUSDA-ARS PGRCU Griffin GA 30223 USA Agricultural Research Organization Plant Sciences Institute 7528809 Rishon LeZion Israel Department of Plant and Soil Science Texas Tech University Lubbock TX 79409-2122 USA Department of Crop and Soil Sciences North Carolina State University Box 7629 Raleigh NC 28695-7629 USA USDA-ARS Tifton GA 31793. USA

Peanut （Arachis hypogaea; 2n = 4x = 40） is a nutritious food and a good source of vitamins, minerals, and healthy fats. Expansion of genetic and genomic resources for genetic enhancement of cultivated peanut has gained momentum from the sequenced genomes of the diploid ancestors of cultivated peanut. To facil- itate high-throughput genotyping of Arachis species, 20 genotypes were re-sequenced and genome-wide single nucleotide poiymorphisms （SNPs） were selected to develop a large-scale SNP genotyping array. For flexibility in genotyping applications, SNPs polymorphic between tetraploid and diploid species were included for use in cultivated and interspecific populations. A set of 384 accessions was used to test the array resulting in 54 564 markers that produced high-quality polymorphic clusters between diploid species, 47 116 polymorphic markers between cultivated and interspecific hybrids, and 15 897 polymorphic markers within A. hypogaea germplasm. An additional 1193 markers were identified that illuminated genomic re- gions exhibiting tetrasomic recombination. Furthermore, a set of elite cultivars that make up the pedigree of US runner germplasm were genotyped and used to identify genomic regions that have undergone pos- itive selection. These observations provide key insights on the inclusion of new genetic diversity in culti- vated peanut and will inform the development of high-resolution mapping populations. Due to its efficiency, scope, and flexibility, the newly developed SNP array will be very useful for further genetic and breeding applications in Arachis.

关键词： single nucleotide polymorphism groundnut Arachis hypogaea

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