Whole genome re-sequencing of cultivated peanut to enable genetic and genomic resources for improvement
Chavarro Fierro, Martha Carolina
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Genotyping of genetically structured populations, such as recombinant inbred lines (RILs), plays a key role in molecular breeding of crop plants by linking genetic markers to traits of interest. In peanut, genotyping has evolved at a slow pace due to the challenges of doing genetics in an allotetraploid species. Peanut has two highly similar subgenomes which complicates the discovery of genetic variants such as single nucleotide polymorphisms (SNPs) as most variation is between subgenomes, not between alleles at a locus. Furthermore, peanut is a segmental allopolyploid, that is, it has both disomic and tetrasomic inheritance, complicating even further the development of molecular markers and associating them with targeted traits. Whole genome re-sequencing was performed for 20 peanut genotypes carrying traits of interest to identify SNPs for genotyping several breeding populations and genotypes of interest. Based on the identified SNPs from the sequencing, a SNP array containing 58,233 SNPs was constructed and used for genotyping. Twenty-three samples including parents of nested association mapping populations (NAM) were genotyped. From this, 11,633 SNPs markers were found to be polymorphic among all the samples of interest and 8,999 SNPs were polymorphic for the parents of a nested association mapping (NAM) panel. Furthermore, a RIL population from the cross between Tifrunner x NC 3033 was genotyped using the SNP array to identify polymorphic markers for saturation of a genetic map and QTL identification of seed and pod traits. This population was used for mapping as the parents contrast for many seed and pod filling traits. The linkage map included 1,524 markers in 29 linkage groups, and forty-nine QTLs were identified including 8 major QTLs with phenotypic effects higher than 20%. To confirm the segmental allopolyploid nature of cultivated peanut, the genotypic data from the RIL populations was used to identify locations in the genome where tetrasomic recombination has taken place. Whole genome re-sequencing of the parents and two RILs of the population was performed to confirm and provide more granularity of the tetrasomic events. This research provides new tools for the understanding of the evolution and domestication of peanut and for molecular improvement.