| dc.description.abstract | Potato (Solanum tuberosum L.) is the world’s fourth most important crop after maize, rice, and wheat. The Texas A&M University (TAMU) Potato Breeding Program is working to produce early maturing russet, specialty, chipping, and red varieties suited to Texas growing conditions. The increasing urgency to develop superior performing varieties to meet the needs of the fresh and processing potato market necessitates the validation and application of new approaches in potato breeding, such as genome-wide association studies (GWAS) and genomic selection (GS). Recent advances in the development of high‐throughput genotyping platforms and whole-genome coverage and affordability have turned single nucleotide polymorphisms (SNPs) into one of the most promising tools for the investigation of genetic diversity and application of GWAS and GS in potato. Two hundred fourteen advanced clones selected over forty years were studied to assess the genetic diversity, population structure, linkage disequilibrium (LD), detect signatures of selection, and find marker trait associations for tuber morphology using the Illumina Infinium 22 K V3 Potato Array. Likewise, 384 unique chipping potato clones were used to evaluate GS for chipping quality in tetraploid potatoes. Results showed that most of the potato clones had high levels of heterozygosity, ranging from 0.22 to 0.80 with a mean of 0.59. Three groups of tetraploid clones, primarily based on potato market classes, were detected using the STRUCTURE software. The highest coefficient of differentiation observed between the groups was 0.14. Signatures of selection were uncovered in genes controlling potato flesh and skin color, length of plant cycle and tuberization, and carbohydrate metabolism. The GWAS experiment yielded putative and novel markers/genes involved with tuber morphology traits. Genomic prediction using fry color, chip quality, specific gravity and yield gave reliabilities of 0.52, 0.17, 0.40 and 0.11, respectively. Even for limited reference populations and traits with low heritability, the accuracies found were encouraging. The comprehensive molecular characterization will help to better understand the genetic diversity of existing potato resources. Results from GWAS and GS will be helpful in increasing breeding efficiency. | |
