Detection of genomic signatures of recent selection in advanced potato clones
Tuesday, July 27, 2021
12:45 PM - 1:00 PM
Natural and artificial selection leads to changes in specific regions of the genome resulting in selection signatures. The identification of causal genomic polymorphisms regulating functionally important traits under selective breeding in potatoes results in the detection of genomic signatures of recent selection. This study aimed at detecting signatures of recent selection in advanced potato clones by conducting genome-wide scans. A total of 214 potato genotypes representing fresh and processing market classes with variation for skin type, flesh and skin color, shape, agronomic, biotic, abiotic, and quality traits were genotyped using the Infinium 22K V3 SNP Potato Array. Signatures of selection analyses were performed using three complementary statistical methods. The PCAdapt procedure was based on allele frequency differentiation whereas, the iHS and the XP-EHH were based on linkage disequilibrium (LD) patterns. Our results revealed genetic differentiation in several genomic windows. Eighteen regions were identified under selection by at least two of the statistics applied and were defined as candidate selection sweep regions. These regions were distributed on ten out of the 12 potato chromosomes. Annotation of the consensus regions of PCAdapt, iHS, and XP-EHH windows revealed genes such as beta-carotene hydroxylase (bch), Dof Zinc Finger Protein-StCDF3, CONSTANTS-CO, LOG3, Adenylyl-sulfate kinase associated with important traits under selection in potato breeding. This study uncovered genes controlling potato flesh and skin color, length of plant cycle and tuberization, and carbohydrate metabolism. Most of the candidate genes controlling traits in the selection regions could be of great interest to better understand past breeding efforts and to guide future breeding endeavors.