Advancing Diploid Potato Breeding Through Genetic Analysis And Genomic Selection

Download or read book Advancing Diploid Potato Breeding Through Genetic Analysis and Genomic Selection written by Lin Song (Ph.D.) and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Breeding gains of commercial autotetraploid potato (Solanum tuberosum L.) have been limited by tetrasomic inheritance for centuries. After mapping a self-compatible gene (Sli) on chromosome 12 at the end of the 20th century, the breeding strategy has shifted towards developing diploid inbred lines that can generate F1 hybrid varieties through sexual hybridization. Overcoming the gametophytic self-incompatibility through Sli is the first step in breeding at the diploid level. Then self-fertilization is performed within each breeding cycle to achieve pure diploid inbred lines. However, reaching full homozygosity is made difficult by severe inbreeding depression in potato. As a result, multiple hybridization events are needed to break linkages with the deleterious alleles. This research aims to create the germplasm and provide the data for future diploid potato breeding. We first focused on genes that were well characterized in potato: Sli and the vine maturity gene StCDF1 (Cycling DOF Factor 1). A modified backcrossing scheme using primary dihaploids of Solanum tuberosum as the recurrent parental background allowed for the selection of self-fertile F2 individuals homozygous for Sli. By integrating haplotype and quantitative trait locus (QTL) analysis, we identified and selected partially inbred lines fixed for the two favorable alleles. They were used to initiate new cycles of selection with the goal of increasing homozygosity while maintaining plant vigor, fertility, and yield. Then we sought to discover new genetic variants by genome-wide association study (GWAS) and joint linkage mapping. Two years of field trials were performed at the Hancock Agricultural Research Station (HARS), WI, using the progeny from Backcross Cycles 1 and 2 (BC1, BC2) in the years 2020 and 2021. The traits evaluated were vine maturity, tuber appearance, tuber yield, tuber size, specific gravity, chip color, and tuber sprouting. 25 significant QTL, including CDF1 and the tuber shape gene StOFP20, were identified in GWAS. Through joint linkage mapping with connected outbred F1 progeny in the 2021 field trial, we determined the three most desirable OFP20 haplotypes for round tuber shape. We further explored the potential of utilizing genomic selection for diploid potato with the two-year field trial data. The narrow-sense heritability estimates ranged from 0.41 to 0.63. Tuber yield showed the highest prediction reliability for marker-assisted genomic selection at 0.78. Both additive and dominance effects were included in the model, and dominance was most important for tuber yield, explaining 12% of the variance through heterosis. We have also discovered that, despite lower prediction accuracy, the historical tetraploid data can be used as a training population to predict traits of diploid potatoes. The prediction ability for diploids with the mixed ploidy training population ranged from 0.1 to 0.3.