Using Haplotype and QTL Analysis to Fix Favorable Alleles in Diploid Potato Breeding

Abstract

AbstractAt present, the potato of international commerce is autotetraploid, and the complexity of this genetic system creates limitations for breeding. Diploid potato breeding has long been used for population improvement, and thanks to improved understanding of the genetics of gametophytic self-incompatibility, there is now sustained interest in the development of uniform F1hybrid varieties based on inbred parents. We report here on the use of haplotype and QTL analysis in a modified backcrossing (BC) scheme, using primary dihaploids ofS.tuberosumas the recurrent parental background. In Cycle 1 we selected XD3-36, a self-fertile F2clone homozygous for the self-compatibility geneSli. Signatures of gametic and zygotic selection were observed at multiple loci in the F2generation, includingSli. In the BC1cycle, an F1population derived from XD3-36 showed a bimodal response for vine maturity, which led to the identification of late vs. early alleles in XD3-36 for the geneStCDF1(Cycling DOF Factor 1). Greenhouse phenotypes and haplotype analysis were used to select a vigorous and self-fertile F2individual with 43% homozygosity, including forSliand the early-maturing alleleStCDF1.3. Partially inbred lines from the BC1and BC2cycles have been used to initiate new cycles of selection, with the goal of reaching higher homozygosity while maintaining plant vigor, fertility, and yield.Core IdeasPartially inbred, diploid potato lines were developed for transitioning to an inbred-hybrid breeding system.Multi-generational linkage analysis was used to track and fix favorable alleles without haplotype-specific markers.Signatures of gametic and zygotic selection were detected by maximum likelihood.