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

Abstract

At 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 F1 hybrid 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 of S.tuberosum as the recurrent parental background. In Cycle 1 we selected XD3-36, a self-fertile F2 clone homozygous for the self-compatibility gene Sli. Signatures of gametic and zygotic selection were observed at multiple loci in the F2 generation, including Sli. In the BC1 cycle, an F1 population 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 gene StCDF1 (Cycling DOF Factor 1). Greenhouse phenotypes and haplotype analysis were used to select a vigorous and self-fertile F2 individual with 43% homozygosity, including for Sli and the early-maturing allele StCDF1.3. Partially inbred lines from the BC1 and BC2 cycles have been used to initiate new cycles of selection, with the goal of reaching higher homozygosity while maintaining plant vigor, fertility, and yield. Core IdeasO_LIPartially inbred, diploid potato lines were developed for transitioning to an inbred-hybrid breeding system. C_LIO_LIMulti-generational linkage analysis was used to track and fix favorable alleles without haplotype-specific markers. C_LIO_LISignatures of gametic and zygotic selection were detected by maximum likelihood. C_LI