Using haplotype and QTL analysis to fix favorable alleles in diploid potato breeding

Abstract

At present, the potato (Solanum tuberosum L.) 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 because of an 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 quantitative trait locus (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 individual homozygous for the self‐compatibility gene Sli (S‐locus inhibitor). 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 versus early alleles in XD3‐36 for the gene CDF1 (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 CDF1.3. 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.

Molecular breeding of flower load related traits in dioecious autotetraploid Actinidia arguta

“…The genetic effects for each haplotype for each locus were then estimated using a Bayesian Linear Mixed Model in “diaQTL” (v. 1.10) in R (R Core Team 2020 ; Amadeu et al 2021 ). “PolyOrigin” in R and “diaQTL” were developed to identify QTL using breeding populations with multiple F1 populations to increase the power of QTL detection, especially when each cross comprises only a few progeny (Amadeu et al 2016 , 2021 ; Lau et al 2022 ; Song and Endelman 2023 ).…”

Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR

“…The 81-bp haplotypes in the MADC file were aligned using MUSCLE v3.8 (Edgar, 2004). DArTag read counts for CDF1 alleles 1, 2, and 4 were tabulated with R/polyBreedR function madc and validated against genotypes determined via whole-genome sequencing with NovaSeq 2x150 reads (Song and Endelman, 2023).…”

Natural variation in potato sexual reproduction facilitates breeding

“…However, insights can be gained from the expanding body of literature on inbred diploid potato. For instance, it is clear that phenotypic selection for vigour and fertility between generations of inbreeding maintain a higher level of heterozygosity than theoretical estimates (Leisner et al, 2018;Peterson et al, 2016;Song and Endelman, 2022;van Lieshout et al, 2020b). Likewise, selection of the most vigorous and fertile descendant during backcross breeding should maintain a level of heterozygosity relatively close to the one of the recurrent parent and thus limit the extent of inbreeding depression.…”

“…Recognizing that breeders would rather introgress Sli from S. tuberosum clones than from S. chacoense accessions, we developed and published KASP markers specific to the Sli haplotype. Those markers were quickly adopted by the potato genetics community (Kaiser et al, 2021;Song and Endelman, 2022). It was subsequently shown, both in S. chacoense and S. tuberosum clones, that the Sli gene encodes for a pollen-expressed F-box protein functioning as a general S-RNase inhibitor (Eggers et al, 2021;Ma et al, 2021).…”

“…It was subsequently shown, both in S. chacoense and S. tuberosum clones, that the Sli gene encodes for a pollen-expressed F-box protein functioning as a general S-RNase inhibitor (Eggers et al, 2021;Ma et al, 2021). The knowledge gained on Sli identity and on its prevalence in S. tuberosum germplasm facilitated the development of selfcompatible diploid potato clones with agronomical value (Alsahlany et al, 2021;Kaiser et al, 2021;Song and Endelman, 2022).…”