Biology subjects

Hartje, S.

Publications and source records attributed to Hartje, S..

3 recordsLinked to original sources

bioRxiv2025

An Axiom SNP genotyping array for potato: development, evaluation and applications

Potato is a versatile food crop and a major component of human nutrition worldwide. Genomic-assisted breeding methods have the potential to increase the gain of selection. We report the development and validation of a high-density Axiom-based SNP array for potato (Solanum tuberosum L.). Whole-genome 10X Genomics based sequencing of 108 diverse clones representing landraces, improved cultivars, and wild relatives identified around 23.8 million sequence variants, from which 929,127 variants, alongside with 18,718 markers from a previously developed Illumina Infinium 21K array (GGP3), were tiled on the array. The array demonstrated high reproducibility, with replicate samples showing an average concordance of 99.88% in genotype calls for PotatoTools specific variants, compared to 99.93% for the Illumina Infinium 21K array variants. A panel of 1,247 diploid and tetraploid clones was genotyped with the developed array. Genotype calling, considering allele dosage, was realized using fitpoly and yielded 852,793 calls. The array informativeness was optimized by applying Euclidean distance, heterozygous strength offset metrics, call rate, minor allele frequency filtering, and diploid-based allele correction, yielding a final set of 206,616 robust and informative markers. The filtered marker set enables precise characterization of genetic variation across diverse germplasm, thereby supporting robust analyses of population structure, genome-wide association studies (GWAS), and genomic prediction in potato. Population structure analysis genotyped clones revealed clear subpopulation differentiation consistent with known ploidy groups. In addition, our discriminant analysis of principal components revealed a weak but structured diversity among clones of different market segments. GWAS analysis of 998 potato clones identified sequence variants significantly associated with polyphenol oxidase (PPO) activity, confirming the platforms efficacy for trait mapping. For the same trait, genomic prediction accuracies of 0.72-0.86 have been observed. The developed potato SNP array provides a robust platform for high-throughput genotyping, supporting genetic diversity studies, association mapping, and genomic-assisted breeding in this important crop.

plant biology↗

bioRxiv2025

Assessment of segregation variance estimates from derivation, simulations, and empirical data in autotetraploid species exemplified in potato

The optimal choice of parents and crosses and, therefore, the prediction of the segregation variance are of high relevance to maximize genetic gain in breeding programs. Several methods have been developed for the prediction of segregation variance, including correlation with genotypic diversity, progeny simulations, or algebraic derivations in case of a diploid inheritance. To the best of our knowledge, no algebraic derivation using parental genotypic information is available to predict segregation variance for autotetraploid species. The objectives of our study were to (1) derive algebraic derivation based on linkage disequilibrium (LD) between linked loci to predict the segregation variance in autotetraploid species; (2) compare the performance of segregation variance estimated based on simulated progenies and the algebraic derivation; (3) investigate by simulations how experimental parameters affect the accuracy of segregation variance prediction; and (4) compare the segregation variance estimated in empirical data of potato and the one based on the algebraic derivation. The segregation variance estimated by the developed derivations showed very high correlations with the one observed in large simulated progenies, but those were lower when phased parental haplotypes were not available or family size decreased. The correlation between segregation variance estimated by the developed derivation and the empirical data was low. This could be attributed to the small family size used in the study, which we could show to increase LD between unlinked loci. The proposed algebraic derivations promise to be a precise alternative to simulations to help breeders in optimizing their family choices and sizes considering the segregation variance.

genetics↗

bioRxiv2024

Optimal implementation of genomic selection in clone breeding programs - exemplified in potato: II. Effect of selection strategy and cross-selection method on long-term genetic gain

Different cross-selection (CS) methods incorporating genomic selection (GS) have been used in diploid species to improve long-term genetic gain and preserve diversity. However, their application to heterozygous and autotetraploid crops such as potato is lacking so far. The objectives of our study were to (i) assess how different CS methods incorporating GS with or without consideration of genetic variability affect both short- and long-term genetic gains compared to strategies using phenotypic selection (PS); (ii) evaluate the changes in genetic variability and the efficiency of converting diversity into genetic gain across different CS methods; and (iii) investigate the interaction effects between different genetic architectures and CS methods on long-term genetic gain. In our simulation results, implementing GS with optimal selection intensities had a higher short- and long-term genetic gain compared to any PS strategy. The CS method considering additive and dominance effects to predict progeny mean based on simulated progenies (MEGV-O) reached the highest long-term genetic gain among the assessed mean-based CS methods. Compared to MEGV-O and usefulness criteria (UC), the linear combination of UC and genome-wide diversity (called EUCD) kept the same level of genetic gain but resulted in a higher diversity and a lower number of fixed QTL. Moreover, EUCD had a relatively high efficiency in converting diversity into genetic gain. However, choosing the most appropriate weight to account for diversity in EUCD depends on the genetic architecture of the target trait and the breeders objectives. Our results provide breeders with concrete methods to improve their potato breeding programs. Key messageCross-selection method considering progeny mean performance and genetic variability can improve long-term genetic gain and keep genetic diversity in clone breeding.

genetics↗