Global multi-environment resistance QTL for foliar late blight resistance in tetraploid potato with tropical adaptation

Abstract

The identification of environmentally-stable and globally-predictable resistance to potato late blight is challenged by the clonal and polyploid nature of the crop and the rapid evolution of the pathogen. A diversity panel of tetraploid potato germplasm bred for multiple resistance and quality traits was genotyped by genotyping by sequencing (GBS) and evaluated for late blight resistance in three countries where the International Potato Center (CIP) has established breeding work. Health-indexed, in vitro plants of 380 clones and varieties were distributed from CIP headquarters and tuber seed was produced centrally in Peru, China and Ethiopia. Phenotypes were recorded following field exposure to local isolates of Phytophthora infestans. QTL explaining resistance in four experiments conducted across the three countries were identified in chromosome IX, and environment-specific QTL were found in chromosomes III, V, and X. Different genetic models were evaluated for prediction ability to identify best performing germplasm in each and all environments. The best prediction ability (0.868) was identified with the genomic best linear unbiased predictors (GBLUPs) when using the diploid marker data and QTL-linked markers as fixed effects. Genotypes with high levels of resistance in all environments were identified from the B3, LBHT, and B3-LTVR populations. The results show that many of the advanced clones bred in Peru for high levels of late blight resistance maintain their resistance in Ethiopia and China, suggesting that the centralized selection strategy has been largely successful.

Potato and sweetpotato breeding at the International Potato Center: approaches, outcomes and the way forward

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Kompetitive Allele Specific PCR (KASP) Markers for Potato: An Effective Tool for Increased Genetic Gains

“…In total, 9 SNP or indels were selected for KASP marker design, and the amplification results were compared with a high-resolution melting (HRM) assay using probe M6P2 [17] on a quality evaluation set of 72 tetraploid potato genotypes from the CIP breeding program. The late blight markers were selected from previous association studies using genotyping by sequencing (GBS) [38] or SolCAP [39] markers, and the KASP results were compared with the original marker scores using a set of 73 and 78 tetraploid potato clones from the CIP breeding program, respectively. Validated SNP markers in the late blight resistance locus on chromosome 9 and in the Ryadg M6 resistance locus on chromosome 11 were converted into KASP markers by LGC, BioSearch Technologies (https: //www.biosearchtech.com/, accessed on 10 September 2021) and analyzed by Intertek ® (https://www.intertek.com/agriculture/agritech/, accessed on 21 July 2020).…”

“…The potato clones originated from the CIP breeding populations A (1 clone), B3 (7 clones), BW (3 clones), and LTVR (67 clones) (Supplementary Table S1 and S2). A detailed description of the CIP potato breeding populations is available in [38]. Assay verification of the PVY markers, snpST0052 and snpST00073, was conducted by comparing the 78 available PVY resistance phenotypes, for which results of enzyme-linked immunosorbent assay (ELISA) tests have previously been recorded as part of the breeding program, with their corresponding genotypes.…”

“…When used for different sets of breeding germplasm, the original markers that were converted into the KASP assay were found to be significantly associated with LB resistance. The snpST0023 marker, originally found when utilizing the B3 population [39], was represented by only seven samples in the validation panel (Supplementary Table S2), while the snpST0020 marker was discovered using a larger diversity panel that included both B3 and LTVR populations [38].…”

“…Further advantages over gel-based assays, such as SCAR or single sequence repeat (SSR), include significantly faster analysis and lower cost and workload since the separation through a gel matrix is not needed. KASP markers were developed from previous efforts on PVY, Ryadg [17], Rysto [19], and late blight [38,39]. Developed KASP markers are now routinely used in the CIP breeding programs for characterizing breeding material with respect to these important diseases affecting potato cultivation.…”