Combining conventional QTL analysis and whole-exome capture-based bulk-segregant analysis provides new genetic insights into tuber sprout elongation and dormancy release in a diploid potato population

Abstract

Tuber dormancy and sprouting are commercially important potato traits as long-term tuber storage is necessary to ensure year-round availability. Premature dormancy release and sprout growth in tubers during storage can result in a significant deterioration in product quality. In addition, the main chemical sprout suppressant chlorpropham has been withdrawn in Europe, necessitating alternative approaches for controlling sprouting. Breeding potato cultivars with longer dormancy and slower sprout growth is a desirable goal, although this must be tempered by the needs of the seed potato industry, where dormancy break and sprout vigour are required for rapid emergence. We have performed a detailed genetic analysis of tuber sprout growth using a diploid potato population derived from two highly heterozygous parents. A dual approach employing conventional QTL analysis allied to a combined bulk-segregant analysis (BSA) using a novel potato whole-exome capture (WEC) platform was evaluated. Tubers were assessed for sprout growth in storage at six time-points over two consecutive growing seasons. Genetic analysis revealed the presence of main QTL on five chromosomes, several of which were consistent across two growing seasons. In addition, phenotypic bulks displaying extreme sprout growth phenotypes were subjected to WEC sequencing for performing BSA. The combined BSA and WEC approach corroborated QTL locations and served to narrow the associated genomic regions, while also identifying new QTL for further investigation. Overall, our findings reveal a very complex genetic architecture for tuber sprouting and sprout growth, which has implications both for potato and other root, bulb and tuber crops where long-term storage is essential.

Genotyping-by-sequencing targets genic regions and improves resolution of genome-wide association studies in autotetraploid potato

“…Due to the very poor resolution of the genetic map in the previous studies, except by Sharma et al ( 2021 ), and largely the deployment of non-sequence-tagged markers, detailed comparisons with the current study are not possible, however, many QTL reported here appear to be in approximately the same genomic locations as reported previously including the detection of novel QTL regions (Table 5 ). A much more recent study (Sharma et al 2021 ) conducted with high map resolution reports tuber dormancy/sprouting QTL on chromosomes 1–8 and 10. Of these, chromosomes 8 and 10 QTL were not detected in the current study but all other QTL (i.e.…”

“…on chromosomes 1–7) find higher correspondence with the GWAS QTL-MTAs reported here. None of the previous studies report QTL for this trait on chromosome 12 except Sharma et al ( 2021 ) who suggest the presence of an effective QTL peak at the bottom end of this chromosome but the required statistical significance in their study was not achieved. The chromosome 12 QTL–MTA (Table 5 ) observed here strongly overlaps, and further strengthens, the chromosome 12 candidate QTL suggested by Sharma et al ( 2021 ).…”

“…Tuber dormancy release and sprout growth are two different physiological phenomena and are often confounded in QTL studies, thereby contributing to the complex genetic architecture of this compound trait. Previous genetic studies (Freyre et al 1994 ; Sharma et al 2021 ; Simko et al 1997 ; Simmonds 1964 ; van den Berg et al 1996 ) on tuber dormancy have detected QTL effects on all chromosomes except chromosome 12. The analysis conducted here also revealed the presence of QTL on several (1, 2, 3, 4, 5, 6, 7, 9, 11 and 12) chromosomes (Table 5 ; Figs.…”

“…Tuber sprouting is one of the commercially important potato traits and critical for the long-term tuber storage required to ensure year-round availability as premature dormancy release and sprout growth in tubers during storage can result in a significant deterioration in product quality. Therefore, breeding potato cultivars with extended or otherwise modified dormancy or sprout vigour is a desirable goal (Alamar et al 2017 ; Sharma et al 2021 ). Tuber dormancy release and sprout growth are two different physiological phenomena and are often confounded in QTL studies, thereby contributing to the complex genetic architecture of this compound trait.…”

Omics-driven exploration and mining of key functional genes for the improvement of food and fiber crops

“…It was inferred that this mutation leads to the retention of the second intron and premature termination of the HvCSLC1 protein (Gajek et al, 2021). The combined bulk segregant analysis and whole exomecapturing methods employed in potatoes for studying tuber sprout elongation corroborated different QTL sites, helped to narrow down the related genomic regions, and discovered novel QTLs (Sharma et al, 2021). Overall, with this focused strategy, crop development efforts are more precisely made while simultaneously speeding up the breeding process.…”