Tuber shape and eye depth variation in a diploid family of Andean potatoes

Abstract

Background: Tuber appearance is highly variable in the Andean cultivated potato germplasm. The diploid backcross mapping population 'DMDD' derived from the recently sequenced genome 'DM' represents a sample of the allelic variation for tuber shape and eye depth present in the Andean landraces. Here we evaluate the utility of morphological descriptors for tuber shape for identification of genetic loci responsible for the shape and eye depth variation.

Results: Subjective morphological descriptors and objective tuber length and width measurements were used for assessment of variation in tuber shape and eye depth. Phenotypic data obtained from three trials and male-female based genetic maps were used for quantitative trait locus (QTL) identification. Seven morphological tuber shapes were identified within the population. A continuous distribution of phenotypes was found using the ratio of tuber length to tuber width and a QTL was identified in the paternal map on chromosome 10. Using toPt-437059, the marker at the peak of this QTL, the seven tuber shapes were classified into two groups: cylindrical and non-cylindrical. In the first group, shapes classified as 'compressed', 'round', 'oblong', and 'long-oblong' mainly carried a marker allele originating from the male parent. The tubers in this group had deeper eyes, for which a strong QTL was found at the same location on chromosome 10 of the paternal map. The non-cylindrical tubers classified as 'obovoid', 'elliptic', and 'elongated' were in the second group, mostly lacking the marker allele originating from the male parent. The main QTL for shape and eye depth were located in the same genomic region as the previously mapped dominant genes for round tuber shape and eye depth. A number of candidate genes underlying the significant QTL markers for tuber shape and eye depth were identified.

Conclusions: Utilization of a molecular marker at the shape and eye depth QTL enabled the reclassification of the variation in general tuber shape to two main groups. Quantitative measurement of the length and width at different parts of the tuber is recommended to accompany the morphological descriptor classification to correctly capture the shape variation.

Fig. 1

Tuber shape and eye depth phenotypes of the DMDD population progenitors. The female grandparent, DM (CIP 801092), had elongated tubers with superficial eyes; the recurrent male parent, DI (CIP 703825), had round tubers and deep eyes; and DMDI (CIP 305156.17) had elliptic tubers and slightly deep eyes

Fig. 2

Tuber shape and eye depth variation in the DMDD progeny in the trial field3. Seven different shapes: ‘compressed’, ‘round’, ‘oblong’, ‘obovoid’, ‘elliptic’, ‘long-oblong’ and ‘elongated’, were found in the progeny. The tuber heel is pointing up

Fig. 3

The ratio of tuber length to width distribution in the DMDD progeny in the three field trials (field 1–3)

Fig. 4

Schematic representation of the QTL detected in chromosome 10 of the paternal genetic map. The marker locations on the linkage map are shown as cumulative distances in cM. The right side of the linkage map shows the QTL for the ratio of tuber length to width obtained by interval mapping and the left side shows the Kruskall-Wallis confidence limits at p < 0.001 for the eye depth and general shape QTL. *QTL for general shape was detected only in trial field1

Fig. 5

The occurrence of the QTL peak marker toPt-437059 genotypes nn and np in categorical tuber shape classes