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

Abstract

BackgroundTuber 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.ResultsSubjective 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.ConclusionsUtilization 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-015-0213-0) contains supplementary material, which is available to authorized users.

Genome Reduction in Tetraploid Potato Reveals Genetic Load, Haplotype Variation, and Loci Associated With Agronomic Traits

“…Bonierbale et al ( 1993 ) reported QTL on chromosomes 2, 4, and 7 for TTY, TS, and ATW, although the QTL on chromosome 2 does not match the chromosome arm location of our QTL. Similarly, several authors have reported a QTL on chromosome 10 for tuber shape (Van Eck et al, 1994 ; Prashar et al, 2014 ; Lindqvist-Kreuze et al, 2015 ), separating mainly compressed, round, and oval from the more elongated shape types oblong and long.…”

“…A cytokinin riboside 5′-monophosphate phosphoribohydrolase LOG3 gene is located in the QTL region at 56 Mb on chromosome 10. For tuber shape, several candidate genes associated with cell structure and function, and pectin metabolism have been reported in the major QTL located around 48 Mb on chromosome 10 (Lindqvist-Kreuze et al, 2015 ). Similarly, in the QTL region discovered in our analysis on chromosome 6, a Pectinesterase gene is located at 58 Mb.…”

QTL for tuber morphology traits in diploid potato

“…Van Eck ( 2007 ) hypothesized on pleiotropic effect of one locus on both traits or two closely linked loci influencing eye depth and tuber shape. In studies of Lindqvist-Kreuze et al ( 2015 ), the QTL for eye depth and QTL for general tuber shape overlap on chromosome X with additional QTL for tuber shape found on chromosome V and QTL for eye depth on chromosome XII. Our results led to the conclusion that tuber shape and eye depth could not be explained by a simple one or two loci model as shown in studies mentioned above.…”

Insight on Genes Affecting Tuber Development in Potato upon Potato spindle tuber viroid (PSTVd) Infection

“…Initially, it was explained by a single locus Ro on chromosome 10, with round being dominant over long [ 27 ]. Other genetics studies identified several Quantitative Trait Loci (QTL) on different chromosomes affecting tuber shape [ 28 – 31 ]. Our previous study identified two QTL on chromosome 2 and 10 for tuber shape; the chromosome 10 QTL can explain the higher variation in the population as seen in other studies.…”