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

Large variability in tuber appearance exists in the Andean cultivated potato germplasm.
While wild potatoes are generally small and round with rather superficial eyes 1] the tubers of early-domesticated landrace cultivars are larger and have great variability
in shape and eye depth 2]. Andean farmers seek to maintain this rich diversity by cultivating mixtures of landraces
in their fields. Cultural rites, folk nomenclature, and the association of certain
shapes with distinct culinary preferences and uses have been passed on through generations
2]. Thus, the user preferences that still persist in the original home of potato domestication
are very distinct from those associated with potato in the areas that adopted this
crop relatively recently. In modern varieties, superficial eyes, uniform color and
round or oblong shape are preferential as these facilitate handling and processing.
Heavy selection has consequently led to low diversity for these traits in modern cultivars.

For the purpose of revealing the genetic control of tuber shape and eye depth, various
classification categories have been used, reflecting the variability present. Some
studies featuring Solanum tuberosum (at either tetraploid or diploid level), have used two (round, long), three (round,
oval and long), or four (round, oval, long oval, very long oval) shape categories
3]–11]. In other cases, such as in a hybrid population between S. verrucosum and S. microdontum, six shape types were recorded (long, long oval, oval, round oval, round, compressed)
12]. In a S. phureja derived population, initially eight shape types were scored, but for genetic mapping
they were grouped into three main classes (round, oval, long) 13], 14]. Eye depth has previously been recorded using three 10], 14], 15] to nine classes 11]–13].

The International Potato Center (CIP) currently holds the largest biodiversity of
cultivated potatoes. The morphological descriptors for tuber shape used by the CIP
genebank include eight basic categories: compressed, round, ovoid, obovoid, elliptic,
oblong, long-oblong and elongated, as well as an additional set of nine unusual shapes
(for example paw-like). For eye depth, the scale has five classes: protuberant, superficial,
slightly deep, deep and very deep 16].

The diploid backcross mapping population ‘DMDD’ was developed at CIP 17] and was used to anchor the first published potato genome sequence of potato (DM)
and to develop a dense genetic map 18]. The female grandparent of the population, DM, belongs to the S. tuberosum Group Phureja 19] and the recurrent male parent, DI, to S. tuberosum diploid Andigenum Group Goniocalyx 20],21], thus providing some of the allelic variation present in the Andean landraces. DMDD
segregates for numerous morphological, reproductive, physiological, biochemical and
abiotic stress related traits 22], 23], which, combined with the high-density genetic map and the high-quality reference
genome sequence, open up great opportunities for trait-QTL and gene discovery studies.

The present work was conducted to evaluate the utility of morphological descriptors
for tuber shape to the identification of genetic loci responsible for the shape and
eye depth variation. In addition, the reference genome sequence of potato was used
to search for potential candidate genes responsible for the QTL effect found.