Agriculture Reference
In-Depth Information
17
Molecular Breeding of Potato
in the Postgenomic Era
Richard E. Veilleux* and T. Boluarte-Medina
Department of Horticulture, Virginia Tech, Blacksburg, USA
Since the potato genome was published in 2011
(Potato Genome Sequencing Consortium, 2011),
with all of its associated tools, including the gen-
ome browser, blast engine, transcriptome with
links to other plant genomes, the Infinium 8303
Potato Array, new possibilities have become
available for potato breeding that complement
the traditional approach described in Chapter
16
of this volume. Amino acid sequences of genes
for which a function has been assigned in model
plants can be blasted against the translated nu-
cleotide sequence database for potato to identify
genes in potato with the most similar structure
to the query. Genetic maps can be constructed in
a matter of days by processing DNA samples
from a segregating population on the Infinium
8303 Potato Array, yielding a dense map with
thousands of markers in a fraction of the time
that was previously required for constructing
maps using simple sequence repeats (SSRs),
amplified fragment length polymorphisms (AFLPs),
or other markers (Felcher
et al
., 2012). Because
of the distribution of single-nucleotide poly-
morphism (SNP) markers across the linkage
groups, the SNP chip presents a convenient op-
tion for the identification of candidate genes
through association genetics. The first genome
available for potato has been assembled for an
obscure cultigen, DM
1-3
516 R44 (hereafter
DM for doubled monoploid), derived by anther
culture of a diploid (2
n
= 2
x
= 24) selection of
Solanum tuberosum
Group Phureja, followed by
chromosome doubling of an anther-derived
monoploid plant. Its fingerling tubers, with little
or no keeping quality, are a far cry from commer-
cial potatoes that comprise the major world
crop. However, it is unmistakably a potato, and
its homozygosity, a rarity for potato, enabled se-
quence assembly from short reads using avail-
able technology, whereas previous attempts to
assemble the genome of a heterozygous diploid
selection had failed. So DM, despite its limita-
tions as a cultivated potato, serves as the draft
potato genome, providing a scaffold for other po-
tato genomes and a set of some
39,000
genes,
most of which are highly similar to those in potato
cultivars, enabling the transcriptome derived
from sequencing cultivar expressed sequence
tags (ESTs) to be aligned to the DM genome. The
potato genome assembly represents 86% of the
844 Mb genome (Potato Genome Sequencing
Consortium, 2011).
17.
1
SNP Chip Development for
Assisting Mapping
Gene mapping (genome mapping) can be ac-
complished by assigning DNA fragments to plant
