Agriculture Reference
In-Depth Information
17.
2
Marker-Assisted Selection
chromosomes based either on recombination
in a segregating population to generate a gen-
etic map or on physical distance between
markers to generate a physical map of an organ-
ism. Genotyping is the identification of alleles,
alternative forms of a gene that differentiate
individuals; differences in the DNA sequences
between alleles comprise any of several types
of molecular markers that can be associated
with phenotypes. New methods of high-
throughput DNA purification, PCR amplifica-
tion, DNA sequencing, and the availability of
bioinformatics tools for handling large data
sets facilitate the development of genetic maps
and molecular genotyping. Molecular mark-
ers on genetic maps enable the identification
of plants with desirable genotypes and pheno-
types at the seedling stage to hasten breeding
programs. SNPs are a powerful type of mo-
lecular marker that differentiate two alleles by
a single nucleotide change, which may be as-
sociated with an amino acid difference (non-
synonymous SNP) that can alter the protein
product of a gene.
A recent addition to the molecular breeding
toolkit for cultivated potato is the Illumina Infin-
ium 8303 Potato Array (Hamilton
et al
., 2011).
RNASeq reads based on cDNA extracted from
three commercial cultivars (Atlantic, Premier
Russet, and Snowden) were used to generate a
28-
to
29-
Mb sequence for each cultivar (Hamilton
et al
., 2011). From more than
2
million SNPs de-
rived from the transcriptome data of the three
cultivars, a set of more than
69,000
high-confidence
SNPs was identified after the application of
various filters. The participation of the potato
research community was solicited to aid in the
selection of SNPs for inclusion on the chip in
order to feature SNPs within genes considered
valuable to various breeding and genetics pro-
grams. Other SNPs were selected to provide
adequate distribution across the genome. An ini-
tial application of the potato array was used
on a panel of
248
genotypes comprising pro-
cessing cultivars, table stocks, diploid breed-
ing lines, and a few non-cultivated potato spe-
cies used in breeding; the SNP chip separated
these four classes of germplasm easily (Hamil-
ton
et al
., 2011). The broad genome coverage
was verified in a mapping study where two
diploid populations that shared a common
parent were mapped based on SNP chip appli-
cation (Felcher
et al
., 2012).
The application of marker-assisted selection in
potato breeding was initially limited by the
paucity of molecular markers, which only
numbered some
350
or so in 2004 (Barone,
2004). The difficult breeding structure of po-
tato, such that backcross breeding cannot be
readily applied to recover the highly heterozy-
gous genotype of a recurrent parent, is an-
other limitation. However, some progress has
been made in the utilization of molecular
markers for breeding and selection in popula-
tions, especially for late blight resistance
(Rickert
et al
., 2003; Bormann
et al
., 2004;
Costanzo
et al
., 2005; Park
et al
., 2005; Colton
et al
., 2006; Malosetti
et al
., 2007; Wick-
ramasinghe
et al
., 2009; DeBolt, 2010; Sliwka
et al
., 2010; Tan
et al
., 2010; Busch
et al
.,
2011; Mori
et al
., 2011; Gyetvai
et al
., 2012),
virus resistance (Hämäläinen
et al
., 1997;
Gebhardt
et al
., 2006; Witek
et al
., 2006;
Velásquez
et al
., 2007; Valkonen
et al
., 2008;
Kelley
et al
., 2009; Whitworth
et al
., 2009;
Mori
et al
., 2011; Ortega and Lopez-Vizcon,
2012), nematode resistance (Pajerowska
et al
.,
2005; Zhang
et al
., 2007; Achenbach
et al
.,
2009; Rüping
et al
., 2010; Milczarek
et al
.,
2011; Mori
et al
., 2011; Schultz
et al
., 2012),
chip color (Kawchuk
et al
., 2008), dry matter
(Bhering
et al
., 2009), cold-induced sweeten-
ing (Baldwin
et al
., 2011), and processing
quality (Li, 2008). An online Sol
R
gene data-
base has been compiled with relevant informa-
tion about resistance genes in tuber-bearing
potato germplasm (Ferreira
et al
., 2010). Yao
et al
. (2011) combined marker-assisted selec-
tion specifically for late blight resistance in
conjunction with background AFLP marker
selection to maintain diversity in their breed-
ing population while increasing the frequency
of resistant individuals. Analysis of data pro-
vided by the potato genome browser promises
to speed up the advance of potato breeding
in the molecular era. Jupe
et al
. (2012) identi-
fied and localized on the potato genome the
nucleotide-binding and leucine-rich repeat
domain (NB-LRR) gene family that comprised
a vast majority of resistance (
R
) genes. These
data elucidate the evolution of the potato
R
genes and facilitate identification of func-
tional NB-LRR genes for further applications
(Agrawal
et al
., 2008).
