Agriculture Reference
In-Depth Information
(IRSC) used the Illumina Infi nium II
system to produce high-throughput SNP
screening methods for genome-wide
evaluation of allelic variation in apple
(
Malus
×
domestica
) germplasm. The
whole-genome sequence from 'Golden
Delicious' was resequenced with 27 apple
cultivars (Chagné
et al.
, 2012). More than 2
million SNPs were detected - equivalent
to one SNP for every 288 bp of genome -
and a subset of 144 SNPs was validated in
160 apple accessions. A total of 7867 apple
SNPs were used to develop the IRSC apple
8K SNP array v1, of which 5554 were
polymorphic after evaluation in
segregating families and a germplasm
collection. This publicly available
genomics resource will allow un-
precedented resolution of SNP haplotypes
and enable structural and functional
genomics studies and marker-locus-trait
association discovery in apple and other
Rosaceaous crops.
short juvenile period. Its self-compatibility
allows the development of F2 progenies,
and homozygous doubled haploids are
available (Pooler and Scorza, 1997).
However, effi cient transformation protocols
have yet to be developed.
An important resource for marker-
assisted breeding is the Genome Database
for Rosaceae (
http://www.rosaceae.org/),
from which the reference
Prunus
map was
created. This consensus map was con-
structed using an interspecifi c almond ×
peach F2 population (Texas 3 Earlygold)
and has hundreds of transportable markers
and several major morphological, quality
and agronomic characters with simple
Mendelian inheritance and QTLs. The
peach doubled haploid 'Lovell' was
selected by the US Department of Energy
Joint Genomics Institute's Community
Sequencing Program for shotgun sequenc-
ing (83-fold genome coverage). The Italian
ESTree database (
http://www.itb.cnr.it/
estree/)
was created by the ESTree Inter-
universitary Centre to develop functional
genomics in drupaceous species. The
Centre produced four cDNA libraries from
P. persica
mesocarps from three different
cultivars at different developmental stages
(postfertilization, endocarp hardening,
preclimateric and postclimateric/fi nal
maturation) and used them to generate
thousands of ESTs. An automated pipeline
was used to mine EST sequences using Perl
scripts. A web interface allowed database
queries. To create this important peach
genomic resource, sequences were
assembled into contig consensus sequences
and annotated against public primary
databases. The resulting database is a
comprehensive tool to link genome
sequences with peach EST sequences,
allowing data to be obtained rapidly for
each sequence/contig.
18.10.5 Peach functional genomics
Fruits from the genus
Prunus
are drupes in
which seeds are enclosed in a hard,
lignifi ed endocarp (the stone) surrounded
by an edible mesocarp. The genus includes
cultivated species like
Prunus
persica
(peach, nectarine),
Prunus
domestica
(European or prune plum),
Prunus salicina
(Japanese plum),
Prunus cerasus
(sour
cherry),
Prunus avium
(sweet cherry),
Prunus
armeniaca
(apricot) and
Prunus
amygdalus
(almond). Peach is self-
compatible, which allows breeding of
cultivars with lower genetic variability
than other
Prunus
crops. Peach is the
genetic and genomic reference species for
the genus
Prunus
because it is both
economically valuable and has a relatively
References
Adams-Phillips, L., Barry, C. and Giovannoni, J. (2004) Signal transduction systems regulating fruit
ripening.
Trends in Plant Science
9, 331-338.
Aharoni, A. and O'Connell, A.P. (2002) Use of DNA microarrays in the identifi cation of genes
involved in strawberry fl avor formation.
Analysis of Taste and Aroma
21, 7-28.
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