EST libraries development in Asparagus officinalis for SNPs discovery

In order to conduct marker-assisted selection (MAS) in asparagus the first
broad survey of EST-SNPs (Expressed Sequence Tag-Single Nucleotide
Polymorphisms) in A. officinalis specie was generated; more than 200,000 Asparagus
officinalis ESTs were sequenced and assembled starting from two GSFLX 454
pyrosequencing runs on two parental genotypes sharing a higher part of their
genetic background and divergent at least for Puccinia asparagi resistance trait
(male genotype named G190 as resistant, female genotype named 1770 as susceptible
ones). Efficient computational SNPs mining pipeline based on a sequence
polymorphisms detection tool was developed, finding more than 1700 putative
G190/1770 SNPs within expressed sequences. Stringent post-processing reduced this
number to 284 putative SNPs and a panel of these was successfully validated by
Sanger sequencing. Expressed sequence tag databases are a valuable resource of
gene-rich DNA sequence information for a species, additionally that can be mined
for the development of genetic markers as SNPs. Once discovered, SNPs can be
converted into genetic markers that can be inexpensively assayed in a highthroughput
manner and it can be used to generate very dense genetic maps. Until
now, there are few deposited Asparagus EST sequences, especially for A. officinalis,
and the repository of a massive number of those from our study can be useful for
genome sequence annotation and, especially, for continued advancement of
Asparagus genomics research