Agriculture Reference
In-Depth Information
F. Software Development
In order to ful
c needs, we developed several programs for
genetic analyses. Most of them can be downloaded free of charge from
http://mapdisto.free.fr/
. The most signi
ll speci
cant programs are MapDisto
(Lorieux 2012), to compute genetic maps with advanced settings; CSSL
Finder, to monitor introgression and to construct CSSLs; SNP Extractor,
to design SNP sets; Paddy Map, to use the Universal Core Genetic Map
(see above); and Paddy Genes Book, to exploit T-DNA phenotypes and
FSTs (see above).
For analysis of whole-genome sequencing data, we developed
NGSEP (Next-Generation Sequencing Eclipse Plugin), a software
tool able to perform integrated detection of SNPs, indels, repetitive
regions, and regions with copy number variations (CNVs). The inte-
grated identi
cation of SNPs and structural variants provided by
NGSEP allowed us to perform a complete, accurate, and ef
cient
bioinformatics analysis of our sequenced samples and to obtain
high-quality SNPs in unique regions of the genome that we can use
for marker-assisted selection. NGSEP is available as an open source
java software package, and is available at
https://sourceforge.net/
G. Outlook
The tools, resources, and methods for molecular breeding developed
by CIAT in collaboration with several research groups have been re-
viewed. Our goal for future would be to integrate and extend our current
approaches in order to take advantage of new technologies available, to
reach an optimized
of breeding and prebreeding.
We must expand precise mapping information on QTL effects and
QTL interactions for important traits, obtained by NAM and GWAS, in
order to design combinations of desired haplotypes. Then, genotypes
will be designed and constructed on the basis of these combinations;
this will be made possible thanks to the availability of ultradense
genotyping technologies and highly ef
“
pipeline
”
cient recombination schemes
such as the recurrent selection. In parallel, genomic selection will be
used for traits that are genetically too complex or too dif
cult to analyze,
which will be addressed by genotype construction.
Although the use and development of DNA technologies and genetic
stocks have been discussed, the importance of phenotyping will be
dealt with in other sections. Efforts to develop phenomics platforms
for important traits must be pursued, for this is the key to obtaining
