Agriculture Reference
In-Depth Information
Because genetics and genomics aim to understand the molecular basis of
traits, these disciplines are tightly linked to breeding. Molecular breeding
uses knowledge generated by genetics and genomics in order to increase
breeding ef
ciency (Coffman et al. 2004). In this section, we illustrate how
CIAT uses genetics and genomics tools in its rice breeding activities.
A. DNA Marker Technologies
Researchers at CIAT started using deoxyribonucleic acid (DNA) marker
technologies for rice breeding since they became available. Restriction
fragment length polymorphism (RFLP) and then ampli
ed fragment
length polymorphism (AFLP) technologies were adopted early. Because
of their unique properties, microsatellites (or SSRs) progressively
replaced them; SSRs are highly polymorphic, abundant, easy to establish
as markers, codominant, reproducible, and relatively cheap. Then,
single-nucleotide polymorphism (SNP) technologies started to appear
on the market and CIAT is currently moving to SNPs for almost all its
DNA marker-based assays in rice. SNP genotyping is more automatable
than SSRs and, although less polymorphic than SSRs, SNPs are even
more abundant in the genome. Automatability is a key property of any
high-throughput (HTP) marker technology. Molecular breeding strongly
needs HTP, as
markers have to be much faster than plants
: This is crucial
for ef
ciency to be able to select genotypes at their early stages of
development
—
less than a month old or so
—
in order to cross, self or
field the selected plants only. First Luminex
and then
Illumina BeadXpress
and Fluidigm SNP platforms were acquired
and are now used routinely to select materials. Although genotyping
by sequencing (GBS) is still more time consuming and complex to use
than SNP platforms
take to the
as it requires high-quality DNA, preparation of
libraries, and complex bioinformatic post-treatment
—
we started to
apply it successfully to obtain high-resolution molecular data on diverse
sets of materials useful for genetic mapping, genome-wide association
studies (GWAS), and diversity analyses. Finally, whole-genome
sequencing (WGS) allows us to de
—
ne targeted SNP sets for any kind
of breeding scheme that involves LAC rice progenitors. In parallel, we
also develop statistical programs and bioinformatic tools for speci
c and
general applications.
B. QTL and Gene Mapping
Mapping genes underlying important traits is a key step in marker-
assisted selection. We present results on major genes and QTL linkage
