Agriculture Reference
In-Depth Information
at least 20,000 SNPs per population, representing a total of 50 million
datapoints, which should be enough to fully represent the expected
128,000 recombination breakpoints, and providing one of the most
saturated and precise genetic maps generated in plants to date. Ultra-
precise QTL mapping for traits of interest is the main expected outcome
of rice NAM-based studies.
C. Marker-Assisted Breeding
1. MABC for Resistance to RHBV.
Resistance to RHBV is an important
trait to consider in rice breeding for LAC. We began a pilot project with
Fedearroz (Bogotá, Colombia) that aims to introgress QTLs found in
variety Fd2000 (see Section IV.B.2) into two elite
indica
backgrounds
—
Fd174 and CT-12. We used marker-assisted backcrossing to generate
two BC
3
F
4
populations, selecting for the favorable QTL allele in each
generation using SSR markers. No phenotypic selection was done at any
step. The families obtained showed signi
cantly increased resistance to
RHBV in both glasshouse and
field experiments. These very encouraging
results led us to start a new marker-aided backcrossing (MABC) experi-
ment in four
indica
elite lines or cultivars. The SNPs were extracted from
the genomic sequences of Fd2000 and eight other
indica
sequences,
obtained by 10 X resequencing on the Illumina HighSeq 2000
platform
in Stephen Dellaporta
s lab (Yale University, CT). SNP Extractor (see
Section IV.F) is used to choose highly informative, evenly dispersed
markers. A total of 177 loci were chosen and converted for the Fluidigm
platform. This technology allows controlling QTL introgression (forward
selection) and genetic background (backward elimination), resulting in
a signi
'
cant increase in ef
ciency and reduction in labor and time.
2. Wild Introgressions.
Interspeci
c hybridization offers an attractive
way of enlarging genetic diversity for crop improvement. Indeed, the
genetic diversity found in wild species is often much larger than that
in their related cultigen pool. These resources are known to contain
many interesting traits for breeding, including grain yield potential
(McCouch et al. 2001; Brondani et al. 2002; McCouch et al. 2007; Fisher
2012), adaptation to abiotic stresses, host plant resistance to pathogens
and pests, and various nutritional traits of interest (Sun et al. 2001). In
the framework of a GCP-funded project, we developed several libraries
of introgression lines that carry genome fragments from wild
Oryza
species and African cultivated rice
O. glaberrima
. This work was done in
collaboration with Dr. Susan McCouch (Cornell University, NY),
Embrapa and AfricaRice (Benin).
