Biology Reference
In-Depth Information
Advances in Genomics and
Applications for
Striga
Resistance Research
tomized bioinformatics pipelines with appropri-
ate computational power, which still remains the
major challenge with handling the large datasets
generated using NGS tools. This extensive cover-
age with a large number of SNPs across genome
helps identify SNPs closest to or inside the genes
associated with
Striga
resistance, and can be a
part of customized SNPs assay using BeadX-
press platform or CAPS markers at lower cost
for further genotyping to transfer this trait to
desired recurrent parent of sorghum. This will
greatly improve the efficiency of introgression
of component traits underlying different
Striga
resistance mechanisms of by reducing breeding
cycles (for recurrent parent recovery) and further
recombining these for development of improved
Striga
-tolerant varieties.
Application of NGS tools like GbS for dis-
secting complex traits such as
Striga
on DNA
sequence level will capture most of the func-
tional factors of genome related to trait expres-
sion. But other application of NGS tools in RNA
sequencing (commonly referred as RNA-seq)
will help capture the regulatory parts (Ozsolak
and Milos 2011). For a complex trait such as
Striga
resistance, involving host-parasite inter-
actions, many growth and development path-
ways from both host and parasite life cycles are
involved in its expression. Application of RNA-
seq platforms can help understand the role of reg-
ulatory and transcription factors (including small
RNA, micro RNA) and their interaction with
other pathways. There is big interest to utilize
recent advances in RNA-seq technologies with
the recombinants identified from fine-mapping
exercise to move toward better understanding the
Striga
resistance in sorghum. As knowledge of
QTL underlying resistance traits increases, com-
parative genomic approaches will aid detection
of
Striga
resistance genes in syntenic regions
of the rice, sorghum, maize, and pearl millet as
sequence information becomes available.
Recently Yoshida et al. (2010) generated a
full-length enriched cDNA library of
S
.
her-
monthica
by sequencing over 37,000 clones and
Simple sequence repeat (SSR) markers are still
the preferred choice of markers in plant-breeding
programs with interest in mapping and intro-
gression of different traits in crop species.
The amenability to simple assays, multiplexing,
reproducibility, and more importantly codomi-
nant nature of SSRs works to the advantage of
plant-breeding science to follow the segregating
population as per principles of Mendelian and
Population genetics for selection of best pheno-
types. SSR markers were greatly exploited for
mapping of different traits in sorghum, includ-
ing
Striga
resistance (Haussmann et al. 2004,
Satish et al. 2012). A major limiting factor for uti-
lization of SSR markers is the resolution power.
Recent advances in sorghum genomics includ-
ing availability of sorghum genome sequence
(Paterson et al. 2009), access to large number
of markers including DArTs (Mace et al. 2009;
Ramu and Deshpande et al. 2010), and alignment
of major trait genes and quantitative trait loci
(QTL) to integrated linkage and physical map
(Mace et al. 2011) had strengthened the founda-
tion for better integration of molecular marker
technologies to dissect complex traits such as
Striga
resistance.
With the invention of Next Generation
Sequencing (NGS) technologies, identification
of a large number of markers, especially Single
Nucleotide Polymorphism (SNPs), has become
cheap as compared to the other marker systems.
Utilizing Illumina NGS platform, Ed Buck-
ler Lab at Cornell University in Ithaca, New
York, developed a technically very simple and
highly multiplexed (96-plex/384-plex) method
for rapid sequencing and associated bioinformat-
ics pipeline for genotyping the germplasm and
is referred as Genotyping-by-Sequencing (GbS)
(Elshire et al. 2011). These sequences produced
are aligned to reference genome, BTx623 (Pater-
son et al. 2009) to identify SNPs with help of cus-
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