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Enhancement of the set of microsatellite (SSR)
markers for improving pearl millet breeding
efficiency in Africa and Asia
Goal of the poject is to develop
a set of 200 novel SSR markers for pearl millet from
genomic, EST and BAC libraries and make these publicly
available. |
Pearl millet [Pennisetum glaucum (L.) R. Br.] is the seventh most important cereal crop globally, and an important coarse grain food crop in Africa and South Asia. Among the cereals, it is a particularly hardy crop that can be grown in very diverse environments from sea level to about 2000 meters in elevation, and is the staple cereal crop for the hottest, driest regions where dryland agriculture is practiced. Pearl millet is grown primarily as a dual-purpose grain plus stover (straw) crop on about 13 million hectares each in Africa and Asia, and primarily as a forage or mulch crop on more than two million hectares in the Americas.
Average pearl millet grain productivity in Asia and Africa is 0.5-0.6 tons per hectare. India, China, Myanmar, Pakistan, and Yemen in Asia and Nigeria, Niger, Burkina Faso, Mali, Sudan, Chad, and Tanzania in Africa are the top countries in each region producing pearl millet grain (FAO and ICRISAT, 1996). The seeds are rich in calcium and iron, and contain 7-14% seed protein that is higher in tryptophan, cysteine, and methionine content than many other cereals.
In comparison to other major cereal crops such as rice, wheat, and maize, there have been very limited crop improvement efforts to boost the production and productivity of this crop in spite of the fact that it is one of the hardiest crops and its grain has high biological food value.
Molecular marker technologies, complemented by good quality phenotyping, can greatly facilitate the crop improvement programs in several ways. For instance, they can be used to assess genetic diversity
at molecular level in a germplasm collection for making appropriate choice of parents for crosses (e.g., hybrid breeding), studying the population structure, mapping and tagging of genes or QTLs (quantitative trait loci) for agronomic and disease resistance traits. As a result, molecular markers permit marker-assisted selection (MAS) in backcross, pedigree, and population improvement programs, which can be especially useful for crop traits that are otherwise difficult or impossible to deal with by conventional means (e.g., due to difficulties in obtaining repeatable field, greenhouse, or laboratory screening conditions “on-demand” as a result of natural variation in rainfall or pest pressure, or due to phytosanitary restrictions).
Eventually, near-isogenic products of marker-assisted backcrossing programs provide useful genetic tools facilitating improved understanding of mechanisms of corresponding traits (reverse crop physiology) such as tolerance to abiotic stress and resistance to pests and diseases. QTL mapping of yield and quality components can provide a better understanding of the basis for genetic correlations between economically important traits such as determining the role of linkage and/or pleiotropy for gene blocks controlling associated traits, such as flowering time and biomass, inflorescence size and inflorescence number, or grain yield and grain protein content.
In case of pearl millet, molecular markers in the form
of RFLPs (restriction fragment length polymorphisms) were
reported as early as 1992. The first molecular marker-based
genetic linkage map of pearl millet, comprised largely
of RFLP loci supplemented by a few isozyme loci was reported
by Liu et al. (1994). In subsequent years, the linkage
map has been expanded (Qi et al., 2004) and its complex
relationships with the foxtail millet, rice, and sorghum
genomes have been established (Devos et al. 1995, 2000,
Bowers et al. 2003).
At present, about 500 homologous RFLP markers are available
for pearl millet that provide a robust and reliable, but
slow system for using molecular markers in applied breeding
programs. Because of the amenability of use in high throughput
and user-friendly assays, PCR-based molecular markers
are preferred over RFLP markers. In an effort to convert
RFLPs to PCR based markers, STS (sequence tagged site)
markers based on primers obtained by end sequencing the
RFLP probes were developed, but these generally failed
to detect polymorphism that can be scored reliably on
gels.
Microsatellite or SSR (simple sequence repeat) markers,
on the other hand generally detect a higher level of polymorphism,
are co-dominant, and therefore, are considered an ideal
class of molecular markers for marker-assisted breeding
applications. By using normal and microsatellite enriched
genomic DNA libraries, a total of 62 SSR markers have
been generated . Other genomic tools such as a modest
(2.5X) bacterial artificial chromosome (BAC) library (Allouis
et al. 2001) and more than 2500 ESTs for pearl millet
have been developed in recent years. As a result, an additional
50 SSR markers based on BAC sequences and 25 SSR markers
based on ESTs have been developed. Further the EST resource
has recently been used to develop SNP (single nucleotide
polymorphism) markers based on single-strand conformation
polymorphism (SSCP-SNP, Bertin et al. 2005) and nearly
100 of these have been mapped (Gale et al. pers. comm.).
To date, about 140 SSR markers are available for pearl
millet, although only 82 of these have been mapped. Interestingly,
the majority of the pearl millet molecular markers mapped
to date are clustered around the seven pearl millet chromosome
centromeres and only a few marker loci are mapped to more
distal regions. Such an uneven distribution of SSR and
RFLP markers on the genetic map may reflect an uneven
distribution of recombination in pearl millet genome,
or is simply the result of the low number of markers that
have been mapped so far. Regardless, the available sets
of RFLP and SSR markers are limiting for mapping QTLs
and for conducting efficient marker-assisted breeding.
While the initial sets of available SSR markers are useful,
we estimate that at least 300 SSRs would be required to
cover the pearl millet genome properly (evenly spaced
on all linkage groups).
Annual reports
» Download
full progress report [PDF 332KB]
Although, to date, about 140 SSR markers are available for pearl millet, only 82 of these have
been mapped and interestingly, the majority of the markers mapped are clustered around the
seven pearl millet chromosome centromeres and only a few marker loci are mapped to more
distal regions (Qi et al. 2004).
» Download
project proposal [PDF 44KB] |
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