Projects
From Azhagu
Research Projects
Post-Doctoral Program Wheat Map-Based Cloning (at TAES, Amarillo, USA)
Greenbug ( Schizaphis graminum (Rondani)) is a type of aphid that infests wheat, barley, oat, rye, corn, sorghum, and forage grasses. It is distributed worldwide, and it is the most economically damaging aphid in wheat of the southern Great Plains, causing over $100 million damage per year in that crop alone. There were seven resistance genes to different greenbug biotypes have been identified in wheat. Gb3, Gb4 and Gb7 were originated from Ae. tauschii , the D genome donor of wheat. Of these Gb3 confers resistance to all three prevailing biotypes (E, I and K) and genetically mapped in the distal 18% region of 7DL. The present major objective is to physically map and clone the gene Gb3. We are having three different mapping populations viz, Largo X TAM 107 a hexaploid cross (RILs), resistant x susceptible of RILs (NILs) and Ae. tauschii PI268210 X AL8/78. High density and high-resolution mapping has been done. Chromosome walking has been initiated by screening Ae. tauschii BAC and 7DL specific wheat libraries to isolate and functionally validate Gb3 resistance gene. Wheat breeding here in Texas AgriLife is also focusing on marker assisted selection for greenbug resistance, translocation of IAIR to get rust resistance ( Plant Breeding doi:10.1111/j.1439-0523.2007.01331.x ) and wheat streak mosaic resistance.
Brachypodium has recently been proposed as a bridge between rice and temperate cereal crops and forage grasses for genomics research. We have explored B. distachyon EST and genomic DNA sequences and developed 160 EST- and 21 genomic microsatellite markers, and used them to evaluate the genetic diversities among the six B. distachyon accessions. Genetic diversity information obtained from this study should be useful in selecting parents for linkage mapping in B. distachyon ( Plant Genetic Resources: Characterization & Utilization, 2008: 1-8 ).
Besides, simple sequence repeats (SSRs) are being explored in the EST and genomic sequences of the pea aphid (Acyrthosiphon pisum (Harris)) and the green peach aphid ( Myzus persicae (Sulzer)). SSR markers were investigated for their cross-species transferability among six aphid species. This is the first attempt of large scale development of SSR markers in aphids, which should have increasing use in aphid genetic, ecological, and evolutionary studies ( Insect Molecular Biology 16(5): 613-622 ).
Post-Doctoral Program Barley Allele Mining (at IPK, Gatersleben, Germany)
Barley yellow mosaic virus (BaYMV) and Barley mild mosaic virus (BaMMV) both belonging to the Bymoviruses are the causal agents of an important soil-borne viral disease seriously affecting winter barley production in large areas of Western Europe and Eastern Asia. Eight independent loci were detected in the barley genome controlling resistance to the viral complex comprising BaMMV, BaYMV-SIL, BaYMV-1 and BaYMV-2. Recently, it was shown that recessive resistance conferred by the gene rym4 is caused by mutations in the âÃÂÃÂeukaryotic translation initiation factor 4EâÃÂà(Hv-eIF4E), which is located on the long arm of barley chromosome 3H. Sequence diversity in the gene Hv-eIF4E indicated the presence of an allelic series conferring different resistance specificities including the already known alleles rym5 and rym6. The genetic diversity of this locus and the availability of ~20,000 independent barley accessions in ex situ Genebank at IPK provides an excellent resource for a comprehensive screening for further genetic diversity and the identification of new alleles that may be implemented into resistance breeding programs. A panel of 2000 barley accessions was selected including 500 chosen based on resistance to either one or a combination of BaMMV, BaYMV1 and BaYMV2. The remaining accessions were selected due to their geographic origin. Identified novel alleles for Hv-eIF4E by Ecotilling analysis were confirmed for its resistance and these could be implemented into resistance breeding programs. A comprehensive review on mutagenesis, TILLING, ecoTILLING and high-throughput functional genomics in cereal crops ( Advances in Agronomy Vol. 98: 358-414 ) has been published.
Post-Doctoral Program Barley Mapping and map-based cloning (at NIAS, Japan)
Barley ( Hordeum vulgare L.) is a model genome of Triticeae family suitable for domestication studies. Among the abundant availability of variations, non-brittle rachis ( btr1/btr2 ) and spikelet (vrs1) morphology are the key characters in studying evolution and domestication pattern in barley. Following research activities were done at Genetic Diversity Department, NIAS, Tsukuba, Japan.
1. Non-brittle rachis of barley is controlled by two tightly linked loci btr1 and btr2 located in the short arm of 3H. AFLP markers linked to btr1/btr2 loci, which were previously mapped, were converted into sequence tagged sites (STS) to exploit the advantages of simple PCR markers ( Plant Science, 170: 1087-1094 ). Ten STS markers were converted and used to screen large-sized segregating mapping populations of F2 crosses between cultivated X cultivated (Azumamugi x Kanto Nakate Gold ; 960 F2 plants), wild x cultivated (Kanto Nakate Gold x OUH602; 672 F2 plants) for high-resolution linkage mapping and comparative mapping. The order of the marker loci is conserved between populations ( JARQ, 40 (3): 239-242 ). The F2 population KNG x OUH602 showed the good separation of the AFLP markers. STS marker e09m25-08STS was mapped 0.21 cM distal and e50m21-01STS was mapped 0.63 cM proximal to the btr1 locus in the high-resolution map ( Plant Science, 170: 1087-1094 ). These identified flanking markers are serving as a basis for map-based cloning of non-brittleness locus, as it will permit the identification of BAC clones spanning the region. Since btr1/btr2 linked STS marker eo9m25-08STS sequence showed high level of polymorphism between the parents, a set of wild barley along with occidental and oriental lines were sequence on this locus. The phylogentic analysis clearly supports diphyletic origin of barley ( Annals of Botany 100: 1009-1015 ).
2. Development and fertility of lateral spikelets of barley is mainly controlled by the vrs1 locus in the long arm of 2H chromosome, with the flanking markers of cMWG699 and MWG865. AFLP marker enrichment were later converted into STS markers, a comparative high resolution genetic map of vrs1 using six different mapping populations has identified the closest flanking markers with a distance of 0.05 cM each on distal and proximal in a well resolved F2 population of Azumamugi x Golden Promise. This highly resolved mapping population made the map-based cloning of vrs1 feasible. We effectively used RICE-BARLEY synteny (As reported 4L of rice and 2HL of barley are having high synteny) and enriched the vrs1 locus, which speeded-up this map based cloning project. A hoemeodomain-leucine zipper I class homeobox gene is responsible for the row type in barley ( PNAS 104 (4):1424-1429 ). These same strategies are followed for fine mapping and positional cloning of non-brittle rachis ( btr1/btr2 ) genes, since barley 3H and rice 1 are having high synteny.
Ph.D Research-Pearl Millet Mapping (At ICRISAT, India)
Worked as a Research Scholar at Pearl millet Breeding, Genetic Resources and Enhancement Division, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Asian Center, India, funded by the UK Department for International Development (DFID) and administered by the Centre for Arid Zone Studies (CAZS), UK for the benefit of developing countries. Completed Ph.D research work on Linkage map construction and identification of QTLs against downy mildew ( Sclerospora graminicola ) resistance in pearl millet ( Pennisetum glaucum (L.) R. Br).
Pearl millet is the sixth most important cereal crop. It is the staple food crop for poor farmers in the semi-arid tropical regions of India and West Africa. The worst disease of pearl millet is downy mildew caused by pseudo-fungal pathogen ( Sclerospora graminicola ). In this study a new pearl millet mapping population was developed from a resistant (IP 18293) x susceptible (Tift 238D1) cross. The downy mildew resistance segregation pattern of F2:F4 progenies from cross (IP 18293 x Tift 238 D1) was studied against six Indian (Patancheru, Jalna, Jamnagar, Jodhpur, Durgapura and New Delhi) and two African pathogen populations (Niger and Mali).
A skeleton linkage map with a length of 561.8 cM has been constructed and identified seven different QTLs controlling resistance to downy mildew, against six Indian and two African pathogen population
Pearl millet dwarfing genes d1 and d2 along with the purple foliage colour P loci were mapped in the new linkage map from (IP 18239 x Tift 238D1)-based cross ( J. Hered. 94: 155-159 )
Involved in Marker-Assisted Selection of downy mildew resistance to improve the elite hybrid parental line PT 732B based on the QTL information from the cross PT 732B x P 1449-2
Research Associate (at TNAU, India)
Worked as a Research Associate in Department of Millets, Center for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, under the scheme of âÃÂÃÂPromotion of Research and Developmental efforts in hybrids in selected crop- Pearl milletâÃÂàfor the period of nearly one year with the following projects. (From 04.09.1997 to 30.08.1998)
1. Evaluation of All India Co-ordinated Pearl millet Improvement Programme/ICRISAT materials for utilization in breeding program.
2. Conservation and utilization of genetics resources in pearl millet breeding program.
3. Production and yearly maintenance of nucleus and breeder seeds in pearl millet and seed distribution.
4. Development of pollinators with good combining ability and resistance to downy mildew / stress in pearl millet.
5. Development of early maturing pearl millet hybrids suited to rain-fed and irrigated situation.
Post Graduation- M.Sc (Agri) - Plant Breeding and Genetics
Postgraduate program in Agriculture specialized in Plant Breeding and Genetics was done during 1994-96 with the thesis the topic of âÃÂÃÂMorphological and molecular characterization of cytosteriles in pearl millet ( Pennisetum glaucum [L.] R. Br)âÃÂÃÂ.
From the ninety hybrids, best parents with high gca effects and the best crosses were identified for exploiting the individual characters.
Correlation studies showed that grain yield having positive correlation with panicle girth. Similarly path analysis showed panicle growth having maximum direct effect on yield followed by plant height and number of productive tillers.
The comparison of diverse cytoplasmic hybrids showed that 732A cytoplasmic hybrids found to be highly variable in fertility restoration (sterile, fertile, partial fertile) when compared to A2 and A1 cytoplasmic hybrids.
Developmental variation in another protein and isozyme expression (Peroxidase and Esterase) was observed in both male sterile and fertile line. Esterase isozyme banding pattern showed variation between diverse cytoplasms, which will help for the differentiation of cytoplasm.
Anther protein study differentiated cytoplasmic male sterile lines by appearance of 18 KD and 53 KD proteins.
Developmental anatomy of pearl millet anthers showed that there is considerable developmental variation observed between male sterile and fertile lines in tapetal layers. Breakdown occurs after tetrad stage of microspore development.
