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Research activities

I. Marker-assisted breeding

I. Marker-Assisted Breeding
I. a. Marker-Assisted Breeding for Abiotic Stress Resistance-Drought tolerant rice
Promising drought tolerant rice cultures viz., CPMB ACM 04 004, CPMB ACM 04 006 and PM 01 011, PM 03 002 and RM 04 001 were developed through marker aided selection (MAS) and farmers participatory plant breeding approach in the Department of Plant Molecular Biology and Biotechnology, CPMB with the help of Department of Plant Breeding and Genetics, AC&RI, Madurai, ARS, Paramakudi and CSRC, Ramnad. Among these drought tolerant rice lines, PM 01 011 performed better over years and across locations. It recorded an average grain yield of 3891 kg/ha, which is 14.40 per cent increased yield over the ruling check variety PMK (R) 3 (3401 kg/ha) and is accepted for release as location specific variety for Ramnad and Sivagangai districts during the year 2008. This culture is being proposed for release during 2009.
Highlights of PMK(R) 4 (PM 01 011)
Higher productivity of 3 .6 t/ha.
Drought tolerant.
Semi dwarf, erect, non-lodging.
Short duration (100 - 105 days) which is a week earlier than PMK ( R )
Suitable for September – October sowing (North East Monsoon) in rainfed rice areas of Ramanathapuram and Sivagangai districts.
Long slender white rice with high head rice recovery (62.1 %)

I. b. Marker-Assisted Breeding for Biotic Stress Resistance
I. b. i. Brown plant hopper resistance in rice
IR 50 and Ratu Heenati were identified as susceptible and resistant parents respectively to develop a mapping population to map the QTLs associated with BPH resistance. Bulked Segregant Analysis was performed in the F3 generation to identify the SSR markers linked to BPH resistance. BSA revealed the association of two SSR markers (on chromosome 3) namely RM 168 and RM 186 with BPH resistance. To identify the QTLs and validate the markers already identified, the population has been forwarded to F7 generation by following SDS method. A recombinant inbred line CB (MAS) 20001 isolated from the mapping population developed for mapping the genes controlling WBPH resistance was recommended for Initial Varietal Trial-Irrigated-Mid Early (IVT-IME).

The details of grain yield of CB (MAS) 20001 are furnished below.
Name of the trial: IVT-IME
Name of the entry: IET-19893
Designation: CB (MAS) 20001
Cross combination: IR50 x Rathu Heenathi
Special features: High yielding, tolerant to WBPH
Further phenotyping and genotyping of the F7 population is in progress.

I. b. ii. Bacterial leaf blight resistance in rice
Evolving high yielding rice genotypes with durable resistance to bacterial leaf blight (BLB) is pertinent considering the extensive damage caused by the disease in most of the rice growing regions. Two high yielding BLB susceptible indica rice cultivars, ADT43 and ASD16 popular among farmers and consumers across South India have been introgressed with three BLB resistance genes xa5, xa13 and Xa21 from isoline IRBB60 using functional markers. The F2 populations of 500 plants from ADT43 x IRBB60 and 806 plants from ASD16 x IRBB60 crosses were screened for the presence of all the three resistance genes. Thirty genotypes with three genes in homozygous and 55 genotypes with two genes in homozygous and one gene in heterozygous condition were identified. These pyramided genotypes with two or three resistance genes exhibited high levels of resistance against two predominant Xanthomonas oryzae isolates of South India. Among the 30 pyramided genotypes (xa5 + xa13 + Xa21), 17 were found to be high yielding with desirable agronomic characteristics and the selection efficiency of the present markers was hundred percent.

I. c. Marker-Assisted breeding for nutritional improvement.
I. c. i. Development of Low Phytate maize

The indigestibility of the primary phosphate reserves in seeds (mostly in the form of phytate) has major nutritional, environmental and economic consequences and the phytic acid problem has attracted substantial interest in animal feed research in maize. Evaluation of germplasm and identification of promising low phytate maize lines can be used to develop a variety/hybrid suitable for poultry industry.

In order to achieve the above objective, a total of 431maize inbreds lines were screened for total P and Phytate P content which resulted in the identification of low phyate maize inbreds viz, UMI 82 ( 2.487 mg/g), UMI 9 ( 2.919 mg/g), UMI 202 ( 2.073 mg/g) UMI 8 ( 2.197 mg/g) and UMI 16 ( 2.269).
Mapping population development has been initiated using the low and high phytate inbred lines. Twenty SSR markers linked to the lpa1 and lpa2 (UMC 1395) region were checked in the inbreds and shows polymorphism and are found suitable for the linkage studies.

II. Bioinformatics
I. PrebZIP: A computational tool to identify bZIP transcription factor in eukaryotes
The basic Leucine zipper (bZIP) protein comprises a family of transcription factors involved in regulating growth, development and environmental stresses in plants and animals. The bZIP transcription factor consists of two structural components namely the basic DNA binding domain and the Leucine zipper. We utilized a simple pattern matching algorithm based on regular expression together with our novel Scoring algorithm to identify the two structural components of bZIP. Our new algorithm performs better than the systems based on Hidden Markov Models (HMM). Accordingly we present PrebZIP, a Java based application to predict the bZIP transcription factor in a given amino acid sequence with a higher degree of accuracy.

II. Differential expression analysis of genes corresponding to well characterized drought QTL's in rice
Gene microarrays contain powerful datasets for studying the changes in gene expression. Gene expression profiling provides a novel way to understand the expression pattern of the gene. It provides greater insight into their expression level under varied experimental level. In this project, we analyzed the drought responsive genes in rice using the published microarray data available in public repositories like Gene Expression Omnibus (GEO). Of the genome wide expression data, only a fraction contains significantly differentially expressed genes (DEG's). DEGs of a drought stress responsive consensus rice QTL falling between 139.9cM - 143.7cM on chromosome was analyzed.

III. Comparative codon usage analysis tool
An important constraint in the development of transgenic crop is achieving a desired level of transgene expression. Codon usage bias is one important factor governing the expression of transgene in the given host. Analyzing synonymous codon usages between the transgene and the host will help in understanding the set in codon bias between them. The same when compared will give a measure of the similarities and differences in codon usage bias shared by transgene and the host. In the present study we worked out the codon usages for indica and japonica genomes based on RSCU and Relative adaptiveness. RSCU (Relative Synonymous Codon Usage) which was the simple measure of non-uniform usage of synonymous codons in a coding sequence. Further the relative adaptiveness was computed. Besides, a list of optimal codons (29 for indica and 28 for japonica) which was already known from an earlier investigation were used to compare codon usage bias between rice (indica and japonica) with that of a query sequence which is presumed to be the transgene.

IV. Establishment of MilletDB: TNAU released Millet varieties with their morphological traits
Millets are small seeded - annual grasses. They grow well, under the marginal conditions of soil fertility and moisture, which provide staple food for millions of people. Millets have strong, deep rooting systems and short life cycles. Breeding research in millets, habitually engages different species, cultivars, and varieties. This makes an immense challenge to maintain the different varieties and their identification characters. On account of this fact, the MilletDB clearly brings out the variations of different morphological traits of the TNAU released varieties. MilletDB is an Internet-accessible database, which is designed by using the front-end language PHP and back-end as MySQL and is equipped with extensive search options. It is a user-friendly database and made publicly available, to improve the research and development of millet crops by making the wealth of available millet varieties.