Ghanta Anuradha

Molecular Genetic Diversity of Major Indian Rice Cultivars over Decadal Periods

Genetic diversity in representative sets of high yielding varieties of rice released in India between 1970 and 2010 was studied at molecular level employing hypervariable microsatellite markers. Of 64 rice SSR primer pairs studied, 52 showed polymorphism, when screened in 100 rice genotypes. A total of 184 alleles was identified averaging 3.63 alleles per locus. Cluster analysis clearly grouped the 100 genotypes into their respective decadal periods i.e., 1970s, 1980s, 1990s and 2000s. The trend of diversity over the decadal periods estimated based on the number of alleles (Na), allelic richness (Rs), Nei’s genetic diversity index (He), observed heterozygosity (Ho) and polymorphism information content (PIC) revealed increase of diversity over the periods in year of releasewise and longevitywise classification of rice varieties. Analysis of molecular variance (AMOVA) suggested more variation in within the decadal periods than among the decades. Pairwise comparison of population differentiation (Fst) among decadal periods showed significant difference between all the pairs except a few. Analysis of trends of appearing and disappearing alleles over decadal periods showed an increase in the appearance of alleles and decrease in disappearance in both the categories of varieties. It was obvious from the present findings, that genetic diversity was progressively on the rise in the varieties released during the decadal periods, between 1970s and 2000s.

Identification of QTLs and possible candidate genes conferring sheath blight resistance in rice ( Oryza sativa L.)

Sheath blight, caused by the pathogenic fungus Rhizoctonia solani Kühn, is one of the most devastating diseases in rice. Breeders have always faced challenges in acquiring reliable and absolute resistance to this disease in existing rice germplasm. In this context, 40 rice germplasm including eight wild, four landraces, twenty- six cultivated and two advanced breeding lines were screened utilizing the colonized bits of typha. Except Tetep and ARC10531 which expressed moderate level of resistance to the disease, none could be found to be authentically resistant. In order to map the quantitative trait loci (QTLs) governing the sheath blight resistance, two mapping populations (F2 and BC1F2) were developed from the cross BPT-5204/ARC10531. Utilizing composite interval mapping analysis, 9 QTLs mapped to five different chromosomes were identified with phenotypic variance ranging from 8.40 to 21.76%. Two SSR markers namely RM336 and RM205 were found to be closely associated with the major QTLs qshb7.3 and qshb9.2 respectively and were attested as well in BC1F2 population by bulk segregant analysis approach. A hypothetical β 1–3 glucanase with other 31 candidate genes were identified in silico utilizing rice database RAP-DB within the identified QTL region qshb9.2. A detailed insight into these candidate genes will facilitate at molecular level the intricate nature of sheath blight, a step forward towards functional genomics.

Assessment of genetic diversity in sesame (Sesamum indicum L.) genotypes, using EST-derived SSR markers

A total of 16,619 ESTs sequences (SSRs) of sesame (Sesamum indicum L.) were mined from Genbank. From sequences, 156 primer pairs were designed and characterized to determine the diversity among 49 sesame accessions. Twenty SSRs were found to be polymorphic and the number of alleles ranged from two to five per locus. The allele size varied from 101 to 399 bp. The average PIC value of the 20 SSR loci was 0.72 ranging from 0.49 (SEM-12-68) to 0.90 (SEM-12-27). Dendrogram analysis grouped the 49 genotypes into five separate clusters exhibiting a genetic similarity coefficient from 0.59 to 1.0. Hence, these EST-derived SSRs markers could be useful in assessing the diversity of sesame accessions and could also help in identifying diverse parents for sesame improvement programs.

Molecular Mapping of QTLs for Yield and its Components under Two Water Supply Conditions in Rice (Oryza sativa L.)

Moisture stress is the major constraint to rice production and its stability in rainfed, mainly irrigated, and aerobic environments. Identification of genomic regions conferring tolerance to stress would improve our understanding of the genetics of stress response and result in the development of drought tolerant cultivars. In the present study, quantitative trait loci for drought response related traits and as well as grain yield were identified using a set of 140 recombinant inbred lines derived from a cross between the popular high-yielding variety, IR64 and the landrace, INRC10192. A total of 36 QTL were identified for grain yield and its components under control and stress conditions. Strikingly, a QTL cluster flanked by the markers RM38 and RM331 on chromosome 8 was found to be associated with grain yield, plant height, no. of productive tillers, chaffy grains, and spikelet fertility on secondary rachis and biomass under stress treatment. The genomic regions associated with these QTL under drought stress will be useful for the development of marker-based breeding for drought tolerant, high-yielding varieties suited to drought-prone areas.

Serine proteases-like genes in the asian rice gall midge show differential expression in compatible and incompatible interactions with rice.

The Asian rice gall midge, Orseolia oryzae (Wood-Mason), is a serious pest of rice. Investigations into the gall midge-rice interaction will unveil the underlying molecular mechanisms which, in turn, can be used as a tool to assist in developing suitable integrated pest management strategies. The insect gut is known to be involved in various physiological and biological processes including digestion, detoxification and interaction with the host. We have cloned and identified two genes, OoprotI and OoprotII, homologous to serine proteases with the conserved His87, Asp136 and Ser241 residues. OoProtI shared 52.26% identity with mosquito-type trypsin from Hessian fly whereas OoProtII showed 52.49% identity to complement component activated C1s from the Hessian fly. Quantitative real time PCR analysis revealed that both the genes were significantly upregulated in larvae feeding on resistant cultivar than in those feeding on susceptible cultivar. These results provide an opportunity to understand the gut physiology of the insect under compatible or incompatible interactions with the host. Phylogenetic analysis grouped these genes in the clade containing proteases of phytophagous insects away from hematophagous insects.

Genetic Variability, Genotype × Environment Interaction, Correlation, and GGE Biplot Analysis for Grain Iron and Zinc Concentration and Other Agronomic Traits in RIL Population of Sorghum (Sorghum bicolor L. Moench)

The low grain iron and zinc densities are well documented problems in food crops, affecting crop nutritional quality especially in cereals. Sorghum is a major source of energy and micronutrients for majority of population in Africa and central India. Understanding genetic variation, genotype × environment interaction and association between these traits is critical for development of improved cultivars with high iron and zinc. A total of 336 sorghum RILs (Recombinant Inbred Lines) were evaluated for grain iron and zinc concentration along with other agronomic traits for 2 years at three locations. The results showed that large variability exists in RIL population for both micronutrients (Iron = 10.8 to 76.4 mg kg−1 and Zinc = 10.2 to 58.7 mg kg−1, across environments) and agronomic traits. Genotype × environment interaction for both micronutrients (iron and zinc) was highly significant. GGE biplots comparison for grain iron and zinc showed greater variation across environments. The results also showed that G × E was substantial for grain iron and zinc, hence wider testing needed for taking care of G × E interaction to breed micronutrient rich sorghum lines. Iron and zinc concentration showed high significant positive correlation (across environment = 0.79; p < 0.01) indicating possibility of simultaneous effective selection for both the traits. The RIL population showed good variability and high heritabilities (>0.60, in individual environments) for Fe and Zn and other traits studied indicating its suitability to map QTL for iron and zinc.

Bulked Segregant Analysis to Detect Main Effect of QTL Associated withSheath Blight Resistance in BPT-5204/ARC10531 Rice (Oryza sativa L)

The population consisting of 210 F2:3 individuals from the cross between BPT-5204 (highly susceptible to sheath blight) and ARC-10531 a land race from Assam (moderately resistant to sheath blight) was analyzed to identify the markers associated with sheath blight resistance and to study any association of any morphological trait to disease incidence. The frequency distribution curve of F2:3 progenies for disease trait were continuous, indicating the polygenic control over the trait. The range of relative lesion height was 21-75% with a mean of 38.59%.No significant association between sheath blight disease and other morphological traits were detected in F2:3 populations. Parental polymorphisms were surveyed with 500 primer pairs of simple sequence repeats (SSR), revealed 70 polymorphic markers between the parents. In order to detect the major effect, QTL associated with sheath blight resistance, a strategy of combining the DNA pooling from selected segregants and genotyping was adopted. The association of putative markers identified based on DNA pooling from selected segregant was established by Single Marker Analysis (SMA).The results of SMA revealed that SSR markers, RM336 (chromosome#7) and RM205 (chromosome#9) showed significant association with sheath blight and accounted for 21.8% and 17.3% of total variation respectively. The results obtained from the DNA pooling of phenotypic extremes could be a useful strategy to detect the genetic loci with major effects of the complex trait such as disease resistance in rice.