Indian Agricultural Statistics Research Institute

About: Indian Agricultural Statistics Research Institute is a facility organization based out in New Delhi, India. It is known for research contribution in the topics: Population & Small area estimation. The organization has 454 authors who have published 870 publications receiving 7987 citations.

Unravelling the epigenomic interactions between parental inbreds resulting in an altered hybrid methylome in pigeonpea.

Abstract: DNA methylation is an important heritable landmark conferring epigenetic changes in hybrids and has fascinated biologists and plant-breeders over the years. Although epigenetic changes have been documented in rice and maize hybrids, such investigations have not been reported in pigeonpea. Here, we report genome-wide methylation profiles of pigeonpea sterile and fertile inbred lines and their fertile F1 hybrid at single base resolution. We found that pigeonpea genome is relatively enriched in CG methylation. Identification of differentially methylated regions (DMRs) in the sterile and fertile parent revealed remarkable differences between their methylation patterns. Investigation of methylation status of parental DMRs in hybrid revealed non-additive methylation patterns resulting from trans-chromosomal methylation and trans-chromosomal demethylation events. Furthermore, we discovered several DMRs negatively associated with gene expression in the hybrid and fertile parent. Interestingly, many of those DMRs belonged to transposable elements and genes encoding pentatricopeptide repeats associated proteins, which may mediate a role in modulating the genes impacting pollen fertility. Overall, our findings provide an understanding of two parental epigenomes interacting to give rise to an altered methylome in pigeonpea hybrids, from genome-wide point of view.

Simple sequence repeats (SSRs) markers in fish genomic research and their acceleration via next-generation sequencing and computational approaches

Abstract: Simple sequence repeats (SSRs) are becoming a choice of markers in fish genetic research due to their abundance in the genome, co-dominant nature, high polymorphism and ability to reproduce. Thus, in this review, we have discussed regarding SSRs markers developed in fishes using different techniques. These markers have been used for revealing genetic variability, strain and species identification, genetic linkage map construction and parentage assignment in fish genetic research. Recently, high-throughput sequencing platform has been widely used in non-model fishes for genome/transcriptome sequencing to understand genomic information. The rapid progress in fish genomic research has been made due to sequencing platform along with their low cost for sequencing and use of the advanced computational tools for generated data analysis. We have shown that different next-generation sequencing platforms have been applied in the genomic studies for SSRs markers identification in fishes with evidence. We have depicted the use of various computational tools/algorithms for the SSRs identification from genome/transcriptome data. However, we also highlighted existing challenges in high-throughput sequencing data analysis as well as the current need of computationally deep analysis software/tools/expertise. The purpose of this review is to get envisage on the various possibilities, which can be harnessed via these new technologies and advanced computational tools for SSRs marker development via genome/transcriptome sequencing of aquaculture species.

Long non-coding RNA ZFAS1 is a major regulator of epithelial-mesenchymal transition through miR-200/ZEB1/E-cadherin, vimentin signaling in colon adenocarcinoma.

Abstract: Colon adenocarcinoma is a common cause of cancer-related deaths worldwide. Epithelial-mesenchymal transition is a major regulator of cancer metastasis, and increased understanding of this process is essential to improve patient outcomes. Long non-coding RNA (lncRNA) are important regulators of carcinogenesis. To identify lncRNAs associated with colon carcinogenesis, we performed an exploratory differential gene expression analysis comparing paired colon adenocarcinoma and normal colon epithelium using an RNA-sequencing data set. This analysis identified lncRNA ZFAS1 as significantly increased in colon cancer compared to normal colon epithelium. This finding was validated in an institutional cohort using laser capture microdissection. ZFAS1 was also found to be principally located in the cellular cytoplasm. ZFAS1 knockdown was associated with decreased cellular proliferation, migration, and invasion in two colon cancer cell lines (HT29 and SW480). MicroRNA-200b and microRNA-200c (miR-200b and miR-200c) are experimentally validated targets of ZFAS1, and this interaction was confirmed using reciprocal gene knockdown. ZFAS1 knockdown regulated ZEB1 gene expression and downstream targets E-cadherin and vimentin. Knockdown of miR-200b or miR-200c reversed the effect of ZFAS1 knockdown in the ZEB1/E-cadherin, vimentin signaling cascade, and the effects of cellular migration and invasion, but not cellular proliferation. ZFAS1 knockdown was also associated with decreased tumor growth in an in vivo mouse model. These results demonstrate the critical importance of ZFAS1 as a regulator of the miR-200/ZEB1/E-cadherin, vimentin signaling cascade.

The Halophile protein database.

Abstract: Halophilic archaea/bacteria adapt to different salt concentration, namely extreme, moderate and low. These type of adaptations may occur as a result of modification of protein structure and other changes in different cell organelles. Thus proteins may play an important role in the adaptation of halophilic archaea/bacteria to saline conditions. The Halophile protein database (HProtDB) is a systematic attempt to document the biochemical and biophysical properties of proteins from halophilic archaea/bacteria which may be involved in adaptation of these organisms to saline conditions. In this database, various physicochemical properties such as molecular weight, theoretical pI, amino acid composition, atomic composition, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (Gravy) have been listed. These physicochemical properties play an important role in identifying the protein structure, bonding pattern and function of the specific proteins. This database is comprehensive, manually curated, non-redundant catalogue of proteins. The database currently contains 59 897 proteins properties extracted from 21 different strains of halophilic archaea/bacteria. The database can be accessed through link. Database URL: http://webapp.cabgrid.res.in/protein/

Soil quality indices in a conservation agriculture based rice-mustard cropping system in North-western Indo-Gangetic Plains.

Abstract: The systematic research on the effect of medium-term conservation agriculture (CA) on soil quality, especially under the rice (Oryza sativa L.)-based cropping systems is limited. Hence, the specific objective of the study was to develop soil quality indices with key soil physical, chemical and biological indicators under the conservation and conventional tillage practices in a rice–mustard [Brassica juncea (L.) Czern.] cropping system. Eight treatment combinations including tillage and crop establishment, crop residue and cropping system intensification with inclusion of short duration summer mungbean [Vigna radiata (L.) Wilczek] were adopted in rice - mustard cropping system in hot semi-arid, sub-tropical north-western Indo-Gangetic Plains agro-ecoregion of India. Soil samples collected from topsoil (0−5 cm) and 5−15 cm soil layer were analyzed for 15 physical, chemical and biological properties to develop unified soil quality index (SQI) through principal component analysis (PCA). The highest SQI was obtained in the zero till direct seeded rice (ZTDSR) – zero till mustard (ZTM) –ZT summer mungbean (ZTSMB (+R) (mungbean residue in ZTDSR - rice residue in ZTM- mustard residue in ZTSMB) treatment followed by the ZTDSR + BM (brown manuring) – ZTM (+R) (mustard residue in ZTDSR with BM – rice residue in ZTM). The lowest SQI was obtained in transplanted puddled rice (TPR) - conventional till mustard (CTM) for both soil layers. The identified key indicators for SQI in this Inceptisol were saturated hydraulic conductivity (Ks), pH, total N, available P, and available K. Besides, the plots under ZTDSR – ZTM – ZTSMB (+R) resulted in 14 % higher total organic C in topsoil and 28 % higher aggregate stability than the TPR - CTM plots. This ZTDSR – ZTM -ZTSMB (+R) treatment had 65 % higher surface soil microbial biomass C than the TPR – CTM treatment. The ZTDSR – ZTM -ZTSMB (+R) treatment also led to higher Ks, which was in the order of triple ZT > double ZT > ZT > conventional tillage. Thus, the medium-term CA with triple or double zero tillage with crop residue retention could lead to maintain agricultural sustainability under rice-mustard system. Hence, it may be recommended to the farmers for adoption.