Molecular Characterization of TGF-Beta Gene Family in Buffalo to Identify Gene Duplication and Functional Mutations.

The TGF-ß superfamily is ubiquitously distributed from invertebrates to vertebrates with diverse cellular functioning such as cell adhesion, motility, proliferation, apoptosis, and differentiation. The present study aimed to characterize the TGF-ß gene superfamily in buffalo through evolutionary, structural, and single nucleotide polymorphism (SNPs) analyses to find the functional effect of SNPs in selected genes. We detected 32 TGF-ß genes in buffalo genome and all TGF-ß proteins exhibited basic nature except INHA, INHBC, MSTN, BMP10, and GDF2, which showed acidic properties. According to aliphatic index, TGF-ß proteins were thermostable but unstable in nature. Except for GDF1 and AMH, TGF-ß proteins depicted hydrophilic nature. Moreover, all the detected buffalo TGF-ß genes showed evolutionary conserved nature. We also identified eight segmental and one tandem duplication event TGF-ß gene family in buffalo, and the ratio of Ka/Ks demonstrated that all the duplicated gene pairs were under selective pressure. Comparative amino acid analysis demonstrated higher variation in buffalo TGF-ß gene family, as a total of 160 amino acid variations in all the buffalo TGF-ß proteins were detected. Mutation analysis revealed that 13 mutations had an overall damaging effect that might have functional consequences on buffalo growth, folliculogenesis, or embryogenesis.

Genome-wide investigation and functional analysis of RNA editing sites in wheat.

Wheat is an important cereal and half of the world population consumed it. Wheat faces environmental stresses and different techniques (CRISPR, gene silencing, GWAS, etc.) were used to enhance its production but RNA editing (RESs) is not fully explored in wheat. RNA editing has a special role in controlling environmental stresses. The genome-wide identification and functional characterization of RESs in different types of wheat genotypes was done. We employed six wheat genotypes by RNA-seq analyses to achieve RESs. The findings revealed that RNA editing events occurred on all chromosomes equally. RNA editing sites were distributed randomly and 10-12 types of RESs were detected in wheat genotypes. Higher number of RESs were detected in drought-tolerant genotypes. A-to-I RNA editing (2952, 2977, 1916, 2576, 3422, and 3459) sites were also identified in six wheat genotypes. Most of the genes were found to be engaged in molecular processes after a Gene Ontology analysis. PPR (pentatricopeptide repeat), OZ1 (organelle zinc-finger), and MORF/RIP gene expression levels in wheat were also examined. Normal growth conditions diverge gene expression of these three different gene families, implying that normal growth conditions for various genotypes can modify RNA editing events and have an impact on gene expression levels. While the expression of PPR genes was not change. We used Variant Effect Predictor (VEP) to annotate RNA editing sites, and Local White had the highest RESs in the CDS region of the protein. These findings will be useful for prediction of RESs in other crops and will be helpful in drought tolerance development in wheat.