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In the present study, Porcine 60K SNP genotype data from 69 Landlly pigs were used to explore Copy Number Variations (CNVs) across the autosomes. A total of 386 CNVs were identified using Hidden Markov Model (HMM) in PennCNV software, which were subsequently aggregated to 115 CNV regions (CNVRs). Among the total detected CNVRs, 58 gain, 49 were loss type while remaining 8 events were both gain and loss types. Identified CNVRs covered 12.5 Mb (0.55%) of Sus scrofa reference 11.1 genome. Comparison of our results with previous investigations on pigs revealed that approximately 75% CNVRs were novel, which may be due to differences in genetic background, environment and implementation of artificial selection in Landlly pigs. Functional annotation and pathway analysis showed the significant enrichment of 267 well-annotated Sus scrofa genes in CNVRs. These genes were involved in different biological functions like sensory perception, meat quality traits, back fat thickness and immunity. Additionally, KIT and FUT1 were two major genes detected on CNVR in our population. This investigation provided a comprehensive overview of CNV distribution in the Indian porcine genome for the first time, which may be useful for further investigating the association of important quantitative traits in Landlly pigs. 115 CNVRs were identified in 69 Landlly pig population. Approximately 75% detected CNVRs were novel for Landlly population. Significant enrichment of 267 well-annotated Sus scrofa genes observed in these CNVRs. These genes were involved in different biological functions like sensory perception, meat quality traits, back fat thickness and immunity. Comprehensive CNV map in the Indian porcine genome developed for the first time. [ABSTRACT FROM AUTHOR]

Keywords: Correlation; heritability; maternal; model; trait; variance; ; ; ; ; ; EN Correlation heritability maternal model trait variance ZH 7948 7955 8 11/21/22 20221220 NES 221220 Introduction Livestock rearing plays a major part in ensuring nutritional security of masses in developing countries (Randolph et al. [14]). Similarly, Wang et al. ([21]) reported moderate heritability (0.40) for fiber diameter and low heritability estimate (0.19) for staple length at yearling stage in Inner Mongolia White Cashmere goats. In concurrence to our study, Di et al. ([4]) reported moderate direct additive heritability estimate of 0.22 for yearling fiber diameter in Chinese superfine Merino sheep on fitting multi-trait animal model. Higher heritability estimates, when compared to the present study, have been reported by Hanford, Van Vleck, and Snowder ([9]) in Rambouillet sheep and Jafari and Hashemi ([10]) in Makuie sheep. [Extracted from the article]

The present study was undertaken to identify the microRNAs (miRNAs) expressed in the mammary tissue of a bubaline heifer. Small RNAs were isolated from the mammary gland tissue and enriched for miRNA fraction. The linker-ligated small RNAs were reverse transcribed to synthesize cDNA and amplified by PCR. The PCR products were ligated to the pGEM-T Easy vector; cloned into DH5 alpha cells and sequenced. Sequencing of 40 clones, randomly chosen from this library, produced 115 concatemerized short sequences. The short sequences were checked for their matches with the help of refseq_rna database, EST database (NCBI) and Ensembl. The analysis was performed for more than 90% identity with miRNAs across different species in miRBase. Alignment of putative small RNA sequences with the bovine genome was attempted in GenBank (NCBI) and Ensembl using BLAST. The small RNA sequences with a partial matches within the bovine genome and/or with flanking sequences (upstream or downstream) were analyzed for hairpin structures using the Mfold web server. Reverse complements were also assessed for the homology search. miRNA sequences showing only a partial match with already reported sequences were considered as a putative bubaline miRNAs. Six developmentally important putative miRNA precursors were identified from this study using cloning and sequencing followed by the Bioinformatics approach. This study will help in the elucidation of pathways involving miRNAs in bubaline species at the heifer stage. [ABSTRACT FROM AUTHOR]

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The improvement in imputation accuracy diminished across different methods of selecting SNPs with increased panel density. 5 O'Brien, A.C., Judge, M.M., Fair, S. & Berry, D.P. (2019) High imputation accuracy from informative low-to-medium density single nucleotide polymorphism genotypes is achievable in sheep1. Genomic technologies have not penetrated enough in livestock, especially in developing nations where animals from a particular breed/population cannot be concurrently genotyped mainly due to financial constraints. [Extracted from the article]

In the present study, to analyze the genomic ROH fragments, haplotypes, inbreeding coefficient and effective population size (Ne), SNP50K data of 72 Vrindavani crossbred cattle strain were obtained. After a quality check, 24,449 biallelic SNPs were retained, which were in HWE, MAF > 0.01 and genotyping rate >95%. A total of 385 ROH were found, and chromosome 25 was mostly covered with 50.86%, while chromosome one was least with 12.42%. We classified ROH into <10Mb, 10-15Mb, 15-20Mb, >20Mb categories and observed a 3% inbreeding coefficient for the population in >20Mb category. Inbreeding from an excess of homozygosity was found to be 6% in the population. Ne was also estimated through Ne Estimator and SNeP and in the recent generation, it was found to be 40 for a census size of 464 cattle. The Ne/Nc ratio was found to be 0.086 and a decreasing trend of Ne was observed for over five generations. 45.95% of the autosomal genome was covered with haplotypic structure with highest total block length in chromosome one and lowest in 28. From all the observations made in this study, it can be concluded that Vrindavani is an admixed cattle strain but have an unstable population structure in the current period. [ABSTRACT FROM AUTHOR]

Biological rhythmicity plays a critical role in the pathophysiology and overall survival of an organism. Period (Per), cryptochrome (Cry), Bmal1 and CLOCK are four important gene families that affect the circadian rhythms to considerable level. However, our understanding regarding the genetic basis of biological rhythmicity is still in its infancy. Biological rhythms are generated through underlying gene expression which is regulated by various control systems. The finely regulated gene expression modulates biological rhythms through various molecular and cell-signaling pathways (metabolic state, endocrine activity and neural excitability). Epigenetics through modifications of histone tags, chromatin remodeling, non-coding RNAs and other mechanisms plays an important role as regulators of gene expression controlling biological rhythmicity in the animal kingdom. MicroRNAs like miR328, miR383, miR192/194, miR122, miRNA-219 and miRNA-132 are some of the noteworthy miRNAs reported to be functionally related to circadian rhythmicity controlling various biological events. Besides miRNAs, histone modification enzyme systems, RNA binding proteins and sirtuins form important ways to regulate the expression of genes related to biological clock in living organisms. In this review, we have made an attempt to understand the epigenetic basis of biological rhythmicity in mammalian organisms and analyze the progress made to date. [ABSTRACT FROM AUTHOR]