Search

Balancing selection is the process of selection that preserves various alleles within a population. Studying the areas undergoing balancing selection is essential, because it preserves genetic diversity in a population. Finding genes that exhibit signs of balancing selection during the domestication of cattle is the goal of this study. To identify regions where polymorphism has persisted in the cattle population for millions of years, we examined the genome of cattle. In this study, we used bovine SNP 50 k data to conduct a detailed genome-wide assessment of selection signatures for balancing selection. We have included the genotyped data from 427 animals, including five taurines, two crossbreds, and eight Indian cattle breeds. For this study, we employed Tajima's D approach to identify signature regions undergoing balancing selection. Using the NCBI database, PANTHER 17.0, and CattleQTL database, the annotation was carried out after finding the relevant areas under balancing selection. The number of genomic regions undergoing balancing selection in Ayrshire, Brown-Swiss, Frieswal, Gir, Guernsey, Hariana, Holstein Friesian, Jersey, Kankrej, Nelore, Ongole, Red Sindhi, Sahiwal, Tharparkar, and Vrindavani was 11, 13, 13, 19, 18, 11, 17, 14, 14, 12, 10, 12, 13, 13, and 11, respectively. We have observed multiple immune system-related genes going through balancing selection, including KIT, NFATC2, GBP4, LRRC32, SYT7, RAG1, RAG2, LOC513659, and ZBTB17. In our study, we found that the majority of the immune-related genes and a few genes associated with growth, reproduction, production, and adaptation are undergoing balancing selection. [ABSTRACT FROM AUTHOR]

Mammalian X and Y chromosomes independently evolved from various autosomes approximately 300 million years ago (MYA). To fully understand the relationship between genomic composition and phenotypic diversity arising due to the course of evolution, we have scanned regions of selection signatures on the X chromosome in different cattle breeds. In this study, we have prepared the datasets of 184 individuals of different cattle breeds and explored the complete X chromosome by utilizing four within-population and two between-population methods. There were 23, 25, 30, 17, 17, and 12 outlier regions identified in Tajima's D, CLR, iHS, ROH, FST, and XP-EHH. Bioinformatics analysis showed that these regions harbor important candidate genes like AKAP4 for reproduction in Brown Swiss, MBTS2 for production traits in Brown Swiss and Guernsey, CXCR3 and CITED1 for health traits in Jersey and Nelore, and BMX and CD40LG for regulation of X chromosome inactivation in Nelore and Gir. We identified genes shared among multiple methods, such as TRNAC-GCA and IL1RAPL1, which appeared in Tajima's D, ROH, and iHS analyses. The gene TRNAW-CCA was found in ROH, CLR and iHS analyses. The X chromosome exhibits a distinctive interaction between demographic factors and genetic variations, and these findings may provide new insight into the X-linked selection in different cattle breeds. [ABSTRACT FROM AUTHOR]

Half a century ago, a seminal article on the hitchhiking effect by Smith and Haigh inaugurated the concept of the selection signature. Selective sweeps are characterised by the rapid spread of an advantageous genetic variant through a population and hence play an important role in shaping evolution and research on genetic diversity. The process by which a beneficial allele arises and becomes fixed in a population, leading to a increase in the frequency of other linked alleles, is known as genetic hitchhiking or genetic draft. Kimura's neutral theory and hitchhiking theory are complementary, with Kimura's neutral evolution as the 'null model' and positive selection as the 'signal'. Both are widely accepted in evolution, especially with genomics enabling precise measurements. Significant advances in genomic technologies, such as next‐generation sequencing, high‐density SNP arrays and powerful bioinformatics tools, have made it possible to systematically investigate selection signatures in a variety of species. Although the history of selection signatures is relatively recent, progress has been made in the last two decades, owing to the increasing availability of large‐scale genomic data and the development of computational methods. In this review, we embark on a journey through the history of research on selective sweeps, ranging from early theoretical work to recent empirical studies that utilise genomic data. [ABSTRACT FROM AUTHOR]

The field of genetics has evolved a lot after the emergence of molecular and advanced genomic technologies. The advent of Next Generation Sequencing, SNP genotyping platforms and simultaneous reduction in the cost of sequencing had opened the door to genomic research in farm animals. There are various applications of genomics in livestock, such as the use of genomic data: (i) to investigate genetic diversity and breed composition/population structure (ii) to identify genetic variants and QTLs related to economically important and ecological traits, genome-wide association studies (GWAS) and genomic signatures of selection; (iii) to enhance breeding programs by genomic selection. Compared to traditional methods, genomic selection is expected to improve selection response by increasing selection accuracy and reducing the generation interval due to early selection. Genomic selection (GS) in developed countries has led to rapid genetic gains, especially in dairy cattle, due to a well-established genetic evaluation system. Indian livestock system is still lagging behind developed nations in adopting these technologies. This review discusses the current status, challenges, and future perspectives of livestock genomics in India. [ABSTRACT FROM AUTHOR]

The process of building a model or copy of a real-world system and assessing its behaviour under various scenarios is referred to as simulation. Simulation in population genetics is the process of simulating a population's genetic makeup and evolutionary history using mathematical models and computer algorithms. It is important in population genetics for a better understanding of the impact of various evolutionary and demographic scenarios on sequence variation and patterns, it allows investigators to better assess and design analytical methods in the study of disease-associated genetic factors. This is an important tool for studying population genetic diversity and how natural selection, genetic drift, mutation, migration, and other evolutionary forces have influenced the genetic makeup of the population. There are three fundamental frameworks for simulation: coalescent, forward, and resampling methods. Numerous simulators that fit under these frameworks can be compared in terms of their evolutionary and demographic scenarios, computing complexity, and particular applications. Population simulation is becoming increasingly important in evolutionary biology, enabling researchers to explore the effects of various genetic models on genetic diversity and DNA sequence patterns. [ABSTRACT FROM AUTHOR]

Copy number variations (CNVs) are major forms of genetic variation with an increasing importance in animal genomics. This study used the Illumina BovineSNP 50 K BeadChip to detect the genome-wide CNVs in the Tharparkar cattle. With the aid of PennCNV software, we noticed a total of 447 copy number variation regions (CNVRs) across the autosomal genome, occupying nearly 2.17% of the bovine genome. The average size of detected CNVRs was found to be 122.2 kb, the smallest CNVR being 50.02 kb in size, to the largest being 1,232.87 Kb. Enrichment analyses of the genes in these CNVRs gave significant associations with molecular adaptation-related Gene Ontology (GO) terms. Most CNVR genes were significantly enriched for specific biological functions; signaling pathways, sensory responses to stimuli, and various cellular processes. In addition, QTL analysis of CNVRs described them to be linked with economically essential traits in cattle. The findings here provide crucial information for constructing a more comprehensive CNVR map for the indigenous cattle genome. [ABSTRACT FROM AUTHOR]

The present broad range of sheep phenotypic variation is the consequence of selection for various production characteristics such as wool, milk, meat, and natural adaptability to diverse situations. In the current study, the genomic data of 79 animals from three Indian sheep breeds (Changthangi, Deccani, and Garole) were explored to decipher regions under positive selection for various productive traits using various statistical tools. We found 61, 102 regions using Tajima's D, CLR and 58, 38, and 71 regions using FST, FLK, and hapFLK, respectively, under selective sweep. Significant candidate genes related to various important traits, such as KLHL for fibre diameter and the OMA1 gene for feed-induced thermogenesis in Changthangi, were identified. In addition, the SYCP2 and NAPAS3 genes were found to be associated with seasonal reproductivity, and BMPR1B for fertilization capacity in Garole. In a previous study, the HSPA6 gene (Garole) was found to be associated with thermo-tolerance in the Angus sheep breed. The outcomes discussed here provide a basis for detecting selective sweeps that underlie genetic variations of traits that have functional importance. [ABSTRACT FROM AUTHOR]

Knowledge about genetic diversity is very essential for the management and sustainable utilization of livestock genetic resources. In this study, we presented a comprehensive genome-wide analysis of genetic diversity, ROH, inbreeding, linkage disequilibrium, effective population size and haplotype block structure in Tharparkar cattle of India. A total of 24 Tharparkar animals used in this study were genotyped with Illumina BovineSNP50 array. After quality control, 22,825 biallelic SNPs were retained, which were in HWE, MAF > 0.05 and genotyping rate >90%. The overall mean observed (HO) and expected heterozygosity (HE) were 0.339 ± 0.156 and 0.325 ± 0.129, respectively. The average minor allele frequency was 0.234 with a standard deviation of ± 0.131. We identified a total of 1832 ROH segments and the highest autosomal coverage of 13.87% was observed on chromosome 23. The genomic inbreeding coefficients estimates by FROH, FHOM, FGRM and FUNI were 0.0589, 0.0215, 0.0532 and 0.0160 respectively. The overall mean linkage disequilibrium (LD) for a total of 133,532 pairwise SNPs measured by D' and r2 was 0.6452 and 0.1339, respectively. In addition, we observed a gradual decline in effective population size over the past generations. [ABSTRACT FROM AUTHOR]

The analysis of genetic diversity is very essential to understand the evolution and adaptability of livestock species to different environmental conditions. Genetic variation is the raw material for selection and foundation for breed improvement programmes. The use of high throughput molecular marker technologies, advanced statistical and software tools have revolutionized the precision of animal genetic diversity analysis in a large number of populations with limited time and resources. SNP genotyping is one of the best methods to study genetic variation due to its abundance in livestock species, stability and cost-effectiveness. In this review, some of the most popularly used diversity analysis software programs in livestock genomics are discussed briefly. Microsatellite-based software such as Genepop, Fstat, Genetix, TFPGA, Stackpack, Arlequin and other multipurpose software such as PLINK, PowerMarker, TASSEL, BEAGLE, R software packages (GenABEL, SNPassoc, snpstats, SNP relate), Gemma, SNP Express, SVS, etc. can be utilized for diversity analysis. [ABSTRACT FROM AUTHOR]

• The review covers livestock genomics of South Asian cattle, buffalo, sheep, goat, pig, camel, horse, yak, mithun, and poultry. • Advancements in next-generation sequencing (NGS) technologies led to the discovery of numerous SNP arrays for different livestock species. • The application of genomics in animal breeding has had the biggest economic impact on livestock production. Livestock plays a central role in sustaining human livelihood in South Asia. There are numerous and distinct livestock species in South Asian countries. Several of them have experienced genetic development in recent years due to the application of genomic technologies and effective breeding programs. This review discusses genomic studies on cattle, buffalo, sheep, goat, pig, horse, camel, yak, mithun, and poultry. The frontiers covered in this review are genetic diversity, admixture studies, selection signature research, QTL discovery, genome-wide association studies (GWAS), and genomic selection. The review concludes with recommendations for South Asian livestock systems to increasingly leverage genomic technologies, based on the lessons learned from the numerous case studies. This paper aims to present a comprehensive analysis of the dichotomy in the South Asian livestock sector and argues that a realistic approach to genomics in livestock can ensure long-term genetic advancements. [ABSTRACT FROM AUTHOR]

• We merged extracted datasets of 11 cattle breeds with our own generated Tharparkar genotypic data to obtain a final dataset of 284 animals. • The PCA indicates the partitioning between Exotic and Indigenous cattle breeds on the two PC axis. • We used several statistical tools (eight) to find out and verify more genomic footprints. • More number of short ROHs in Tharparkar shows a more historical relationship. • Combined analysis of all the methods may provide refined information about selective sweep regions in different methods. • We extracted out various candidate genes associated with economically important traits. In the present study, the population genomic data of different cattle breeds were explored to decipher the genomic regions affected due to selective events and reflected in the productive, reproductive, thermo-tolerance, and health-related traits. To find out these genomic deviations due to selective sweeps, we used eight different statistical tools (Tajima's D, Fu & Li's D*, CLR, ROH, iHS, F ST , FLK, and hapFLK) on seven indigenous and five exotic cattle breeds. We further performed composite analysis by comparing their covariance matrix. Several candidate genes were found to be related to milk production (ADARB, WDR70, and CA8), reproductive (PARN, FAM134B2, and ZBTB20), and health-related traits (SP110, CXCL2, CLXCL3 , CXCL5 , IRF8, and MYOM1). The outcome of this investigation provides a basis for detecting selective sweeps that explain the genetic variation of traits. They may possess functional importance for multiple cattle breeds in different subcontinents. However, further studies are required to improve the findings using high-density arrays or whole-genome sequencing with higher resolution and greater sample sizes. [ABSTRACT FROM AUTHOR]

• The review highlights the potential applications of genomic techniques in conservation purposes as well as discusses few case studies regarding the applications of conservation genomics in livestock and wildlife species. • Advancements in next-generation sequencing (NGS) technologies has generated a massive amount of data that is more fine-scaled and accurate and has thus resulted in more and more species becoming "genome enabled" • The conservation genetics-based "one gene, many individuals" strategy has given way to a conservation genomics-based "few individuals, several genes" approach. Due to environmental change and anthropogenic activities, global biodiversity has suffered an unprecedented loss, and the world is now heading toward the sixth mass extinction event. This urges the need to step up our efforts to promote the sustainable use of animal genetic resources and plan effective strategies for their conservation. Although habitat preservation and restoration are the primary means of conserving biodiversity, genomic technologies offer a variety of novel tools for identifying biodiversity hotspots and thus, support conservation efforts. Conservation genomics is a broad area of science that encompasses the application of genomic data from thousands or tens of thousands of genome-wide markers to address important conservation biology concerns. Genomic approaches have revolutionized the way we understand and manage animal populations, providing tools to identify and preserve unique genetic variants and alleles responsible for adaptive genetic variation, reducing the deleterious consequences of inbreeding, and increasing the adaptive potential of threatened species. The advancement of genomic technologies, particularly comparative genomic approaches, and the increased accessibility of genomic resources in the form of genome-enabled taxa for non-model organisms, provides a distinct advantage in defining conservation units over traditional genetics approaches. The objective of this review is to provide an exhaustive overview of the concept of conservation genomics, discuss the rationale behind the transition from conservation genetics to genomic approaches, and emphasize the potential applications of genomic techniques for conservation purposes. We also highlight interesting case studies in both livestock and wildlife species where genomic techniques have been used to accomplish conservation goals. Finally, we address some challenges and future perspectives in this field. [ABSTRACT FROM AUTHOR]