Selection signatures for fiber production in commercial species: A review

Single cell RNA-seq: a novel tool to unravel virus-host interplay

Over the last decade, single cell RNA sequencing (scRNA-seq) technology has caught the momentum of being a vital revolutionary tool to unfold cellular heterogeneity by high resolution assessment. It evades the inadequacies of conventional sequencing technology which was able to detect only average expression level among cell populations. In the era of twenty-first century, several epidemic and pandemic viruses have emerged. Being an intracellular entity, viruses totally rely on host. Complex virus-host dynamics result when the virus tend to obtain factors from host cell required for its replication and establishment of infection. As a prevailing tool, scRNA-seq is able to understand virus-host interplay by comprehensive transcriptome profiling. Because of technological and methodological advancement, this technology is capable to recognize viral genome and host cell response heterogeneity. Further development in analytical methods with multiomics approach and increased availability of accessible scRNA-seq datasets will improve the understanding of viral pathogenesis that can be helpful for development of novel antiviral therapeutic strategies.

Dissecting the genomic regions of selection on the X chromosome in different cattle breeds

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.

Relevance of pharmacogenetics and pharmacogenomics in veterinary clinical practice: A review

The recent advances in high-throughput next-generation sequencing technologies have heralded the arrival of the Big Data era. As a result, the use of pharmacogenetics in drug discovery and individualized drug therapy has transformed the field of precision medicine. This paradigm shift in drug development programs has effectively reshaped the old drug development practices, which were primarily concerned with the physiological status of patients for drug development. Pharmacogenomics bridges the gap between pharmacodynamics and pharmacokinetics, advancing current diagnostic and treatment strategies and enabling personalized and targeted drug therapy. The primary goals of pharmacogenetic studies are to improve drug efficacy and minimize toxicities, to identify novel drug targets, to estimate drug dosage for personalized medicine, and to incorporate it as a routine diagnostic for disease susceptibility. Although pharmacogenetics has numerous applications in individualized drug therapy and drug development, it is in its infancy in veterinary medicine. The objective of this review is to present an overview of historical landmarks, current developments in various animal species, challenges and future perspectives of genomics in drug development and dosage optimization for individualized medicine in veterinary subjects.

Whole-Genome Resequencing Reveals Genetic Diversity and Wool Trait-Related Genes in Liangshan Semi-Fine-Wool Sheep

Understanding the genetic makeup of local sheep breeds is essential for their scientific conservation and sustainable utilization. The Liangshan semi-fine-wool sheep (LSS), a Chinese semi-fine-wool breed renowned for its soft wool, was analyzed using whole-genome sequencing data including 35 LSS, 84 sheep from other domestic breeds, and 20 Asiatic mouflons. We investigated the genetic composition of LSS by conducting analyses of the population structure, runs of homozygosity, genomic inbreeding coefficients, and selection signature. Our findings indicated that LSS shares greater genetic similarity with Border Leicester and Romney sheep than with Tibetan (TIB), Yunnan (YNS), and Chinese Merino sheep. Genomic analysis indicated low to moderate inbreeding coefficients, ranging from 0.014 to 0.154. In identifying selection signals across the LSS genome, we pinpointed 195 candidate regions housing 74 annotated genes (e.g., IRF2BP2, BVES, and ALOX5). We also found the overlaps between the candidate regions and several known quantitative trait loci related to wool traits, such as the wool staple length and wool fiber diameter. A selective sweep region, marked by the highest value of cross-population extended haplotype homozygosity, encompassed IRF2BP2-an influential candidate gene affecting fleece fiber traits. Furthermore, notable differences in genotype frequency at a mutation site (c.1051 + 46T > C, Chr25: 6,784,190 bp) within IRF2BP2 were observed between LSS and TIB and YNS sheep (Fisher's exact test, p < 2.2 × 10-16). Taken together, these findings offer insights crucial for the conservation and breeding enhancement of LSS.

Deciphering climate resilience in Indian cattle breeds by selection signature analyses

The signature of selection is a crucial concept in evolutionary biology that refers to the pattern of genetic variation which arises in a population due to natural selection. In the context of climate adaptation, the signature of selection can reveal the genetic basis of adaptive traits that enable organisms to survive and thrive in changing environmental conditions. Breeds living in diverse agroecological zones exhibit genetic "footprints" within their genomes that mirror the influence of climate-induced selective pressures, subsequently impacting phenotypic variance. It is assumed that the genomes of animals residing in these regions have been altered through selection for various climatic adaptations. These regions are known as signatures of selection and can be identified using various summary statistics. We examined genotypic data from eight different cattle breeds (Gir, Hariana, Kankrej, Nelore, Ongole, Red Sindhi, Sahiwal, and Tharparkar) that are adapted to diverse regional climates. To identify selection signature regions in this investigation, we used four intra-population statistics: Tajima's D, CLR, iHS, and ROH. In this study, we utilized Bovine 50 K chip data and four genome scan techniques to assess the genetic regions of positive selection for high-temperature adaptation. We have also performed a genome-wide investigation of genetic diversity, inbreeding, and effective population size in our target dataset. We identified potential regions for selection that are likely to be caused by adverse climatic conditions. We observed many adaptation genes in several potential selection signature areas. These include genes like HSPB2, HSPB3, HSP20, HSP90AB1, HSF4, HSPA1B, CLPB, GAP43, MITF, and MCHR1 which have been reported in the cattle populations that live in varied climatic regions. The findings demonstrated that genes involved in disease resistance and thermotolerance were subjected to intense selection. The findings have implications for marker-assisted breeding, understanding the genetic landscape of climate-induced adaptation, putting breeding and conservation programs into action.

Comprehensive selection signature analyses in dairy cattle exploiting purebred and crossbred genomic data

The main objective of the current research was to locate, annotate, and highlight specific areas of the bovine genome that are undergoing intense positive selection. Here, we are analyzing selection signatures in crossbred (Bos taurus X Bos indicus), taurine (Bos taurus), and indicine (Bos indicus) cattle breeds. Indicine cattle breeds found throughout India are known for their higher heat tolerance and disease resilience. More breeds and more methods can provide a better understanding of the selection signature. So, we have worked on nine distinct cattle breeds utilizing seven different summary statistics, which is a fairly extensive approach. In this study, we carried out a thorough genome-wide investigation of selection signatures using bovine 50K SNP data. We have included the genotyped data of two taurine, two crossbreds, and five indicine cattle breeds, for a total of 320 animals. During the 1950s, these indicine (cebuine) cattle breeds were exported with the aim of enhancing the resilience of taurine breeds in Western countries. For this study, we employed seven summary statistics, including intra-population, i.e., Tajima's D, CLR, iHS, and ROH and inter-population statistics, i.e., FST, XP-EHH, and Rsb. The NCBI database, PANTHER 17.0, and CattleQTL database were used for annotation after finding the important areas under selection. Some genes, including EPHA6, CTNNA2, NPFFR2, HS6ST3, NPR3, KCNIP4, LIPK, SDCBP, CYP7A1, NSMAF, UBXN2B, UGDH, UBE2K, and DAB1, were shown to be shared by three or more different approaches. Therefore, it gives evidence of the most intense selection in these areas. These genes are mostly linked to milk production and adaptability traits. This study also reveals selection regions that contain genes which are crucial to numerous biological functions, including those associated with milk production, coat color, glucose metabolism, oxidative stress response, immunity and circadian rhythms.

Landmarks in the history of selective sweeps

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.

Genomic insights into the conservation of wild and domestic animal diversity: A review

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.

Genome-wide analysis emancipates genomic diversity and signature of selection in Altay white-headed cattle of Xinjiang, China

Altay white-headed cattle have not received enough attention for several reasons. Due to irrational breeding and selection practices, the number of pure Altay white-headed cattle has decreased significantly and the breed is now on the eve of extinction. The genomic characterization will be a crucial step towards understanding the genetic basis of productivity and adaptability to survival under native Chinese agropastoral systems; nevertheless, no attempt has been made in Altay white-headed cattle. In the current study, we compared the genomes of 20 Altay white-headed cattle to the genomes of 144 individuals in representative breeds. Population genetic diversity revealed that the nucleotide diversity of Altay white-headed cattle was less than that of indicine breeds and comparable to that of Chinese taurus cattle. Using population structure analysis, we also found that Altay white-headed cattle carried the ancestry of the European and East Asian cattle lineage. In addition, we used three different methods (FST, θπ ratio and XP-EHH) to investigate the adaptability and white-headed phenotype of Altay white-headed cattle and compared it with Bohai black cattle. We found EPB41L5, SCG5 and KIT genes on the list of the top one percent genes, these genes might have an association with environmental adaptability and the white-headed phenotype for this breed. Our research reveals the distinctive genomic features of Altay white-headed cattle at the genome-wide level.