Identification of important genomic footprints using eight different selection signature statistics in domestic cattle breeds

Genome-wide selection signatures address trait specific candidate genes in cattle indigenous to arid regions of India

The peculiarity of Indian cattle lies in milk quality, resistance to diseases and stressors as well as adaptability. The investigation addressed selection signatures in Gir and Tharparkar cattle, belonging to arid ecotypes of India. Double digest restriction-site associated DNA sequencing (ddRAD-seq) yielded nearly 26 million high-quality reads from unrelated seven Gir and seven Tharparkar cows. In all, 19,127 high-quality SNPs were processed for selection signature analysis. An approach involving within-population composite likelihood ratio (CLR) statistics and between-population FST statistics was used to capture selection signatures within and between the breeds, respectively. A total of 191 selection signatures were addressed using CLR and FST approaches. Selection signatures overlapping 86 and 73 genes were detected as Gir- and Tharparkar-specific, respectively. Notably, genes related to production (CACNA1D, GHRHR), reproduction (ESR1, RBMS3), immunity (NOSTRIN, IL12B) and adaptation (ADAM22, ASL) were annotated to selection signatures. Gene pathway analysis revealed genes in insulin/IGF pathway for milk production, gonadotropin releasing hormone pathway for reproduction, Wnt signalling pathway and chemokine and cytokine signalling pathway for adaptation. This is the first study where selection signatures are identified using ddRAD-seq in indicine cattle breeds. The study shall help in conservation and leveraging genetic improvements in Gir and Tharparkar cattle.

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.

Association of three single nucleotide polymorphisms in the LPIN1 gene with milk production traits in cows of the Yaroslavl breed

Lipin-1 is a member of the evolutionarily conserved family of proteins and is expressed predominantly in adipose tissue and skeletal muscle. On the one hand, lipin-1 is an enzyme that catalyzes the dephosphorylation of phosphatidic acid to diacylglycerol (DAG) and thus participates in the metabolic pathways of biosynthesis of storage lipids in the cell, membrane phospholipids, and intracellular signaling molecules. On the other hand, lipin-1 is able to be transported from the cytoplasm to the nucleus and is a coactivator of lipid metabolism gene transcription. It was shown, using the analysis of single nucleotide polymorphism (SNP) associations, that the lipin-1 coding gene (LPIN1) is a promising candidate gene for milk production traits in Holstein and Brown Swiss cows. However, it is unclear how much of its effect depends on the breed. The Yaroslavl dairy cattle breed was created in the 18-19 centuries in Russia by breeding northern Great Russian cattle, which were short and poor productive, but well adapted to local climatic conditions and bad food base. It was shown by whole genome genotyping and sequencing that the Yaroslavl breed has unique genetics compared to Russian and other cattle breeds. The aim of the study was to assess the frequency of alleles and genotypes of three SNPs in the LPIN1 gene and to study the association of these SNPs with milk production traits in Yaroslavl cows. Blood samples from 142 cows of the Yaroslavl breed were obtained from two farms in the Yaroslavl region. Genotyping of SNPs was carried out by polymerase chain reaction-restriction fragment length polymorphism method. Associations of SNPs with 305-day milk yield, fat yield, fat percentages, protein yield, and protein percentages were studied from the first to the fourth lactation. Statistical tests were carried out using a mixed linear model, taking into account the relationship between individuals. We identified three SNPs - rs110871255, rs207681322 and rs109039955 with a frequency of a rare allele of 0.042-0.261 in Yaroslavl cows. SNP rs110871255 was associated with fat yield during the third and fourth lactations. SNP rs207681322 was associated with milk yield for the second, third and fourth lactations, as well as protein yield for the third lactation. Thus, we identified significant associations of SNPs rs207681322 and rs110871255 in the LPIN1 gene with a number of milk production traits during several lactations in Yaroslavl cows.

Unique footprints of balancing selection in bovine genome

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.

Genomics and conservation: Guidance from training to analyses and applications

Environmental change is intensifying the biodiversity crisis and threatening species across the tree of life. Conservation genomics can help inform conservation actions and slow biodiversity loss. However, more training, appropriate use of novel genomic methods and communication with managers are needed. Here, we review practical guidance to improve applied conservation genomics. We share insights aimed at ensuring effectiveness of conservation actions around three themes: (1) improving pedagogy and training in conservation genomics including for online global audiences, (2) conducting rigorous population genomic analyses properly considering theory, marker types and data interpretation and (3) facilitating communication and collaboration between managers and researchers. We aim to update students and professionals and expand their conservation toolkit with genomic principles and recent approaches for conserving and managing biodiversity. The biodiversity crisis is a global problem and, as such, requires international involvement, training, collaboration and frequent reviews of the literature and workshops as we do here.

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.

Detection of genome-wide copy number variation in Murrah buffaloes

Riverine Buffaloes, especially the Murrah breed because of their adaptability to harsh climatic conditions, is farmed in many countries to convert low-quality feed into valuable dairy products and meat. Here, we investigated the copy number variations (CNVs) in 296 Murrah buffalo using the Axiom® Buffalo Genotyping Array 90K (Affymetrix, Santa Clara, CA, USA). The CNVs were detected on the autosomes, using the Copy Number Analysis Module (CNAM) using the univariate analysis. 7937 CNVs were detected in 279 Buffaloes, the average length of the CNVs was 119,048.87 bp that ranged between 7800 and 4,561,030 bp. These CNVs were accounting for 10.33% of the buffalo genome, which was comparable to cattle, sheep, and goat CNV analyses. Further, CNVs were merged and 1541 CNVRs were detected using the Bedtools-mergeBed command. 485 genes were annotated within 196 CNVRs that were identified in at least 10 animals of Murrah population. Out of these, 40 CNVRs contained 59 different genes that were associated with 69 different traits. Overall, the study identified a significant number of CNVs and CNVRs in the Murrah breed of buffalo, with a wide range of lengths and frequencies across the autosomes. The identified CNVRs contained genes associated with important traits related to production and reproduction, making them potentially important targets for future breeding and genetic improvement efforts.

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.

Study on lactation performance and development of KASP marker for milk traits in Xinjiang donkey (Equus asinus)

Donkey milk has high nutritional and medicinal value, but there are few researches in donkey milk traits, especially on genome. The whole lactation of 89 donkeys was recorded and it was found that Xinjiang donkey had good lactation performance while great differences among individuals. In our previous study, four genes including LGALS2, NUMB, ADCY8 and CA8 were identified as milk-associated with Chinese Kazakh house, based on Equine 670k Chip genomic analysis. And then 15 SNPs of the four key genes were conducted for genotyping in Xinjiang donkey in this study, one of Chinese indigenous breed, 14 SNPs were successful classified. And those SNPs were correlation analysis with milk yield of Xinjiang donkeys. The results showed that NUMB g.46709914T > G was significantly correlated with daily milk yield of Xinjiang donkey in the early, middle, and late periods, while ADCY8 g.48366302T > C, CA8 g.89567442T > G and CA8 g.89598328T > A were significantly correlated with lactation in the late periods. These results indicate that NUMB g.46709914T > G can be as markers of candidate genes for lactating traits in donkeys, SNPs of ADCY8 and CA8 as potential. Our findings will not only help confirm key genes for donkey milk traits, but also provide future for genomic selection in donkeys.

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.

Evidence for selective sweeps in the MHC gene repertoire of various cattle breeds

Major Histocompatibility Complex (MHC) genes are among the immune genes that have been extensively studied in vertebrates and are necessary for adaptive immunity. In the immunological response to infectious diseases, they play several significant roles. This research paper provides the selection signatures in the MHC region of the bovine genome as well as how certain genes related to innate immunity are undergoing a positive selective sweep. Here, we investigated signatures of historical selection on MHC genes in 15 different cattle populations and a total of 427 individuals. To identify the selection signatures, we have used three separate summary statistics. The findings show potential selection signatures in cattle from whom we isolated genes involved in the MHC. The most significant regions related to the bovine MHC are BOLA, non-classical MHC class I antigen (BOLA-NC1), Microneme protein 1 (MIC1) , Cluster of Differentiation 244 (CD244), Gap Junction Alpha-5 Protein (GJA5). It will be possible to gain new insight into immune system evolution by understanding the distinctive characteristics of MHC in cattle.

Signatures of selection in riverine buffalo populations revealed by genome-wide SNP data

The detection of selection signatures assists in understanding domestication, evolution, and the identification of genomic regions related to adaptation and production traits in buffaloes. The emergence of high-throughput technologies like Next Generation Sequencing and SNP genotyping had expanded our ability to detect these signatures of selection. In this study, we sought to identify signatures of selection in five buffalo populations (Brazilian Murrah, Bulgarian Murrah, Indian Murrah, Nili-Ravi, and Kundi) using Axiom Buffalo 90 K Genotyping Array data. Using seven different methodologies (Tajima's D, CLR, ROH, iHS, FST, FLK and hapFLK), we identified selection signatures in 374 genomic regions, spanning a total of 381 genes and 350 quantitative trait loci (QTLs). Among these, several candidate genes were associated with QTLs for milk production, reproduction, growth and carcass traits. The genes and QTLs reported in this study provide insight into selection signals shaping the genome of buffalo breeds. Our findings can aid in further genomic association studies, genomic prediction, and the implementation of breeding programmes in Indian buffaloes.

Genome-wide screening for selection signatures in native and cosmopolitan cattle breeds reared in Türkiye

Via long-term natural and artificial selection pressure, homozygosity may extend across the genome, leaving genomic patterns called selection signatures. This study is the first attempt to assess genome-wide selection signatures in six native Turkish and two cosmopolitan cattle breeds by 211.119 bi-allelic SNPs recovered using the double digest restriction associated DNA sequencing method. The integrated haplotype score (iHS) statistic was utilised to reveal selection signatures within populations, whereas the cross-population extended haplotype homozygosity (XP-EHH) and fixation index (FST ) approaches were preferred to reveal differently fixed genomic regions between native Turkish and cosmopolitan cattle breeds. Selection signatures in 142 genomic regions containing 305 genes were detected within eight cattle breeds by iHS statistics. The XP-EHH and FST approaches revealed that 197 and 114 SNPs were under selection pressure, respectively, which overlapped with 144 and 190 genes, respectively. A total of 18 genes were detected by at least two approaches. Six genes related to disease resistance (TTP2), meat yield (DIAPH3 and METTL21C), meat quality (ZNF24 and ZNF397) and first calving interval (ZSCAN30) turned out to be differently fixed between native Turkish and cosmopolitan cattle breeds, as they were identified by both XP-EHH and FST approaches. In addition, the iHS approach revealed that eight genes associated with visual modality (LSGN), olfaction (MOXD2, OR4C1F and OR4C1F), and immune response (TRBV3-1 and CLDN10) were under selection pressure in both native and cosmopolitan cattle breeds. Owing to their being significantly related to survival traits, these regions may have played a key role in cattle genome evolution. Future studies utilising denser genetic data are required to obtain deeper knowledge on effects of natural and artificial selection in Anatolian cattle breeds. © 2023 Stichting International Foundation for Animal Genetics.

Uncovering genes underlying coat color variation in indigenous cattle breeds through genome-wide positive selection

The identification of candidate genes related to pigmentation and under selective sweep provides insights into the genetic basis of pigmentation and the evolutionary forces that have shaped this variation. The selective sweep events in the genes responsible for normal coat color in Indian cattle groups are still unknown. To find coat color genes displaying signs of selective sweeps in the indigenous cattle, we compiled a list of candidate genes previously investigated for their association with coat color and pigmentation. After that, we performed a genome-wide scan of positive selection signatures using the BovineSNP50K Bead Chip in 187 individuals of seven indigenous breeds. We applied a wide range of methods to find evidence of selection, such as Tajima's D, CLR, iHS, varLD, ROH, and FST. We found a total of sixteen genes under selective sweep, that were involved in coat color and pigmentation physiology. These genes are CRIM1 in Gir, MC1R in Sahiwal, MYO5A, PMEL and POMC in Tharparkar, TYRP1, ERBB2, and ASIP in Red Sindhi, MITF, LOC789175, PAX3 and TYR in Ongole, and IRF2, SDR165 and, KIT in Nelore, ADAMTS19 in Hariana. These genes are related to melanin synthesis, the biology of melanocytes and melanosomes, and the migration and survival of melanocytes during development.

Progress and future perspectives of livestock genomics in India: a mini review

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.

Candidate genes associated with heat stress and breeding strategies to relieve its effects in dairy cattle: a deeper insight into the genetic architecture and immune response to heat stress

The need for food products of animal origin is increasing worldwide. Satisfying these needs in a way that has minimal impact on the environment requires cutting-edge technologies and techniques to enhance the genetic quality of cattle. Heat stress (HS), in particular, is affecting dairy cattle with increasing frequency and severity. As future climatic challenges become more evident, identifying dairy cows that are more tolerant to HS will be important for breeding dairy herds that are better adapted to future environmental conditions and for supporting the sustainability of dairy farming. While research into the genetics of HS in the context of the effect of global warming on dairy cattle is gaining momentum, the specific genomic regions involved in heat tolerance are still not well documented. Advances in omics information, QTL mapping, transcriptome profiling and genome-wide association studies (GWAS) have identified genomic regions and variants associated with tolerance to HS. Such studies could provide deeper insights into the genetic basis for response to HS and make an important contribution to future breeding for heat tolerance, which will help to offset the adverse effects of HS in dairy cattle. Overall, there is a great interest in identifying candidate genes and the proportion of genetic variation associated with heat tolerance in dairy cattle, and this area of research is currently very active worldwide. This review provides comprehensive information pertaining to some of the notable recent studies on the genetic architecture of HS in dairy cattle, with particular emphasis on the identified candidate genes associated with heat tolerance in dairy cattle. Since effective breeding programs require optimal knowledge of the impaired immunity and associated health complications caused by HS, the underlying mechanisms by which HS modulates the immune response and renders animals susceptible to various health disorders are explained. In addition, future breeding strategies to relieve HS in dairy cattle and improve their welfare while maintaining milk production are discussed.

Exploring genome-wide differentiation and signatures of selection in Italian and North American Holstein populations

Among Italian dairy cattle, the Holstein is the most reared breed for the production of Parmigiano Reggiano protected designation of origin cheese, which represents one of the most renowned products in the entire Italian dairy industry. In this work, we used a medium-density genome-wide data set consisting of 79,464 imputed SNPs to study the genetic structure of Italian Holstein breed, including the population reared in the area of Parmigiano Reggiano cheese production, and assessing its distinctiveness from the North American population. Multidimensional scaling and ADMIXTURE approaches were used to explore the genetic structure among populations. We also investigated putative genomic regions under selection among these 3 populations by combining 4 different statistical methods based either on allele frequencies (single marker and window-based) or extended haplotype homozygosity (EHH; standardized log-ratio of integrated EHH and cross-population EHH). The genetic structure results allowed us to clearly distinguish the 3 Holstein populations; however, the most remarkable difference was observed between Italian and North American stock. Selection signature analyses identified several significant SNPs falling within or closer to genes with known roles in several traits such as milk quality, resistance to disease, and fertility. In particular, a total of 22 genes related to milk production have been identified using the 2 allele frequency approaches. Among these, a convergent signal has been found in the VPS8 gene which resulted to be involved in milk traits, whereas other genes (CYP7B1, KSR2, C4A, LIPE, DCDC1, GPR20, and ST3GAL1) resulted to be associated with quantitative trait loci related to milk yield and composition in terms of fat and protein percentage. In contrast, a total of 7 genomic regions were identified combining the results of standardized log-ratio of integrated EHH and cross-population EHH. In these regions candidate genes for milk traits were also identified. Moreover, this was also confirmed by the enrichment analyses in which we found that the majority of the significantly enriched quantitative trait loci were linked to milk traits, whereas the gene ontology and pathway enrichment analysis pointed to molecular functions and biological processes involved in AA transmembrane transport and methane metabolism pathway. This study provides information on the genetic structure of the examined populations, showing that they are distinguishable from each other. Furthermore, the selection signature analyses can be considered as a starting point for future studies in the identification of causal mutations and consequent implementation of more practical application.

Genetic diversity and signatures of selection in four indigenous horse breeds of Iran

Indigenous Iranian horse breeds were evolutionarily affected by natural and artificial selection in distinct phylogeographic clades, which shaped their genomes in several unique ways. The aims of this study were to evaluate the genetic diversity and genomewide selection signatures in four indigenous Iranian horse breeds. We evaluated 169 horses from Caspian (n = 21), Turkmen (n = 29), Kurdish (n = 67), and Persian Arabian (n = 52) populations, using genomewide genotyping data. The contemporary effective population sizes were 59, 98, 102, and 113 for Turkmen, Caspian, Persian Arabian, and Kurdish breeds, respectively. By analysis of the population genetic structure, we classified the north breeds (Caspian and Turkmen) and west/southwest breeds (Persian Arabian and Kurdish) into two phylogeographic clades reflecting their geographic origin. Using the de-correlated composite of multiple selection signal statistics based on pairwise comparisons, we detected a different number of significant SNPs under putative selection from 13 to 28 for the six pairwise comparisons (FDR < 0.05). The identified SNPs under putative selection coincided with genes previously associated with known QTLs for morphological, adaptation, and fitness traits. Our results showed HMGA2 and LLPH as strong candidate genes for height variation between Caspian horses with a small size and the other studied breeds with a medium size. Using the results of studies on human height retrieved from the GWAS catalog, we suggested 38 new putative candidate genes under selection. These results provide a genomewide map of selection signatures in the studied breeds, which represent valuable information for formulating genetic conservation and improved breeding strategies for the breeds.

Comparative genomic analysis uncovers candidate genes related with milk production and adaptive traits in goat breeds

During the process of animal domestication, both natural and artificial selection cause variation in allele frequencies among populations. Identifying genomic areas of selection in domestic animals may aid in the detection of genomic areas linked to ecological and economic traits. We studied genomic variation in 140 worldwide goat individuals, including 75 Asian, 30 African and 35 European goats. We further carried out comparative population genomics to detect genomic regions under selection for adaptability to harsh conditions in local Asian ecotypes and also milk production traits in European commercial breeds. In addition, we estimated the genetic distances among 140 goat individuals. The results showed that among all studied goat groups, local breeds from West and South Asia emerged as an independent group. Our search for selection signatures in local goats from West and South Asia revealed candidate genes related to adaptation to hot climate (HSPB6, HSF4, VPS13A and NBEA genes) and immune response (IL7, IL5, IL23A and LRFN5) traits. Furthermore, selection signatures in European commercial goats involved several milk production related genes, such as VPS13C, NCAM2, TMPRSS15, CSN3 and ABCG2. The identified candidate genes could be the fundamental genetic resource for enhancement of goat production and environmental-adaptive traits, and as such they should be used in goat breeding programs to select more efficient breeds.

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.

Genomic diversity and signals of selection processes in wild and farm-reared red-legged partridges (Alectoris rufa)

The genetic dynamics of wild populations with releases of farm-reared reinforcements are very complex. These releases can endanger wild populations through genetic swamping or by displacing them. We assessed the genomic differences between wild and farm-reared red-legged partridges (Alectoris rufa) and described differential selection signals between both populations. We sequenced the whole genome of 30 wild and 30 farm-reared partridges. Both partridges had similar nucleotide diversity (π). Farm-reared partridges had a more negative Tajima's D and more and longer regions of extended haplotype homozygosity than wild partridges. We observed higher inbreeding coefficients (F_IS and F_ROH) in wild partridges. Selective sweeps (Rsb) were enriched with genes that contribute to the reproductive, skin and feather colouring, and behavioural differences between wild and farm-reared partridges. The analysis of genomic diversity should inform future decisions for the preservation of wild populations.

Genome-wide search reveals the uniqueness of DNA regions associated with coat color and innate immunity in Hokkaido Native Horse

Hokkaido Native Horse (HKD) is a horse breed native to Hokkaido in Japan known for the traits such as coat color with no white spots and adaptability to the local cold climate. To examine whether those traits of HKD are conferred at the DNA level, we attempted to identify fixed DNA regions in HKD individuals, that is, the selection signatures of HKD. A comparison of genome-wide single nucleotide polymorphism genotypes in 58 HKD individuals by principal component analysis, and cluster analysis between breeds, including HKD, and within the HKD individuals indicated the genetic independence of HKD as a breed. Tajima's D analysis and runs of homozygosity analysis identified 23 selection signatures unique to HKD (P < 0.05), and following database search found 20 traits that were associated with those selection signatures; among these traits, coat color traits, face and body markings, showed the highest important value (0.50 and 0.46). Enrichment analysis of genes in the selection signatures identified six gene ontology terms (P < 0.05), and a term related to innate immunity (regulation of defense response; GO:0031347) showed the highest positive fold enrichment value (7.13). These results provide the first scientific evidence of a genetic basis for the traits of HKD.

Genome-wide analysis identified candidate variants and genes associated with heat stress adaptation in Egyptian sheep breeds

Heat stress caused by climatic changes is one of the most significant stresses on livestock in hot and dry areas. It has particularly adverse effects on the ability of the breed to maintain homeothermy. Developing countries are advised to protect and prepare their animal resources in the face of potential threats such as climate change. The current study was conducted in Egypt’s three hot and dry agro-ecological zones. Three local sheep breeds (Saidi, Wahati, and Barki) were studied with a total of 206 ewes. The animals were exercised under natural heat stress. The heat tolerance index of the animals was calculated to identify animals with high and low heat tolerance based on their response to meteorological and physiological parameters. Genomic variation in these breeds was assessed using 64,756 single nucleotide polymorphic markers (SNPs). From the perspective of comparative adaptability to harsh conditions, our objective was to investigate the genomic structure that might control the adaptability of local sheep breeds to environmental stress under hot and dry conditions. In addition, indices of population structure and diversity of local breeds were examined. Measures of genetic diversity showed a significant influence of breed and location on populations. The standardized index of association (rbarD) ranged from 0.0012 (Dakhla) to 0.026 (Assuit), while for the breed, they ranged from 0.004 (Wahati) to 0.0103 (Saidi). The index of association analysis (I^a) ranged from 1.42 (Dakhla) to 35.88 (Assuit) by location and from 6.58 (Wahati) to 15.36 (Saidi) by breed. The most significant SNPs associated with heat tolerance were found in the MYO5A, PRKG1, GSTCD, and RTN1 genes (p ≤ 0.0001). MYO5A produces a protein widely distributed in the melanin-producing neural crest of the skin. Genetic association between genetic and phenotypic variations showed that OAR1_18300122.1, located in ST3GAL3, had the greatest positive effect on heat tolerance. Genome-wide association analysis identified SNPs associated with heat tolerance in the PLCB1, STEAP3, KSR2, UNC13C, PEBP4, and GPAT2 genes.

Trajectory of livestock genomics in South Asia: A comprehensive review

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.