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

A comprehensive review of livestock development: insights into domestication, phylogenetics, diversity, and genomic advances

Livestock plays an essential role in sustaining human livelihoods, offering a diverse range of species integral to food security, economic stability, and cultural traditions. The domestication of livestock, which began over 10,000 years ago, has driven significant genetic changes in species such as cattle, buffaloes, sheep, goats, and pigs. Recent advancements in genomic technologies, including next-generation sequencing (NGS), genome-wide association studies (GWAS), and genomic selection, have dramatically enhanced our understanding of these genetic developments. This review brings together key research on the domestication process, phylogenetics, genetic diversity, and selection signatures within major livestock species. It emphasizes the importance of admixture studies and evolutionary forces like natural selection, genetic drift, and gene flow in shaping livestock populations. Additionally, the integration of machine learning with genomic data offers new perspectives on the functional roles of genes in adaptation and evolution. By exploring these genomic advancements, this review provides insights into genetic variation and evolutionary processes that could inform future approaches to improving livestock management and adaptation to environmental challenges, including climate change.

The evolution of contemporary livestock species: Insights from mitochondrial genome

The domestication of animals marks a pivotal moment in human history, profoundly influencing our demographic and cultural progress. This process has led to significant genetic, behavioral, and physical changes in livestock species compared to their wild ancestors. Understanding the evolutionary history and genetic diversity of livestock species is crucial, and mitochondrial DNA (mtDNA) has emerged as a robust marker for investigating molecular diversity in animals. Its highly conserved gene content across animal species, minimal duplications, absence of introns, and short intergenic regions make mtDNA analysis ideal for such studies. Mitochondrial DNA analysis has uncovered distinct cattle domestication events dating back to 8000 years BC in Southwestern Asia. The sequencing of water buffalo mtDNA in 2004 provided important insights into their domestication history. Caprine mtDNA analysis identified three haplogroups, indicating varied maternal origins. Sheep, domesticated 12,000 years ago, exhibit diverse mtDNA lineages, suggesting multiple domestication events. Ovine mtDNA studies revealed clades A, B, C, and a fourth lineage, group D. The origins of domestic pigs were traced to separate European and Asian events followed by interbreeding. In camels, mtDNA elucidated the phylogeographic structure and genetic differentiation between wild and domesticated species. Horses, domesticated around 3500 BC, show significant mtDNA variability, highlighting their diverse origins. Yaks exhibit unique adaptations for high-altitude environments, with mtDNA analysis providing insights into their adaptation. Chicken mtDNA studies supported a monophyletic origin from Southeast Asia's red jungle fowl, with evidence of multiple origins. This review explores livestock evolution and diversity through mtDNA studies, focusing on cattle, water buffalo, goat, sheep, pig, camel, horse, yak and chicken. It highlights mtDNA's significance in unraveling maternal lineages, genetic diversity, and domestication histories, concluding with insights into its potential application in improving livestock production and reproduction dynamics.

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.

Genome-wide association study of genetic markers of coat color patterns in Sumatran native cattle

Background and Aim

Coat color is a phenotypic trait that is affected by many functional genes. In addition, coat color is an important characteristic of breeds in livestock. This study aimed to determine functional genes for coat color patterns in Sumatran native cattle in Indonesia using a genome-wide association study method.

Materials and Methods

A bovine single nucleotide polymorphism (SNP) 50K BeadChip was used for the investigation. A total of 46. Sumatran native cattle of three colors as follows: Brown (36 animals), white (9 animals), and black (1 animal), were used as experimental animals.

Results

Results showed that the SNP markers ARS-BFGL-NGS-75486 (p = 2.46 × 10-7) and BTB-01992588 (p = 1.06 × 10-5) were selected as two genetic markers for coat color variation in animals under study, which were located at the cytoplasmic FMR1-interacting protein 2 (CYFIP2) gene at BTA7 and small G protein signaling modulator 1(SGSM1) genes at BTA17, respectively. The polymorphic informative content values of both SNP markers were 0.33 (ARS-BFGL-NGS-75486) and 0.13 (BTB-01992588). In this study, a genetic marker for coat color patterns in Sumatran native cattle was obtained based on the haplotypes of both SNP markers.

Conclusion

It can be concluded that CYFIP2 and SGSM1 are two coloration genes that affect the phenotype characteristics of Sumatran native cattle.

Whole-genome resequencing reveals melanin deposition candidate genes of Luning chicken

BACKGROUND

Melanin in the black-bone chicken's body is considered the material basis for its medicinal effects and is an economically important trait. Therefore, improving the melanin content is a crucial focus in the breeding process of black-bone chickens. Luning chickens are black-bone chickens, with black beaks, skin, and meat. To investigate the genetic diversity and molecular mechanisms of melanin deposition in Luning chickens, we conducted whole-genome resequencing to analyze their breeding history and identify candidate genes influencing their black phenotype, along with transcriptome sequencing of dorsal skin tissues of male Luning chickens.

RESULTS

Population structure analysis revealed that Luning chickens tend to cluster independently and are closely related to Tibetan chickens. Runs of homozygosity analysis suggested potential inbreeding in the Luning chicken and Tibetan chicken population. By combining genetic differentiation index (Fst) and nucleotide diversity (θπ) ratios, we pinpointed selected regions associated with melanin deposition. Gene annotation identified 540 genes with the highest Fst value in LOC101750371 and LOC121108313, located on the 68.24-68.58 Mb interval of chromosome Z. Combining genomic and transcriptomic data, we identified ATP5E, EDN3, and LOC101750371 as candidate genes influencing skin color traits in black-bone chickens.

CONCLUSIONS

This study characterized the evolutionary history of Luning chickens and preliminarily excavated candidate genes influencing the genetic mechanism of pigmentation in black-bone chickens, providing valuable insights for the study of animal melanin deposition.

Genomic patterns of selection in morphometric traits across diverse Indian cattle breeds

This study seeks a comprehensive exploration of genome-wide selective processes impacting morphometric traits across diverse cattle breeds, utilizing an array of statistical methods. Morphometric traits, encompassing both qualitative and quantitative variables, play a pivotal role in characterizing and selecting livestock breeds based on their external appearance, size, and physical attributes. While qualitative traits, such as color, horn structure, and coat type, contribute to adaptive features and breed identification, quantitative traits like body weight and conformation measurements bear a closer correlation with production characteristics. This study employs advanced genotyping technologies, including the Illumina BovineSNP50 Bead Chip and next-generation sequencing methods like Reduced Representation sequencing, to identify genomic signatures associated with these traits. We applied four intra-population methods to find evidence of selection, such as Tajima's D, CLR, iHS, and ROH. We found a total of 40 genes under the selection signature, that were associated with morphometric traits in five cattle breeds (Kankrej, Tharparkar, Nelore, Sahiwal, and Gir). Crucial genes such as ADIPDQ, DPP6, INSIG1, SLC35D2 in Kankrej, LPL, ATP6V1B2, CDC14B in Tharparkar, HPSE2, PLAG1 in Nelore, PCSK1, PRKD1 in Sahiwal, and GNAQ, HPCAL1 in Gir were identified in our study. This approach provides valuable insights into the genetic basis of variations in body weight and conformation traits, facilitating informed selection processes and offering a deeper understanding of the evolutionary and domestication processes in diverse cattle breeds.

Genomic regions associated with coat color in Gir cattle

Indicine cattle breeds are adapted to the tropical climate, and their coat plays an important role in this process. Coat color influences thermoregulation and the adhesion of ectoparasites and may be associated with productive and reproductive traits. Furthermore, coat color is used for breed qualification, with breeders preferring certain colors. The Gir cattle is characterized by a wide variety of coat colors. Therefore, we performed genome-wide association studies to identify candidate genes for coat color in Gir cattle. Different phenotype scenarios were considered in the analyses and regions were identified on eight chromosomes. Some regions and many candidate genes are influencing coat color in the Gir cattle, which was found to be a polygenic trait. The candidate genes identified have been associated with white spotting patterns and base coat color in cattle and other species. In addition, a possible epistatic effect on coat color determination in the Gir cattle was suggested. This is the first published study that identified genomic regions and listed candidate genes associated with coat color in Gir cattle. The findings provided a better understanding of the genetic architecture of the trait in the breed and will allow to guide future fine-mapping studies for the development of genetic markers for selection.

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.

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.

Genome-Wide Association Analysis Identifies the PMEL Gene Affecting Coat Color and Birth Weight in Simmental × Holstein

Coat color and birth weight, as easily selected traits in cattle, play important roles in cattle breeding. Therefore, we carried out a genome-wide association study on birth weight and coat color to identify loci or potential linkage regions in 233 Simmental × Holstein crossbred beef cattle. The results revealed that nine SNPs were significantly associated with coat color (rs137169378, rs110022687, rs136002689, Hypotrichosis_PMel17, PMEL_1, rs134930689, rs383170073, rs109924971, and rs109146332), and these were in RNF41, ZC3H10, ERBB3, PMEL, and OR10A7 on BTA5. Interestingly, rs137169378, rs110022687, rs136002689, Hypotrichosis_PMel17, and PMEL_1 showed strong linkage disequilibrium (r2 > 0.8) and were significantly associated with coat color. Notably, Hypotrichosis_PMel17 and PMEL_1 were located in the gene PMEL (p = 2.22 × 10-18). Among the five significant SNPs associated with coat color, the birth weight of heterozygous individuals (AB) was greater than that of homozygous individuals (AA). Notably, the birth weight of heterozygous individuals with Hypotrichosis_PMel17 and PMEL_1 genotypes was significantly greater than that of homozygous individuals (0.01 < p < 0.05). Interestingly, the two loci were homozygous in black/white individuals and heterozygous in gray/white individuals, and the birth weight of heterozygous brown/white individuals (43.82 ± 5.25 kg) was greater than that of homozygous individuals (42.58 ± 3.09 kg). The birth weight of calves with the parental color (41.95 ± 3.53 kg) was significantly lower than that of calves with a non-parental color (43.54 ± 4.78 kg) (p < 0.05), and the birth weight of gray/white individuals (49.40 ± 7.11 kg) was the highest. Overall, PMEL appears to be a candidate gene affecting coat color in cattle, and coat color may have a selective effect on birth weight. This study provides a foundation for the breeding of beef cattle through GWAS for coat color and birth weight.

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.