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Current IssueSpecial IssueEditorial BoardOnline First ArticlesArchive

Review Article

Exploring Genetic Diversity of the X Chromosome in Livestock: A Critical Review

K
Karan Mahar1
R
Rangasai Chandra Goli1
P
Pritam Pal1
P
Pradyut Das1
G
Gopal R.Gowane1
R
Ranjit Singh Kataria2
M
Mahesh Shivanand Dige2
A
Anil Kumar Mishra2,*
1Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal-132 001, Haryana, India.
2Division of Animal Genetic Resources, ICAR-National Bureau of Animal Genetic Resources, Karnal-132 001, Haryana, India.

ABSTRACT

The X chromosome plays a crucial role in domestic animal genetics due to its unique inheritance pattern and evolutionary dynamics. First identified in 1891, the X chromosome, although comparable to autosomes in size and cytogenetic appearance, exhibits a distinct evolutionary trajectory driven largely by its hemizygous state in males. Advances in high-throughput sequencing technologies have enabled comprehensive investigations of X-chromosomal structure and variation across species. This review highlights the architectural features of the X chromosome in major domestic species, including cattle, sheep, pigs and horses and compares them with autosomal characteristics. Understanding these differences provides valuable insights into genetic diversity, population structure and evolutionary history. Furthermore, X-chromosome diversity has significant implications for conservation genetics, particularly in the preservation of indigenous breeds and the management of genetic bottlenecks. The potential for X-chromosome-based research in domestic animals is growing quickly due to the continuous advancement of high-resolution molecular techniques, which holds promise for advancing both scientific knowledge and useful results in animal breeding and conservation.

INTRODUCTION

The X chromosome, a critical player in sex determination, has a rich history of discovery and study. Its journey began in 1891 when Hermann Henking, working on the firebug (Pyrrhocoris apterus), observed an anomalous behavior in one chromosome, which he termed “Element X.” This pioneering observation laid the foundation for future research on sex chromosomes. In 1902, Erwin M. McClung expanded on Henking’s work while studying the slender meadow katydid (Xiphidium fasciatum). McClung identified a similar chromosome, which he named the “Accessory chromosome,” and elucidated its role in sex determination. This work significantly advanced our understanding of chromosomal mechanisms underlying sex determination. Further breakthroughs came in 1910 with Thomas Hunt Morgan’s experiments on Drosophila melanogaster at Columbia University. Morgan discovered a rare white-eyed mutant among a predominantly red-eyed population, noting that the mutation was exclusive to males. This discovery, published as “Sex Limited Inheritance in Drosophila,” provided compelling evidence for the role of the X chromosome in genetic inheritance. The understanding of the X chromosome continued to evolve with the work of  Barr and Bertram (1949). Barr, a Canadian physician, identified darkly stained bodies within the nuclei of female cells, which he termed “sex chromatin.” These structures, later known as “Barr bodies,” were shown to be condensed, inactive X chromosomes, providing insights into X chromosome inactivation.
       
Lyon (1961) proposed the X-chromosome inactivation (XCI) hypothesis, now commonly termed lyonization, to explain dosage compensation between XX females and XY males in placental mammals. XCI is mediated by the long non-coding RNA XIST, which coats and transcriptionally silences one X chromosome in female somatic cells. Silencing is incomplete: a subset of X-linked genes escapes XCI and remains expressed from the inactive X. An early systematic survey estimated that approximately 10% of tested X-linked transcripts escaped inactivation (Carrel et al., 1999).
       
The first phylogenetic tree for human mtDNA was published in 1987 (Cann et al., 1987), marking a significant milestone in the study of human genetics. Shortly thereafter, in 1989, the first phylogenetic tree for the Y chromosome was introduced (Lucotte et al., 1989), further advancing our understanding of human evolutionary history. However, population genetic studies of the X chromosome lagged behind, primarily due to the limitations in DNA sequencing technology at the time. It was only with the advent of practical DNA-sequencing techniques that comprehensive population genetic analyses of the X chromosome became feasible. Studies on X-chromosome were overshadowed by mt-DNA and Y-chromosome studies due to their uniparental inheritance despite its genetically rich repertoire than either.
       
This review seeks to improve our understanding of genetic diversity by surveying existing literature on X-chromosome studies across various domestic animal species. It emphasizes key findings and evaluates the role of X-chromosome analyses in elucidating genetic diversity and evolutionary patterns.
 
Structure of X-chromosome
 
X chromosome is the second-largest chromosome in the bovine genome and comprises 1132 annotated genes (Ensembl version 107 - January 2023), i.e., more than 4% of all annotated genes in the whole genome, with the majority (1098) situated in the non-PAR region. The pseudoautosomal region (PAR) refers to small regions of sequence homology found on tip of short arms of both the X and Y chromosomes (Fig 1). These regions facilitate pairing and recombination between the X and Y chromosomes during meiosis, which is crucial for proper segregation of the sex chromosomes. Unlike Humans who have 2 PAR regions, livestock comprises of single PAR region. Usually, mammals span few hundred Kbs to several Mbs of PAR region in length (Johnson et al., 2019; Raudsepp and Chowdhary; 2008; Das et al., 2009).  Johnson et al. (2019) identified the position of the pseudoautosomal boundary (PAB) on the X chromosome at ChrX:133,300,518. This determination was based on the observation that it is the last location within the zone of reduced homology. Previously, in 2008, Van Laere and colleagues characterized the bovine PAB and found a perfect match with this position. Accordingly in ARS-UCD1.2 reference genome assembly, the pseudoautosomal region (PAR) measured 5,708,626 base pairs in size (Van Laere et al., 2008). Information on PAB and PAR becomes useful particularly in genetic analyses (GWAS studies) on X-chromosome to differentiate the sex-specific region as it requires different statistical model for evaluation.

Fig 1: Simplified illustration of Bovine X-chromosome.


       
Studies on Human X-chromosome has revealed a lower GC content (39%) than the typical genome, which is 41%. Apart from that, X-chromosome is represented by having low gene density and small gene length i.e., 1.7% of X-chromosome constitutes exonic region (Ross et al., 2005).
 
Properties of X-chromosome
 
The X-chromosome is noteworthy due to its distinctive inheritance patterns in males and females. It is passed down two-thirds of the time through the female lineage, but only one-third of the time through the male lineage. Consequently, only two-thirds of X chromosomes recombine per generation, resulting in higher linkage disequilibrium (LD), longer haplotype blocks and amplified sensitivity to selection, drift and sex-biased demography compared to autosomes (Zhu et al., 2015; Chen et al., 2018). X-chromosome markers therefore provide powerful tools for population genetics, domestication studies and breeding in livestock due to their sex-specific inheritance and recombination dynamics. Compared to autosomes, the X-chromosome exhibits a divergent evolutionary trajectory, which can be attributed to its hemizygous state in males. Additionally, X diversity is generally lower than autosomal diversity due to its effective population size (approx 3:4 ratio) and female-biased transmission (Rajawat et al., 2024). These features make the X particularly informative for detecting breed-specific adaptations and domestication signatures. Unique properties of the X-chromosome include dosage compensation, sex-biased transmission and sexual antagonistic behavior. Additionally, the X-chromosome is characterized by a smaller genome size, lower mutation rate, reduced effective population size, decreased recombination rates and consequently, elevated linkage disequilibrium (Shihabi et al., 2022; Schaffner, 2004). These distinctive features make the X-chromosome a vital genetic tool for kinship analysis, forensic investigations and population genetics research (Gomes et al., 2020).
 
Attainment of H-W Equilibrium
 
Assuming large random mating population, in absence of systematic evolutionary forces (Mutation, migration and selection), one generation of random mating will bring Hardy-Weinberg gene frequencies if the two sexes have different gene frequency on Autosomal loci. The case is however different in case of sex-linked loci, where the gene frequency oscillates between the two sexes as population approaches equilibrium. The difference between the gene frequency subsequently halves in every generation till equilibrium between two sexes is achieved (Falconer and Mackay, 1983).
 
Influences moulding the evolution of X-chromosome
 
There are systematic (Migration, Mutation and Selection) and dispersive processes (Genetic drift, Population growth, etc) which shapes the trajectory of evolution of X-chromosome in different livestock species. The X chromosome can reveal information about demographic processes that autosome analysis alone is unable to reveal (Ramachandran et al., 2004; Schaffner, 2004; Bustamante and Ramachandran, 2009; Bryc et al., 2010; Goldberg and Rosenberg, 2015; Shringarpure et al., 2016).
 
Mutation
 
Mutation rate for X-chromosome is different from Autosomes and Y-chromosomes. Mutational changes occur in all somatic cells of the body. It is only the mutational changes in the germ line that are transferred to subsequent generation. Male requires a greater number of cell division to produce spermatogonia, more cell division causes replication error which tend to accumulate more on Y-chromosomes since it is transferred uniparentally in paternal line and also spermatogenesis occurs in the oxidative environment of the testis where there is lack of repair enzymes (Graves, 2006). Mutation rate for autosomes is the average of mutation rate across both sexes. However, in case of X-chromosome mutation rate will be lower than both autosomes and Y-chromosomes because there are only 3 X-chromosomes and mostly, they spend time in female sex i.e., 2/3rd time. Since females are less mutagenic, X- chromosome mutation rate is lowered. For instance, in a Human-Chimpanzee comparison (Ebersberger et al., 2002), they have obtained Ka/Kx value of 1.3 (K is no. of mutations that become fixed in a population per unit of evolutionary time). According to theoretical models of evolutionary rates, the X chromosome should, in some circumstances, accrue advantageous mutations more quickly than the autosomes (Charlesworth et al., 1987; Kirkpatrick and Hall 2004). This is particularly because the X chromosome allows for more effective selection on recessive or partially recessive mutations since the consequences of these changes are not hidden by the ancestral alleles in men (Haldane, 1924; Rice, 1984; Charlesworth et al., 1987; Vicoso and Charlesworth, 2006).
 
Migration
 
Migration pattern in livestock is a major systematic force which can shape the genome. Uniparental genetic marker i.e., Y-chromosome and Mitochondrial genome have been very useful for determining migration pattern of male and female sexes in within and across countries. These uniparental marker gives sex-specific demographic history. Major problem with these uniparental markers is their reduced effective population size (Ne) when compared to autosomes and X-chromosome. Lower Ne value will indicate high rate of genetic drift. Recent demographic process will have more effect on Y-chromosome and Mitochondrial genome. Another limitation of these uniparental markers is that they cannot differentiate the effect of drift from that of migration (Heyer and Segurel, 2010). Comparing genetic diversity between X-chromosomes and autosomes can provide crucial insights in sex-specific migration intensity in the populations.
       
Discordant genealogies are produced when employing autosomal, mitochondrial and Y-chromosomal loci, indicating sex-biased migratory patterns in the past (Tosi et al., 2000). Similar findings have been reported in 7 macaque species (Osada et al., 2021) where they have obtained incongruency between the phylogeny created using Y-chromosome, Mitochondrial loci and autosomes. They deduced that X-chromosome retains more original genetic component particularly in strong male-biased migration.
       
Effective population size and inbreeding coefficient: Effective population size is the size of an idealized population that would experience the same rate of genetic drift or inbreeding as the population under study (Falconer and Mackay, 1983). Under an ideal population with equal numbers of breeding males and females, the expected effective population size of the X chromosome is approximately three-quarters (3/4) that of the autosomes. The X-to-autosome effective-size ratio can deviate from 3/4 because of unequal sex ratios, sex-biased variance in reproductive success, inbreeding, population-size changes and other demographic processes (Wright, 1931; Wright, 1933; Caballero, 1995; Laporte and Charlesworth, 2002; Hitchcock, 2024). Estimates of effective population size for autosomes, the X chromosome, mitochondrial DNA and the Y chromosome are given in Table 1.

Table 1: Estimates of ne for autosomes, X-chromosome, mitochondrial DNA and Y-chromosome.


       
Inbreeding also affects effective population size (Caballero and Hill, 1992; Wang, 1996; Hedrick and Parker, 1997; Laporte and Charlesworth, 2002). The inbreeding coefficient is F, the probability that the two alleles at a diploid locus are identical by descent. For X-linked loci outside the pseudoautosomal region, males are hemizygous whereas females carry two alleles; consequently, X-linked inbreeding and coancestry depend on sex-specific pedigree pathways and should not be interpreted using exactly the same assumptions as autosomal inbreeding.
 
Selection
 
Genome wide scans for footprints related to selection are abundant and are studied on autosomes mainly. X-chromosome have not been included in these studies mainly due to lack of chromosome mapping due to large blocks of repetitive sequences. Now, due to advancement in newer generation sequencing technologies X-chromosome is being explored. Signatures of selection on X-chromosome can be crucial for studying sex-specific selection. Selection acts more efficiently on X-chromosome particularly for recessive alleles because they are exposed in hemizygous males. Genes on X-chromosome are under direct and effective selection (Graves et al., 2006).
 
Evolutionary significance of X-chromosome diversity
 
Many genomic studies have historically prioritized autosomes because autosomal loci have the same ploidy in both sexes. The X chromosome requires sex-aware treatment because males are hemizygous outside the pseudoautosomal region, females are diploid and the chromosome differs from autosomes in effective population size, recombination and inheritance. Consequently, autosomal and X-chromosomal data should not be analysed using identical assumptions (Schaffner, 2004). Previous X-chromosome selection scans have identified regions potentially involved in domestication and adaptation in pigs, horses and sheep (Ma et al., 2014; Liu et al., 2018; Zhu et al., 2015; Shihabi et al., 2022).
 
Cattle
 
The X-chromosomes of Bos taurus and Bos indicus exhibit distinct patterns of genetic variation, autozygosity, selection signatures and ancestral contributions that reflect their separate domestication histories, environmental adaptations and differing intensities of artificial selection. In Bos taurus breeds (e.g., Holstein-Friesian, Jersey, Brown Swiss), often shaped by intensive selection for dairy and beef production in temperate systems, the X chromosome typically shows reduced overall heterozygosity, elevated autozygosity in some regions and pronounced selection signatures tied to production efficiency, fertility and health. These patterns arise from historical bottlenecks, founder effects and strong directional selection, leading to targeted sweeps in regions influencing milk yield, growth and reproductive performance (Sanchez et al., 2023; Rajawat et al., 2024). In contrast, Bos indicus breeds (e.g., Nellore, Gir, Sahiwal, Tharparkar), domesticated in tropical/subtropical regions with larger effective population sizes near centers of origin and historically milder artificial selection, generally retain higher X-chromosome genetic diversity. This includes more polymorphic sites, less severe reductions in variation and signatures associated with adaptation to heat stress, disease resistance and immune function. For instance, comprehensive scans across indicine-influenced breeds have identified breed-specific selection regions on the X chromosome linked to environmental resilience, with overall higher nucleotide diversity and fewer fixed haplotypes compared to highly selected taurine lines (Rajawat et al., 2024). While studies for selection signatures on autosomal region is prevalent, very few studies target X-chromosomes (Dash et al., 2025).
       
X-inclusive association analyses also demonstrate that the chromosome contributes to economically important traits: Cole et al., (2011) included X-linked markers in a multi-trait Holstein GWAS, while de Carvalho et al. (2025) quantified substantial X-chromosomal contributions to male and female reproductive traits in Nellore cattle.
       
Bahbahani et al., (2015) analysed East African Shorthorn Zebu cattle (n = 425) genotyped with the Illumina BovineSNP50 BeadChip v1, together with Holstein-Friesian (n = 64), Jersey (n = 28), N’Dama (n = 25) and Nellore (n = 21) reference populations. X-chromosomal candidate regions were identified using inter-population (Rsb and FST) and intra-population (iHS) statistics and included loci associated with immune function. This interpretation is biologically relevant because East African cattle are exposed to substantial tick-borne and infectious-disease pressure (Latif et al., 1991; Bock et al., 2004; de Clare Bronsvoort et al., 2013; Thumbi et al., 2014). However, functional associations inferred from selection scans should be presented as candidate relationships unless experimentally validated.
       
Similarly, Rajawat et al., (2024), used different statistics (iHS, ROH, Tajima’s D, CLR, FST and XP-EHH) in their study to exclusively study X-chromosome based selection signatures. 6 Cattle breeds (Brown Swiss, Gir, Guernsey, H.F., Jersey and Nelore) with a total sample size of 184 individuals were genotyped with Illumina 50k SNP chip were utilized. Outlier regions were identified in Tajima’s D, CLR, iHS, ROH, FST and XP-EHH. These regions harbored several important candidate genes like AKAP4 for reproduction in Brown Swiss, MBTPS2 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. Most of the genes in their study were related with Health and Immunity.
       
Zavarez et al., (2015), found that X chromosome had much higher average autozygosity (runs of homozygosity) than autosomes, based on high-density SNP genotyping in Nellore cows (Bos indicus). Their study comprised of 1,278 Nellore cattle samples, genotyped with Illumina® BovineHD Genotyping BeadChip assay (HD). Their study suggests increased selective pressure due to gene content and sex-specific dosage effects (diploid in females, hemizygous in males) in X-chromosomes. Notably, despite theoretical predictions of three-quarters Ne, there was no evidence to suggest a smaller effective population size (Ne) for the X in comparison to autosomes. According to the authors, even under balanced demographic assumptions, the X chromosome is more vulnerable to bottlenecks and drift because of its hemizygous male inheritance.
       
Mehla et al., (2025) used X chromosomes to estimate ROH based inbreeding and hotspots in seven Indian cattle breeds (Dairy, Draft and dual-purpose). They utilised 132 samples which were genotyped using Illumina BovineHD BeadChip (777 K) platform. Compared to draft breeds (~19%), dairy breeds showed increased autozygosity, with ROH coverage of ~36-54% of the genome. They detected ROH islands on the X chromosome that contained genes and quantitative trait loci (QTLs) linked to reproduction, immunity and milk production. Additionally, Goli et al., (2026) analysed whole genome sequence data from 50 cattle samples, encompassing breeds from Indian indicine (Ladakhi (LC) = 9, Kangayam (KG) = 6,  Sahiwal (SW)=6, Gir (GR) = 4 and Nelore (NEL = 4), Chinese  indicine (Guangfeng (GUA) = 4 and Wannan (WAN) = 4) and taurine (Hereford (HER) = 4; Simmental (SIM) = 4 and Hanwoo (HA) = 5). They found that X chromosome diversity estimations were lower than those of autosomes. They also discovered selection signatures in the distal regions of the X chromosome related to metabolism, reproduction, disease resistance and immunological response, which is consistent with earlier research. Their 1st ever detailed whole genome resequencing study on X-linked markers also revealed locus specific adaptive admixture analysis in Indian cattle through precise introgression of alleles from other cattle populations.
 
Sheep
 
Shihabi et al., 2022 conducted a comprehensive selection signature analysis on the X-chromosome of 8 East Adriatic sheep breeds and 10 mouflons. Their findings identified 12 regions across the 135.4 Mb long sheep X-chromosome that exhibited signs of selection. The study emphasizes the pivotal role of the X-chromosome in the adaptive framework of these ruminant species. Moreover, the researchers developed a novel approach, termed HRiD (Haplotype richness drop), for detecting selection signals using haplotype information from male individuals. Zhu et al., (2015), conducted genome-wide scans for selection signatures using the OvineSNP50 BeadChip in 3 sheep breeds (German Mutton, Dorper and Sunit) using integrated haplotype score (iHS) and fixation index (FST) methods, identified 49, 34 and 55 candidate regions on the X chromosome, respectively (totalling 27.49 Mb, 16.47 Mb and 25.42 Mb). Downstream functional annotation highlighted genes with human orthologs implicated in reproduction (e.g., BMP15), immunity and disease resistance (VSIG4, PCDH11X), biosynthetic pathways (PDHA1) and nervous system/skin functions (PCDH19, PLP1, MSN, GUCY2F, SRPX2, BKT, CENPI). These results indicate that post-domestication selection targeted X-linked loci to enhance fertility, immune competence and adaptation to production environments. Complementary analyses in Chinese indigenous sheep breeds with distinct tail types (large-tailed Han, Altay and Tibetan) detected breed-specific copy number variations (CNVRs) and selection signatures on the X chromosome using FST and PennCNV software. The Tibetan sheep X chromosome contained the highest number of CNVRs (22), followed by large-tailed Han (6) and Altay (4). Two CNVRs were shared between large-tailed Han and Altay sheep, with genes in these regions associated with fat metabolism (DHRSX, CACNA1F, PNPLA4), energy metabolism (FAM58A), skeletal muscle development (SRPK3) and immunity (IL2RG). Reproduction-associated genes consistently showed selection signatures across multiple studies (Zhu et al., 2019). Goli et al., (2025) have recently analysed role of X-chromosome in high-altitude adaptation in Changthangi breed of Sheep. They have utilised dataset comprising 292 animals from seven breeds i.e., Changthangi, Garole, Deccani, Tibetan, Rambouillet, Australian Merino and European Mouflon, genotyped with the Illumina OvineSNP50 BeadChip. Cross population extended haplotype homozygosity (XP-EHH) method identified 9 candidate genes under selection in Changthangi breed which plays a role in their adaptation. Broader comparative genomic analyses of wild and domestic sheep revealed contrasting patterns: accelerated genetic drift on the X chromosome but reduced directional (positive) selection compared to autosomes, with X-to-autosome diversity ratios (~0.6) lower than the neutral expectation (~0.75). These observations are consistent with sex-biased demographic processes and stronger purifying selection acting on X-linked loci (Chen et al., 2018). Despite species-specific differences, convergent domestication signals are shared between sheep and goats which include X-linked regions under selection for immune function, nervous system development and productivity traits, suggesting parallel genomic responses to human management across small ruminants (Alberto et al., 2018). Together, these results show that the ovine X chromosome complements autosomal and uniparental markers by capturing female-mediated gene flow, recombination dynamics and sex-specific selective pressures. Future breeding strategies to preserve genetic diversity and improve productivity in sheep populations can be informed by the X-linked signatures, which offer crucial insights into post-domestication adaptation, breed differentiation and the genetic basis of traits like reproduction, tail morphology, fat deposition and environmental resilience (Zhu et al., 2015; Chen et al., 2018; Alberto et al., 2018).
 
Pigs
 
The first assembly of the swine genome, was published by Groenen et al., (2012) as part of the initial description of the pig genome sequence. Research on the X chromosome in domestic pigs (Sus scrofa) has revealed unique patterns of genetic diversity and selection signatures that support breed differentiation, especially between Asian and European lineages. Ma et al., 2014, conducted study on Landrace, Yorkshire and Chinese Songliao to identify putative selection imprints on the X chromosome using intrapopulation (iHS, Tajima’s D) and interpopulation (XPEHH, XPCLR, FST) technique employing high-density SNP data. They analysed a total of 515 pig sample representing three breeds. There are 67 individuals (32 boars and 35 sows) in Landrace, 375 individuals (207 boars and 168 sows) in Yorkshire and 73 individuals (39 boars and 34 sows) in Chinese Songliao. They have identified X-chromosome regions, spanning several megabases, harbouring genes associated with key production traits, including immunity, reproduction and potentially meat quality, reflecting artificial selection pressures during breed development and adaptation to diverse environments. In another study by Tong et al., (2020), whole genome sequences of 24 individual pigs representing 22 breeds distributed throughout China were compared with European and commercial breeds. The study revealed chinese indigenous pigs, has unique haplotype structures and large-scale linkage disequilibrium (LD) blocks on the X chromosome, with three major haplotypes identified: one unique to southern Chinese domestic and wild pigs, another in northern wild pigs and a recombinant form predominantly in northern domestic pigs (Tong et al., 2020). These haplotype patterns highlight regional genetic differentiation within Asian pigs and potential adaptive responses to local conditions. Unlike the Y chromosome, where European lineages (e.g., HY1) have introgressed into Asian populations via unidirectional paternal gene flow over the past ~200 years-often under positive selection for traits like lean meat and growth-the X chromosome reflects more complex, bidirectional influences. Historical hybridization during the Industrial Revolution introduced Asian genetic material into European commercial breeds (e.g., Large White, Landrace), with introgressed Asian haplotypes showing signatures of selection for economically important traits such as meat quality, development and fertility (Bosse et al., 2014). This admixture has contributed to increased genetic diversity in European pigs compared to their wild ancestors, though X-linked regions often display intermediate diversity patterns due to hemizygosity in males and sex-biased selection. In contrast, many Chinese indigenous breeds retain higher X-chromosome variation consistent with milder artificial selection and greater retention of ancestral diversity, while commercial European breeds show stronger sweeps in regions linked to production efficiency. These findings illustrate how the X chromosome captures female-mediated gene flow, recombination dynamics and sex-specific selection, complementing uniparental markers to explain breed-specific phenotypes like reproductive performance and immune competence. Overall, X-chromosome studies underscore the role of human-mediated admixture and targeted breeding in shaping modern pig genetic architecture across continents (Ma et al., 2014; Tong et al., 2020).
 
Horse
 
The horse X chromosome makes up 4.6% of the horse genome and is about 124 Mb in size. According to Liu et al., (2018), ponies are small-type horses that are under intense selection pressure to develop their diminutive stature. In order to find footprints of selection utilising FST and XP-EHH, Liu et al., (2018) performed a genome-wide scan of three Chinese horse breeds using an Equine SNP 70 BeadChip. A total of 64 unrelated adult mares were randomly sampled from three geographic regions in China. They detected, five X chromosomal sites under intense selection pressure in their study. Ninety-five overlapping genes were found by downstream analysis of those regions; twelve to seventeen of these genes, including SMS, PHEX, ACSL4, CHRDL1, CACNA1F, DKC1 and CDKL5, are involved in fat deposition, growth hormone production and bone development.
               
The X chromosome is a useful target for comprehending adaptation, quantitative traits and conservation in equine genomics because, in contrast to the severely bottlenecked Y chromosome in contemporary horse populations, X-chromosome retains more moderate variation due to female-mediated recombination and gene flow (Salek Ardestani et al., 2020; Liu et al., 2018). A cross-species comparison of the analytical approaches, candidate loci, principal findings and study limitations discussed above is summarized in Table 2.

Table 2: Comparative summary of X-chromosome studies across major livestock species.

CONCLUSION

The X chromosome serves as a critical component in understanding the evolutionary dynamics and genetic diversity of domestic animals due to its unique inheritance and recombination patterns. Its comparative analysis with autosomes provides valuable insights into population structure, selection pressures and breed differentiation. With advances in high-resolution molecular technologies, X-chromosome research will continue to enhance breeding strategies and conservation efforts in domestic species. Future work should prioritize complete sex-chromosome assemblies, X-specific variant calling and imputation, sex-aware statistical models, long-read structural-variant analysis and functional validation of candidate X-linked loci.

ACKNOWLEDGEMENT

The authors thank the Director, ICAR-National Dairy Research Institute, Karnal, India and Director, ICAR- National Bureau of Animal Genetic Resources, Karnal, India for providing necessary facilities and support.

DECLARATIONS

Consent for publication
 
The manuscript has consent of all the authors for its publication in current format.
 
Funding
 
This study was not supported by any external grants.

CONFLICT OF INTEREST

The authors declare that there is no conflict of interest.

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    Review Article

    Exploring Genetic Diversity of the X Chromosome in Livestock: A Critical Review

    K
    Karan Mahar1
    R
    Rangasai Chandra Goli1
    P
    Pritam Pal1
    P
    Pradyut Das1
    G
    Gopal R.Gowane1
    R
    Ranjit Singh Kataria2
    M
    Mahesh Shivanand Dige2
    A
    Anil Kumar Mishra2,*
    1Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal-132 001, Haryana, India.
    2Division of Animal Genetic Resources, ICAR-National Bureau of Animal Genetic Resources, Karnal-132 001, Haryana, India.

    ABSTRACT

    The X chromosome plays a crucial role in domestic animal genetics due to its unique inheritance pattern and evolutionary dynamics. First identified in 1891, the X chromosome, although comparable to autosomes in size and cytogenetic appearance, exhibits a distinct evolutionary trajectory driven largely by its hemizygous state in males. Advances in high-throughput sequencing technologies have enabled comprehensive investigations of X-chromosomal structure and variation across species. This review highlights the architectural features of the X chromosome in major domestic species, including cattle, sheep, pigs and horses and compares them with autosomal characteristics. Understanding these differences provides valuable insights into genetic diversity, population structure and evolutionary history. Furthermore, X-chromosome diversity has significant implications for conservation genetics, particularly in the preservation of indigenous breeds and the management of genetic bottlenecks. The potential for X-chromosome-based research in domestic animals is growing quickly due to the continuous advancement of high-resolution molecular techniques, which holds promise for advancing both scientific knowledge and useful results in animal breeding and conservation.

    INTRODUCTION

    The X chromosome, a critical player in sex determination, has a rich history of discovery and study. Its journey began in 1891 when Hermann Henking, working on the firebug (Pyrrhocoris apterus), observed an anomalous behavior in one chromosome, which he termed “Element X.” This pioneering observation laid the foundation for future research on sex chromosomes. In 1902, Erwin M. McClung expanded on Henking’s work while studying the slender meadow katydid (Xiphidium fasciatum). McClung identified a similar chromosome, which he named the “Accessory chromosome,” and elucidated its role in sex determination. This work significantly advanced our understanding of chromosomal mechanisms underlying sex determination. Further breakthroughs came in 1910 with Thomas Hunt Morgan’s experiments on Drosophila melanogaster at Columbia University. Morgan discovered a rare white-eyed mutant among a predominantly red-eyed population, noting that the mutation was exclusive to males. This discovery, published as “Sex Limited Inheritance in Drosophila,” provided compelling evidence for the role of the X chromosome in genetic inheritance. The understanding of the X chromosome continued to evolve with the work of  Barr and Bertram (1949). Barr, a Canadian physician, identified darkly stained bodies within the nuclei of female cells, which he termed “sex chromatin.” These structures, later known as “Barr bodies,” were shown to be condensed, inactive X chromosomes, providing insights into X chromosome inactivation.
           
    Lyon (1961) proposed the X-chromosome inactivation (XCI) hypothesis, now commonly termed lyonization, to explain dosage compensation between XX females and XY males in placental mammals. XCI is mediated by the long non-coding RNA XIST, which coats and transcriptionally silences one X chromosome in female somatic cells. Silencing is incomplete: a subset of X-linked genes escapes XCI and remains expressed from the inactive X. An early systematic survey estimated that approximately 10% of tested X-linked transcripts escaped inactivation (Carrel et al., 1999).
           
    The first phylogenetic tree for human mtDNA was published in 1987 (Cann et al., 1987), marking a significant milestone in the study of human genetics. Shortly thereafter, in 1989, the first phylogenetic tree for the Y chromosome was introduced (Lucotte et al., 1989), further advancing our understanding of human evolutionary history. However, population genetic studies of the X chromosome lagged behind, primarily due to the limitations in DNA sequencing technology at the time. It was only with the advent of practical DNA-sequencing techniques that comprehensive population genetic analyses of the X chromosome became feasible. Studies on X-chromosome were overshadowed by mt-DNA and Y-chromosome studies due to their uniparental inheritance despite its genetically rich repertoire than either.
           
    This review seeks to improve our understanding of genetic diversity by surveying existing literature on X-chromosome studies across various domestic animal species. It emphasizes key findings and evaluates the role of X-chromosome analyses in elucidating genetic diversity and evolutionary patterns.
     
    Structure of X-chromosome
     
    X chromosome is the second-largest chromosome in the bovine genome and comprises 1132 annotated genes (Ensembl version 107 - January 2023), i.e., more than 4% of all annotated genes in the whole genome, with the majority (1098) situated in the non-PAR region. The pseudoautosomal region (PAR) refers to small regions of sequence homology found on tip of short arms of both the X and Y chromosomes (Fig 1). These regions facilitate pairing and recombination between the X and Y chromosomes during meiosis, which is crucial for proper segregation of the sex chromosomes. Unlike Humans who have 2 PAR regions, livestock comprises of single PAR region. Usually, mammals span few hundred Kbs to several Mbs of PAR region in length (Johnson et al., 2019; Raudsepp and Chowdhary; 2008; Das et al., 2009).  Johnson et al. (2019) identified the position of the pseudoautosomal boundary (PAB) on the X chromosome at ChrX:133,300,518. This determination was based on the observation that it is the last location within the zone of reduced homology. Previously, in 2008, Van Laere and colleagues characterized the bovine PAB and found a perfect match with this position. Accordingly in ARS-UCD1.2 reference genome assembly, the pseudoautosomal region (PAR) measured 5,708,626 base pairs in size (Van Laere et al., 2008). Information on PAB and PAR becomes useful particularly in genetic analyses (GWAS studies) on X-chromosome to differentiate the sex-specific region as it requires different statistical model for evaluation.

    Fig 1: Simplified illustration of Bovine X-chromosome.


           
    Studies on Human X-chromosome has revealed a lower GC content (39%) than the typical genome, which is 41%. Apart from that, X-chromosome is represented by having low gene density and small gene length i.e., 1.7% of X-chromosome constitutes exonic region (Ross et al., 2005).
     
    Properties of X-chromosome
     
    The X-chromosome is noteworthy due to its distinctive inheritance patterns in males and females. It is passed down two-thirds of the time through the female lineage, but only one-third of the time through the male lineage. Consequently, only two-thirds of X chromosomes recombine per generation, resulting in higher linkage disequilibrium (LD), longer haplotype blocks and amplified sensitivity to selection, drift and sex-biased demography compared to autosomes (Zhu et al., 2015; Chen et al., 2018). X-chromosome markers therefore provide powerful tools for population genetics, domestication studies and breeding in livestock due to their sex-specific inheritance and recombination dynamics. Compared to autosomes, the X-chromosome exhibits a divergent evolutionary trajectory, which can be attributed to its hemizygous state in males. Additionally, X diversity is generally lower than autosomal diversity due to its effective population size (approx 3:4 ratio) and female-biased transmission (Rajawat et al., 2024). These features make the X particularly informative for detecting breed-specific adaptations and domestication signatures. Unique properties of the X-chromosome include dosage compensation, sex-biased transmission and sexual antagonistic behavior. Additionally, the X-chromosome is characterized by a smaller genome size, lower mutation rate, reduced effective population size, decreased recombination rates and consequently, elevated linkage disequilibrium (Shihabi et al., 2022; Schaffner, 2004). These distinctive features make the X-chromosome a vital genetic tool for kinship analysis, forensic investigations and population genetics research (Gomes et al., 2020).
     
    Attainment of H-W Equilibrium
     
    Assuming large random mating population, in absence of systematic evolutionary forces (Mutation, migration and selection), one generation of random mating will bring Hardy-Weinberg gene frequencies if the two sexes have different gene frequency on Autosomal loci. The case is however different in case of sex-linked loci, where the gene frequency oscillates between the two sexes as population approaches equilibrium. The difference between the gene frequency subsequently halves in every generation till equilibrium between two sexes is achieved (Falconer and Mackay, 1983).
     
    Influences moulding the evolution of X-chromosome
     
    There are systematic (Migration, Mutation and Selection) and dispersive processes (Genetic drift, Population growth, etc) which shapes the trajectory of evolution of X-chromosome in different livestock species. The X chromosome can reveal information about demographic processes that autosome analysis alone is unable to reveal (Ramachandran et al., 2004; Schaffner, 2004; Bustamante and Ramachandran, 2009; Bryc et al., 2010; Goldberg and Rosenberg, 2015; Shringarpure et al., 2016).
     
    Mutation
     
    Mutation rate for X-chromosome is different from Autosomes and Y-chromosomes. Mutational changes occur in all somatic cells of the body. It is only the mutational changes in the germ line that are transferred to subsequent generation. Male requires a greater number of cell division to produce spermatogonia, more cell division causes replication error which tend to accumulate more on Y-chromosomes since it is transferred uniparentally in paternal line and also spermatogenesis occurs in the oxidative environment of the testis where there is lack of repair enzymes (Graves, 2006). Mutation rate for autosomes is the average of mutation rate across both sexes. However, in case of X-chromosome mutation rate will be lower than both autosomes and Y-chromosomes because there are only 3 X-chromosomes and mostly, they spend time in female sex i.e., 2/3rd time. Since females are less mutagenic, X- chromosome mutation rate is lowered. For instance, in a Human-Chimpanzee comparison (Ebersberger et al., 2002), they have obtained Ka/Kx value of 1.3 (K is no. of mutations that become fixed in a population per unit of evolutionary time). According to theoretical models of evolutionary rates, the X chromosome should, in some circumstances, accrue advantageous mutations more quickly than the autosomes (Charlesworth et al., 1987; Kirkpatrick and Hall 2004). This is particularly because the X chromosome allows for more effective selection on recessive or partially recessive mutations since the consequences of these changes are not hidden by the ancestral alleles in men (Haldane, 1924; Rice, 1984; Charlesworth et al., 1987; Vicoso and Charlesworth, 2006).
     
    Migration
     
    Migration pattern in livestock is a major systematic force which can shape the genome. Uniparental genetic marker i.e., Y-chromosome and Mitochondrial genome have been very useful for determining migration pattern of male and female sexes in within and across countries. These uniparental marker gives sex-specific demographic history. Major problem with these uniparental markers is their reduced effective population size (Ne) when compared to autosomes and X-chromosome. Lower Ne value will indicate high rate of genetic drift. Recent demographic process will have more effect on Y-chromosome and Mitochondrial genome. Another limitation of these uniparental markers is that they cannot differentiate the effect of drift from that of migration (Heyer and Segurel, 2010). Comparing genetic diversity between X-chromosomes and autosomes can provide crucial insights in sex-specific migration intensity in the populations.
           
    Discordant genealogies are produced when employing autosomal, mitochondrial and Y-chromosomal loci, indicating sex-biased migratory patterns in the past (Tosi et al., 2000). Similar findings have been reported in 7 macaque species (Osada et al., 2021) where they have obtained incongruency between the phylogeny created using Y-chromosome, Mitochondrial loci and autosomes. They deduced that X-chromosome retains more original genetic component particularly in strong male-biased migration.
           
    Effective population size and inbreeding coefficient: Effective population size is the size of an idealized population that would experience the same rate of genetic drift or inbreeding as the population under study (Falconer and Mackay, 1983). Under an ideal population with equal numbers of breeding males and females, the expected effective population size of the X chromosome is approximately three-quarters (3/4) that of the autosomes. The X-to-autosome effective-size ratio can deviate from 3/4 because of unequal sex ratios, sex-biased variance in reproductive success, inbreeding, population-size changes and other demographic processes (Wright, 1931; Wright, 1933; Caballero, 1995; Laporte and Charlesworth, 2002; Hitchcock, 2024). Estimates of effective population size for autosomes, the X chromosome, mitochondrial DNA and the Y chromosome are given in Table 1.

    Table 1: Estimates of ne for autosomes, X-chromosome, mitochondrial DNA and Y-chromosome.


           
    Inbreeding also affects effective population size (Caballero and Hill, 1992; Wang, 1996; Hedrick and Parker, 1997; Laporte and Charlesworth, 2002). The inbreeding coefficient is F, the probability that the two alleles at a diploid locus are identical by descent. For X-linked loci outside the pseudoautosomal region, males are hemizygous whereas females carry two alleles; consequently, X-linked inbreeding and coancestry depend on sex-specific pedigree pathways and should not be interpreted using exactly the same assumptions as autosomal inbreeding.
     
    Selection
     
    Genome wide scans for footprints related to selection are abundant and are studied on autosomes mainly. X-chromosome have not been included in these studies mainly due to lack of chromosome mapping due to large blocks of repetitive sequences. Now, due to advancement in newer generation sequencing technologies X-chromosome is being explored. Signatures of selection on X-chromosome can be crucial for studying sex-specific selection. Selection acts more efficiently on X-chromosome particularly for recessive alleles because they are exposed in hemizygous males. Genes on X-chromosome are under direct and effective selection (Graves et al., 2006).
     
    Evolutionary significance of X-chromosome diversity
     
    Many genomic studies have historically prioritized autosomes because autosomal loci have the same ploidy in both sexes. The X chromosome requires sex-aware treatment because males are hemizygous outside the pseudoautosomal region, females are diploid and the chromosome differs from autosomes in effective population size, recombination and inheritance. Consequently, autosomal and X-chromosomal data should not be analysed using identical assumptions (Schaffner, 2004). Previous X-chromosome selection scans have identified regions potentially involved in domestication and adaptation in pigs, horses and sheep (Ma et al., 2014; Liu et al., 2018; Zhu et al., 2015; Shihabi et al., 2022).
     
    Cattle
     
    The X-chromosomes of Bos taurus and Bos indicus exhibit distinct patterns of genetic variation, autozygosity, selection signatures and ancestral contributions that reflect their separate domestication histories, environmental adaptations and differing intensities of artificial selection. In Bos taurus breeds (e.g., Holstein-Friesian, Jersey, Brown Swiss), often shaped by intensive selection for dairy and beef production in temperate systems, the X chromosome typically shows reduced overall heterozygosity, elevated autozygosity in some regions and pronounced selection signatures tied to production efficiency, fertility and health. These patterns arise from historical bottlenecks, founder effects and strong directional selection, leading to targeted sweeps in regions influencing milk yield, growth and reproductive performance (Sanchez et al., 2023; Rajawat et al., 2024). In contrast, Bos indicus breeds (e.g., Nellore, Gir, Sahiwal, Tharparkar), domesticated in tropical/subtropical regions with larger effective population sizes near centers of origin and historically milder artificial selection, generally retain higher X-chromosome genetic diversity. This includes more polymorphic sites, less severe reductions in variation and signatures associated with adaptation to heat stress, disease resistance and immune function. For instance, comprehensive scans across indicine-influenced breeds have identified breed-specific selection regions on the X chromosome linked to environmental resilience, with overall higher nucleotide diversity and fewer fixed haplotypes compared to highly selected taurine lines (Rajawat et al., 2024). While studies for selection signatures on autosomal region is prevalent, very few studies target X-chromosomes (Dash et al., 2025).
           
    X-inclusive association analyses also demonstrate that the chromosome contributes to economically important traits: Cole et al., (2011) included X-linked markers in a multi-trait Holstein GWAS, while de Carvalho et al. (2025) quantified substantial X-chromosomal contributions to male and female reproductive traits in Nellore cattle.
           
    Bahbahani et al., (2015) analysed East African Shorthorn Zebu cattle (n = 425) genotyped with the Illumina BovineSNP50 BeadChip v1, together with Holstein-Friesian (n = 64), Jersey (n = 28), N’Dama (n = 25) and Nellore (n = 21) reference populations. X-chromosomal candidate regions were identified using inter-population (Rsb and FST) and intra-population (iHS) statistics and included loci associated with immune function. This interpretation is biologically relevant because East African cattle are exposed to substantial tick-borne and infectious-disease pressure (Latif et al., 1991; Bock et al., 2004; de Clare Bronsvoort et al., 2013; Thumbi et al., 2014). However, functional associations inferred from selection scans should be presented as candidate relationships unless experimentally validated.
           
    Similarly, Rajawat et al., (2024), used different statistics (iHS, ROH, Tajima’s D, CLR, FST and XP-EHH) in their study to exclusively study X-chromosome based selection signatures. 6 Cattle breeds (Brown Swiss, Gir, Guernsey, H.F., Jersey and Nelore) with a total sample size of 184 individuals were genotyped with Illumina 50k SNP chip were utilized. Outlier regions were identified in Tajima’s D, CLR, iHS, ROH, FST and XP-EHH. These regions harbored several important candidate genes like AKAP4 for reproduction in Brown Swiss, MBTPS2 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. Most of the genes in their study were related with Health and Immunity.
           
    Zavarez et al., (2015), found that X chromosome had much higher average autozygosity (runs of homozygosity) than autosomes, based on high-density SNP genotyping in Nellore cows (Bos indicus). Their study comprised of 1,278 Nellore cattle samples, genotyped with Illumina® BovineHD Genotyping BeadChip assay (HD). Their study suggests increased selective pressure due to gene content and sex-specific dosage effects (diploid in females, hemizygous in males) in X-chromosomes. Notably, despite theoretical predictions of three-quarters Ne, there was no evidence to suggest a smaller effective population size (Ne) for the X in comparison to autosomes. According to the authors, even under balanced demographic assumptions, the X chromosome is more vulnerable to bottlenecks and drift because of its hemizygous male inheritance.
           
    Mehla et al., (2025) used X chromosomes to estimate ROH based inbreeding and hotspots in seven Indian cattle breeds (Dairy, Draft and dual-purpose). They utilised 132 samples which were genotyped using Illumina BovineHD BeadChip (777 K) platform. Compared to draft breeds (~19%), dairy breeds showed increased autozygosity, with ROH coverage of ~36-54% of the genome. They detected ROH islands on the X chromosome that contained genes and quantitative trait loci (QTLs) linked to reproduction, immunity and milk production. Additionally, Goli et al., (2026) analysed whole genome sequence data from 50 cattle samples, encompassing breeds from Indian indicine (Ladakhi (LC) = 9, Kangayam (KG) = 6,  Sahiwal (SW)=6, Gir (GR) = 4 and Nelore (NEL = 4), Chinese  indicine (Guangfeng (GUA) = 4 and Wannan (WAN) = 4) and taurine (Hereford (HER) = 4; Simmental (SIM) = 4 and Hanwoo (HA) = 5). They found that X chromosome diversity estimations were lower than those of autosomes. They also discovered selection signatures in the distal regions of the X chromosome related to metabolism, reproduction, disease resistance and immunological response, which is consistent with earlier research. Their 1st ever detailed whole genome resequencing study on X-linked markers also revealed locus specific adaptive admixture analysis in Indian cattle through precise introgression of alleles from other cattle populations.
     
    Sheep
     
    Shihabi et al., 2022 conducted a comprehensive selection signature analysis on the X-chromosome of 8 East Adriatic sheep breeds and 10 mouflons. Their findings identified 12 regions across the 135.4 Mb long sheep X-chromosome that exhibited signs of selection. The study emphasizes the pivotal role of the X-chromosome in the adaptive framework of these ruminant species. Moreover, the researchers developed a novel approach, termed HRiD (Haplotype richness drop), for detecting selection signals using haplotype information from male individuals. Zhu et al., (2015), conducted genome-wide scans for selection signatures using the OvineSNP50 BeadChip in 3 sheep breeds (German Mutton, Dorper and Sunit) using integrated haplotype score (iHS) and fixation index (FST) methods, identified 49, 34 and 55 candidate regions on the X chromosome, respectively (totalling 27.49 Mb, 16.47 Mb and 25.42 Mb). Downstream functional annotation highlighted genes with human orthologs implicated in reproduction (e.g., BMP15), immunity and disease resistance (VSIG4, PCDH11X), biosynthetic pathways (PDHA1) and nervous system/skin functions (PCDH19, PLP1, MSN, GUCY2F, SRPX2, BKT, CENPI). These results indicate that post-domestication selection targeted X-linked loci to enhance fertility, immune competence and adaptation to production environments. Complementary analyses in Chinese indigenous sheep breeds with distinct tail types (large-tailed Han, Altay and Tibetan) detected breed-specific copy number variations (CNVRs) and selection signatures on the X chromosome using FST and PennCNV software. The Tibetan sheep X chromosome contained the highest number of CNVRs (22), followed by large-tailed Han (6) and Altay (4). Two CNVRs were shared between large-tailed Han and Altay sheep, with genes in these regions associated with fat metabolism (DHRSX, CACNA1F, PNPLA4), energy metabolism (FAM58A), skeletal muscle development (SRPK3) and immunity (IL2RG). Reproduction-associated genes consistently showed selection signatures across multiple studies (Zhu et al., 2019). Goli et al., (2025) have recently analysed role of X-chromosome in high-altitude adaptation in Changthangi breed of Sheep. They have utilised dataset comprising 292 animals from seven breeds i.e., Changthangi, Garole, Deccani, Tibetan, Rambouillet, Australian Merino and European Mouflon, genotyped with the Illumina OvineSNP50 BeadChip. Cross population extended haplotype homozygosity (XP-EHH) method identified 9 candidate genes under selection in Changthangi breed which plays a role in their adaptation. Broader comparative genomic analyses of wild and domestic sheep revealed contrasting patterns: accelerated genetic drift on the X chromosome but reduced directional (positive) selection compared to autosomes, with X-to-autosome diversity ratios (~0.6) lower than the neutral expectation (~0.75). These observations are consistent with sex-biased demographic processes and stronger purifying selection acting on X-linked loci (Chen et al., 2018). Despite species-specific differences, convergent domestication signals are shared between sheep and goats which include X-linked regions under selection for immune function, nervous system development and productivity traits, suggesting parallel genomic responses to human management across small ruminants (Alberto et al., 2018). Together, these results show that the ovine X chromosome complements autosomal and uniparental markers by capturing female-mediated gene flow, recombination dynamics and sex-specific selective pressures. Future breeding strategies to preserve genetic diversity and improve productivity in sheep populations can be informed by the X-linked signatures, which offer crucial insights into post-domestication adaptation, breed differentiation and the genetic basis of traits like reproduction, tail morphology, fat deposition and environmental resilience (Zhu et al., 2015; Chen et al., 2018; Alberto et al., 2018).
     
    Pigs
     
    The first assembly of the swine genome, was published by Groenen et al., (2012) as part of the initial description of the pig genome sequence. Research on the X chromosome in domestic pigs (Sus scrofa) has revealed unique patterns of genetic diversity and selection signatures that support breed differentiation, especially between Asian and European lineages. Ma et al., 2014, conducted study on Landrace, Yorkshire and Chinese Songliao to identify putative selection imprints on the X chromosome using intrapopulation (iHS, Tajima’s D) and interpopulation (XPEHH, XPCLR, FST) technique employing high-density SNP data. They analysed a total of 515 pig sample representing three breeds. There are 67 individuals (32 boars and 35 sows) in Landrace, 375 individuals (207 boars and 168 sows) in Yorkshire and 73 individuals (39 boars and 34 sows) in Chinese Songliao. They have identified X-chromosome regions, spanning several megabases, harbouring genes associated with key production traits, including immunity, reproduction and potentially meat quality, reflecting artificial selection pressures during breed development and adaptation to diverse environments. In another study by Tong et al., (2020), whole genome sequences of 24 individual pigs representing 22 breeds distributed throughout China were compared with European and commercial breeds. The study revealed chinese indigenous pigs, has unique haplotype structures and large-scale linkage disequilibrium (LD) blocks on the X chromosome, with three major haplotypes identified: one unique to southern Chinese domestic and wild pigs, another in northern wild pigs and a recombinant form predominantly in northern domestic pigs (Tong et al., 2020). These haplotype patterns highlight regional genetic differentiation within Asian pigs and potential adaptive responses to local conditions. Unlike the Y chromosome, where European lineages (e.g., HY1) have introgressed into Asian populations via unidirectional paternal gene flow over the past ~200 years-often under positive selection for traits like lean meat and growth-the X chromosome reflects more complex, bidirectional influences. Historical hybridization during the Industrial Revolution introduced Asian genetic material into European commercial breeds (e.g., Large White, Landrace), with introgressed Asian haplotypes showing signatures of selection for economically important traits such as meat quality, development and fertility (Bosse et al., 2014). This admixture has contributed to increased genetic diversity in European pigs compared to their wild ancestors, though X-linked regions often display intermediate diversity patterns due to hemizygosity in males and sex-biased selection. In contrast, many Chinese indigenous breeds retain higher X-chromosome variation consistent with milder artificial selection and greater retention of ancestral diversity, while commercial European breeds show stronger sweeps in regions linked to production efficiency. These findings illustrate how the X chromosome captures female-mediated gene flow, recombination dynamics and sex-specific selection, complementing uniparental markers to explain breed-specific phenotypes like reproductive performance and immune competence. Overall, X-chromosome studies underscore the role of human-mediated admixture and targeted breeding in shaping modern pig genetic architecture across continents (Ma et al., 2014; Tong et al., 2020).
     
    Horse
     
    The horse X chromosome makes up 4.6% of the horse genome and is about 124 Mb in size. According to Liu et al., (2018), ponies are small-type horses that are under intense selection pressure to develop their diminutive stature. In order to find footprints of selection utilising FST and XP-EHH, Liu et al., (2018) performed a genome-wide scan of three Chinese horse breeds using an Equine SNP 70 BeadChip. A total of 64 unrelated adult mares were randomly sampled from three geographic regions in China. They detected, five X chromosomal sites under intense selection pressure in their study. Ninety-five overlapping genes were found by downstream analysis of those regions; twelve to seventeen of these genes, including SMS, PHEX, ACSL4, CHRDL1, CACNA1F, DKC1 and CDKL5, are involved in fat deposition, growth hormone production and bone development.
                   
    The X chromosome is a useful target for comprehending adaptation, quantitative traits and conservation in equine genomics because, in contrast to the severely bottlenecked Y chromosome in contemporary horse populations, X-chromosome retains more moderate variation due to female-mediated recombination and gene flow (Salek Ardestani et al., 2020; Liu et al., 2018). A cross-species comparison of the analytical approaches, candidate loci, principal findings and study limitations discussed above is summarized in Table 2.

    Table 2: Comparative summary of X-chromosome studies across major livestock species.

    CONCLUSION

    The X chromosome serves as a critical component in understanding the evolutionary dynamics and genetic diversity of domestic animals due to its unique inheritance and recombination patterns. Its comparative analysis with autosomes provides valuable insights into population structure, selection pressures and breed differentiation. With advances in high-resolution molecular technologies, X-chromosome research will continue to enhance breeding strategies and conservation efforts in domestic species. Future work should prioritize complete sex-chromosome assemblies, X-specific variant calling and imputation, sex-aware statistical models, long-read structural-variant analysis and functional validation of candidate X-linked loci.

    ACKNOWLEDGEMENT

    The authors thank the Director, ICAR-National Dairy Research Institute, Karnal, India and Director, ICAR- National Bureau of Animal Genetic Resources, Karnal, India for providing necessary facilities and support.

    DECLARATIONS

    Consent for publication
     
    The manuscript has consent of all the authors for its publication in current format.
     
    Funding
     
    This study was not supported by any external grants.

    CONFLICT OF INTEREST

    The authors declare that there is no conflict of interest.

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