Genome-wide analysis reveals genomic diversity and signatures of selection in Qinchuan beef cattle.

BACKGROUND: Indigenous Chinese cattle have abundant genetic diversity and a long history of artificial selection, giving local breeds advantages in adaptability, forage tolerance and resistance. The detection of selective sweeps and comparative genome analysis of selected breeds and ancestral populations provide a basis for understanding differences among breeds and for the identification and utilization of candidate genes. We investigated genetic diversity, population structure, and signatures of selection using genome-wide sequencing data for a new breed of Qinchuan cattle (QNC, n = 21), ancestral Qinchuan cattle (QCC, n = 20), and Zaosheng cattle (ZSC, n = 19). RESULTS: A population structure analysis showed that the ancestry components of QNC and ZSC were similar. In addition, the QNC and ZSC groups showed higher proportions of European taurine ancestry than that of QCC, and this may explain the larger body size of QNC, approaching that of European cattle under long-term domestication and selection. A neighbor-joining tree revealed that QCC individuals were closely related, whereas QNC formed a distinct group. To search for signatures of selection in the QNC genome, we evaluated nucleotide diversity (θπ), the fixation index (FST) and Tajima's D. Overlapping selective sweeps were enriched for one KEGG pathway, the apelin signaling pathway, and included five candidate genes (MEF2A, SMAD2, CAMK4, RPS6, and PIK3CG). We performed a comprehensive review of genomic variants in QNC, QCC, and ZSC using whole-genome sequencing data. QCC was rich in novel genetic diversity, while diversity in QNC and ZSC cattle was reduced due to strong artificial selection, with divergence from the original cattle. CONCLUSIONS: We identified candidate genes associated with production traits. These results support the success of selective breeding and can guide further breeding and resource conservation of Qinchuan cattle.

Whole-genome selection signature differences between Chaohu and Ji'an red ducks.

Assessing the genetic structure of local varieties and understanding their genetic data are crucial for effective management and preservation. However, the genetic differences among local breeds require further explanation. To enhance our understanding of their population structure and genetic diversity, we conducted a genome-wide comparative study of Chaohu and Ji'an Red ducks using genome sequence and restriction site-associated DNA sequencing technology. Our analysis revealed a distinct genetic distinction between the two breeds, leading to divided groups. The phylogenetic tree for Chaohu duck displayed two branches, potentially indicating minimal impact from artificial selection. Additionally, our ROH (runs of homozygosity) analysis revealed that Chaohu ducks had a lower average inbreeding coefficient than Ji'an Red ducks. We identified several genomic regions with high genetic similarity in these indigenous duck breeds. By conducting a selective sweep analysis, we identified 574 candidate genes associated with muscle growth (BMP2, ITGA8, MYLK, and PTCH1), fat deposits (ELOVL1 and HACD2), and pigmentation (ASIP and LOC101797494). These results offer valuable insights for the further enhancement and conservation of Chinese indigenous duck breeds.

Comparative whole-genome resequencing to uncover selection signatures linked to litter size in Hu Sheep and five other breeds.

Hu sheep (HS), a breed of sheep carrying the FecB mutation gene, is known for its "year-round estrus and multiple births" and is an ideal model for studying the high fecundity mechanisms of livestock. Through analyzing and comparing the genomic selection features of Hu sheep and other sheep breeds, we identified a series of candidate genes that may play a role in Hu sheep's high fecundity mechanisms. In this study, we conducted whole-genome resequencing on six breeds and screened key mutations significantly correlated with high reproductive traits in sheep. Notably, the CC2D1B gene was selected by the fixation index (FST) and the cross-population composite likelihood ratio (XP-CLR) methods in HS and other five breeds. It was worth noting that the CC2D1B gene in HS was different from that in other sheep breeds, and seven missense mutations have been identified. Furthermore, the linkage disequilibrium (LD) analysis revealed a strong linkage disequilibrium in this specific gene region. Subsequently, by performing different grouping based on FecB genotypes in Hu sheep, genome-wide selective signal analysis screened several genes related to reproduction, such as BMPR1B and PPM1K. Besides, FST analysis identified functional genes related to reproductive traits, including RHEB, HSPA2, PPP1CC, HVCN1, and CCDC63. Additionally, a missense mutation was found in the CCDC63 gene and the haplotype was different between the high reproduction (HR) group and low reproduction (LR) group in HS. In summary, we discovered genetic differentiation among six distinct breeding sheep breeds at the whole genome level. Additionally, we identified a set of genes which were associated with reproductive performance in Hu sheep and visualized how these genes differed in different breeds. These findings laid a theoretical foundation for understanding genetic mechanisms behind high prolific traits in sheep.

Genome-wide detection of selection signatures in Jianli pigs reveals novel cis-regulatory haplotype in EDNRB associated with two-end black coat color.

BACKGROUND: Jianli pig, a renowned indigenous breed in China, has the characteristics of a two-end black (TEB) coat color, excellent meat quality, strong adaptability and increased prolificacy. However, there is limited information available regarding the genetic diversity, population structure and genomic regions under selection of Jianli pig. On the other hand, the genetic mechanism of TEB coat color has remained largely unknown. RESULTS: In this study, the whole genome resequencing of 30 Jianli pigs within a context of 153 individuals representing 13 diverse breeds was performed. The population structure analysis revealed that Jianli pigs have close genetic relationships with the Tongcheng pig breed, their geographical neighbors. Three methods (observed heterozygosity, expected heterozygosity, and runs of homozygosity) implied a relatively high level of genetic diversity and, a low inbreeding coefficient in Jianli compared with other pigs. We used Fst and XP-EHH to detect the selection signatures in Jianli pigs compared with Asian wild boar. A total of 451 candidate genes influencing meat quality (CREBBP, ADCY9, EEPD1 and HDAC9), reproduction (ESR1 and FANCA), and coat color (EDNRB, MITF and MC1R), were detected by gene annotation analysis. Finally, to fine-map the genomic region for the two-end black (TEB) coat color phenotype in Jianli pigs, we performed three signature selection methods between the TEB coat color and no-TEB coat color pig breeds. The current study, further confirmed that the EDNRB gene is a candidate gene for TEB color phenotype found in Chinese pigs, including Jinhua pigs, and the haplotype harboring 25 SNPs in the EDNRB gene may promote the formation of TEB coat color. Further ATAC-seq and luciferase reporter assays of these regions suggest that the 25-SNPs region was a strong candidate causative mutation that regulates the TEB coat color phenotype by altering enhancer function. CONCLUSION: Our results advanced the understanding of the genetic mechanism behind artificial selection, and provided further resources for the protection and breeding improvement of Jianli pigs.

Selective sweep analysis of the adaptability of the Yarkand hare (Lepus yarkandensis) to hot arid environments using SLAF-seq.

The Yarkand hare (Lepus yarkandensis) inhabits arid desert areas and is endemic to China. It has evolved various adaptations to survive in hot arid environments, including stress responses, the ability to maintain water homeostasis and heat tolerance. Here, we performed a selective sweep analysis to identify the candidate genes for adaptation to hot arid environments in the Yarkand hare. A total of 397 237 single-nucleotide polymorphisms were obtained from 80 Yarkand hares, which inhabit hot arid environments, and 36 Tolai hares (Lepus tolai), which inhabit environments with a mild climate, via specific-locus amplified fragment sequencing. We identified several candidate genes that were associated with the heat stress response (HSPE1), oxidative stress response (SLC23A and GLRX2), immune response (IL1R1 and IRG1), central nervous system development (FGF13, THOC2, FMR1 and MECP2) and regulation of water homeostasis (CDK1) according to fixation index values and θπ ratios in the selective sweep analysis, and six of these genes (GLRX2, IRG1, FGF13, FMR1, MECP2 and CDK1) are newly discovered genes. To the best of our knowledge, this is the first study to identify candidate genes for adaptation to hot arid environments in the Yarkand hare. The results of this study enhance our understanding of the adaptation of the Yarkand hare to hot arid environments and will aid future studies aiming to functionally verify these candidate genes.

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.

Sorghum Association Panel whole-genome sequencing establishes cornerstone resource for dissecting genomic diversity.

Association mapping panels represent foundational resources for understanding the genetic basis of phenotypic diversity and serve to advance plant breeding by exploring genetic variation across diverse accessions. We report the whole-genome sequencing (WGS) of 400 sorghum (Sorghum bicolor (L.) Moench) accessions from the Sorghum Association Panel (SAP) at an average coverage of 38× (25-72×), enabling the development of a high-density genomic marker set of 43 983 694 variants including single-nucleotide polymorphisms (approximately 38 million), insertions/deletions (indels) (approximately 5 million), and copy number variants (CNVs) (approximately 170 000). We observe slightly more deletions among indels and a much higher prevalence of deletions among CNVs compared to insertions. This new marker set enabled the identification of several novel putative genomic associations for plant height and tannin content, which were not identified when using previous lower-density marker sets. WGS identified and scored variants in 5-kb bins where available genotyping-by-sequencing (GBS) data captured no variants, with half of all bins in the genome falling into this category. The predictive ability of genomic best unbiased linear predictor (GBLUP) models was increased by an average of 30% by using WGS markers rather than GBS markers. We identified 18 selection peaks across subpopulations that formed due to evolutionary divergence during domestication, and we found six Fst peaks resulting from comparisons between converted lines and breeding lines within the SAP that were distinct from the peaks associated with historic selection. This population has served and continues to serve as a significant public resource for sorghum research and demonstrates the value of improving upon existing genomic resources.

Selection signatures for local and regional adaptation in Chinese Mongolian horse breeds reveal candidate genes for hoof health.

BACKGROUND: Thousands of years of natural and artificial selection since the domestication of the horse has shaped the distinctive genomes of Chinese Mongolian horse populations. Consequently, genomic signatures of selection can provide insights into the human-mediated selection history of specific traits and evolutionary adaptation to diverse environments. Here, we used genome-wide SNPs from five distinct Chinese Mongolian horse populations to identify genomic regions under selection for the population-specific traits, gait, black coat colour, and hoof quality. Other global breeds were used to identify regional-specific signatures of selection. RESULTS: We first identified the most significant selection peak for the Wushen horse in the region on ECA23 harbouring DMRT3, the major gene for gait. We detected selection signatures encompassing several genes in the Baicha Iron Hoof horse that represent good biological candidates for hoof health, including the CSPG4, PEAK1, EXPH5, WWP2 and HAS3 genes. In addition, an analysis of regional subgroups (Asian compared to European) identified a single locus on ECA3 containing the ZFPM1 gene that is a marker of selection for the major domestication event leading to the DOM2 horse clade. CONCLUSIONS: Genomic variation at these loci in the Baicha Iron Hoof may be leveraged in other horse populations to identify animals with superior hoof health or those at risk of hoof-related pathologies. The overlap between the selection signature in Asian horses with the DOM2 selection peak raises questions about the nature of horse domestication events, which may have involved a prehistoric clade other than DOM2 that has not yet been identified.

A whole genome scan reveals distinct features of selection in Zhaotong cattle of Yunnan province.

Over the years, indigenous cattle have not only played an essential role in securing primary food sources but have also been utilized for labor by humans, making them invaluable genetic resources. The Zhaotong cattle, a native Chinese breed from the Yunnan province, possess excellent meat quality and resistance to heat and humidity. Here we used whole genome sequencing data of 104 animals to delve into the population structure, genomic diversity and potential positive selection signals in Zhaotong cattle. The findings of this study demonstrate that the genetic composition of Zhaotong cattle was primarily derived from Chinese indicine cattle and East Asian cattle. The nucleotide diversity of Zhaotong cattle was only lower than that of Chinese indicine cattle, which was much higher than that of other taurine cattle. Genome-wide selection scans detected a series of positive candidate regions containing multiple key genes related to bone development and metabolism (CA10, GABRG3, GLDN and NOTUM), meat quality traits (ALG8, LINGO2, MYO5B, PRKG1 and GABRB1), immune response (ADA2, BMF, LEF1 and PAK6) and heat resistance (EIF2AK4 and LEF1). In summary, this study supplies essential genetic insights into the genome diversity within Zhaotong cattle and provides a foundational framework for comprehending the genetic basis of indigenous cattle breeds.

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.

Integrated testis transcriptome and whole genome analysis of sexual maturity in Large White and Tongcheng pigs.

Testicular development and spermatogenesis play critical roles in male fertility and sexual maturation. To explore the genetic basis and key genes related to sexual maturity, we measured serum testosterone content and analysed testis tissue sections of Large White (LW) and Tongcheng (TC) boars at an immature age. We then screened differentially expressed genes (DEGs) in testis development in both breeds using RNA-seq. Finally, we analysed the selection signatures of both breeds to investigate which DEGs were subjected to positive selection. Our findings showed that serum testosterone contents in TC pigs (~4 ng/mL) were much higher than those in LW pigs (<0.95 ng/mL). Haematoxylin and eosin staining of testicular sections showed that the cross-sectional areas and perimeters of the seminiferous tubules in TC testes were larger and longer than those in LW pigs. A total of 5068 DEGs were selected by filtering criteria of q value <0.05 and |log2 (fold change)| ≥ 1. Gene Ontology analysis revealed that 250 genes were enriched in 11 biological process categories involved in sexual maturity. Most candidate genes, including TRIP13, NR6A1, STRA8, PCSK4, ACRBP, TSSK1B and TSSK6, were under positive selection. These results provide a better understanding of the genetic basis for testicular maturation and are useful for enhancing boar reproductive traits through molecular breeding.

Mitonuclear incompatibility as a hidden driver behind the genome ancestry of African admixed cattle.

BACKGROUND: Africa is an important watershed in the genetic history of domestic cattle, as two lineages of modern cattle, Bos taurus and B. indicus, form distinct admixed cattle populations. Despite the predominant B. indicus nuclear ancestry of African admixed cattle, B. indicus mitochondria have not been found on the continent. This discrepancy between the mitochondrial and nuclear genomes has been previously hypothesized to be driven by male-biased introgression of Asian B. indicus into ancestral African B. taurus. Given that this hypothesis mandates extreme demographic assumptions relying on random genetic drift, we propose a novel hypothesis of selection induced by mitonuclear incompatibility and assess these hypotheses with regard to the current genomic status of African admixed cattle. RESULTS: By analyzing 494 mitochondrial and 235 nuclear genome sequences, we first confirmed the genotype discrepancy between mitochondrial and nuclear genome in African admixed cattle: the absence of B. indicus mitochondria and the predominant B. indicus autosomal ancestry. We applied approximate Bayesian computation (ABC) to assess the posterior probabilities of two selection hypotheses given this observation. The results of ABC indicated that the model assuming both male-biased B. indicus introgression and selection induced by mitonuclear incompatibility explains the current genomic discrepancy most accurately. Subsequently, we identified selection signatures at autosomal loci interacting with mitochondria that are responsible for integrity of the cellular respiration system. By contrast with B. indicus-enriched genome ancestry of African admixed cattle, local ancestries at these selection signatures were enriched with B. taurus alleles, concurring with the key expectation of selection induced by mitonuclear incompatibility. CONCLUSIONS: Our findings support the current genome status of African admixed cattle as a potential outcome of male-biased B. indicus introgression, where mitonuclear incompatibility exerted selection pressure against B. indicus mitochondria. This study provides a novel perspective on African cattle demography and supports the role of mitonuclear incompatibility in the hybridization of mammalian species.

Genome-wide scan for selective sweeps identifies novel loci associated with resistance to mastitis in German Holstein cattle.

Domestication and selection significantly changed phenotypic and behavioural traits in modern domestic animals. In this study, to identify the genomic regions associated with mastitis, genomic data of German Holstein dairy cattle were analysed. The samples were genotyped using the Bovine 50 K SNP chip. For each defined healthy and sick group, 133 samples from 13,276 genotyped dairy cows were selected based on mastitis random residual effects. Grouping was done to infer selection signatures based on XP-EHH statistic. The results revealed that for the top 0.01 percentile of the obtained XP-EHH values, five genomic regions on chromosomes 8, 11, 12, 14 and 26 of the control group, and four regions on chromosomes 3, 4 (two regions) and 22 of the case group, have been under selection. Also, consideration of the top 0.1 percentile of the XP-EHH values, clarified 21 and 15 selective sweeps in the control and case group, respectively. This study identified some genomic regions containing potential candidate genes associated with resistance and susceptibility to mastitis, immune system and inflammation, milk traits, udder morphology and different types of cancers. In addition, these regions overlap with some quantitative trait loci linked to clinical mastitis, immunoglobulin levels, somatic cell score, udder traits, milk fat and protein, milk yield, milking speed and veterinary treatments. It is noteworthy that we found two regions in the healthy group (on chromosomes 12 and 14) with strong signals, which were not described previously. It is likely that future research could link these identified genomic regions to mastitis. The results of the current study contribute to the identification of causal mutations, genomic regions and genes affecting mastitis incidence in dairy cows.

A genome-wide comparison between selected and unselected Valle del Belice sheep reveals differences in population structure and footprints of recent selection.

About three decades of breeding and selection in the Valle del Belìce sheep are expected to have left several genomic footprints related to milk production traits. In this study, we have assembled a dataset with 451 individuals of the Valle del Belìce sheep breed: 184 animals that underwent directional selection for milk production and 267 unselected animals, genotyped for 40,660 single-nucleotide polymorphisms (SNPs). Three different statistical approaches, both within (iHS and ROH) and between (Rsb) groups, were used to identify genomic regions potentially under selection. Population structure analyses separated all individuals according to their belonging to the two groups. A total of four genomic regions on two chromosomes were jointly identified by at least two statistical approaches. Several candidate genes for milk production were identified, corroborating the polygenic nature of this trait and which may provide clues to potential new selection targets. We also found candidate genes for growth and reproductive traits. Overall, the identified genes may explain the effect of selection to improve the performances related to milk production traits in the breed. Further studies using high-density array data, would be particularly relevant to refine and validate these results.

Convergent Genomic Signatures of Cashmere Traits: Evidence for Natural and Artificial Selection.

Convergent evolution provides powerful opportunities to investigate the genetic basis of complex traits. The Tibetan antelope (Pantholops hodgsonii) and Siberian ibex (Capra sibirica) belong to different subfamilies in Bovidae, but both have evolved similar superfine cashmere characteristics to meet the cold temperature in plateau environments. The cashmere traits of cashmere goats underwent strong artificial selection, and some traces of domestication also remained in the genome. Hence, we investigated the convergent genomic signatures of cashmere traits between natural and artificial selection. We compared the patterns of convergent molecular evolution between Tibetan antelope and Siberian ibex by testing positively selected genes, rapidly evolving genes and convergent amino acid substitutions. In addition, we analyzed the selected genomic features of cashmere goats under artificial selection using whole-genome resequencing data, and skin transcriptome data of cashmere goats were also used to focus on the genes involved in regulating cashmere traits. We found that molecular convergent events were very rare, but natural and artificial selection genes were convergent enriched in similar functional pathways (e.g., ECM-receptor interaction, focal adhesion, PI3K-Akt signaling pathway) in a variety of gene sets. Type IV collagen family genes (COL4A2, COL4A4, COL4A5, COL6A5, COL6A6) and integrin family genes (ITGA2, ITGA4, ITGA9, ITGB8) may be important candidate genes for cashmere formation and development. Our results provide a comprehensive approach and perspective for exploring cashmere traits and offer a valuable reference for subsequent in-depth research on the molecular mechanisms regulating cashmere development and fineness.

Genetic Diversity, Population Structure, and Environmental Adaptation Signatures of Chinese Coastal Hard-Shell Mussel Mytilus coruscus Revealed by Whole-Genome Sequencing.

The hard-shell mussel (Mytilus coruscus) is widespread in the temperate coastal areas of the northwest Pacific and holds a significant position in the shellfish aquaculture market in China. However, the natural resources of this species have been declining, and population genetic studies of M. coruscus are also lacking. In this study, we conducted whole-genome resequencing (WGR) of M. coruscus from eight different latitudes along the Chinese coast and identified a total of 25,859,986 single nucleotide polymorphism (SNP) markers. Our findings indicated that the genetic diversity of M. coruscus from the Zhoushan region was lower compared with populations from other regions. Furthermore, we observed that the evolutionary tree clustered into two primary branches, and the Zhangzhou (ZZ) population was in a separate branch. The ZZ population was partly isolated from populations in other regions, but the distribution of branches was not geographically homogeneous, and a nested pattern emerged, consistent with the population differentiation index (FST) results. To investigate the selection characteristics, we utilized the northern M. coruscus populations (Dalian and Qingdao) and the central populations (Zhoushan and Xiangshan) as reference populations and the southern ZZ population as the target population. Our selection scan analysis identified several genes associated with thermal responses, including Hsp70 and CYP450. These genes may play important roles in the adaptation of M. coruscus to different living environments. Overall, our study provides a comprehensive understanding of the genomic diversity of coastal M. coruscus in China and is a valuable resource for future studies on genetic breeding and the evolutionary adaptation of this species.

Genomic selection pressure discovery using site-frequency spectrum and reduced local variability statistics in Pakistani Dera-Din-Panah goat.

BACKGROUND: Population geneticists have long sought to comprehend various selection traces accumulated in the goat genome due to natural or human driven artificial selection through breeding practices, which led the wild animals to domestication, so understanding evolutionary process may helpful to utilize the full genetic potential of goat genome. METHODS AND RESULTS: As a step forward to pinpoint the selection signals in Pakistani Dera-Din-Panah (DDP) goat, whole-genome pooled sequencing (n = 12) was performed, and 618,236,192 clean paired-end reads were mapped against ARS1 reference goat assembly. Five different selection signature statistics were applied using four site-frequency spectrum (SFS) methods (Tajima's D ([Formula: see text]), Fay and Wu's H ([Formula: see text]), Zeng's E ([Formula: see text]), [Formula: see text]) and one reduced local variability approach named pooled heterozygosity ([Formula: see text]). The under-selection regions were annotated with significant threshold values of [Formula: see text]≥4.7, [Formula: see text]≥6, [Formula: see text]≥2.5, Pool-HMM ≥ 12, and [Formula: see text]≥5 that resulted in accumulative 364 candidate gene hits. The highest genomic selection signals were observed on Chr. 4, 6, 10, 12, 15, 16, 18, 20, and 27 and harbor ADAMTS6, CWC27, RELN, MYCBP2, FGF14, STIM1, CFAP74, GNB1, CALML6, TMEM52, FAM149A, NADK, MMP23B, OPN3, FH, MFHAS1, KLKB1, RRM1, KMO, SPEF2, F11, KIT, KMO, ERI1, ATP8B4, and RHOG genes. Next, the validation of our captured genomic hits was also performed by more than one applied statistics which harbor meat production, immunity, and reproduction associated genes to strengthen our hypothesis of under-selection traits in this Pakistani goat breed. Furthermore, common candidate genes captured by more than one statistical method were subjected to gene ontology and KEGG pathway analysis to get insights of particular biological processes associated with this goat breed. CONCLUSION: Current perception of genomic architecture of DDP goat provides a better understanding to improve its genetic potential and other economically important traits of medium to large body size, milk, and fiber production by updating the genomic insight driven breeding strategies to boost the livestock and agriculture-based economy of the country.

Simultaneous testing of rule- and model-based approaches for runs of homozygosity detection opens up a window into genomic footprints of selection in pigs.

BACKGROUND: Past selection events left footprints in the genome of domestic animals, which can be traced back by stretches of homozygous genotypes, designated as runs of homozygosity (ROHs). The analysis of common ROH regions within groups or populations displaying potential signatures of selection requires high-quality SNP data as well as carefully adjusted ROH-defining parameters. In this study, we used a simultaneous testing of rule- and model-based approaches to perform strategic ROH calling in genomic data from different pig populations to detect genomic regions under selection for specific phenotypes. RESULTS: Our ROH analysis using a rule-based approach offered by PLINK, as well as a model-based approach run by RZooRoH demonstrated a high efficiency of both methods. It underlined the importance of providing a high-quality SNP set as input as well as adjusting parameters based on dataset and population for ROH calling. Particularly, ROHs ≤ 20 kb were called in a high frequency by both tools, but to some extent covered different gene sets in subsequent analysis of ROH regions common for investigated pig groups. Phenotype associated ROH analysis resulted in regions under potential selection characterizing heritage pig breeds, known to harbour a long-established breeding history. In particular, the selection focus on fitness-related traits was underlined by various ROHs harbouring disease resistance or tolerance-associated genes. Moreover, we identified potential selection signatures associated with ear morphology, which confirmed known candidate genes as well as uncovered a missense mutation in the ABCA6 gene potentially supporting ear cartilage formation. CONCLUSIONS: The results of this study highlight the strengths and unique features of rule- and model-based approaches as well as demonstrate their potential for ROH analysis in animal populations. We provide a workflow for ROH detection, evaluating the major steps from filtering for high-quality SNP sets to intersecting ROH regions. Formula-based estimations defining ROHs for rule-based method show its limits, particularly for efficient detection of smaller ROHs. Moreover, we emphasize the role of ROH detection for the identification of potential footprints of selection in pigs, displaying their breed-specific characteristics or favourable phenotypes.

Genomic consequences of artificial selection during early domestication of a wood fibre crop.

From its origins in Australia, Eucalyptus grandis has spread to every continent, except Antarctica, as a wood crop. It has been cultivated and bred for over 100 yr in places such as South Africa. Unlike most annual crops and fruit trees, domestication of E. grandis is still in its infancy, representing a unique opportunity to interrogate the genomic consequences of artificial selection early in the domestication process. To determine how a century of artificial selection has changed the genome of E. grandis, we generated single nucleotide polymorphism genotypes for 1080 individuals from three advanced South African breeding programmes using the EUChip60K chip, and investigated population structure and genome-wide differentiation patterns relative to wild progenitors. Breeding and wild populations appeared genetically distinct. We found genomic evidence of evolutionary processes known to have occurred in other plant domesticates, including interspecific introgression and intraspecific infusion from wild material. Furthermore, we found genomic regions with increased linkage disequilibrium and genetic differentiation, putatively representing early soft sweeps of selection. This is, to our knowledge, the first study of genomic signatures of domestication in a timber species looking beyond the first few generations of cultivation. Our findings highlight the importance of intra- and interspecific hybridization during early domestication.

Detection of Common Copy Number of Variants Underlying Selection Pressure in Middle Eastern Horse Breeds Using Whole-Genome Sequence Data.

Dareshouri, Arabian, and Akhal-Teke are 3 Middle Eastern horse breeds that have been selected for endurance and adaptation to harsh climates. Deciphering the genetic characteristics of these horses by tracing selection footprints and copy number of variations will be helpful in improving our understanding of equine breeds' development and adaptation. For this purpose, we sequenced the whole genome of 4 Dareshouri horses using Illumina Hiseq panels and compared them with publicly available whole-genome sequences of Arabian (n = 3) and Akhal-Teke (n = 3) horses. Three tests of FLK, hapFLK, and pooled heterozygosity were applied using a sliding window (window size = 100 kb, step size = 50 kb) approach to detect putative selection signals. Copy number variation analysis was applied to investigate copy number of variants (CNVs), and the results were used to suggest selection signatures involving CNVs. Whole-genome sequencing demonstrated 8 837 950 single-nucleotide polymorphisms (SNPs) in autosomal chromosomes. We suggested 58 genes and 3 quantitative trait loci, including some related to horse gait, insect bite hypersensitivity, and withers height, based on selective signals detected by adjusted P-value of Mahalanobis distance based on the rank-based P-values (Md-rank-P) method. We proposed 12 genomic regions under selection pressure involving CNVs that were previously reported to be associated with metabolism energy (SLC5A8), champagne dilution in horses (SLC36A1), and synthesis of polyunsaturated fatty acids (FAT2). Only 10 Middle Eastern horses were tested in this study; therefore, the conclusions are speculative. Our findings are useful to better understanding the evolution and adaptation of Middle Eastern horse breeds.