All sheeps and sizes: a genetic investigation of mature body size across sheep breeds reveals a polygenic nature

Characterizing differences in the muscle transcriptome between cattle with alternative LCORL-NCAPG haplotypes

BACKGROUND

The LCORL-NCAPG locus is a major quantitative trait locus (QTL) on bovine chromosome 6 (BTA6) that influences growth and carcass composition in cattle. To further understand the molecular mechanism responsible for the phenotypic changes associated with this locus, twenty-four Charolais-sired calves were selected for muscle transcriptome analysis based on alternative homozygous LCORL-NCAPG haplotypes (i.e., 12 "QQ" and 12 "qq", where "Q" is a haplotype harboring variation associated with increased growth). At 300 days of age, a biopsy of the longissimus dorsi muscle was collected from each animal for RNA sequencing.

RESULTS

Gene expression analysis identified 733 genes as differentially expressed between QQ and qq animals (q-value < 0.05). Notably, LCORL and genes known to be important regulators of growth such as IGF2 were upregulated in QQ individuals, while genes associated with adiposity such as FASN and LEP were downregulated, reflecting the increase in lean growth associated with this locus. Gene set enrichment analysis demonstrated QQ individuals had downregulation of pathways associated with adipogenesis, alongside upregulation of transcripts for cellular machinery essential for protein synthesis and energy metabolism, particularly ribosomal and mitochondrial components.

CONCLUSIONS

The differences in the muscle transcriptome between QQ and qq animals imply that muscle hypertrophy may be metabolically favored over accumulation of fat in animals with the QQ haplotype. Our findings also suggest this haplotype could be linked to a difference in LCORL expression that potentially influences the downstream transcriptional effects observed, though further research will be needed to confirm the molecular mechanisms underlying the associated changes in phenotype.

Identification of Candidate Genes and Functional Pathways Associated with Body Size Traits in Hulunbuir Sheep Through GWAS Analysis

(1) Background: The Hulunbuir sheep is a Chinese local sheep breed with good meat quality and exceptional cold-stress resilience. However, the growth performance of the Hulunbuir sheep is lower when compared to that of commercial breeds. Growth traits such as body weight and body size are critical, as they directly influence the meat production in sheep farming. Employing genome-wide association studies can identify SNPs and candidate genes related to growth traits in Hulunbuir sheep. (2) Methods: The chest girth (CG), cannon circumference (CC), hip width (HW), body height (BH), and body length (BL) of 799 Hulunbuir sheep were measured. All the animals were divided into three groups according to their age (Group 1: 0-6 months old, Group 2: 12-24 months old, Group 3: 48-70 months old). Subsequently, genotyping was carried out using the Sheep 40K liquid chip. A multi-trait genome-wide association study (MT-GWAS) was performed for each group of animals. (3) Results: A total of three candidate genes (SLC9C1, VSTM2A, FRG1) associated with body size traits were identified through GWAS analysis and KEGG pathway enrichment for Group 2. (4) Conclusions: This study identified three candidate genes related to body size in Hulunbuir sheep, providing genetic targets for marker-assisted selection (MAS) in Hulunbuir sheep.

Genome-wide association study identifies candidate genes affecting body conformation traits of Zhongwei goat

BACKGROUND

Identifying markers or genes crucial for growth traits in Zhongwei goats is pivotal for breeding. Pinpointing genetic factors linked to body size gain enhances breeding efficiency and economic value. In this study, we used the MGISEQ-T7 platform to re-sequence 240 Zhongwei goats (133 male; 107 female) belonging to 5 metrics of growth traits at different growth stages (40 days and 6 months, here in after referred to as 40d and 6 m), namely, Body Weight (BW), Body Height (BH), Body Length (BL), Chest Circumference (CC), Tube Circumference (TC) were examined. A Genome-wide association study (GWAS) was conducted to identify candidate genes associated with the five indicators of body conformation traits, thereby establishing a foundation for subsequent investigations into the biological functions of these genes.

RESULTS

A total of 19.89 Tb of raw data was generated with an average sequencing depth of about 20×. After quality control, 15,958,716 SNPs were available for the analysis. A total of 342 genome-wide significant SNPs were obtained. Among them, in the two physiological stages of 40d and 6 m, 147 and 32 SNPs were significantly associated with BW; 1 and 4 SNPs were significantly associated with BH; 19 and 6 SNPs were significantly associated with BL; 33 and 64 SNPs were significantly associated with CC, 34 and 2 SNPs were significantly associated with TC. These SNPs were annotated to 425 candidate genes. Finally, A total of 39 candidate genes are closely related to biological processes such as skeletal muscle development, skeletal formation, carcass quality, and embryonic development, where ADIPOQ, CCDD39, PTPRT, ZNF215, VRTN, ABCD4, DLST, ADAMTS2, ROBO1, AKAP13, AQPI, SOX2, and AHSG were identified as an important component of the genetic framework that may control somatic conformational traits in Zhongwei goats. which warrants further investigation and review. We verified the polymorphism of 11 SNPs by KASP, and found that Chr13_g.11,700,438 A > G, Chr15_g.37,120,328 A > G, Chr6_g.7,209,383 C > T, Chr20_g.51277932T > A, Chr19_g.17,078,199 A > G, and Chr1_g.79,943,276 C > T were significantly genotyped in verified populations (P < 0.001).

CONCLUTION

It is the first GWAS study to analyze genomic data from 40d and 6 m of Zhongwei goats to understand the molecular genetic mechanisms of growth. Our research identified a series of SNPs and candidate genes associated with growth traits, which could assist us in developing the meat production trait in Zhongwei goats.

Genome-wide association studies of body size traits in Tibetan sheep

BACKGROUND

Elucidating the genetic variation underlying phenotypic diversity will facilitate improving production performance in livestock species. The Tibetan sheep breed in China holds significant historical importance, serving as a fundamental pillar of Qinghai's animal husbandry sector. The Plateau-type Tibetan sheep, comprising 90% of the province's population, are characterized by their tall stature and serve as the primary breed among Tibetan sheep. In contrast, Zhashijia sheep exhibit larger size and superior meat quality. These two species provide an excellent model for elucidating the genetic basis of body size variation. Therefore, this study aims to conduct a comprehensive genome-wide association study on these two Tibetan sheep breeds to identify single nucleotide polymorphism loci and regulatory genes that influence body size traits in Tibetan sheep.

RESULT

In this study, the phenotypic traits of body weight, body length, body height, chest circumference, chest depth, chest width, waist angle width, and pipe circumference were evaluated in two Tibetan sheep breeds: Plateau-type sheep and Zhashijia Tibetan sheep. Whole genome sequencing generated 48,215,130 high-quality SNPs for genome-wide association study. Four methods were applied and identified 623 SNPs significantly associated with body size traits. The significantly associated single nucleotide polymorphisms identified in this study are located near or within 111 candidate genes. These genes exhibit enrichment in the cAMP and Rap1 signaling pathways, significantly affecting animal growth, and body size. Specifically, the following genes were associated: ASAP1, CDK6, FRYL, NAV2, PTPRM, GPC6, PTPRG, KANK1, NTRK2 and ADCY8.

CONCLUSION

By genome-wide association study, we identified 16 SNPs and 10 candidate genes associated with body size traits in Tibetan sheep, which hold potential for application in genomic selection breeding programs in sheep. Identifying these candidate genes will establish a solid foundation for applying molecular marker-assisted selection in sheep breeding and improve our understanding of body size control in farmed animals.

Genome-wide association analysis identify candidate genes for feed efficiency and growth traits in Wenchang chickens

BACKGROUND

Wenchang chickens are one of the most popular local chicken breeds in the Chinese chicken industry. However, the low feed efficiency is the main shortcoming of this breed. Therefore, there is a need to find a more precise breeding method to improve the feed efficiency of Wenchang chickens. In this study, we explored important candidate genes and variants for feed efficiency and growth traits through genome-wide association study (GWAS) analysis.

RESULTS

Estimates of genomic heritability for growth and feed efficiency traits, including residual feed intake (RFI) of 0.05, average daily food intake (ADFI) of 0.21, average daily weight gain (ADG) of 0.24, body weight (BW) at 87, 95, 104, 113 days of age (BW87, BW95, BW104 and BW113) ranged from 0.30 to 0.44. Important candidate genes related to feed efficiency and growth traits were identified, such as PLCE1, LAP3, MED28, QDPR, LDB2 and SEL1L3 genes.

CONCLUSION

The results identified important candidate genes for feed efficiency and growth traits in Wenchang chickens and provide a theoretical basis for the development of new molecular breeding technology.

Genomic analyses of withers height and linear conformation traits in German Warmblood horses using imputed sequence-level genotypes

BACKGROUND

Body conformation, including withers height, is a major selection criterion in horse breeding and is associated with other important traits, such as health and performance. However, little is known about the genomic background of equine conformation. Therefore, the aim of this study was to use imputed sequence-level genotypes from up to 4891 German Warmblood horses to identify genomic regions associated with withers height and linear conformation traits. Furthermore, the traits were genetically characterised and putative causal variants for withers height were detected.

RESULTS

A genome-wide association study (GWAS) for withers height confirmed the presence of a previously known quantitative trait locus (QTL) on Equus caballus (ECA) chromosome 3 close to the LCORL/NCAPG locus, which explained 16% of the phenotypic variance for withers height. An additional significant association signal was detected on ECA1. Further investigations of the region on ECA3 identified a few promising candidate causal variants for withers height, including a nonsense mutation in the coding sequence of the LCORL gene. The estimated heritability for withers height was 0.53 and ranged from 0 to 0.34 for the conformation traits. GWAS identified significantly associated variants for more than half of the investigated conformation traits, among which 13 showed a peak on ECA3 in the same region as withers height. Genetic parameter estimation revealed high genetic correlations between these traits and withers height for the QTL on ECA3.

CONCLUSIONS

The use of imputed sequence-level genotypes from a large study cohort led to the discovery of novel QTL associated with conformation traits in German Warmblood horses. The results indicate the high relevance of the QTL on ECA3 for various conformation traits, including withers height, and contribute to deciphering causal mutations for body size in horses.

Defining a Haplotype Encompassing the LCORL-NCAPG Locus Associated with Increased Lean Growth in Beef Cattle

Numerous studies have shown genetic variation at the LCORL-NCAPG locus is strongly associated with growth traits in beef cattle. However, a causative molecular variant has yet to be identified. To define all possible candidate variants, 34 Charolais-sired calves were whole-genome sequenced, including 17 homozygous for a long-range haplotype associated with increased growth (QQ) and 17 homozygous for potential ancestral haplotypes for this region (qq). The Q haplotype was refined to an 814 kb region between chr6:37,199,897-38,014,080 and contained 218 variants not found in qq individuals. These variants include an insertion in an intron of NCAPG, a previously documented mutation in NCAPG (rs109570900), two coding sequence mutations in LCORL (rs109696064 and rs384548488), and 15 variants located within ATAC peaks that were predicted to affect transcription factor binding. Notably, rs384548488 is a frameshift variant likely resulting in loss of function for long isoforms of LCORL. To test the association of the coding sequence variants of LCORL with phenotype, 405 cattle from five populations were genotyped. The two variants were in complete linkage disequilibrium. Statistical analysis of the three populations that contained QQ animals revealed significant (p < 0.05) associations with genotype and birth weight, live weight, carcass weight, hip height, and average daily gain. These findings affirm the link between this locus and growth in beef cattle and describe DNA variants that define the haplotype. However, further studies will be required to define the true causative mutation.

Assessing the performance of Moghani crossbred lambs derived from different mating systems with Texel and Booroola sheep

In our ongoing project, which focuses on the introgression of Booroola/FecB gene and the myostatin (MSTN) gene into purebred Moghani sheep, we assessed the performance of second-generation Moghani crossbreds such as second crossbreds (F2) and initial backcross generation (BC1). These crossbreds were generated through different mating systems, including in-breeding, outcrossing, first paternal backcrossing (PBC1), and first maternal backcrossing (MBC1). Notably, F2 strains exhibited lean tail, woolly fleece and a higher percentage of white coat color compared to BC1. The impact of mating systems and birth types on pre-weaning survival rates was found to be statistically significant (P < 0.0001), with singleton offspring resulting from paternal backcross showing a particularly substantial effect. The F2 crossbred lambs carrying the Booroola gene did not show a statistically significant difference in survivability compared to those carrying the MSTN gene, implying the Booroola prolificacy gene had no significant impact on survival outcomes. However, the occurrence of multiple births had a significant negative impact on lamb survival (P < 0.0001). The PBC1 sheep strains, specifically Texel Tamlet ram strains carrying the MSTN mutation, exhibited superior growth rates compared to others (P < 0.05). Interestingly, the MSTN mutation in the homozygous variant genotype significantly impacts growth rate before weaning compared to other genotypes and pure Moghani sheep (P < 0.05). In conclusion, this study objectively underscores the pivotal role of genetic factors, specifically through strategic mating systems like paternal backcrossing, in enhancing desired traits and growth rates in Moghani sheep, thereby contributing valuable insights to the field of sheep breeding programs.

Whole-Genome Scanning for Selection Signatures Reveals Candidate Genes Associated with Growth and Tail Length in Sheep

Compared to Chinese indigenous sheep, Western sheep have rapid growth rate, larger physique, and higher meat yield. These excellent Western sheep were introduced into China for crossbreeding to expedite the enhancement of production performance and mutton quality in local breeds. Here, we investigated population genetic structure and genome-wide selection signatures among the Chinese indigenous sheep and the introduced sheep based on whole-genome resequencing data. The PCA, N-J tree and ADMIXTURE results showed significant genetic difference between Chinese indigenous sheep and introduced sheep. The nucleotide diversity (π) and linkage disequilibrium (LD) decay results indicated that the genomic diversity of introduced breeds were lower. Then, Fst & π ratio, XP-EHH, and de-correlated composite of multiple signals (DCMS) methods were used to detect the selection signals. The results showed that we identified important candidate genes related to growth rate and body size in the introduced breeds. Selected genes with stronger selection signatures are associated with growth rate (CRADD), embryonic development (BVES, LIN28B, and WNT11), body size (HMGA2, MSRB3, and PTCH1), muscle development and fat metabolism (MSTN, PDE3A, LGALS12, GGPS1, and SAR1B), wool color (ASIP), and hair development (KRT71, KRT74, and IRF2BP2). Thus, these genes have the potential to serve as candidate genes for enhancing the growth traits of Chinese indigenous sheep. We also identified tail-length trait-related candidate genes (HOXB13, LIN28A, PAX3, and VEGFA) in Chinese long-tailed breeds. Among these genes, HOXB13 is the main candidate gene for sheep tail length phenotype. LIN28A, PAX3, and VEGFA are related to embryonic development and angiogenesis, so these genes may be candidate genes for sheep tail type traits. This study will serve as a foundation for further genetic improvement of Chinese indigenous sheep and as a reference for studies related to growth and development of sheep.

Characterization of HMGA2 variants expands the spectrum of Silver-Russell syndrome

Silver-Russell syndrome (SRS) is a heterogeneous disorder characterized by intrauterine and postnatal growth retardation. HMGA2 variants are a rare cause of SRS and its functional role in human linear growth is unclear. Patients with suspected SRS negative for 11p15LOM/mUPD7 underwent whole-exome and/or targeted-genome sequencing. Mutant HMGA2 protein expression and nuclear localization were assessed. Two Hmga2-knockin mouse models were generated. Five clinical SRS patients harbored HMGA2 variants with differing functional impacts: 2 stop-gain nonsense variants (c.49G>T, c.52C>T), c.166A>G missense variant, and 2 frameshift variants (c.144delC, c.145delA) leading to an identical, extended-length protein. Phenotypic features were highly variable. Nuclear localization was reduced/absent for all variants except c.166A>G. Homozygous knockin mice recapitulating the c.166A>G variant (Hmga2K56E) exhibited a growth-restricted phenotype. An Hmga2Ter76-knockin mouse model lacked detectable full-length Hmga2 protein, similarly to patient 3 and 5 variants. These mice were infertile, with a pygmy phenotype. We report a heterogeneous group of individuals with SRS harboring variants in HMGA2 and describe the first Hmga2 missense knockin mouse model (Hmga2K56E) to our knowledge causing a growth-restricted phenotype. In patients with clinical features of SRS but negative genetic screening, HMGA2 should be included in next-generation sequencing testing approaches.

Genome-wide association study of growth traits and validation of key mutations (MSTN c.C861T) associated with the muscle mass of meat pigeons

Selective breeding of meat pigeons is primarily based on growth traits, especially muscle mass (MM). Identification of functional genes and molecular markers of growth and slaughter traits through a genome-wide association study (GWAS) will help to elucidate the underlying molecular mechanisms and provide a theoretical basis for the selective breeding of meat pigeons. The phenotypic data of body weight (BW) and body size (BS) of 556 meat pigeons at 52 and 80 weeks of age were collected. In total, 160 434 high-quality single nucleotide polymorphism sites were obtained by restriction site-associated DNA sequencing. The GWAS analysis revealed that MSTN, IGF2BP3 and NCAPG/LCORL were important candidate genes affecting the growth traits of meat pigeons. IGF2BP3 and NCAPG/LCORL were highly correlated to BW and BS, which are related to overall growth and development, while MSTN was associated with pectoral thickness and BW. Phenotypic association validation with the use of two meat pigeon populations found that the MSTN mutation c.C861T determines the MM. These results provide new insights into the genetic mechanisms underlying phenotypic variations of growth traits and MM in commercial meat pigeons. The identified markers and genes provide a theoretical basis for the selective breeding of meat pigeons.

A mutation in POLR2A gene associated with body size traits in Dezhou donkeys revealed with GWAS

The Dezhou donkey is a famous local donkey breed in China. The aim of the present study was to identify the genes associated with the body size traits of the Dezhou donkey and facilitate the breeding activities of the donkeys. A total of 349 donkeys from 2 generations (113 individuals in F0 and 236 in F1) were analyzed with restriction-site-associated DNA sequencing. A genome-wide association study revealed that the region between 13.7 and 15.6 Mb of chromosome 13 is significantly associated with body sizes. Candidate genes related to body size development, including POLR2A, CHRNB1, FGF11, and ZBTB4, were identified. The results of GO and KEGG analysis indicated that the genes involved in many GO terms were related to metabolic processes and developmental processes. Additionally, a T>C mutation (Chr13:14312485) was found at intron 10 of the POLR2A gene. The association analysis showed significant differences among genotypes for the size traits. The body size of the individuals with the TT genotype was significantly higher than that with the CC genotype. The results showed that the polymorphism of POLR2A has the potential to be used as a marker in the breeding programs of the Dezhou donkeys.

Genomic Selection for Live Weight in the 14th Month in Alpine Merino Sheep Combining GWAS Information

Alpine Merino Sheep is a novel breed reared from Australian Merino Sheep as the father and Gansu Alpine Fine-Wool Sheep as the mother, living all year in cold and arid alpine areas with exceptional wool quality and meat performance. Body weight is an important economic trait of the Alpine Merino Sheep, but there is limited research on identifying the genes associated with live weight in the 14th month for improving the accuracy of the genomic prediction of this trait. Therefore, this study's sample comprised 1310 Alpine Merino Sheep ewes, and the Fine Wool Sheep 50K Panel was used for genome-wide association study (GWAS) analysis to identify candidate genes. Moreover, the trial population (1310 ewes) in this study was randomly divided into two groups. One group was used as the population for GWAS analysis and screened for the most significant top 5%, top 10%, top 15%, and top 20% SNPs to obtain prior marker information. The other group was used to estimate the genetic parameters based on the weight assigned by heritability combined with different prior marker information. The aim of this study was to compare the accuracy of genomic breeding value estimation when combined with prior marker information from GWAS analysis with the optimal linear unbiased prediction method for genome selection (GBLUP) for the breeding value of target traits. Finally, the accuracy was evaluated using the five-fold cross-validation method. This research provides theoretical and technical support to improve the accuracy of sheep genome selection and better guide breeding. The results demonstrated that eight candidate genes were associated with GWAS analysis, and the gene function query and literature search results suggested that FAM184B, NCAPG, MACF1, ANKRD44, DCAF16, FUK, LCORL, and SYN3 were candidate genes affecting live weight in the 14th month (WT), which regulated the growth of muscle and bone in sheep. In genome selection analysis, the heritability of GBLUP to calculate the WT was 0.335-0.374, the accuracy after five-fold cross-verification was 0.154-0.190, and after assigning different weights to the top 5%, top 10%, top 15%, and top 20% of the GWAS results in accordance with previous information to construct the G matrix, the accuracy of the WT in the GBLUP model was improved by 2.59-7.79%.

Genomic signatures of selection, local adaptation and production type characterisation of East Adriatic sheep breeds

BACKGROUND

The importance of sheep breeding in the Mediterranean part of the eastern Adriatic has a long tradition since its arrival during the Neolithic migrations. Sheep production system is extensive and generally carried out in traditional systems without intensive systematic breeding programmes for high uniform trait production (carcass, wool and milk yield). Therefore, eight indigenous Croatian sheep breeds from eastern Adriatic treated here as metapopulation (EAS), are generally considered as multipurpose breeds (milk, meat and wool), not specialised for a particular type of production, but known for their robustness and resistance to certain environmental conditions. Our objective was to identify genomic regions and genes that exhibit patterns of positive selection signatures, decipher their biological and productive functionality, and provide a "genomic" characterization of EAS adaptation and determine its production type.

RESULTS

We identified positive selection signatures in EAS using several methods based on reduced local variation, linkage disequilibrium and site frequency spectrum (eROHi, iHS, nSL and CLR). Our analyses identified numerous genomic regions and genes (e.g., desmosomal cadherin and desmoglein gene families) associated with environmental adaptation and economically important traits. Most candidate genes were related to meat/production and health/immune response traits, while some of the candidate genes discovered were important for domestication and evolutionary processes (e.g., HOXa gene family and FSIP2). These results were also confirmed by GO and QTL enrichment analysis.

CONCLUSIONS

Our results contribute to a better understanding of the unique adaptive genetic architecture of EAS and define its productive type, ultimately providing a new opportunity for future breeding programmes. At the same time, the numerous genes identified will improve our understanding of ruminant (sheep) robustness and resistance in the harsh and specific Mediterranean environment.

Community-wide genome sequencing reveals 30 years of Darwin's finch evolution

A fundamental goal in evolutionary biology is to understand the genetic architecture of adaptive traits. Using whole-genome data of 3955 of Darwin's finches on the Galápagos Island of Daphne Major, we identified six loci of large effect that explain 45% of the variation in the highly heritable beak size of Geospiza fortis, a key ecological trait. The major locus is a supergene comprising four genes. Abrupt changes in allele frequencies at the loci accompanied a strong change in beak size caused by natural selection during a drought. A gradual change in Geospiza scandens occurred across 30 years as a result of introgressive hybridization with G. fortis. This study shows how a few loci with large effect on a fitness-related trait contribute to the genetic potential for rapid adaptive radiation.

Identification of Candidate Genes and Functional Pathways Associated with Body Size Traits in Chinese Holstein Cattle Based on GWAS Analysis

Body size is one of the most economically important traits of dairy cattle, as it is significantly associated with cow longevity, production, health, fertility, and environmental adaptation. The identification and application of genetic variants using a novel genetic approach, such as genome-wide association studies (GWASs), may give more insights into the genetic architecture of complex traits. The identification of genes, single nucleotide polymorphisms (SNPs), and pathways associated with the body size traits may offer a contribution to genomic selection and long-term planning for selection in dairy cows. In this study, we performed GWAS analysis to identify the genetic markers and genes associated with four body size traits (body height, body depth, chest width, and angularity) in 1000 Chinese Holstein cows. We performed SNPs genotyping in 1000 individuals, based on the GeneSeek Genomic Profiler Bovine 100 K. In total, we identified 11 significant SNPs in association with body size traits at the threshold of Bonferroni correction (5.90 × 10−7) using the fixed and random model circulating probability unification (FarmCPU) model. Several genes within 200 kb distances (upstream or downstream) of the significant SNPs were identified as candidate genes, including MYH15, KHDRBS3, AIP, DCC, SQOR, and UBAP1L. Moreover, genes within 200 kb of the identified SNPs were significantly enriched (p ≤ 0.05) in 25 Gene Ontology terms and five Kyoto Encyclopedia of Genes and Genomes pathways. We anticipate that these results provide a foundation for understanding the genetic architecture of body size traits. They will also contribute to breeding programs and genomic selection work on Chinese Holstein cattle.

Disentangling clustering configuration intricacies for divergently selected chicken breeds

Divergently selected chicken breeds are of great interest not only from an economic point of view, but also in terms of sustaining diversity of the global poultry gene pool. In this regard, it is essential to evaluate the classification (clustering) of varied chicken breeds using methods and models based on phenotypic and genotypic breed differences. It is also important to implement new mathematical indicators and approaches. Accordingly, we set the objectives to test and improve clustering algorithms and models to discriminate between various chicken breeds. A representative portion of the global chicken gene pool including 39 different breeds was examined in terms of an integral performance index, i.e., specific egg mass yield relative to body weight of females. The generated dataset was evaluated within the traditional, phenotypic and genotypic classification/clustering models using the k-means method, inflection points clustering, and admixture analysis. The latter embraced SNP genotype datasets including a specific one focused on the performance-associated NCAPG-LCORL locus. The k-means and inflection points analyses showed certain discrepancies between the tested models/submodels and flaws in the produced cluster configurations. On the other hand, 11 core breeds were identified that were shared between the examined models and demonstrated more adequate clustering and admixture patterns. These findings will lay the foundation for future research to improve methods for clustering as well as genome- and phenome-wide association/mediation analyses.

Effects of the Level and Composition of Concentrate Supplements before Breeding and in Early Gestation on Production of Different Hair Sheep Breeds

Female hair sheep, 27 Dorper (DOR), 41 Katahdin (KAT), and 39 St. Croix (STC), were used to determine influences of the nutritional plane before breeding and in early gestation on feed intake, body weight, body condition score, body mass indexes, blood constituent concentrations, and reproductive performance. There were 35 multiparous and 72 primiparous sheep, with initial ages of 5.6 ± 0.25 years and 1.5 ± 0.01 years, respectively (average overall initial age of 2.8 ± 0.20 years). Wheat straw (4% crude protein; dry matter [DM] basis) was consumed ad libitum and supplemented with approximately 0.15% initial body weight (BW) of soybean meal (LS) or a 1:3 mixture of soybean meal and rolled corn at 1% BW (HS; DM). The supplementation period was 162 days, with the breeding of animals in two sets sequentially, with the pre-breeding period 84 and 97 days, and that after breeding began at 78 and 65 days, respectively. Wheat straw DM intake (1.75, 1.30, 1.57, 1.15, 1.80, and 1.38% BW; SEM = 0.112) was lower (p < 0.05), but average daily gain (-46, 42, -44, 70, -47, and 51 g for DOR-LS, DOR-HS, KAT-LS, KAT-HS, STC-LS, and STC-HS, respectively; SEM = 7.3) was greater (p < 0.05) for HS than LS treatment during the supplementation period. Additionally, changes in body condition score during the supplementation period (-0.61, 0.36, -0.53, 0.27, -0.39, and -0.18; SEM = 0.058), and changes in body mass index based on height at the withers and body length from the point of the shoulder to the pin bone (BW/[height × length], g/cm2) from 7 days before supplementation (day -7) to day 162 were -1.99, 0.07, -2.19, -0.55, -2.39, and 0.17 for DOR-LS, DOR-HS, KAT-LS, KAT-HS, STC-LS, and STC-HS, respectively; (SEM = 0.297) were affected by supplement treatment. All blood constituent concentrations and characteristics addressed varied with the day of sampling (-7, 14, 49, 73, and 162) as well as the interaction between the supplement treatment and the day (p < 0.05), with few effects of interactions involving breed. Birth rate (66.7, 93.5, 84.6, 95.5, 82.8, and 100.0; SEM = 9.83) and individual lamb birth weight (4.50, 4.61, 4.28, 3.98, 3.73, and 3.88 kg; SEM = 0.201) were not affected by supplement treatment (p = 0.063 and 0.787, respectively), although litter size (0.92, 1.21, 1.17, 1.86, 1.12, and 1.82; SEM = 0.221) and total litter birth weight (5.84, 5.74, 5.92, 7.52, 5.04, and 6.78 kg for DOR-LS, DOR-HS, KAT-LS, KAT-HS, STC-LS, and STC-HS, respectively; SEM = 0.529) were greater (p < 0.05) for HS than for LS. In conclusion, although there was some compensation in wheat straw intake for the different levels of supplementation, soybean meal given alone rather than with cereal grain adversely affected BW, BCS, BMI, and reproductive performance, the latter primarily through litter size but also via a trend for an effect on the birth rate. Hence, the supplementation of low-protein and high-fiber forage such as wheat straw should include a consideration of the inclusion of a feedstuff(s) high in energy in addition to nitrogen.

Epigenetics and island-mainland divergence in an insectivorous small mammal

Geographically isolated populations, specifically island-mainland counterparts, tend to exhibit phenotypic variation in many species. The so-called island syndrome occurs when different environmental pressures lead to insular divergence from mainland populations. This phenomenon can be seen in an island population of Nova Scotia masked shrews (Sorex cinereus), which have developed a specialized feeding habit and digestive enzyme compared to their mainland counterparts. Epigenetic modifications, such as DNA methylation (DNAm), can impact phenotypes by altering gene expression without changing the DNA sequence. Here, we used a de novo masked shrew genome assembly and a mammalian methylation array profiling 37 thousand conserved CpGs to investigate morphological and DNA methylation patterns between island and mainland populations. Island shrews were morphologically and epigenetically different than their mainland counterparts, exhibiting a smaller body size. A gene ontology enrichment analyses of differentially methylated CpGs implicated developmental and digestive system related pathways. Based on our shrew epigenetic clock, island shrews might also be aging faster than their mainland counterparts. This study provides novel insight on phenotypic and epigenetic divergence in island-mainland mammal populations and suggests an underlying role of methylation in island-mainland divergence.

High-density SNP markers elucidate the genetic divergence and population structure of Noticiana sheep breed in the Mediterranean context

Among livestock species, sheep have played an early major role in the Mediterranean area. Italy has a long history of sheep breeding and, despite a dramatic contraction in numbers, still raise several local populations that may represent a unique source of genetic diversity. The Noticiana is a breed of the south-eastern part of Sicily appreciated both for its dairy products and for its resistance to harsh environment. In this study, the high-density Illumina Ovine SNP600K BeadChip array was used for the first genome-wide characterization of 48 individuals of Noticiana sheep to investigate its diversity, the genome structure and the relationship within the context of worldwide and Italian breeds. Moreover, the runs of homozygosity (ROH) pattern and the pairwise F_ST-outliers were examined. Noticiana reported moderate levels of genetic diversity. The high percentage of short and medium length ROH segments (93% under 4 Mb) is indicative of a within breed relatedness dating back to ancient times, despite the absence of management for the mating plans and the reduced population size. In the worldwide context, the Southern Italian, Spanish and Albanian breeds overlapped in a macro cluster which also included the Noticiana sheep. The results highlighted ancestral genetic components of Noticiana shared with Comisana breed, and showed the clear separation from the other Italian sheep. This is likely the consequence of the combined effects of genetic drift, small population size and reproductive isolation. ROH islands and F_ST-outliers approaches in Noticiana identified genes and QTLs involved in milk and meat production, as well as related to the local adaptation, and therefore are consistent with the phenotypic traits of the studied breed. Although a wider sampling could be useful to deepen the genomic survey on Noticiana, these results represent a crucial starting point for the characterization of an important local genetic resource, with a view of supporting the local economy and preserving the biodiversity of the sheep species.

Genetic architecture and selection of Anhui autochthonous pig population revealed by whole genome resequencing

The genetic resources among pigs in Anhui Province are diverse, but their value and potential have yet to be discovered. To illustrate the genetic diversity and population structure of the Anhui pigs population, we resequenced the genome of 150 pigs from six representative Anhui pigs populations and analyzed this data together with the sequencing data from 40 Asian wild boars and commercial pigs. Our results showed that Anhui pigs were divided into two distinct types based on ancestral descent: Wannan Spotted pig (WSP) and Wannan Black pig (WBP) origins from the same ancestor and the other four populations origins from another ancestor. We also identified several potential selective sweep regions associated with domestication characteristics among Anhui pigs, including reproduction-associated genes (CABS1, INSL6, MAP3K12, IGF1R, INSR, LIMK2, PATZ1, MAPK1), lipid- and meat-related genes (SNX19, MSTN, MC5R, PRKG1, CREBBP, ADCY9), and ear size genes (MSRB3 and SOX5). Therefore, these findings expand the catalogue and how these genetic differences among pigs and this newly generated data will be a valuable resource for future genetic studies and for improving genome-assisted breeding of pigs and other domesticated animals.

Favored single nucleotide variants identified using whole genome Re-sequencing of Austrian and Chinese cattle breeds

Cattle have been essential for the development of human civilization since their first domestication few thousand years ago. Since then, they have spread across vast geographic areas following human activities. Throughout generations, the cattle genome has been shaped with detectable signals induced by various evolutionary processes, such as natural and human selection processes and demographic events. Identifying such signals, called selection signatures, is one of the primary goals of population genetics. Previous studies used various selection signature methods and normalized the outputs score using specific windows, in kbp or based on the number of SNPs, to identify the candidate regions. The recent method of iSAFE claimed for high accuracy in pinpointing the candidate SNPs. In this study, we analyzed whole-genome resequencing (WGS) data of ten individuals from Austrian Fleckvieh (Bos taurus) and fifty individuals from 14 Chinese indigenous breeds (Bos taurus, Bos taurus indicus, and admixed). Individual WGS reads were aligned to the cattle reference genome of ARS. UCD1.2 and subsequently undergone single nucleotide variants (SNVs) calling pipeline using GATK. Using these SNVs, we examined the population structure using principal component and admixture analysis. Then we refined selection signature candidates using the iSAFE program and compared it with the classical iHS approach. Additionally, we run Fst population differentiation from these two cattle groups. We found gradual changes of taurine in north China to admixed and indicine to the south. Based on the population structure and the number of individuals, we grouped samples to Fleckvieh, three Chinese taurines (Kazakh, Mongolian, Yanbian), admixed individuals (CHBI_Med), indicine individuals (CHBI_Low), and a combination of admixed and indicine (CHBI) for performing iSAFE and iHS tests. There were more significant SNVs identified using iSAFE than the iHS for the candidate of positive selection and more detectable signals in taurine than in indicine individuals. However, combining admixed and indicine individuals decreased the iSAFE signals. From both within-population tests, significant SNVs are linked to the olfactory receptors, production, reproduction, and temperament traits in taurine cattle, while heat and parasites tolerance in the admixed individuals. Fst test suggests similar patterns of population differentiation between Fleckvieh and three Chinese taurine breeds against CHBI. Nevertheless, there are genes shared only among the Chinese taurine, such as PAX5, affecting coat color, which might drive the differences between these yellowish coated breeds, and those in the greater Far East region.

Co-expression of candidate genes regulating growth performance and carcass traits of Barki lambs in Egypt

Sheep are considered one of the main sources of animal protein in Egypt and the producers of sheep mutton eagers to find biological criteria for selecting fast-growing lambs that reach market weight early. Therefore, the present study aimed to find a link between the expression profile of selected candidate genes with growth performance and carcass traits of Barki lambs. Thirty-eight Barki lambs were kept and fed individually after weaning till 12 months of age and were divided into 3 groups according to growth performance (fast, intermediate, and slow-growing). Three samples were taken from different body tissues (eye muscle, liver, and fat tail) of each group, directly during slaughtering and stored at − 80 °C until RNA isolation. Real-time PCR was used to profile selected candidate genes (RPL7, CTP1, FABP4, ADIPOQ, and CAPN3) and GAPDH was used as a housekeeping gene. The results indicated that the final body weight was significantly (P ≤ 0.05) greater in the fast (49.9 kg) and intermediate (40.7 kg) compared to slow-growing animals (30.8 kg). The hot carcass weight was heavier (P ≤ 0.05) in the fast and intermediate-growing (24.57 and 19.07 kg) than slow-growing lambs (15.10 kg). The blood profiles of T3 and T4 hormones in addition to other parameters such as total protein, total lipids, and calcium level showed no clear variations among different experimental groups. At the molecular level, our data demonstrated upregulation of genes involved in protein biosynthesis (RPL7), fatty acid oxidation (CPT1), and lipolysis (FABP4) in the fast and intermediate-growing lambs in all studied tissues which facilitate protein accretion, energy expenditure, and fatty acid partitioning required for muscle building up. Moreover, the expression profile of the gene involved in muscle development (CAPN3) was increased in fast and intermediate-growing compared to slow-growing lambs in order to support muscle proper development. On the other hand, a candidate gene involved in lipogenesis (ADIPOQ) was expressed similarly in fat and liver tissues; however, its expression was increased in muscles of fast and intermediate-growing lambs compared to slow-growing animals. In conclusion, the current study indicated that the expression profile of genes involved in metabolic activities of liver, muscle, and adipose tissue is linked with the growth performance of lambs although no variations were detected in blood parameters. This provides an evidence for the importance of co-expression of these genes in body tissues to determine the final body weight and carcass characteristics of Barki sheep.

Genetic architectures and selection signatures of body height in Chinese indigenous donkeys revealed by next-generation sequencing

Donkeys are widely distributed labour animals in the world. During the process of the domestication and artificial selection of domestic donkeys, body sizes show significant differences among different breeds of donkeys. Based on the genome resequencing data of 103 Chinese indigenous donkeys from 11 breeds (Biyang, Dezhou, Guangling, Hetian, Jiami, Kulun, Qingyang, Turfan, Tibetan, Xinjiang, and Yunnan), seven Spanish donkeys from two breeds (Zamorano~Leonés and Andalusian), and three wild donkeys, we investigated the population structures of Chinese domestic donkeys with different body sizes. We used F_ST and XP-EHH analyses to explore the selected regions related to body sizes. The results showed that Chinese indigenous donkeys have a closer relationship with African wild donkeys than with Asian wild donkeys. LCORL/NCAPG, FAM184B, TBX3, and IHH were identified as genes with strong signals in analysis of selection signature (F_ST and XP-EHH) in large and small donkeys. The seven identified variants can be served as candidate loci affecting the body size of Chinese donkeys. Five of seven loci were located in intron 9 of FAM184B and were in a haplotype block, and one of the identified variants (Chr03:112664848) located in the CDS region of the LCORL gene was found to cause stop-loss. These candidate genes and variants shed new light on the molecular basis of donkey body size and will facilitate the breeding activities of donkeys.

Evolution of the sheep industry and genetic research in the United States: opportunities for convergence in the twenty-first century

The continuous development and application of technology for genetic improvement is a key element for advancing sheep production in the United States. The US sheep industry has contracted over time but appears to be at a juncture where a greater utilization of technology can facilitate industry expansion to new markets and address inefficiencies in traditional production practices. Significant transformations include the increased value of lamb in relation to wool, and a downtrend in large-scale operations but a simultaneous rise in small flocks. Additionally, popularity of hair breeds not requiring shearing has surged, particularly in semi-arid and subtropical US environments. A variety of domestically developed composite breeds and newly established technological approaches are now widely available for the sheep industry to use as it navigates these ongoing transformations. These genetic resources can also address long-targeted areas of improvement such as growth, reproduction and parasite resistance. Moderate progress in production efficiency has been achieved by producers who have employed estimated breeding values, but widespread adoption of this technology has been limited. Genomic marker panels have recently shown promise for reducing disease susceptibility, identifying parentage and providing a foundation for marker-assisted selection. As the ovine genome is further explored and genomic assemblies are improved, the sheep research community in the USA can capitalize on new-found information to develop and apply genetic technologies to improve the production efficiency and profitability of the sheep industry.

The GWAS Analysis of Body Size and Population Verification of Related SNPs in Hu Sheep

Body size is an important indicator of growth and health in sheep. In the present study, we performed Genome-Wide Association Studies (GWAS) to detect significant single-nucleotide polymorphisms (SNPs) associated with Hu sheep's body size. After genotyping parental (G1) and offspring (G2) generation of the nucleus herd for meat production of Hu sheep and conducting GWAS on the body height, chest circumference, body length, tail length, and tail width of the two groups, 5 SNPs associated with body height and 4 SNPs correlated with chest circumference were identified at the chromosomal significance level. No SNPs were significantly correlated to body length, tail length, and width. Four out of the 9 SNPs were found to be located within the 4 genes. KITLG and CADM2 are considered as candidate functional genes related to body height; MCTP1 and COL4A6 are candidate functional genes related to chest circumference. The 9 SNPs found in GWAS were verified using the G3 generation of the nucleus herd for meat production. Nine products were amplified around the 9 sites, and 29 SNPs were found; 3 mutation sites, G > C mutation at 134 bp downstream of s554331, T > G mutation at 19 bp upstream of s26859.1, and A > G mutation at 81 bp downstream of s26859.1, were significantly correlated to the body height. Dual-luciferase reporter gene experiments showed that the 3 SNPs could significantly impact dual-luciferase and gene transcription activity.

A QTL for conformation of back and croup influences lateral gait quality in Icelandic horses

BACKGROUND

The back plays a vital role in horse locomotion, where the spine functions as a spring during the stride cycle. A complex interaction between the spine and the muscles of the back contribute to locomotion soundness, gait ability, and performance of riding and racehorses. Conformation is commonly used to select horses for breeding and performance in multiple horse breeds, where the back and croup conformation plays a significant role. The conformation of back and croup plays an important role on riding ability in Icelandic horses. However, the genes behind this trait are still unknown. Therefore, the aim of this study was to identify genomic regions associated with conformation of back and croup in Icelandic horses and to investigate their effects on riding ability. One hundred seventy-seven assessed Icelandic horses were included in the study. A genome-wide association analysis was performed using the 670 K+ Axiom Equine Genotyping Array, and the effects of different haplotypes in the top associated region were estimated for riding ability and additional conformation traits assessed during breeding field tests.

RESULTS

A suggestive quantitative trait loci (QTL) for the score of back and croup was detected on Equus caballus (ECA) 22 (p-value = 2.67 × 10- 7). Haplotype analysis revealed two opposite haplotypes, which resulted in higher and lower scores of the back and croup, respectively (p-value < 0.001). Horses with the favorable haplotype were more inclined to have a well-balanced backline with an uphill conformation and had, on average, higher scores for the lateral gaits tölt (p-value = 0.02) and pace (p-value = 0.004). This genomic region harbors three genes: C20orf85, ANKRD60 and LOC100056167. ANKRD60 is associated with body height in humans. C20orf85 and ANKRD60 are potentially linked to adolescent idiopathic scoliosis in humans.

CONCLUSIONS

Our results show that the detected QTL for conformation of back and croup is of importance for quality of lateral gaits in Icelandic horses. These findings could result in a genetic test to aid in the selection of breeding horses, thus they are of major interest for horse breeders. The results may also offer a gateway to comparative functional genomics by potentially linking both motor laterality and back inclination in horses with scoliosis in humans.

ASAS-NANP SYMPOSIUM: prospects for interactive and dynamic graphics in the era of data-rich animal science1

Statistical graphics, and data visualization, play an essential but under-utilized, role for data analysis in animal science, and also to visually illustrate the concepts, ideas, or outputs of research and in curricula. The recent rise in web technologies and ubiquitous availability of web browsers enables easier sharing of interactive and dynamic graphics. Interactivity and dynamic feedback enhance human-computer interaction and data exploration. Web applications such as decision support systems coupled with multimedia tools synergize with interactive and dynamic graphics. However, the importance of graphics for effectively communicating data, understanding data uncertainty, and the state of the field of interactive and dynamic graphics is underappreciated in animal science. To address this gap, we describe the current state of graphical methodology and technology that might be more broadly adopted. This includes an explanation of a conceptual framework for effective graphics construction. The ideas and technology are illustrated using publicly available animal datasets. We foresee that many new types of big and complex data being generated in precision livestock farming create exciting opportunities for applying interactive and dynamic graphics to improve data analysis and make data-supported decisions.