Gene polymorphisms in PROP1 associated with growth traits in sheep

A Genome-Wide Association Study of the Chest Circumference Trait in Xinjiang Donkeys Based on Whole-Genome Sequencing Technology

Animal genotyping by means of genome-wide association studies is important for connecting phenotypes of interest with their underlying genetics in livestock. However, the use of whole genome sequencing to investigate chest circumference (CC) in donkeys has rarely been reported. We aimed to use the genome-wide association study approach to detect significant single nucleotide polymorphisms (SNPs) and key genes associated with chest circumference traits in Xinjiang donkeys. We assessed 112 Xinjiang donkeys in this study. The chest circumference of each was measured 2 h before milking. We re-sequenced blood samples from the Xinjiang donkeys, and genome-wide association study analyses were performed using a mixed model with the PLINK, GEMMA, and REGENIE programs. We tested 38 donkeys for candidate SNPs for genome-wide association study using three software programs. Additionally, 18 SNP markers reached genome-wide significance (p < 1.61 × 10^-9). On the basis of these, 41 genes were identified. Previously proposed candidate genes for CC traits were supported by this study, including NFATC2 (Nuclear Factor of Activated T Cells 2), PROP1 (PROP Paired-Like Homeobox 1), UBB (Ubiquitin B), and HAND2 (Heart and Neural Crest Derivatives Expressed 2). These promising candidates provide a valuable resource for validating potential meat production genes and will facilitate the development of high-yielding Xinjiang donkey breeds through marker-assisted selection or gene editing.

Whole-genome sequence analysis reveals selection signatures for important economic traits in Xiang pigs

Xiang pig (XP) is one of the best-known indigenous pig breeds in China, which is characterized by its small body size, strong disease resistance, high adaptability, favorite meat quality, small litter sizes, and early sexual maturity. However, the genomic evidence that links these unique traits of XP is still poorly understood. To identify the genomic signatures of selection in XP, we performed whole-genome resequencing on 25 unrelated individual XPs. We obtained 876.70 Gb of raw data from the genomic libraries. The LD analysis showed that the lowest level of linkage disequilibrium was observed in Xiang pig. Comparative genomic analysis between XPs and other breeds including Tibetan, Meishan, Duroc and Landrace revealed 3062, 1228, 907 and 1519 selected regions, respectively. The genes identified in selected regions of XPs were associated with growth and development processes (IGF1R, PROP1, TBX19, STAC3, RLF, SELENOM, MSTN), immunity and disease resistance (ZCCHC2, SERPINB2, ADGRE5, CYP7B1, STAT6, IL2, CD80, RHBDD3, PIK3IP1), environmental adaptation (NR2E1, SERPINB8, SERPINB10, SLC26A7, MYO1A, SDR9C7, UVSSA, EXPH5, VEGFC, PDE1A), reproduction (CCNB2, TRPM6, EYA3, CYP7B1, LIMK2, RSPO1, ADAM32, SPAG16), meat quality traits (DECR1, EWSR1), and early sexual maturity (TAC3). Through the absolute allele frequency difference (ΔAF) analysis, we explored two population-specific missense mutations occurred in NR6A1 and LTBP2 genes, which well explained that the vertebrae numbers of Xiang pigs were less than that of the European pig breeds. Our results indicated that Xiang pigs were less affected by artificial selection than the European and Meishan pig breeds. The selected candidate genes were mainly involved in growth and development, disease resistance, reproduction, meat quality, and early sexual maturity. This study provided a list of functional candidate genes, as well as a number of genetic variants, which would provide insight into the molecular basis for the unique traits of Xiang pig.

Genetic variations in the Myostatin gene affecting growth traits in sheep

Background and Aim

Sheep productivity in developing countries is crucial, as this animal is an essential source of meat and wool. Myostatin (MSTN) plays an important role in the regulation of muscle mass through the regulation of muscle growth, differentiation, and regeneration. The present study sought to investigate genetic variation in the first intron of the MSTN gene and the association of variants with growth traits in major sheep breeds in Egypt (Barki, Ossimi, and Rahmani) and Saudi Arabia (Najdi) using polymerase chain reaction (PCR) and sequencing.

Materials and Methods

Blood samples were collected, and DNA was extracted from 75 animals. A 386 bp fragment in the first intron of the MSTN gene was amplified using PCR. Polymorphic sites were detected using direct sequencing and then correlated with growth traits using a general linear model.

Results

Sequence analysis of the first intron of MSTN gene identified six single-nucleotide polymorphisms (SNPs) in the studied breeds. Four mutual SNPs were determined: c.18 G>T, c.241 T>C, c.243 G>A, and c.259 G>T. In addition, two SNPs c.159 A>T and c.173 T>G were monomorphic (AA and TT, respectively) in the Ossimi, Rahmani, and Najdi breeds and polymorphic in the Barki breed. The association analysis revealed that the c.18 G>T and c.241 C>T significantly associated (p<0.05) with birth weight and average daily weight gain, respectively.

Conclusion

Our results strongly support MSTN as a candidate gene for marker-assisted selection in sheep breeding programs. Furthermore, the identified variants may be considered as putative markers to improve growth traits in sheep.

Selection Signatures Analysis Reveals Genes Associated with High-Altitude Adaptation in Tibetan Goats from Nagqu, Tibet

Simple Summary

In the process of domestication, goats have undergone long-term artificial and natural selection, leading to differences among goat breeds and leaving different selection traces on the genome. However, the genetic components underlying high-altitude adaptation remain largely unknown. Here, we genotyped four goat breeds using the Illumina Caprine 50K single nucleotide polymorphism (SNP) Chip. One highland breed (Tibetan goat) compared with three lowland breeds (Huanghuai goat, Taihang goat and Xinjiang goat) to identify the molecular basis of high-altitude adaptation. So, we investigated selection signatures using the di statistic of four goat breeds and some genes in Tibetan goats related to high-altitude adaptation were identified. In addition, q-PCR validated the gene expression level in Tibetan goats and Huanghuai goats. This information may be valuable for the study of the genetic uniqueness of Tibetan goats and increased understanding of the hypoxic adaptation mechanism of Tibetan goats on the plateau.

Abstract

Tibetan goat is an ancient breed, which inhabits the adverse conditions of the plateaus in China. To investigate the role of selection in shaping its genomes, we genotyped Tibetan goats (Nagqu Prefecture, above 4500 m) and three lowland populations (Xinjiang goats, Taihang goats and Huanghuai goats). The result of PCA, neighbor-joining (N-J) tree and model-based clustering showed that the genetic structure between the Tibetan goat and the three lowland populations has significant difference. As demonstrated by the di statistic, we found that some genes were related to the high-altitude adaptation of Tibetan goats. Functional analysis revealed that these genes were enriched in the VEGF (vascular endothelial growth factor) signaling pathway and melanoma, suggesting that nine genes (FGF2, EGFR, AKT1, PTEN, MITF, ENPEP, SIRT6, KDR, and CDC42) might have important roles in the high-altitude adaptation of Nagqu Tibetan goats. We also found that the LEPR gene was under the strongest selection (di value = 16.70), and it could induce upregulation of the hypoxic ventilatory response. In addition, five genes (LEPR, LDB1, EGFR, NOX4 and FGF2) with high di values were analyzed using q-PCR. Among them, we found that LEPR, LDB1 and FGF2 exhibited higher expression in the lungs of the Tibetan goats; LEPR, EGFR and LDB1 exhibited higher expression in the hearts of the Huanghuai goat. Our results suggest that LEPR, LDB1, EGFR and FGF2 genes may be related to the high-altitude adaptation of the goats. These findings improve our understanding of the selection of the high-altitude adaptability of the Nagqu Tibetan goats and provide new theoretical knowledge for the conservation and utilization of germplasm resources.

Genetics of Omega-3 Long-Chain Polyunsaturated Fatty Acid Metabolism and Meat Eating Quality in Tattykeel Australian White Lambs

Meat eating quality with a healthy composition hinges on intramuscular fat (IMF), fat melting point (FMP), tenderness, juiciness, flavour and omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA) content. These health-beneficial n-3 LC-PUFA play significant roles in optimal cardiovascular, retinal, maternal and childhood brain functions, and include alpha linolenic (ALA), eicosapentaenoic (EPA), docosahexaenoic (DHA) and docosapentaenoic (DPA) acids. The primary objective of this review was to access, retrieve, synthesise and critically appraise the published literature on the synthesis, metabolism and genetics of n-3 LC-PUFA and meat eating quality. Studies on IMF content, FMP and fatty acid composition were reviewed to identify knowledge gaps that can inform future research with Tattykeel Australian White (TAW) lambs. The TAW is a new sheep breed exclusive to MARGRA brand of lamb with an outstanding low fat melting point (28-39°C), high n-3 LC-PUFA EPA+DHA content (33-69mg/100g), marbling (3.4-8.2%), tenderness (20.0-38.5N) and overall consumer liking (7.9-8.5). However, correlations between n-3 LC-PUFA profile, stearoyl-CoA desaturase (SCD), fatty acid binding protein 4 (FABP4), fatty acid synthase (FASN), other lipogenic genes and meat quality traits present major knowledge gaps. The review also identified research opportunities in nutrition-genetics interactions aimed at a greater understanding of the genetics of n-3 LC-PUFA, feedlot finishing performance, carcass traits and eating quality in the TAW sheep. It was concluded that studies on IMF, FMP and n-3 LC-PUFA profiles in parental and progeny generations of TAW sheep will be foundational for the genetic selection of healthy lamb eating qualities and provide useful insights into their correlations with SCD, FASN and FABP4 genes.

A novel 23 bp indel mutation in PRL gene is associated with growth traits in Luxi Blackhead sheep

Prolactin is a highly versatile pituitary hormone with multiple biological functions. PRL expression is regulated by POU1F1 and the prophet of POU1F1 (PROP1). The aim of this study was to investigate the indel variations in ovine PRL and the directly related (PROP1 and POU1F1) genes, and their associations with growth traits in Luxi Blackhead (LXBH) sheep. A monomorphism in PROP1 and POU1F1 genes, and one novel 23-bp insertion mutation in the PRL gene, were identified in LXBH sheep. The 23 bp insertion mutation within PRL gene was significantly associated with several body measurements (e.g., body weight, body height) in sheep of different ages (p < 0.05). Ram lambs (p = 0.036) of genotype insertion/insertion (II) had significantly higher body weights. Weaners (p = 0.018) of genotypes insertion/insertion (II) and insertion/deletion (ID) also had significantly higher body weights compared with male sheep of deletion/deletion (DD) genotype. Moreover, among ewe lambs, individuals of genotype insertion/insertion (II) had a higher paunch girth compared to those with other genotypes (p = 0.044). These findings indicate that a 23 bp indel variant of the ovine PRL gene is correlated with body measurements in LXBH sheep. The findings have potential utility for sheep breeding programs based on marker-assisted selection.

Copy Number Variation of the CADM2 Gene and Its Association with Growth Traits in Yak

Simple Summary

Cell adhesion molecule 2 (CADM2), also known as synaptic cell adhesion molecule 2 (SYNCAM2), is the mediator of synaptic signals enriched in the brain. Overlaps between copy number variation (CNV) regions in CADM2 and quantitative trait loci (QTL) related to body weight have been clarified in a previous study. In this study, two loci were amplified in the CADM2 gene (CNV1: 235,915 bp, exon 1 and partial intron 1; CNV2: 60,430 bp, intron 9) to explore the relationship between CNV types in the CADM2 gene and growth traits in 350 Ashidan yaks. Association analysis illustrated that no significant effect was found on growth traits in CNV1. However, the CNV2 mutation had a significant effect on body weight at the sixth month (p < 0.05). Individuals with the gain-type copy number variation CNV2 were significantly superior to those with loss- or normal-type in terms of body weight (p < 0.05). In summary, this study confirmed that CADM2-CNVs affect growth traits in yaks, and may be candidate genes for successful yak breeding and genetics projects.

Abstract

Copy number variation (CNV) is currently accepted as a common source of genetic variation. It is reported that CNVs may influence the resistance to disease and complex economic traits, such as residual feed intake, muscle formation, and fat deposition in livestock. Cell adhesion molecule 2 (CADM2) is expressed widely in the brain and adipose tissue and can regulate body weight through the central nervous system. Growth traits are important economic traits for animal selection. In this study, we aimed to explore the effect of CADM2 gene copy number variants on yak growth traits. Here, two CNVs in the CADM2 gene were investigated using the quantitative polymerase chain reaction (qPCR), and the association of the CNVs with growth traits in yak was analyzed using statistical methods by SPSS software. Differences were considered significant if the p value was < 0.05. Statistical analysis indicated significant association of CADM2-CNV2 with the body weight of the Chinese Ashidan yak. A significant effect of CNV2 (p < 0.05) was found on body weight at 6 months. In CNV2, the gain-type copy number variation exhibited greater performance than the other variants, with greater body weight observed at 6 months (p < 0.05). To the best of our knowledge, this is the first attempt to investigate the function of CADM2-CNVs and their association with growth traits in animals. This may be a useful candidate marker in marker-assisted selection of yaks.

Associations between genetic variants of the POU1F1 gene and production traits in Saanen goats

This study was conducted to determine the polymorphisms of the POU1F1 gene and their relationships with milk yield and components, litter size, birth weight, and weaning weight in goats. For this purpose, a total of 108 Saanen goats from two different farms (Bornova and Manisa) were used as animal materials. Polymorphisms at the exon 6 and the 3' flanking region of the POU1F1 gene were determined by using PCR-RFLP with PstI and AluI restriction enzymes and DNA sequencing analyses. Two alleles and three genotypes were identified by AluI or PstI digestions of the POU1F1 gene. The genotypes frequencies of TT, TC, and CC were 64.8 %, 31.5 % and 3.7 % for the PstI locus; 54.6 %, 31.5 % and 13.9 % for the AluI locus, respectively. T allele frequencies (0.56 and 0.88 for the AluI locus, 0.80 and 0.81 for the PstI locus, respectively) were predominant in both loci at the Bornova and Manisa farms. In terms of POU1F1-AluI and POU1F1-PstI loci, two populations were found to be in Hardy-Weinberg equilibrium. In the POU1F1-AluI locus, significant associations were found between genotypes and lactation milk yield and litter size. Similarly, a significant relationship between genotypes and birth weight in the POU1F1-PstI locus ( p < 0.05 ) was determined. The TC and CC genotypes were observed to be higher than the TT genotype for lactation milk yield and litter size at the POU1F1-AluI locus. Birth weight was found to be higher in animals that have the CC genotype at the POU1F1-PstI locus. In conclusion, the POU1F1 gene can be used as a molecular marker for economic features like reproduction, growth, milk content and yield in Saanen goats.