Genome‐wide re‐sequencing and transcriptome analysis reveal candidate genes associated with the pendulous comb phenotype in domestic chickens

To determine the causative variations associated with two chicken comb phenotypes, pendulous comb (PC) or upright comb (UC), two pooled genomic DNA samples from PC and UC chickens were re‐sequenced by Next‐Generation Sequencer, and genome‐wide Single nucleotide polymorphisms (SNPs) were detected. Using three selective sweep approaches, F_ST, θπ, and Tajima's D, with top 5% window values serving as the threshold, a total of 84 positively selective genes (PSGs) were identified. There were no SNPs in exons of the PSGs with significant differences in allele frequencies between the two comb phenotype groups. Then, 515 differentially expressed genes (DEGs) between the PC and UC were identified by RNA‐seq. Three genes including CD36 (CD36 molecule), ADAMTSL3 (ADAMTS‐like 3), and AOX1 (aldehyde oxidases 1) are overlapped between PSGs and DEGs. After genotyping seven candidate SNPs in the regulatory regions of the three overlapping genes in 120 chickens from two other breeds, two variants (rs14607046 and rs731818051) in the regulatory regions of AOX1 and ADAMTSL3 were found to have significant differences in allele frequency between the PC and UC, suggesting that the two variants may be causative mutations for PC. Overall, our study shed light on the genetic basis underlying the PC phenotype in chickens.     

Association of PCSK1 gene polymorphisms with abdominal fat content in broilers

Protein proteolytic enzymes (Proprotein Convertase, PC) is a Ca²⁺‐dependent serine protease family, whose main function is to cleave precursors of biologically inactive proteins or peptide chains into active functional molecules. Proprotein convertase subtilisin/kexin type 1 (PCSK1) gene is mainly expressed in nerve and endocrine tissues. In this study, PCSK1 was selected as an important candidate gene for abdominal fat content in broilers. We cloned the exon region of chicken PCSK1 gene and found six single‐nucleotide polymorphisms (SNPs). Association analysis was carried out and we found that the polymorphisms of these six SNPs were significantly associated with abdominal fat content in G19 and G20 populations. Five of these SNPs were significantly associated with abdominal fat content in G19 and G20 combined population. The polymorphism of these five SNPs was significantly correlated with the abdominal fat content of AA broilers. Together, our study demonstrated that c.927T>C, c.1880C>T, c.*900G>A, and c.*1164C>T were significantly associated with abdominal fat content in populations used in this study, which means that these SNPs in PCSK1 gene could be used as candidate markers to select lean broiler lines.     

Use of high‐density SNP data to identify patterns of diversity and signatures of selection in broiler chickens

The development of broiler chickens over the last 70 years has been accompanied by large phenotypic changes, so that the resulting genomic signatures of selection should be detectable by current statistical techniques with sufficiently dense genetic markers. Using two approaches, this study analysed high‐density SNP data from a broiler chicken line to detect low‐diversity genomic regions characteristic of past selection. Seven regions with zero diversity were identified across the genome. Most of these were very small and did not contain many genes. In addition, fifteen regions were identified with diversity increasing asymptotically from a low level. These regions were larger and thus generally included more genes. Several candidate genes for broiler traits were found within these ‘regression regions’, including IGF1, GPD2 and MTNR1AI. The results suggest that the identification of zero‐diversity regions is too restrictive for characterizing regions under selection, but that regions showing patterns of diversity along the chromosome that are consistent with selective sweeps contain a number of genes that are functional candidates for involvement in broiler development. Many regions identified in this study overlap or are close to regions identified in layer chicken populations, possibly due to their shared precommercialization history or to shared selection pressures between broilers and layers.     

Intracerebroventricular administration of chicken glucagon‐like peptide‐2 potently suppresses food intake in chicks

Glucagon‐related peptides, such as glucagon‐like peptide (GLP)‐1, GLP‐2 and oxyntomodulin (OXM), are processed from an identical precursor proglucagon. In mammals, all of these peptides are suggested to be involved in the central regulation of food intake. We previously showed that intracerebroventricular administration of chicken OXM and GLP‐1 significantly suppressed food intake in chicks. Here, we show that central administration of chicken GLP‐2 potently suppresses food intake in chicks. Male 8‐day‐old chicks (Gallus gallus domesticus) were used in all experiments. Intracerebroventricular administration of chicken GLP‐2 significantly suppressed food intake in chicks. Plasma glucose concentration was significantly decreased by chicken GLP‐2, whereas plasma nonesterified fatty acid concentration was significantly increased. Intracerebroventricular administration of chicken GLP‐2 did not affect plasma corticosterone concentration. In addition, the anorexigenic effect of GLP‐2 was not reversed by the corticotropin‐releasing factor (CRF) receptor antagonist α‐helical CRF, suggesting that CRF is not a downstream mediator of the anorexigenic pathway of GLP‐2 in chicks. Intracerebroventricular administration of an equimolar amount of GLP‐1 and GLP‐2, but not OXM, significantly suppressed food intake in both broiler and layer chicks. All our findings suggest that GLP‐2 functions as a potent anorexigenic peptide in the brain, as well as GLP‐1, in chicks.     

Cloning,tissue expression and polymorphisms of chicken Krüppel‐like factor 7 gene

Krüppel‐like factor 7 (KLF7) has been extensively studied in mammalian species, but its role in birds is still unclear. In the current study, cloning and sequencing showed that the full‐length coding region of chicken KLF7 (Gallus gallus KLF7, gKLF7) was 891 bp long, encoding 296 amino acids. In addition, real‐time RT‐PCR analysis showed that gKLF7 was broadly expressed in all 15 chicken tissues selected, and its expression was significantly different in spleen, proventriculus, abdominal fat, brain, leg muscle, gizzard and heart between fat and lean broilers at 7 weeks of age. Additionally, one novel single nucleotide polymorphism (SNP), XM_426569.3: c. A141G, was identified in the second exon of gKLF7. Association analysis showed that this locus was significantly associated with fatness traits in Arbor Acres broiler random population and the eighth generation of Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF) population (P < 0.05). These results suggest that gKLF7 might be a candidate gene for chicken fatness traits.     

Genome‐wide association study for fatty acid composition in Japanese Black cattle

Fatty acid composition is one of the important traits in beef. The aim of this study was to identify candidate genomic regions for fatty acid composition by genome‐wide association study with 50 K single nucleotide polymorphism (SNP) array in Japanese Black cattle. A total of 461 individuals and 40 657 SNPs were used in this study. We applied genome‐wide rapid association using mixed model and regression (GRAMMAR) and genomic control approaches to estimate the associations between genotypes and fatty acid composition. In addition, two SNPs in fatty acid synthase (FASN) (T1952A) and stearoyl‐CoA desaturase (SCD) (V293A) genes were also genotyped. Association analysis revealed that 30 significant SNPs for several fatty acids (C14:0, C14:1, C16:1 and C18:1) were located in the BTA19 FASN gene located within this region but the FASN mutation had no significant effect on any traits. We also detected one significant SNP for C18:1 on BTA23 and two SNPs for C16:0 on BTA25. The region around 17 Mb on BTA26 harbored two significant SNPs for C14:1 and SNP in SCD in this region showed the strongest association with C14:1. This study demonstrated novel candidate regions in BTA19, 23 and 25 for fatty acid composition.     

Genome‐wide association studies revealed candidate genes for tail fat deposition and body size in the Hulun Buir sheep

Fat‐tailed sheep have a unique characteristic of depositing fat in their tails. In the present study, we conducted genome‐wide association studies (GWAS) on traits related to tail fat deposition and body size in the Hulun Buir sheep. A total number of 300 individuals belonging to two fat‐tailed lines of the Hulun Buir sheep breed genotyped with the Ovine Infinium HD SNP BeadChip were included in the current study. Two mixed models, one for continuous and one for binary phenotypic traits, were employed to analyse ten traits, that is, body length (BL), body height (BH), chest girth (CG), tail length (TL), tail width (TW), tail circumference (TC), carcass weight (CW), tail fat weight (TF), ratio of CW to TF (RCT) and tail type (TT). We identified 7, 6, 7, 2, 10 and 1 SNPs significantly associated with traits TF, CW, RCT, TW, TT and CG, respectively. Their associated genomic regions harboured 42 positional candidate genes. Out of them, 13 candidate genes including SMURF2, FBF1, DTNBP1, SETD7 and RBM11 have been associated with fat metabolism in sheep. The RBM11 gene has already been identified in a previous study on signatures of selection in this specific sheep population. Two more genes, that is, SMARCA5 and GAB1 were associated with body size in sheep. The present study has identified candidate genes that might be implicated in tail fat deposition and body size in sheep.     

Development of divergent lines of lean and fat broilers using plasma very low density lipoprotein concentration as selection criterion: The first three generations

1. Male and female broilers of a pure line were selected over three generations on the basis of high or low plasma very low density lipoprotein (VLDL) concentration at 7 weeks of age.

2. Heritability of plasma VLDL was high (h ² = 0·50 ± 0·08) and by the third generation mean values in the two lines differed by a factor of 2·5.

3. Correlated responses to selection for low plasma VLDL included a relative decrease in abdominal fat and total body lipid and an increase in body protein, together with improvements in the conversion efficiences of food and dietary protein.

4. There was no difference between the lines in 7‐week body weight.

     

A genome‐wide SNP scan in a porcine Large White × Minzhu intercross population reveals a locus influencing muscle mass on chromosome 2

A high‐density single nucleotide polymorphism (SNP) array containing 62 163 markers was employed for a genome‐wide association study (GWAS) to identify variants associated with lean meat in ham (LMH, %) and lean meat percentage (LMP, %) within a porcine Large White × Minzhu intercross population. For each individual, LMH and LMP were measured after slaughter at the age of 240 ± 7 days. A total of 557 F2 animals were genotyped. The GWAS revealed that 21 SNPs showed significant genome‐wide or chromosome‐wide associations with LMH and LMP by the Genome‐wide Rapid Association using Mixed Model and Regression‐Genomic Control approach. Nineteen significant genome‐wide SNPs were mapped to the distal end of Sus Scrofa Chromosome (SSC) 2, where a major known gene responsible for muscle mass, IGF2 is located. A conditioned analysis, in which the genotype of the strongest associated SNP is included as a fixed effect in the model, showed that those significant SNPs on SSC2 were derived from a single quantitative trait locus. The two chromosome‐wide association SNPs on SSC1 disappeared after conditioned analysis suggested the association signal is a false association derived from using a F2 population. The present result is expected to lead to novel insights into muscle mass in different pig breeds and lays a preliminary foundation for follow‐up studies for identification of causal mutations for subsequent application in marker‐assisted selection programs for improving muscle mass in pigs.     

Characterization and expression of non‐polymorphic liver expressed antimicrobial peptide 2: LEAP‐2 in the Japanese quail,Coturnix japonica

Liver‐expressed antimicrobial peptide 2 (LEAP‐2) is a cationic peptide that plays an important role in innate immunity for host defense. The aim of this study was to characterize the LEAP‐2 gene in the Japanese quail (Coturnix japonica). Japanese quail LEAP‐2 (CjLEAP‐2) was identified from the Japanese quail draft genome database by a local BLAST analysis using chicken LEAP‐2 (GgLEAP‐2). The exon‐intron structure of CjLEAP‐2, analyzed from three quails, is composed of three exons, as is the chicken LEAP‐2 homolog (GgLEAP‐2). An analysis of the coding sequence revealed that CjLEAP‐2 is 231 bp long, like GgLEAP‐2, and 93% identical to GgLEAP‐2 at the nucleic acid level. The predicted amino acid sequence of CjLEAP‐2 contained the liver‐expressed antimicrobial peptide 2‐precursor domain and four cysteine residues characteristic of the LEAP‐2 protein. The amino acid sequence of the mature peptide of CjLEAP‐2 was 100% identical to that of GgLEAP‐2. We confirmed that CjLEAP‐2 was transcribed in at least seven tissues, including the digestive system. Additionally, the mature peptide region of CjLEAP‐2 exhibited no polymorphisms in 99 quails from six strains. Taken together, these findings indicate that CjLEAP‐2 is non‐polymorphic and therefore, it likely plays an important role in the innate immunity of quail as it does in chicken.     

Polymorphism in promoter region of growth hormone receptor is associated with potential production capacity of insulin‐like growth factor‐1 in pre‐pubertal Holstein heifers

Insulin‐like growth factor‐1 (IGF‐1) is one of the important factors for growth, milk production and reproductive functions and mainly released from the liver in response to growth hormone (GH) via GH receptor (GHR) in cattle. Recently, some single nucleotide polymorphisms (SNPs) were identified in the bovine GHR gene. Some GHR‐SNPs were shown to be related to plasma IGF‐1 concentration in cattle. Hence, the capacity to IGF‐1 production in the liver might be affected by GHR‐SNP and associated with performance in the future. This study examined whether GHR‐SNP is associated with IGF‐1 production in the liver of pre‐pubertal heifers. In 71 Holstein calves, blood samples for genomic DNA extraction were obtained immediately after birth. To genotype the GHR‐SNPs in the promoter region, polymerase chain reaction (PCR) products were digested with restriction enzyme NsiI (cutting sites: AA, AG and GG). All heifers at 4 months of age were intramuscularly injected with 0.4 mg oestradiol benzoate. Blood samples were obtained from the jugular vein just before (0 h) and 24 h after injection. The number of AA, AG and GG at the NsiI site was 0, 17 and 54 respectively. In AG and GG, plasma GH concentrations were higher pre‐injection than 24 h post‐injection (p < 0.01). Moreover, plasma GH concentrations in AG post‐injection were higher than in GG (p < 0.05). In contrast, the GG genotype exhibited higher plasma IGF‐1 concentrations in pre‐injection than post‐injection (p < 0.01), although oestradiol did not change IGF‐1 concentration in the AG genotype. We conclude that the GG polymorphism in the promoter region of GHR is associated with a higher potential capacity of IGF‐1 production in the liver of cattle.     

Aspartame supplementation in starter accelerates small intestinal epithelial cell cycle and stimulates secretion of glucagon‐like peptide‐2 in pre‐weaned lambs

The objective of this study was to test the hypothesis that aspartame supplementation in starter diet accelerates small intestinal cell cycle by stimulating secretion and expression of glucagon‐like peptide ?2 (GLP‐2) in pre‐weaned lambs using animal and cell culture experiments. In vivo, twelve 14‐day‐old lambs were selected and allocated randomly to two groups; one was treated with plain starter diet (Con, n = 6) and the other was treated with starter supplemented with 200 mg of aspartame/kg starter (APM, n = 6). Results showed that the lambs received APM treatment for 35 d had higher (p < .05) GLP‐2 concentration in the plasma and greater jejunum weight/live body weight (BW) and jejunal crypt depth. Furthermore, APM treatment significantly upregulated (p < .05) the mRNA expression of cyclin D1 in duodenum; and cyclin A2, cyclin D1, cyclin‐dependent kinases 6 (CDK6) in jejunum; and cyclin A2, cyclin D1, CDK4 in ileum. Moreover, APM treatment increased (p < .05) the mRNA expression of glucagon (GCG), insulin‐like growth factor 1 (IGF‐1) in the jejunum and ileum and mRNA expression of GLP‐2 receptor (GLP‐2R) in the jejunum. In vitro, when jejunal cells were treated with GLP‐2 for 2 hr, the 3‐(4,5‐dimethyl‐2‐thiazolyl)‐2,5‐diphenyl‐2‐H‐tetrazolium bromide (MTT) OD, IGF‐1 concentration, and the mRNA expression of IGF‐1, cyclin D1 and CDK6 were increased (p < .05). Furthermore, IGF‐1 receptor (IGF‐1R) inhibitor decreased (p < .05) the mRNA expression of IGF‐1, cyclin A2, cyclin D1 and CDK6 in GLP‐2 treatment jejunal cells. These results suggest that aspartame supplementation in starter accelerates small intestinal cell cycle that may, in part, be related to stimulate secretion and expression of GLP‐2 in pre‐weaning lambs. Furthermore, GLP‐2 can indirectly promote the proliferation of jejunal cells mainly through the IGF‐1 pathway. These findings provide new insights into nutritional interventions that promote the development of small intestines in young ruminants.     

An imputation‐based genome‐wide association study on traits related to male reproduction in a White Duroc × Erhualian F2 population

Boar reproductive traits are economically important for the pig industry. Here we conducted a genome‐wide association study (GWAS) for 13 reproductive traits measured on 205 F₂ boars at day 300 using 60 K single nucleotide polymorphism (SNP) data imputed from a reference panel of 1200 pigs in a White Duroc × Erhualian F₂ intercross population. We identified 10 significant loci for seven traits on eight pig chromosomes (SSC). Two loci surpassed the genome‐wide significance level, including one for epididymal weight around 60.25 Mb on SSC7 and one for semen temperature around 43.69 Mb on SSC4. Four of the 10 significant loci that we identified were consistent with previously reported quantitative trait loci for boar reproduction traits. We highlighted several interesting candidate genes at these loci, including APN, TEP1, PARP2, SPINK1 and PDE1C. To evaluate the imputation accuracy, we further genotyped nine GWAS top SNPs using PCR restriction fragment length polymorphism or Sanger sequencing. We found an average of 91.44% of genotype concordance, 95.36% of allelic concordance and 0.85 of r² correlation between imputed and real genotype data. This indicates that our GWAS mapping results based on imputed SNP data are reliable, providing insights into the genetic basis of boar reproductive traits.     

Genetic differences in oestrous signs and oestrogen metabolism‐related genes between Chinese Mi and European Landrace‐Large White pigs

Oestrous signs affect timely mating and reproductive efficiency in swine breeding herds. To study the genetic difference of oestrous signs between Chinese and European pigs, 100 Landrace‐Large White (LLW) cross gilts and 50 Chinese Mi gilts were assessed for oestrous signs and the concentrations of serum estradiol‐17β and progesterone were determined. The genotype of 39 single nucleotide polymorphisms (SNPs) in 11 oestrogen metabolism and function‐related genes was determined by Sequenom iPLEX platform. Compared with LLW gilts, Mi gilts had longer time of standing reflex (p < .001), higher scores of vulva reddening (p = .001) and greater serum estradiol‐17β concentration (p < .01). Gilts with greater serum estradiol‐17β concentrations also had greater (p < .05) scores for oestrous signs. Genetic polymorphisms of nine genes in oestrogen metabolism pathways had significant differences (p < .05) between LLW and Mi gilts. There were three and six haploblocks of SNPs in LLW and Mi, respectively. Compared with LLW, the distribution of haplotypes was more centralized in Mi pigs. Genetic polymorphisms of oestrogen metabolism‐related genes have considerable differences between Chinese Mi and European LLW pigs. Because of the important roles of oestrogen during the oestrus, some genes of oestrogen metabolism pathway could be considered as candidate genes for oestrous signs.     

Identification of Stably Expressed Reference Genes for RT‐qPCR Data Normalization in Defined Localizations of Cyclic Bovine Ovaries

Ovaries are highly complex organs displaying morphological, molecular and functional differences between their cortical zona parenchymatosa and medullary zona vasculosa, and also between the different cyclic luteal stages. Objective of the present study was to validate expression stability of twelve putative reference genes (RGs) in bovine ovaries, considering the intrinsic heterogeneity of bovine ovarian tissue with regard to different luteal stages and intra‐ovarian localizations. The focus was on identifying RGs, which are suitable to normalize RT‐qPCR results of ovaries collected from clinical healthy cattle, irrespective of localization and the hormonal stage. Expression profiles of twelve potential reference genes (GAPDH, ACTB, YWHAZ, HPRT1, SDHA, UBA52, POLR2C, RPS9, ACTG2, H3F3B, RPS18 and RPL19) were analysed. Evaluation of gene expression differences was performed using genorm , normfinder , and bestkeeper software. The most stably expressed genes according to genorm , normfinder and bestkeeper approaches contained the candidates H3F3B, RPS9, YWHAZ, RPS18, POLR2C and UBA52. Of this group, the genes YWHAZ, H3F3B and RPS9 could be recommended as best‐suited RGs for normalization purposes on healthy bovine ovaries irrespective of the luteal stage or intra‐ovarian localization.     

Cytogenetic mapping of 11 functional genes to chicken chromosomes by fluorescence in situ hybridization

With chicken bacterial artificial chromosome (BAC) DNA as probes, 11 non‐assigned functional genes were localized to chicken chromosomes 1 or 2 by fluorescence in situ hybridization (FISH). The 11 genes and their chromosomal positions are as follows: ALVEB5, 1p26‐24; ACO2, 1p16‐14; HSP108, 1p14‐13; CD4, 1q11; HSD3B; 1q11; SOD1, 1q14‐21; LAMP1, 1q24‐31; P2Y5, 1q35‐36; EN2, 2p31‐24; NPY, 2p14‐13 and CA2, 2q31‐32. Metaphase chromosome spreads used for hybridization were prepared from embryonic chicken fibroblast cultures. The gene position was identified according to the international standardized G‐banded karyotype of chicken by measuring the relative fractional length from the telomere of the p‐arm to the hybridization signal (FLpter). The 11 genes mapped newly will enrich the cytogenetic map and serve as additional anchor markers for integrating the cytogenetic map with the genetic map of chicken.     

Effects of β‐hydroxybutyricacid on the synthesis and assembly of very low‐density lipoprotein in bovine hepatocytes in vitro

β‐Hydroxybutyricacid (BHBA) is an important metabolite that involved in the development of ketosis and fatty liver in dairy cows. Dairy cows with fatty liver displayed high blood concentration of BHBA and very low‐density lipoprotein (VLDL) assembly. The effects of BHBA on VLDL synthesis and assembly in hepatocytes of cows were unclear. In this study, bovine hepatocytes were cultured and treated with different concentrations of BHBA. We found that BHBA treatment upregulated the mRNA and protein levels of apolipoprotein B100 (ApoB 100), apolipoprotein E (ApoE) and microsomal triglyceride transfer protein (MTTP) and showed in a firstly increased and then decreased trend. Meanwhile, the mRNA and protein levels of LDLR showed in a reverse trend. Consequently, VLDL content was significantly increased in medium‐dose BHBA treatment group, while decreased in high‐dose group. These results indicate that the effects of BHBA on the VLDL synthesis showed in a dose‐dependent manner that low levels of BHBA increase VLDL synthesis and high levels of BHBA decrease VLDL synthesis.     

Genome‐wide association study for feedlot average daily gain in Nellore cattle (Bos indicus)

The genome‐wide association study (GWAS) results are presented for average daily gain (ADG) in Nellore cattle. Phenotype of 720 male Bos indicus animals with information of ADG in feedlots and 354 147 single‐nucleotide polymorphisms (SNPs) obtained from a database added by information from Illumina Bovine HD (777 962 SNPs) and Illumina BovineSNP50 (54 609) by imputation were used. After quality control and imputation, 290 620 SNPs remained in the association analysis, using R package Genome‐wide Rapid Association using Mixed Model and Regression method GRAMMAR‐Gamma. A genomic region with six significant SNPs, at Bonferroni‐corrected significance, was found on chromosome 3. The most significant SNP (rs42518459, BTA3: 85849977, p = 9.49 × 10^?8) explained 5.62% of the phenotypic variance and had the allele substitution effect of ?0.269 kg/day. Important genes such as PDE4B, LEPR, CYP2J2 and FGGY are located near this region, which is overlapped by 12 quantitative trait locus (QTLs) described for several production traits. Other regions with markers with suggestive effects were identified in BTA6 and BTA10. This study showed regions with major effects on ADG in Bos indicus in feedlots. This information may be useful to increase the efficiency of selecting this trait and to understand the physiological processes involved in its regulation.