Genome‐wide association study of cell‐mediated immune response in chicken

Cell‐mediated immunity (CMI) causes the intracellular destruction of the antigen or elimination of the host cell to make animals resistant against exogenous antigens and cancers. In this study, a genome‐wide association study (GWAS) was carried out to identify genomic regions associated with CMI in chicken using chicken 60k high‐density single nucleotide polymorphism (SNP) array. Genomic relationships were taken into account to adjust for population structure. In order to account for multiple testing, chromosome‐wise false discovery rate was controlled at 5% and 10% levels. Moreover, a comparison of the power of fixed and mixed linear models based on genomic inflation factor was carried out. Mixed linear model (MLM) had better inflation rate, and therefore the results from MLM were used for subsequent analysis. Three significantly associated SNPs (FDR < 0.05) on chromosome 24 and linkage group E22C19W28_E50C23, and three suggestively associated SNPs (FDR < 0.1) on chromosome 1, 5 and 16 were identified. Pathway analysis showed that two biological pathways, which are related to immune response, were strongly associated with the candidate genes surrounding identified SNPs, and their influences were mostly on antigen processing and presentation, and cellular structure.     

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 identified variants for taurine concentration in Japanese Black beef

We performed genome‐wide association studies (GWAS) using the BovineSNP50 array to detect significant single nucleotide polymorphisms (SNPs) that may affect the concentration of 22 free amino acids and three peptides in Japanese Black beef cattle. A total of 574 Japanese Black cattle and 40,657 SNPs from the array were used for this study. Genome‐wide significant SNPs were detected for β‐alanine (three SNPs on chromosomes 22 and 29) and taurine (26 SNPs on chromosome 22). Importantly, the top two SNPs for taurine were highly significant (p = 6.2 × 10^?21), and the frequency of the increase‐concentration allele (Q) for taurine was found to be 0.73. The Q allele frequency of this population was similar to that of the other unrelated Japanese Black cattle, but different from that of the other breeds. In addition, the significant SNPs were not associated with carcass traits or fatty acid compositions. Interestingly, the top three of the four most significant SNPs for taurine were located near solute carrier family 6, member 6 (SLC6A6), which is a membrane transporter for taurine. We also found two associated variants in the 5′‐upstream region of SLC6A6; however, they were less significantly associated than the SNPs from the BovineSNP50 array.     

肉种鸡血浆极低密度脂蛋白质量浓度双向选择的效应

以父母代肉种鸡为材料，以血浆极低密度脂蛋白（very low density lipoprotein，VLDL）质量浓度为选择指标建立肉鸡高脂系和低脂系，个体测定一世代高、低脂系母鸡产蛋性能、种蛋受精率、孵化率、二世代6周龄体质量，观察血浆VLDL质量浓度选择效应。结果显示，一世代低脂系比高脂系早开产6．7d，低脂系40周龄和54周龄产蛋量显著高于高脂系零世代，一世代低脂系种蛋受精率、受精蛋孵化率、入孵蛋孵化率均优于高脂系；二世代高、低脂系6周龄体质量差异不显著。结果表明，对血浆VLDL质量浓度的低向选择使种鸡产蛋性能、种蛋受精率、孵化率产生了有益的间接反应，但对早期体质量没有影响。     

蛋用型鸡血浆极低密度脂蛋白浓度,肥度,生产性能之间的相关研究

以褐壳蛋鸡祖代母本种鸡为研究材料，用比浊法测定血浆极低密度脂蛋白浓度。试验结果表明，母鸡８１周龄腹脂重，腹脂率，鲜肝脂肪含量的变异系数分别高达４７％，３９％，４７％。表明这些性状在鸡群中未做过选择。血浆ＶＬＤＬ浓度与腹脂重，腹脂度，肝重，肝脂含量均呈正表型相关趋势。     

肉鸡血浆VLDL浓度的选择效应—肉仔鸡体重和血浆VLDL

以父线代肉种鸡为材料,用比浊法测定血浆ＶＬＤＬ浓度,分别以１６周龄,６周龄血浆ＶＬＤＬ浓度为选择指标建立零世代,一世代肉鸡高脂系和低脂系地肉鸡体重和血浆ＶＬＤＬ浓度的选择反应。结果：１．零世代,一世代肉鸡血浆ＶＬＤＬ浓度变异很大,变异系数分别为４３．６％－７４．６％和３８．７％－７９．９％,二个世代选择后,血浆ＶＬＤＬ浓度变异系数在高,低脂质中分别为３７％－５２％和３１％－４６％,表明对血浆ＶＬＤ     

Genome‐wide association studies for two exterior traits in Chinese Dongxiang spotted pigs

Pigs show extensive variation in exterior appearance. This variation has been explored as one of the selection targets to form breeding features in the pig industry. In this study, a customized Affymetrix Axiom Pig1.4M array plate was used to conduct genome‐wide association studies (GWAS) for two exterior traits—spotted coat color (SC) and facial type (FT)—in Chinese Dongxiang spotted pigs. Two and 12 single nucleotide polymorphisms (SNPs) were identified to be associated with SC and FT at the 5% genome‐wide significant level, respectively. Of these SNPs, two associated with SC were located around the DACH1 gene on Sus Scrofa chromosome (SSC)11. Eleven SNPs associated with FT were located within a 7.68 Mb region (29.03–36.71 Mb) on SSC7. Based on the GWAS results and the biological functions of genes, we highlight EDNRB as a candidate gene for SC and HMGA1 and RPS10 as the potential genes affecting facial variation. The findings contribute to the final characterization of causative genes and mutations underlying the effects of the SSC7 and SSC11 loci and improve our understanding of the genetic basis of phenotypic variation in Chinese indigenous pigs.     

肉鸡血浆极低密度脂蛋白浓度与屠体肥度性状的相关研究

以白羽肉仔鸡为研究材料，４９日龄采血，用此法浊法测定血浆极低密度脂蛋白浓度。试验结果表明，血浆ＶＬＤＬ浓度的变异系数为５５％，其与腹脂重，腹脂率呈显著的正表型相关。体重和屠体重与腹膜重呈极显著的正表型相关，对血浆ＶＬＤＬ浓度的低向选择将间接低体重。为防止肉仔鸡上市体重的下降，应该同时考虑对血浆ＶＬＤＬ浓度和体重的选择。对血浆ＶＬＤＬ浓度的低向选择将降低腹膜重，腹脂率，肝脂含量和肝脂重而对胸肌脂肪含     

Genome‐wide association study and genomic evaluation of feed efficiency traits in Japanese Black cattle using single‐step genomic best linear unbiased prediction method

The objectives of this study were to better understand the genetic architecture and the possibility of genomic evaluation for feed efficiency traits by (i) performing genome‐wide association studies (GWAS), and (ii) assessing the accuracy of genomic evaluation for feed efficiency traits, using single‐step genomic best linear unbiased prediction (ssGBLUP)‐based methods. The analyses were performed in residual feed intake (RFI), residual body weight gain (RG), and residual intake and body weight gain (RIG) during three different fattening periods. The phenotypes from 4,578 Japanese Black steers, which were progenies of 362 progeny‐tested bulls and the genotypes from the bulls were used in this study. The results of GWAS showed that a total of 16, 8, and 12 gene ontology terms were related to RFI, RG, and RIG, respectively, and the candidate genes identified in RFI and RG were involved in olfactory transduction and the phosphatidylinositol signaling system, respectively. The realized reliabilities of genomic estimated breeding values were low to moderate in the feed efficiency traits. In conclusion, ssGBLUP‐based method can lead to understand some biological functions related to feed efficiency traits, even with small population with genotypes, however, an alternative strategy will be needed to enhance the reliability of genomic evaluation.     

Genome‐wide association study for egg production and quality in layer chickens

Discovery of genes with large effects on economically important traits has for many years been of interest to breeders. The development of SNP panels which cover the whole genome with high density and, more importantly, that can be genotyped on large numbers of individuals at relatively low cost, has opened new opportunities for genome‐wide association studies (GWAS). The objective of this study was to find genomic regions associated with egg production and quality traits in layers using analysis methods developed for the purpose of whole genome prediction. Genotypes on over 4500 birds and phenotypes on over 13 000 hens from eight generations of a brown egg layer line were used. Birds were genotyped with a custom 42K Illumina SNP chip. Recorded traits included two egg production and 11 egg quality traits (puncture score, albumen height, yolk weight and shell colour) at early and late stages of production, as well as body weight and age at first egg. Egg weight was previously analysed by Wolc et al. ( 2012 ). The Bayesian whole genome prediction model – BayesB (Meuwissen et al. 2001 ) was used to locate 1 Mb regions that were most strongly associated with each trait. The posterior probability of a 1 Mb window contributing to genetic variation was used as the criterion for suggesting the presence of a quantitative trait locus (QTL) in that window. Depending upon the trait, from 1 to 7 significant (posterior probability >0.9) 1 Mb regions were found. The largest QTL, a region explaining 32% of genetic variance, was found on chr4 at 78 Mb for body weight but had pleiotropic effects on other traits. For the other traits, the largest effects were much smaller, explaining <7% of genetic variance, with regions on chromosomes 2, 12 and 17 explaining above 5% of genetic variance for albumen height, shell colour and egg production, respectively. In total, 45 of 1043 1 Mb windows were estimated to have a non‐zero effect with posterior probability > 0.9 for one or more traits.     

Practical capability of a DNA pool‐based genome‐wide association study using BovineSNP50 array in a cattle population

Genome‐wide association mapping for complex traits in cattle populations is a powerful, but expensive, selection tool. The DNA pooling technique can potentially reduce the cost of genome‐wide association studies. However, in DNA pooling design, the additional variance generated by pooling‐specific errors must be taken into account. Therefore, this study aimed to investigate factors such as: (i) the accuracy of allele frequency estimation; (ii) the magnitude of errors in pooling construction and in the array; and (iii) the effect of the number of replicate arrays on P‐values estimated by a genome‐wide association study. Results showed that the Illumina correction method is the most effective method to correct the allele frequency estimation; pooling errors, especially array variance, should be taken into account in DNA pooling design; and the risk of a type I error can be reduced by using at least two replicate arrays. These results indicate the practical capability and cost‐effectiveness of pool‐based genome‐wide association studies using the BovineSNP50 array in a cattle population.     

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.     

Genome‐wide association study for carcass traits,fatty acid composition,chemical composition,sugar, and the effects of related candidate genes in Japanese Black cattle

We performed a genome‐wide association study (GWAS) and candidate gene analysis to: (i) evaluate the effectiveness of the GWAS in our small population by performing GWAS for carcass weight (CW) and fatty acid composition; (ii) detect novel candidate regions affecting non‐CW carcass traits, chemical composition and sugar; and (iii) evaluate the association of the candidate genes previously detected in CW and fatty acid composition with other economically important traits. A total of 574 Japanese Black cattle and 40 657 Single nucleotide polymorphisms were used. In addition, candidate gene analyses were performed to evaluate the association of three CW‐related genes and two fatty acid‐related genes with carcass traits, fatty acid composition, chemical composition and sugar. The significant regions with the candidate genes were detected for CW and fatty acid composition, and these results showed that a significant region would be detectable despite the small sample size. The novel candidate regions were detected on BTA23 for crude protein and on BTA19 for fructose. CW‐related genes associated with the rib‐eye area and fatty acid composition were identified, and fatty acid‐related genes had no relationship with other traits. Moreover, the favorable allele of CW‐related genes had an unfavorable effect on fatty acid composition.     

A genome‐wide association study for fat‐related traits computed by image analysis in Japanese Black cattle

The objective of this study was to identify genomic regions associated with fat‐related traits using a Japanese Black cattle population in Hyogo. From 1836 animals, those with high or low values were selected on the basis of corrected phenotype and then pooled into high and low groups (n = 100 each), respectively. DNA pool‐based genome‐wide association study (GWAS) was performed using Illumina BovineSNP50 BeadChip v2 with three replicate assays for each pooled sample. GWAS detected that two single nucleotide polymorphisms (SNPs) on BTA7 (ARS‐BFGL‐NGS‐35463 and Hapmap23838‐BTA‐163815) and one SNP on BTA12 (ARS‐BFGL‐NGS‐2915) significantly affected fat percentage (FAR). The significance of ARS‐BFGL‐NGS‐35463 on BTA7 was confirmed by individual genotyping in all pooled samples. Moreover, association analysis between SNP and FAR in 803 Japanese Black cattle revealed a significant effect of SNP on FAR. Thus, further investigation of these regions is required to identify FAR‐associated genes and mutations, which can lead to the development of DNA markers for marker‐assisted selection for the genetic improvement of beef quality.     

Pool‐based genome‐wide association study identified novel candidate regions on BTA9 and 14 for oleic acid percentage in Japanese Black cattle

Fatty acid composition is an important indicator of beef quality. The objective of this study was to search the potential candidate region for fatty acid composition. We performed pool‐based genome‐wide association studies (GWAS) for oleic acid percentage (C18:1) in a Japanese Black cattle population from the Hyogo prefecture. GWAS analysis revealed two novel candidate regions on BTA9 and BTA14. The most significant single nucleotide polymorphisms (SNPs) in each region were genotyped in a population (n = 899) to verify their effect on C18:1. Statistical analysis revealed that both SNPs were significantly associated with C18:1 (p = .0080 and .0003), validating the quantitative trait loci (QTLs) detected in GWAS. We subsequently selected VNN1 and LYPLA1 genes as candidate genes from each region on BTA9 and BTA14, respectively. We sequenced full‐length coding sequence (CDS) of these genes in eight individuals and identified a nonsynonymous SNP T66M on VNN1 gene as a putative candidate polymorphism. The polymorphism was also significantly associated with C18:1, but the p value (p = .0162) was higher than the most significant SNP on BTA9, suggesting that it would not be responsible for the QTL. Although further investigation will be needed to determine the responsible gene and polymorphism, our findings would contribute to development of selective markers for fatty acid composition in the Japanese Black cattle of Hyogo.     

Genome‐wide association study for milk somatic cell score in holstein cattle using copy number variation as markers

Mastitis, the most common and expensive disease in dairy cows, implies significant losses in the dairy industry worldwide. Many efforts have been made to improve genetic mastitis resistance in dairy populations, but low heritability of this trait made this process not as effective as desired. The purpose of this study was to identify genomic regions explaining genetic variation of somatic cell count using copy number variations (CNVs) as markers in the Holstein population, genotyped with the Illumina BovineHD BeadChip. We found 24 and 47 copy number variation regions significantly associated with estimated breeding values for somatic cell score (SCS_EBVs) using SVS 8.3.1 and PennCNV‐CNVRuler software, respectively. The association analysis performed with these two software allowed the identification of 18 candidate genes (TERT, NOTCH1, SLC6A3, CLPTM1L, PPARα, BCL‐2, ABO, VAV2, CACNA1S, TRAF2, RELA, ELF3, DBH, CDK5, NF2, FASN, EWSR1 and MAP3K11) that result classified in the same functional cluster. These genes are also part of two gene networks, whose genes share the ‘stress’, ‘cell death’, ‘inflammation’ and ‘immune response’ GO terms. Combining CNV detection/association analysis based on two different algorithms helps towards a more complete identification of genes linked to phenotypic variation of the somatic cell count.     

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.     

Changes in lipoprotein metabolism and body composition in chickens in response to divergent selection for plasma very low density lipoprotein concentration

1. Plasma lipoprotein metabolism and body composition in lines of chicken selected for high- and low-plasma very low density lipoprotein (VLDL) concentrations were compared to the commercial broiler (meat-type) line from which they were derived. 2. Selection for low-plasma VLDL concentration for 10 generations has reduced the rate of VLDL secretion by at least 50% in males whereas selection for high-VLDL concentration has increased the rate of VLDL secretion over 2-fold. 3. Body fat content was highly correlated with rate of secretion of plasma triglyceride-rich (TGR) lipoproteins (r = 0.88 over the three lines). However, extrapolation of the data suggests that birds secreting no TGR-lipoproteins into the plasma would still have substantial amounts of body fat. 4. Selection for high VLDL has increased the proportion of circulating VLDL-triglyceride taken up by the abdominal fat pad by over 2-fold but there was no difference between high- and low-VLDL lines in the proportion of VLDL-triglyceride taken up by tissues and oxidised to [14C]-carbon dioxide. 5. The results confirm the importance of plasma lipoprotein metabolism in determining body composition in the chicken but suggest there are limits to further reduction in body fat content by manipulation of plasma lipoprotein metabolism.     

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.