Genetic Architecture of Abdominal Fat Deposition Revealed by a Genome-Wide Association Study in the Laying Chicken.

Fat has a high energy density, and excessive fatness has been recognized as a problem for egg production and the welfare of chickens. The identification of a genetic polymorphism controlling fat deposition would be helpful to select against excessive fatness in the laying hen. This study aimed to estimate genomic heritability and identify the genetic architecture of abdominal fat deposition in a population of chickens from a Dongxiang blue-shelled local breed crossbred with the White Leghorn. A genome-wide association study was conducted on abdominal fat percentage, egg production and body weights using a sample of 1534 hens genotyped with a 600 K Chicken Genotyping Array. The analysis yielded a heritability estimate of 0.19 ± 0.04 for abdominal fat percentage; 0.56 ± 0.04 for body weight at 72 weeks; 0.11 ± 0.03 for egg production; and 0.24 ± 0.04 for body weight gain. The genetic correlation of abdominal fat percentage with egg production between 60 and 72 weeks of age was -0.35 ± 0.18. This implies a potential trade-off between these two traits related to the allocation of resources. Strong positive genetic correlations were found between fat deposition and weight traits. A promising locus close to COL12A1 on chromosome 3, associated with abdominal fat percent, was found in the present study. Another region located around HTR2A on chromosome 1, where allele substitution was predicted to be associated with body weight gain, accounted for 2.9% of phenotypic variance. Another region located on chromosome 1, but close to SOX5, was associated with egg production. These results may be used to influence the balanced genetic selection for laying hens.

Effects of Energy-Restricted Feeding during Rearing on the Performance, Uniformity, and Development of Rugao Layer Breeders at the Initiation of the Laying Period.

The aim of this study was to assess the effects of energy-restricted feeding during rearing on the performance, uniformity, and development of layer breeders at the initiation of the laying period. A total of 2400 8-week-old Rugao layer breeders were randomly assigned to one of five groups (480 pullets per group) with eight replicates and were fed one of five diets that were nutritionally equal with the exception of apparent metabolizable energy corrected for nitrogen (AMEn) content (2850, 2750, 2650, 2550, and 2450 kcal AMEn/kg) from 8 to 18 weeks of age. The daily amount of feed was restricted to the absolute quantity of the diet consumed by laying hens fed 2850 kcal AMEn per kg diet ad libitum (control). From 18 to 21 weeks of age, all hens were fed a basal diet ad libitum. The body weight (BW) of the laying pullets decreased linearly with increasing energy restriction (p < 0.001) but recovered within 3 weeks of ad libitum feeding (p = 0.290). A gradual increase in the degree of energy restriction resulted in a gradual decrease in average daily weight gain (ADG) and a gradual increase in the feed conversion ratio (FCR) and energy conversion ratio (ECR) from 8 to 18 weeks of age (p < 0.001, p < 0.001, p = 0.008). In contrast, the ADG and ADFI (p < 0.001, p < 0.001) gradually increased, while the FCR and ECR (p < 0.001, p < 0.001) gradually improved from 18 to 21 weeks of age. From 8 to 21 weeks of age, ECR improved (p = 0.005) with an increasing degree of energy restriction. The energy-restricted feeding for 6 weeks to the end of the trial improved BW uniformity (p < 0.05). The relative length and circumference of tarsus (p < 0.001, p < 0.001), and the relative weights and lengths of the small intestine, duodenum, jejunum, ileum, and caeca increased linearly (p < 0.001, p = 0.012, p < 0.007, p = 0.012, p = 0.040; p < 0.001, p = 0.003, p = 0.032, p = 0.029, p = 0.040) with increasing energy restriction at 18 weeks of age. After switching to ad libitum feeding for 3 weeks, the relative weights and lengths of the small intestine, duodenum, and jejunum of laying pullets increased linearly with increasing energy restriction (p < 0.001, p = 0.016, p = 0.011; p = 0.009, p = 0.028, p = 0.032). In conclusion, moderate energy restriction (85.97%, 2450 vs. 2850 kcal AMEn/kg) from 8 to 18 weeks of age and switching to ad libitum feeding from 18 to 21 weeks of age can be used to improve BW uniformity and stimulate the development of the duodenum and jejunum of native layer breeders at the initiation of the laying period without compromising BW.

Lipolytic gene DAGLA is targeted by miR-223 in chicken hepatocytes.

miR-223 is an important miRNA. It plays important roles in lipid metabolism by targeting related genes in mammals. It may be related to fatty liver in laying hens and its functions and target genes need further study. Through bioinformatics, we found that 349 genes were predicted as target genes of miR-223. Lipid-related gene DAGLA was among the predicted target genes. Dual-luciferase reporter assays showed that DAGLA was the target gene of miR-223 and the site mutation assays validated the target site of miR-223 in DAGLA. Overexpression of miR-223 in chicken hepatocytes LMH decreased the mRNA and protein expression of DAGLA, while knockdown of miR-223 increased expression of DAGLA in LMH cells, further indicating that miR-223 targets DAGLA and downregulates its expression. Since the target site of miR-223 in chicken DAGLA is not conserved, these findings suggest that miR-223 plays a specific role in chicken liver by regulating expression of target gene DAGLA.

Genetic evaluation of eggshell color based on additive and dominance models in laying hens.

OBJECTIVE: Eggshells with a uniform color and intensity are important for egg production because many consumers assess the quality of an egg according to the shell color. In the present study, we evaluated the influence of dominant effects on the variations in eggshell color after 32 weeks in a crossbred population. METHODS: This study was conducted using 7,878 eggshell records from 2,626 hens. Heritability was estimated using a univariate animal model, which included inbreeding coefficients as a fixed effect and animal additive genetic, dominant genetic, and residuals as random effects. Genetic correlations were obtained using a bivariate animal model. The optimal diagnostic criteria identified in this study were: L* value (lightness) using a dominance model, and a* (redness), and b* (yellowness) value using an additive model. RESULTS: The estimated heritabilities were 0.65 for shell lightness, 0.42 for redness, and 0.60 for yellowness. The dominance heritability was 0.23 for lightness. The estimated genetic correlations were 0.61 between lightness and redness, -0.84 between lightness and yellowness, and -0.39 between redness and yellowness. CONCLUSION: These results indicate that dominant genetic effects could help to explain the phenotypic variance in eggshell color, especially based on data from blue-shelled chickens. Considering the dominant genetic variation identified for shell color, this variation should be employed to produce blue eggs for commercial purposes using a planned mating system.

Genome-wide association study provides insights into the genetic architecture of bone size and mass in chickens.

Bone size is an important trait for chickens because of its association with osteoporosis in layers and meat production in broilers. Here, we employed high density genotyping platforms to detect candidate genes for bone traits. Estimates of the narrow heritabilities ranged from 0.37 ± 0.04 for shank length to 0.59 ± 0.04 for tibia length. The dominance heritability was 0.12 ± 0.04 for shank length. Using a linear mixed model approach, we identified a promising locus within NCAPG on chromosome 4, which was associated with tibia length and mass, femur length and area, and shank length. In addition, three other loci were associated with bone size or mass at a Bonferroni-corrected genome-wide significance threshold of 1%. One region on chicken chromosome 1 between 168.38 and 171.82 Mb harbored HTR2A, LPAR6, CAB39L, and TRPC4. A second region that accounted for 2.2% of the phenotypic variance was located around WNT9A on chromosome 2, where allele substitution was predicted to be associated with tibia length. Four candidate genes identified on chromosome 27 comprising SPOP, NGFR, GIP, and HOXB3 were associated with tibia length and mass, femur length and area, and shank length. Genome partitioning analysis indicated that the variance explained by each chromosome was proportional to its length.

Identification of potential genomic regions and candidate genes for egg albumen quality by a genome-wide association study.

Albumen quality is a leading economic trait in the chicken industry. Major studies have paid attention to genetic architecture underlying albumen quality. However, the putative quantitative trait locus (QTL) for this trait is still unclear. In this genome-wide association study, we used an F 2 resource population to study longitudinal albumen quality. Seven single-nucleotide polymorphism (SNP) loci were found to be significantly ( p < 8.43 × 10 - 7 ) related to albumen quality by univariate analysis, while 11 SNPs were significantly ( p < 8.43 × 10 - 7 ) associated with albumen quality by multivariate analysis. A QTL on GGA4 had a pervasive function on albumen quality, including a SNP at the missense of NCAPG, and a SNP at the intergenic region of FGFPB1. It was further found that the putative QTLs at GGA1, GGA2, and GGA7 had the strongest effects on albumen height (AH) at 32 weeks, Haugh units (HU) at 44 weeks, and AH at 55 weeks. Moreover, novel SNPs on GGA5 and GGA3 were associated with AH and HU at 32, 44, and 48 weeks of age. These results confirmed the regions for egg weight that were detected in a previous study and were similar with QTL for albumen quality. These results showed that GGA4 had the strongest effect on albumen quality. Only a few significant loci were detected for most characteristics probably reflecting the attributes of a pleiotropic gene and a minor-polygene in quantitative traits.

Genetic architecture related to contour feathers density in an F2 resource population via a genome-wide association study.

The density of contour feathers is an important trait as it is closely related to heat dissipation in birds. Thus, identification of the major genes that control this trait will be useful to improve heat tolerance in chicken. So far, no GWAS study for the density of contour feathers in birds has been previously published; therefore, this study was aimed to identify genomic regions controlling the density of contour feathers. A total of 1252 hens were genotyped, using the 600 K Affymetrix Axiom Chicken Genotyping Array. The association analyses were performed using the GenABEL package in the R program. In brief, 146 significant SNP markers were mainly located on chromosome 1 and were identified to associate with the density of contour feathers in the current GWAS analysis. Moreover, we identified several within/nearby candidate genes (SUCLA2, DNAJC15, DHRS12, MLNR, and RB1) that are either directly or indirectly involved in the genetic control of the density of contour feathers in chicken. This study laid the foundation for studying the mechanism that underlies the density of chicken feathers. Furthermore, it is feasible to shear the back feathers of live chickens and measure the density of the feathers to improve heat tolerance in breeding practice.

Genetic architecture and candidate genes detected for chicken internal organ weight with a 600 K single nucleotide polymorphism array.

OBJECTIVE: Internal organs indirectly affect economic performance and well-being of animals. Study of internal organs during later layer period will allow full utilization of layer hens. Hence, we conducted a genome-wide association study (GWAS) to identify potential quantitative trait loci or genes that potentially contribute to internal organ weight. METHODS: A total of 1,512 chickens originating from White Leghorn and Dongxiang Blue-Shelled chickens were genotyped using high-density Affymetrix 600 K single nucleotide polymorphism (SNP) array. We conducted a GWAS, linkage disequilibrium analysis, and heritability estimated based on SNP information by using GEMMA, Haploview and GCTA software. RESULTS: Our results displayed that internal organ weights show moderate to high (0.283 to 0.640) heritability. Variance partitioned across chromosomes and chromosome lengths had a linear relationship for liver weight and gizzard weight (R2 = 0.493, 0.753). A total of 23 highly significant SNPs that associated with all internal organ weights were mainly located on Gallus gallus autosome (GGA) 1 and GGA4. Six SNPs on GGA2 affected heart weight. After the final analysis, five top SNPs were in or near genes 5-Hydroxytryptamine receptor 2A, general transcription factor IIF polypeptide 2, WD repeat and FYVE domain containing 2, non-SMC condensin I complex subunit G, and sonic hedgehog, which were considered as candidate genes having a pervasive role in internal organ weights. CONCLUSION: Our findings provide an understanding of the underlying genetic architecture of internal organs and are beneficial in the selection of chickens.

A genome-wide study to identify genes responsible for oviduct development in chickens.

Molecular genetic tools provide a method for improving the breeding selection of chickens (Gallus gallus). Although some studies have identified genes affecting egg quality, little is known about the genes responsible for oviduct development. To address this issue, here we used a genome-wide association (GWA) study to detect genes or genomic regions that are related to oviduct development in a chicken F2 resource population by employing high-density 600 K single-nucleotide polymorphism (SNP) arrays. For oviduct length and weight, which exhibited moderate heritability estimates of 0.35 and 0.39, respectively, chromosome 1 (GGA1) explained 9.45% of the genetic variance, while GGA4 to GGA8 and GGA11 explained over 1% of the variance. Independent univariate genome-wide screens for oviduct length and weight detected 69 significant SNPs on GGA1 and 49 suggestive SNPs on GGA1, GGA4, and GGA8. One hundred and fourteen suggestive SNPs were associated with oviduct length, while 73 SNPs were associated with oviduct weight. The significant genomic regions affecting oviduct weight ranged from 167.79-174.29 Mb on GGA1, 73.16-75.70 Mb on GGA4, and 4.88-4.92 Mb on GGA8. The genes CKAP2, CCKAR, NCAPG, IGFBP3, and GORAB were shown to have potential roles in oviduct development. These genes are involved in cell survival, appetite, and growth control. Our results represent the first GWA analysis of genes controlling oviduct weight and length. The identification of genomic loci and potential candidate genes affecting oviduct development greatly increase our understanding of the genetic basis underlying oviduct development, which could have an impact on the selection of egg quality.

Genetic Architecture and Candidate Genes Identified for Follicle Number in Chicken.

Follicular development has a major impact on reproductive performance. Most previous researchers focused on molecular mechanisms of follicular development. The genetic architecture underlying the number of follicle, however, has yet not to be thoroughly defined in chicken. Here we report a genome-wide association study for the genetic architecture determining the numbers of follicles in a large F2 resource population. The results showed heritability were low to moderate (0.05-0.28) for number of pre-ovulatory follicles (POF), small yellow follicles (SYF) and atresia follicles (AF). The highly significant SNPs associated with SYF were mainly located on GGA17 and GGA28. Only four significant SNPs were identified for POF on GGA1. The variance partitioned across chromosomes and chromosome lengths had a linear relationship for SYF (R2 = 0.58). The enriched genes created by the closest correspondent significant SNPs were found to be involved in biological pathways related to cell proliferation, cell cycle and cell survival. Two promising candidate genes, AMH and RGS3, were suggested to be prognostic biomarkers for SYF. In conclusion, this study offers the first evidence of genetic variance and positional candidate genes which influence the number of SYF in chicken. These identified informative SNPs may facilitate selection for an improved reproductive performance of laying hens.

Genetic architecture of bone quality variation in layer chickens revealed by a genome-wide association study.

Skeletal problems in layer chickens are gaining attention due to animal welfare and economic losses in the egg industry. The genetic improvement of bone traits has been proposed as a potential solution to these issues; however, genetic architecture is not well understood. We conducted a genome-wide association study (GWAS) on bone quality using a sample of 1534 hens genotyped with a 600 K Chicken Genotyping Array. Using a linear mixed model approach, a novel locus close to GSG1L, associated with femur bone mineral density (BMD), was uncovered in this study. In addition, nine SNPs in genes were associated with bone quality. Three of these genes, RANKL, ADAMTS and SOST, were known to be associated with osteoporosis in humans, which makes them good candidate genes for osteoporosis in chickens. Genomic partitioning analysis supports the fact that common variants contribute to the variations of bone quality. We have identified several strong candidate genes and genomic regions associated with bone traits measured in end-of-lay cage layers, which accounted for 1.3-7.7% of the phenotypic variance. These SNPs could provide the relevant information to help elucidate which genes affect bone quality in chicken.

Genome-Wide Association Studies for Comb Traits in Chickens.

The comb, as a secondary sexual character, is an important trait in chicken. Indicators of comb length (CL), comb height (CH), and comb weight (CW) are often selected in production. DNA-based marker-assisted selection could help chicken breeders to accelerate genetic improvement for comb or related economic characters by early selection. Although a number of quantitative trait loci (QTL) and candidate genes have been identified with advances in molecular genetics, candidate genes underlying comb traits are limited. The aim of the study was to use genome-wide association (GWA) studies by 600 K Affymetrix chicken SNP arrays to detect genes that are related to comb, using an F2 resource population. For all comb characters, comb exhibited high SNP-based heritability estimates (0.61-0.69). Chromosome 1 explained 20.80% genetic variance, while chromosome 4 explained 6.89%. Independent univariate genome-wide screens for each character identified 127, 197, and 268 novel significant SNPs with CL, CH, and CW, respectively. Three candidate genes, VPS36, AR, and WNT11B, were determined to have a plausible function in all comb characters. These genes are important to the initiation of follicle development, gonadal growth, and dermal development, respectively. The current study provides the first GWA analysis for comb traits. Identification of the genetic basis as well as promising candidate genes will help us understand the underlying genetic architecture of comb development and has practical significance in breeding programs for the selection of comb as an index for sexual maturity or reproduction.

Genome-wide association studies for feed intake and efficiency in two laying periods of chickens.

BACKGROUND: Feed contributes to over 60 % of the total production costs in the poultry industry. Increasing feed costs prompt geneticists to include feed intake and efficiency as selection goals in breeding programs. In the present study, we used an F2 chicken population in a genome-wide association study (GWAS) to detect potential genetic variants and candidate genes associated with daily feed intake (FI) and feed efficiency, including residual feed intake (RFI) and feed conversion ratio (FCR). METHODS: A total of 1534 F2 hens from a White Leghorn and Dongxiang reciprocal cross were phenotyped for feed intake and efficiency between 37 and 40 weeks (FI1, RFI1, and FCR1) and between 57 and 60 weeks (FI2, RFI2, and FCR2), and genotyped using the chicken 600 K single nucleotide polymorphism (SNP) genotyping array. Univariate, bivariate, and conditional genome-wide association studies (GWAS) were performed with GEMMA, a genome-wide efficient mixed model association algorithm. The statistical significance threshold for association was inferred by the simpleM method. RESULTS: We identified eight genomic regions that each contained at least one genetic variant that showed a significant association with FI. Genomic regions on Gallus gallus (GGA) chromosome 4 coincided with known quantitative trait loci (QTL) that affect feed intake of layers. Of particular interest, eight SNPs on GGA1 in the region between 169.23 and 171.55 Mb were consistently associated with FI in both univariate and bivariate GWAS, which explained 3.72 and 2.57 % of the phenotypic variance of FI1 and FI2, respectively. The CAB39L gene can be considered as a promising candidate for FI1. For RFI, a haplotype block on GGA27 harbored a significant SNP associated with RFI2. The major allele of rs315135692 was favorable for a lower RFI, with a phenotypic difference of 3.35 g/day between opposite homozygous genotypes. Strong signals on GGA1 were detected in the bivariate GWAS for FCR. CONCLUSIONS: The results demonstrated the polygenic nature of feed intake. GWAS identified novel variants and confirmed a QTL that was previously reported for feed intake in chickens. Genetic variants associated with feed efficiency may be used in genomic breeding programs to select more efficient layers.

Genome-wide association study dissects genetic architecture underlying longitudinal egg weights in chickens.

BACKGROUND: As a major economic trait in chickens, egg weight (EW) receives widespread interests in breeding, production and consumption. However, limited information is available for underlying genetic architecture of longitudinal trend in EW. Herein, we measured EWs at nine time points from onset of laying to 60 week of age, and conducted comprehensive genome-wide association studies (GWAS) in 1,534 F2 hens derived from reciprocal crosses between White Leghorn and Dongxiang chickens. RESULTS: Egg weights at all ages except the first egg weight (FEW) exhibited high SNP-based heritability estimates (0.47~0.60). Strong pair-wise genetic correlations (0.77~1.00) were found among all EWs. Nine separate univariate genome-wide screens suggested 73 signals showing significant associations with longitudinal EWs. After multivariate and conditional analyses, four variants on three chromosomes remained independent contributions. The minor alleles at two loci exerted consistent and positive substitution effects on EWs, and other two were negative. The four loci together accounted for 3.84 % of the phenotypic variance for FEW and 7.29~11.06 % for EWs from 32 to 60 week of age. We obtained five candidate genes, of which NCAPG harbors a non-synonymous SNP (rs14491030) causing a valine-to-alanine amino-acid substitution. Genome partitioning analysis indicated a strong linear correlation between the variance explained by each chromosome and its length, which provided evidence that EW follows a highly polygenic nature of inheritance. CONCLUSIONS: Identification of significant genetic causes that together implicate EWs at different ages will greatly advance our understanding of the genetic basis behind longitudinal EWs, and would be helpful to illuminate the future breeding direction on how to select desired egg size.

Identification of Promising Mutants Associated with Egg Production Traits Revealed by Genome-Wide Association Study.

Egg number (EN), egg laying rate (LR) and age at first egg (AFE) are important production traits related to egg production in poultry industry. To better understand the knowledge of genetic architecture of dynamic EN during the whole laying cycle and provide the precise positions of associated variants for EN, LR and AFE, laying records from 21 to 72 weeks of age were collected individually for 1,534 F2 hens produced by reciprocal crosses between White Leghorn and Dongxiang Blue-shelled chicken, and their genotypes were assayed by chicken 600 K Affymetrix high density genotyping arrays. Subsequently, pedigree and SNP-based genetic parameters were estimated and a genome-wide association study (GWAS) was conducted on EN, LR and AFE. The heritability estimates were similar between pedigree and SNP-based estimates varying from 0.17 to 0.36. In the GWA analysis, we identified nine genome-wide significant loci associated with EN of the laying periods from 21 to 26 weeks, 27 to 36 weeks and 37 to 72 weeks. Analysis of GTF2A1 and CLSPN suggested that they influenced the function of ovary and uterus, and may be considered as relevant candidates. The identified SNP rs314448799 for accumulative EN from 21 to 40 weeks on chromosome 5 created phenotypic differences of 6.86 eggs between two homozygous genotypes, which could be potentially applied to the molecular breeding for EN selection. Moreover, our finding showed that LR was a moderate polygenic trait. The suggestive significant region on chromosome 16 for AFE suggested the relationship between sex maturity and immune in the current population. The present study comprehensively evaluates the role of genetic variants in the development of egg laying. The findings will be helpful to investigation of causative genes function and future marker-assisted selection and genomic selection in chickens.

Genetic parameters of feed efficiency traits in laying period of chickens.

Laying records on 1,534 F2 hens, derived from a reciprocal cross between White Leghorns and Dongxiang blue-shelled chickens, were used to estimate genetic parameters for residual feed intake (RFI), feed conversion ratio (FCR), daily feed intake (FI), metabolic BW (MBW), BW gain (BWG), and daily egg mass (EM) at 37 to 40 (T1) and 57 to 60 wk age (T2), respectively. Genetic analysis was subsequently conducted with the AI-REML method using an animal model. Estimates for heritability of RFI, FCR, and FI were 0.21, 0.19, and 0.20 in T1, and 0.29, 0.13, and 0.26 in T2, respectively. In T1 and T2, RFI showed high and positive genetic correlations with FCR (0.51, 0.43) and FI (0.72, 0.84), whereas the genetic correlation between FI and FCR was very low (-0.09, 0.11). Genetically, negative correlations were found between RFI and its component traits (-0.01 to -0.47). In addition, high genetic correlations, from 0.76 to 0.94, were observed between T1 and T2 for RFI, FCR, and FI, suggesting that feed efficiency traits in the 2 stages had a similar genetic background. The results indicate that selection for low RFI could reduce FI without significant changes in EM, while selection on FCR will increase EM. The present study lays the foundation for genetic improvement of feed efficiency during the laying period of chickens.