A genome-wide SNP scan reveals novel loci for egg production and quality traits in white leghorn and brown-egg dwarf layers

Genome-wide re-sequencing reveals selection signatures for important economic traits in Taihang chickens

Taihang chickens is precious genetic resource with excellent adaptability and disease resistance, as well as high-quality eggs and meat. However, the genetic mechanism underlying important economic traits remain largely unknown. To address this gap, we conducted whole-genome resequencing of 66 Taihang and 15 White Plymouth rock chicken (Baiyu). The population structure analysis revealed that Taihang chickens and Baiyu are 2 independent populations. The genomic regions with strong selection signals and some candidate genes related to economic and appearance traits were identified. Additionally, we found a continuously selected 1.2 Mb region on chromosome 2 that is closely related to disease resistance. Therefore, our findings were helpful in further understanding the genetic architecture of the Taihang chickens and provided a worthy theoretical basis and technological support to improve high-quality Taihang chickens.

Calcium deposition in chicken eggshells: role of host genetics and gut microbiota

Eggshell is predominantly composed of calcium carbonate, making up about 95% of its composition. Eggshell quality is closely related to the amount of calcium deposition in the shell, which requires chickens to maintain a robust state of calcium metabolism. In this study, we introduced a novel parameter, Total Eggshell Weight (TESW), which measures the total weight of eggshells produced by chickens over a period of 10 consecutive d, providing valuable information on the intensity of calcium metabolism in chickens. Genome-wide association study (GWAS) was conducted to explore the genetic determinants of eggshell calcification in a population of 570 Rhode Island Red laying hens at 90 wk of age. This study revealed a significant association between a specific SNP (rs14249431) and TESW. Additionally, using random forest modeling and 2-tailed testing, we identified 3 genera, Lactobacillus in the jejunum, Lactobacillus, and Fournierella in the cecum, that exhibited a significant association with TESW. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis of claudin-1 and occludin genes in individuals with low TESW and high abundance of jejunal Lactobacillus confirmed that the inhibitory effect of jejunal Lactobacillus on calcium uptake was achieved through the up-regulation of tight junctions in intestinal epithelial cells. Notably, both host and microbial factors influence TESW, displaying a mutually influential relationship between them. The microbiome-wide Genome-Wide Association Study (mb-GWAS) identified significant associations between these 3 genera and specific genomic variants, such as rs316115020 and rs316420452 on chromosome 5, rs313198529 on chromosome 11, linked to Lactobacillus in the cecum. Moreover, rs312552529 on chromosome 1 exhibited potential association with Fournierella in the cecum. This study highlights the influence of host genetics and gut microbiota on calcium deposition in eggshells during the late laying phase, providing a foundational reference for studying calcium metabolism in hens.

Genome-wide association study identified candidate genes for egg production traits in the Longyan Shan-ma duck

Egg production is an important economic trait in layer ducks and understanding the genetics basis is important for their breeding. In this study, a genome-wide association study (GWAS) for egg production traits in 303 female Longyan Shan-ma ducks was performed based on a genotyping-by-sequencing strategy. Sixty-two single nucleotide polymorphisms (SNPs) associated with egg weight traits were identified (P < 9.48 × 10-5), including 8 SNPs at 5% linkage disequilibrium (LD)-based Bonferroni-corrected genome-wide significance level (P < 4.74 × 10-6). One hundred and nineteen SNPs were associated with egg number traits (P < 9.48 × 10-5), including 13 SNPs with 5% LD-based Bonferroni-corrected genome-wide significance (P < 4.74 × 10-6). These SNPs annotated 146 target genes which contained known candidate genes for egg production traits, such as prolactin and prolactin releasing hormone receptor. This study identified that these associated genes were significantly enriched in egg production-related pathways (P < 0.05), such as the oxytocin signaling, MAPK signaling, and calcium signaling pathways. It was notable that 18 genes were differentially expressed in ovarian tissues between higher and lower egg production in Shan-ma ducks. The identified potential candidate genes and pathways provide insight into the genetic basis underlying the egg production trait of layer ducks.

Runs of homozygosity and selection signature analyses reveal putative genomic regions for artificial selection in layer breeding

BACKGROUND

The breeding of layers emphasizes the continual selection of egg-related traits, such as egg production, egg quality and eggshell, which enhance their productivity and meet the demand of market. As the breeding process continued, the genomic homozygosity of layers gradually increased, resulting in the emergence of runs of homozygosity (ROH). Therefore, ROH analysis can be used in conjunction with other methods to detect selection signatures and identify candidate genes associated with various important traits in layer breeding.

RESULTS

In this study, we generated whole-genome sequencing data from 686 hens in a Rhode Island Red population that had undergone fifteen consecutive generations of intensive artificial selection. We performed a genome-wide ROH analysis and utilized multiple methods to detect signatures of selection. A total of 141,720 ROH segments were discovered in whole population, and most of them (97.35%) were less than 3 Mb in length. Twenty-three ROH islands were identified, and they overlapped with some regions bearing selection signatures, which were detected by the De-correlated composite of multiple signals methods (DCMS). Sixty genes were discovered and functional annotation analysis revealed the possible roles of them in growth, development, immunity and signaling in layers. Additionally, two-tailed analyses including DCMS and ROH for 44 phenotypes of layers were conducted to find out the genomic differences between subgroups of top and bottom 10% phenotype of individuals. Combining the results of GWAS, we observed that regions significantly associated with traits also exhibited selection signatures between the high and low subgroups. We identified a region significantly associated with egg weight near the 25 Mb region of GGA 1, which exhibited selection signatures and has higher genomic homozygosity in the low egg weight subpopulation. This suggests that the region may be play a role in the decline in egg weight.

CONCLUSIONS

In summary, through the combined analysis of ROH, selection signatures, and GWAS, we identified several genomic regions that associated with the production traits of layers, providing reference for the study of layer genome.

Genome-wide association studies of egg production traits by whole genome sequencing of Laiwu Black chicken

Compared to high-yield commercial laying hens, Chinese indigenous chicken breeds have poor egg laying capacity due to the lack of intensive selection. However, as these breeds have not undergone systematic selection, it is possible that there is a greater abundance of genetic variations related to egg laying traits. In this study, we assessed 5 egg number (EN) traits at different stages of the egg-laying period: EN1 (from the first egg to 23 wk), EN2 (from 23 to 35 wk), EN3 (from 35 to 48 wk), EN4 (from the first egg to 35 wk), and EN5 (from the first egg to 48 wk). To investigate the molecular mechanisms underlying egg number traits in a Chinese local chicken breed, we conducted a genome-wide association study (GWAS) using data from whole-genome sequencing (WGS) of 399 Laiwu Black chickens. We obtained a total of 3.01 Tb of raw data with an average depth of 7.07 × per individual. A total of 86 genome-wide suggestive or significant single-nucleotide polymorphisms (SNP) contained within a set of 45 corresponding candidate genes were identified and found to be associated with stages EN1-EN5. The genes vitellogenin 2 (VTG2), lipase maturation factor 1 (LMF1), calcium voltage-gated channel auxiliary subunit alpha2delta 3 (CACNA2D3), poly(A) binding protein cytoplasmic 1 (PABPC1), programmed cell death 11 (PDCD11) and family with sequence similarity 213 member A (FAM213A) can be considered as the candidate genes associated with egg number traits, due to their reported association with animal reproduction traits. Noteworthy, results suggests that VTG2 and PDCD11 are not only involved in the regulation of EN3, but also in the regulation of EN5, implies that VTG2 and PDCD11 have a significant influence on egg production traits. Our study offers valuable genomic insights into the molecular genetic mechanisms that govern egg number traits in a Chinese indigenous egg-laying chicken breed. These findings have the potential to enhance the egg-laying performance of chickens.

Genome-wide association study identifies a novel candidate gene for egg production traits in chickens

Qingyuan partridge chicken is a renowned indigenous yellow broiler breed in China. Egg production traits are important economic traits for chickens. With the decreasing cost of whole genome resequencing, identifying candidate genes with more precision has become possible. In order to identify molecular markers and candidate genes associated with egg production traits, we conducted genome-wide association studies based on the resequencing data of 287 female Qingyuan partridge chickens. For each hen, age at first egg and egg laying rate were recorded and calculated, respectively. With a univariate linear mixed model, we detected one genome-wide significant single nucleotide polymorphism (SNP) and three chromosome-wide significant SNPs associated with egg laying rate. MTA2 is highly likely to be a functional gene for egg laying rate. Our study identifies MTA2 as the first time to be associated with egg laying rate. Findings in our study will advance our understanding of the genetic basis of egg production and have the potential to improve the efficiency of genomic selection in chickens.

A large-scale comparison of the meat quality characteristics of different chicken breeds in South China

Meat quality traits are essential for producing high-quality broilers, but the genetic improvement has been limited by the complexity of measurement methods and the numerous traits involved. To systematically understand the meat quality characteristics of different broiler breeds, this study collected data on slaughter performance, skin color, fat deposition, and meat quality traits of 434 broilers from 12 different breeds in South China. The results showed that there was no significant difference in the live weight and slaughter weight of various broiler breeds at their respective market ages. Commercial broiler breeds such as Xiaobai and Huangma chickens had higher breast muscle and leg muscle rates. The skin and abdominal fat of Huangma chickens cultivated in the consumer market in South China exhibited significantly higher levels of yellowness compared to other varieties. Concerning fat traits, we observed that Wenchang chickens exhibited a strong ability to fat deposition, while the younger breeds showed lower fat deposition. Additionally, there were significant positive correlations found among different traits, including traits related to weight, traits related to fat, and skin color of different parts. Hierarchical clustering analysis revealed that fast-growing and large broiler Xiaobai chickens formed a distinct cluster based on carcass characteristics, skin color, and meat quality traits. Principal component analysis (PCA) was used to extract multiple principal components as substitutes for complex meat quality indicators, establishing a chicken meat quality evaluation model to differentiate between different breeds of chickens. At the same time, we identified 46, 22, and 20 SNP loci and their adjacent genes that were significantly associated with muscle mass traits, fat deposition, and skin color through genome-wide association studies (GWAS). The above results are helpful for systematically understanding the differences and characteristics of meat quality traits among different breeds.

Integration of Whole-Genome Resequencing and Transcriptome Sequencing Reveals Candidate Genes in High Glossiness of Eggshell

Eggshell gloss is an important characteristic for the manifestation of eggshell appearance. However, no study has yet identified potential candidate genes for eggshell gloss between high-gloss (HG) and low-gloss (LG) chickens. The aim of this study was to perform a preliminary investigation into the formation mechanism of eggshell gloss and to identify potential genes. The eggshell gloss of 300-day-old Rhode Island Red hens was measured from three aspects. Uterine tissues of the selected HG and LG (n = 5) hens were collected for RNA-seq. Blood samples were also collected for whole-genome resequencing (WGRS). RNA-seq analysis showed that 150 differentially expressed genes (DEGs) were identified in the uterine tissues of HG and LG hens. These DEGs were mainly enriched in the calcium signaling pathway and the neuroactive ligand-receptor interaction pathway. Importantly, these two pathways were also significantly enriched in the WGRS analysis results. Further joint analysis of WGRS and RNA-seq data revealed that 5-hydroxytryptamine receptor 1F (HTR1F), zinc finger protein 536 (ZNF536), NEDD8 ubiquitin-like modifier (NEDD8), nerve growth factor (NGF) and calmodulin 1 (CALM1) are potential candidate genes for eggshell gloss. In summary, our research provides a reference for the study of eggshell gloss and lays a foundation for improving egg glossiness in layer breeding.

Genetic patterns and genome-wide association analysis of eggshell quality traits of egg-type chicken across an extended laying period

The industry of egg-type chicken has shown a trend of extending the rearing period, with the goal of breeding chicken breeds capable of producing 500 qualified eggs by 700 d of age. However, the rapid decline in eggshell quality during the late laying period is one of the major challenges. In this study, a total of 3,261 Rhode Island Red chickens were used to measure eggshell quality traits including eggshell strength (ESS), eggshell thickness (EST), eggshell color (ESC) and eggshell gloss (ESG) at seven age points ranging from 36 to 90 wk of age. Phenotypic variations increased with the aging process, especially during the late laying period (> 55 wk), and the heritability during this period decreased by 22.7 to 81.4% compared to the initial and peak laying periods. Then we performed genome-wide association study (GWAS) to identify the genomic variants that associated with eggshell quality, with a custom Illumina 50K BeadChip, named PhenoixChip-I. The results indicated that 2 genomic regions on GGA1(23.24-25.15Mb; 175.95-176.05 Mb) were significantly (P < 4.48E-06) or suggestively (P < 8.97E-05) associated with ESS, which can explain 9.59% and 0.48% of the phenotypic variations of ESS46 and ESS36, respectively. Three genes, FRY, PCNX2, and ENSGALG00000052468, were considered to be the candidate genes for ESS. For other traits, the genome-wide suggestive SNPs were identified at each age point, exhibiting a certain trend with aging process. Additionally, SNP enrichment analysis and functional annotation of cross-tissue regulatory elements to ESS36 revealed a high concentration of enhancer elements specific to shell gland and kidney tissues. This study, deepened our knowledge of eggshells and laying a valued scientific foundation for chicken molecular breeding.

Association analysis of production traits of Japanese quail (Coturnix japonica) using restriction-site associated DNA sequencing

This study was designed to perform an association analysis and identify SNP markers associated with production traits of Japanese quail using restriction-site-associated DNA sequencing. Weekly body weight data from 805 quail were collected from hatching to 16 weeks of age. A total number of 3990 eggs obtained from 399 female quail were used to assess egg quality traits. Egg-related traits were measured at the beginning of egg production (first stage) and at 12 weeks of age (second stage). Five eggs were analyzed at each stage. Traits, such as egg weight, egg length and short axes, eggshell strength and weight, egg equator thickness, yolk weight, diameter, and colour, albumen weight, age of first egg, total number of laid eggs, and egg production rate, were assessed. A total of 383 SNPs and 1151 associations as well as 734 SNPs and 1442 associations were identified in relation to quail production traits using general linear model (GLM) and mixed linear model (MLM) approaches, respectively. The GLM-identified SNPs were located on chromosomes 1-13, 15, 17-20, 24, 26-28, and Z, underlying phenotypic traits, except for egg and albumen weight at the first stage and yolk yellowness at the second stage. The MLM-identified SNPs were positioned on defined chromosomes associated with phenotypic traits except for the egg long axis at the second stage of egg production. Finally, 35 speculated genes were identified as candidate genes for the targeted traits based on their nearest positions. Our findings provide a deeper understanding and allow a more precise genetic improvement of production traits of Galliformes, particularly in Japanese quail.

Genome-Wide Association Study of Egg Production Traits in Shuanglian Chickens Using Whole Genome Sequencing

Egg production is the most important economic trait in laying hens. To identify molecular markers and candidate genes associated with egg production traits, such as age at first egg (AFE), weight at first egg (WFE), egg weight (EW), egg number (EN), and maximum consecutive egg laying days (MCD), a genome-wide analysis by whole genome sequencing was performed in Shuanglian chickens. Through whole genome sequencing and quality control, a total of 11,006,178 SNPs were obtained for further analysis. Heritability estimates ranged from moderate to high for EW (0.897) and MCD (0.632), and from low to moderate (0.193~0.379) for AFE, WFE, and EN. The GWAS results showed 11 genome-wide significant SNPs and 23 suggestive significant SNPs were identified to be associated with EN, MCD, WFE, and EW. Linkage disequilibrium analysis revealed twenty-seven SNPs associated with EN were located in a 0.57 Mb region on GGA10, and clustered into five blocks. Through functional annotation, three candidate genes NEO1, ADPGK, and CYP11A1, were identified to be associated with EN, while the S1PR4, LDB2, and GRM8 genes was linked to MCD, WFE, and EW, respectively. These findings may help us to better understand the molecular mechanisms underlying egg production traits in chickens and contribute to genetic improvement of these traits.

Estimation of genetic parameters of eggshell translucency and production traits in different genotypes of laying hens

The translucency of eggshells is a ubiquitous appearance problem caused by moisture translocation and the accumulation of egg contents into the eggshell ultrastructure. Previous studies have mainly investigated the causes of eggshell translucency from nutritional and environmental perspectives. However, little is known of the effect of genetics the causes of eggshell translucency on hen production performance. To evaluate the genetic parameters of eggshell translucency and other production performance indicators, we performed an experiment on 3 pure hen lines: 624 Dwarf Layer-White, 1,612 Rhode Island Red, and 813 Rhode Island Red-White. We collected eggs from each hen over 5 d and measured eggshell translucent level (TL) using the grading method. Additionally we measured indicators of each hen during the laying period, including age at laying of the first egg (AFE), body weight at laying of the first egg (BWFE), weight of the first egg (FEW), body weight at 40 wk (BW40), egg weight at 40 wk (EW40), egg production up to 40 wk of age (EN), and calculated the genetic parameters among the indicators. The results showed that the estimated heritability of TL in the 3 genotypes were 0.30, 0.24, and 0.20, respectively, suggesting a low or moderate level of heritability. We found a positive correlation between TL and AFE, with genetic correlation coefficients 0.19 to 0.41, and negative genetic correlation between TL and EN, with correlation coefficient -0.36 to -0.19. Additionally, we observed positive correlation exists between AFE and FEW, BWFE and FEW, and BW40 and EW40; and negative correlation between AFE and EN in the 3 pure lines. These results enriched the research on heritability of eggshell translucency in different hen breeds and demonstrated moderate or low heritability of the indicator. Furthermore, eggshell translucency was negatively affected by AFE and EN. Our results provide a valuable reference for predicting selection response of eggshell translucency and production performance in brood hens, and locating the genes regulating eggshell translucency.

Genome-Wide Associative Study of Phenotypic Parameters of the 3D Body Model of Aberdeen Angus Cattle with Multiple Depth Cameras

Simple Summary

This article aims to develop a new approach to the lifetime evaluation of cattle by 3-D visualization of economic-biological and genetic features. The following indicators were selected as phenotypic features: chest width and chest girth retrieved by 3-D model and meat output on the bones. Correlation analysis showed a reliable positive relationship between chest width and meat output on the bones, which can potentially be used for lifetime evaluation of meat productivity of animals. Genome-wide associations analysis revealed the following potential loci of quantitative traits on cattle chromosomes for chest width, chest girth, and meat output on bones.

Abstract

In beef cattle breeding, genome-wide association studies (GWAS) using single nucleotide polymorphisms (SNPs) arrays can reveal many loci of various production traits, such as growth, productivity, and meat quality. With the development of genome sequencing technologies, new opportunities are opening up for more accurate identification of areas associated with these traits. This article aims to develop a novel approach to the lifetime evaluation of cattle by 3-D visualization of economic-biological and genetic features. The purpose of this study was to identify significant variants underlying differences in the qualitative characteristics of meat, using imputed data on the sequence of the entire genome. Samples of biomaterial of young Aberdeen-Angus breed cattle (n = 96) were the material for carrying out genome-wide SNP genotyping. Genotyping was performed using a high-density DNA chip Bovine GPU HD BeadChip (Illumina Inc., San Diego, CA, USA), containing ~150 thousand SNPs. The following indicators were selected as phenotypic features: chest width and chest girth retrieved by 3-D model and meat output on the bones. Correlation analysis showed a reliable positive relationship between chest width and meat output on the bones, which can potentially be used for lifetime evaluation of meat productivity of animals.

Genome-Wide Association Studies and Haplotype-Sharing Analysis Targeting the Egg Production Traits in Shaoxing Duck

Age at first egg (AFE) and egg number (EN) are economically important traits related to egg production, as they directly influence the benefits of the poultry industry, but the molecular genetic research that affects those traits in laying ducks is still sparse. Our objective was to identify the genomic regions and candidate genes associated with AFE, egg production at 43 weeks (EP43w), and egg production at 66 weeks (EP66w) in a Shaoxing duck population using genome-wide association studies (GWASs) and haplotype-sharing analysis. Single-nucleotide polymorphism (SNP)-based genetic parameter estimates showed that the heritability was 0.15, 0.20, and 0.22 for AFE, EP43w, and EP66w, respectively. Subsequently, three univariate GWASs for AFE, EP43w, and EP66w were carried out independently. Twenty-four SNPs located on chromosome 25 within a 0.01-Mb region that spans from 4.511 to 4.521 Mb were associated with AFE. There are two CIs that affect EP43w, i.e., twenty-five SNPs were in strong linkage disequilibrium region spanning from 3.186 to 3.247 Mb on chromosome 25, a region spanning from 4.442 to 4.446 Mb on chromosome 25, and two interesting genes, ACAD8 and THYN1, that may affect EP43w in laying ducks. There are also two CIs that affect EP66w, i.e., a 2.412-Mb region that spans from 127.497 to 129.910 Mb on chromosome 2 and a 0.355-Mb region that spans from 4.481 to 4.837 Mb on chromosome 29, and CA2 and GAMT may be the putative candidate genes. Our study also found some haplotypes significantly associated with these three traits based on haplotype-sharing analysis. Overall, this study was the first publication of GWAS on egg production in laying ducks, and our findings will be helpful to provide some candidate genes and haplotypes to improve egg production performance based on breeding in laying duck. Additionally, we learned from a method called bootstrap test to verify the reliability of a GWAS with small experimental samples that users can access at https://github.com/xuwenwu24/Bootstrap-test.

Genome-wide association studies for egg quality traits in White Leghorn layers using low-pass sequencing and SNP chip data

Low-pass sequencing data have been proposed as an alternative to single nucleotide polymorphism (SNP) chips in genome-wide association studies (GWAS) of several species. However, it has not been used in layer chickens yet. This study aims at comparing the GWAS results of White Leghorn chickens using low-pass sequencing data (1×) and 54 k SNP chip data. Ten commercially relevant egg quality traits including albumen height, shell strength, shell colour, egg weight and yolk weight collected from up to 1,420 White Leghorn chickens were analysed. The results showed that the genomic heritability estimates based on low-pass sequencing data were higher than those based on SNP chip data. Although two GWAS analyses showed similar overall landscape for most traits, low-pass sequencing captured some significant SNPs that were not on the SNP chip. In GWAS analysis using 54 k SNP chip data, after including more individuals (up to 5,700), additional significant SNPs not detected by low-pass sequencing data were found. In conclusion, GWAS using low-pass sequencing data showed similar results to those with SNP chip data and may require much larger sample sizes to show measurable advantages.

Transcriptomic analyses of the HPG axis-related tissues reveals potential candidate genes and regulatory pathways associated with egg production in ducks

BACKGROUND

Egg production is one of the most important economic traits in the poultry industry. The hypothalamic-pituitary-gonadal (HPG) axis plays an essential role in regulating reproductive activities. However, the key genes and regulatory pathways within the HPG axis dominating egg production performance remain largely unknown in ducks.

RESULTS

In this study, we compared the transcriptomic profiles of the HPG-related tissues between ducks with high egg production (HEP) and low egg production (LEP) to reveal candidate genes and regulatory pathways dominating egg production. We identified 543, 759, 670, and 181 differentially expressed genes (DEGs) in the hypothalamus, pituitary, ovary stroma, and F5 follicle membrane, respectively. Gene Ontology (GO) analysis revealed that DEGs from four HPG axis-related tissues were enriched in the "cellular component" category. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that the neuroactive ligand-receptor interaction pathway was significantly enriched based on DEGs commonly identified in all four HPG axis-related tissues. Gene expression profiles and Protein-Protein Interaction (PPI) network were performed to show the regulatory relationships of the DEGs identified. Five DEGs encoding secreted proteins in the hypothalamus and pituitary have interaction with DEGs encoding targeted proteins in the ovary stroma and F5 follicle membrane, implying that they were these DEGs might play similar roles in the regulation of egg production.

CONCLUSIONS

Our results revealed that neuroactive ligand-receptor interaction pathway and five key genes(VEGFC, SPARC, BMP2, THBS1, and ADAMTS15) were identified as the key signaling pathways and candidate genes within the HPG axis responsible for different egg production performance between HEP and LEP. This is the first study comparing the transcriptomic profiles of all HPG axis-related tissues in HEP and LEP using RNA-seq in ducks to the best of our knowledge. These data are helpful to enrich our understanding of the classical HPG axis regulating the egg production performance and identify candidate genes that can be used for genetic selection in ducks.

Identification of Key Candidate Genes in Runs of Homozygosity of the Genome of Two Chicken Breeds, Associated with Cold Adaptation

Simple Summary

The search for genomic regions related to adaptive abilities preserved in the chicken gene pool of two breeds, which have not been under intensive selection pressure, is of great importance for breeding in the future. This study aimed to identify key candidate genes associated with the adaptation of chickens to cold environments (using the example of the Russian White breed) by using molecular genetic methods. A total of 12 key genes on breed-specific ROH (runs of homozygosity) islands were identified, which may be potential candidate genes associated with the high level of adaptability of chickens to cold environments in the early postnatal period. These genes were associated with lipid metabolism, maintaining body temperature in cold environments, non-shivering thermogenesis and muscle development and are perspectives for further research.

Abstract

It is well known that the chicken gene pools have high adaptive abilities, including adaptation to cold environments. This research aimed to study the genomic distribution of runs of homozygosity (ROH) in a population of Russian White (RW) chickens as a result of selection for adaptation to cold environments in the early postnatal period, to perform a structural annotation of the discovered breed-specific regions of the genome (compared to chickens of the Amroks breed) and to suggest key candidate genes associated with the adaptation of RW chickens to cold environments. Genotyping of individual samples was performed using Illumina Chicken 60K SNP BeadChip^® chips. The search for homozygous regions by individual chromosomes was carried out using the PLINK 1.9 program and the detectRuns R package. Twelve key genes on breed-specific ROH islands were identified. They may be considered as potential candidate genes associated with the high adaptive ability of chickens in cold environments in the early postnatal period. Genes associated with lipid metabolism (SOCS3, NDUFA4, TXNRD2, IGFBP 1, IGFBP 3), maintaining body temperature in cold environments (ADIPOQ, GCGR, TRPM2), non-shivering thermogenesis (RYR2, CAMK2G, STK25) and muscle development (METTL21C) are perspectives for further research. This study contributes to our understanding of the mechanisms of adaptation to cold environments in chickens and provides a molecular basis for selection work.

Transcriptome analysis reveals the potential roles of long non-coding RNAs in feed efficiency of chicken

Feed efficiency is an important economic trait and reduces the production costs per unit of animal product. Up to now, few studies have conducted transcriptome profiling of liver tissue in feed efficiency-divergent chickens (Ross vs native breeds). Also, molecular mechanisms contributing to differences in feed efficiency are not fully understood, especially in terms of long non-coding RNAs (lncRNAs). Hence, transcriptome profiles of liver tissue in commercial and native chicken breeds were analyzed. RNA-Seq data along with bioinformatics approaches were applied and a series of lncRNAs and target genes were identified. Furthermore, protein-protein interaction network construction, co-expression analysis, co-localization analysis of QTLs and functional enrichment analysis were used to functionally annotate the identified lncRNAs. In total, 2,290 lncRNAs were found (including 1,110 annotated, 593 known and 587 novel), of which 53 (including 39 known and 14 novel), were identified as differentially expressed genes between two breeds. The expression profile of lncRNAs was validated by RT-qPCR. The identified novel lncRNAs showed a number of characteristics similar to those of known lncRNAs. Target prediction analysis showed that these lncRNAs have the potential to act in cis or trans mode. Functional enrichment analysis of the predicted target genes revealed that they might affect the differences in feed efficiency of chicken by modulating genes associated with lipid metabolism, carbohydrate metabolism, growth, energy homeostasis and glucose metabolism. Some gene members of significant modules in the constructed co-expression networks were reported as important genes related to feed efficiency. Co-localization analysis of QTLs related to feed efficiency and the identified lncRNAs suggested several candidates to be involved in residual feed intake. The findings of this study provided valuable resources to further clarify the genetic basis of regulation of feed efficiency in chicken from the perspective of lncRNAs.

Identification of candidate genomic regions for chicken egg number traits based on genome-wide association study

Background

Since the domestication of chicken, various breeds have been developed for food production, entertainment, and so on. Compared to indigenous chicken breeds which generally do not show elite production performance, commercial breeds or lines are selected intensely for meat or egg production. In the present study, in order to understand the molecular mechanisms underlying the dramatic differences of egg number between commercial egg-type chickens and indigenous chickens, we performed a genome-wide association study (GWAS) in a mixed linear model.

Results

We obtained 148 single nucleotide polymorphisms (SNPs) associated with egg number traits (57 significantly, 91 suggestively). Among them, 4 SNPs overlapped with previously reported quantitative trait loci (QTL), including 2 for egg production and 2 for reproductive traits. Furthermore, we identified 32 candidate genes based on the function of the screened genes. These genes were found to be mainly involved in regulating hormones, playing a role in the formation, growth, and development of follicles, and in the development of the reproductive system. Some genes such as NELL2 (neural EGFL like 2), KITLG (KIT ligand), GHRHR (Growth hormone releasing hormone receptor), NCOA1 (Nuclear receptor coactivator 1), ITPR1 (inositol 1, 4, 5-trisphosphate receptor type 1), GAMT (guanidinoacetate N-methyltransferase), and CAMK4 (calcium/calmodulin-dependent protein kinase IV) deserve our attention and further study since they have been reported to be closely related to egg production, egg number and reproductive traits. In addition, the most significant genomic region obtained in this study was located at 48.61–48.84 Mb on GGA5. In this region, we have repeatedly identified four genes, in which YY1 (YY1 transcription factor) and WDR25 (WD repeat domain 25) have been shown to be related to oocytes and reproductive tissues, respectively, which implies that this region may be a candidate region underlying egg number traits.

Conclusion

Our study utilized the genomic information from various chicken breeds or populations differed in the average annual egg number to understand the molecular genetic mechanisms involved in egg number traits. We identified a series of SNPs, candidate genes, or genomic regions that associated with egg number, which could help us in developing the egg production trait in chickens.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07755-3.

Identification and Validation of Marketing Weight-Related SNP Markers Using SLAF Sequencing in Male Yangzhou Geese

Growth performance is a complex economic trait for avian production. The swan goose (Anser cygnoides) has never been exploited genetically like chickens or other waterfowl species such as ducks. Traditional phenotypic selection is still the main method for genetic improvement of geese body weight. In this study, specific locus amplified fragment sequencing (SLAF-seq) with bulked segregant analysis (BSA) was conducted for discovering and genotyping single nucleotide polymorphisms (SNPs) associated with marketing weight trait in male geese. A total of 149,045 SNPs were obtained from 427,093 SLAF tags with an average sequencing depth of 44.97-fold and a Q30 value of 93.26%. After SNPs' filtering, a total of 12,917 SNPs were included in the study. The 31 highest significant SNPs-which had different allelic frequencies-were further validated by individual-based AS-PCR genotyping in two populations. The association between 10 novel SNPs and the marketing weight of male geese was confirmed. The 10 significant SNPs were involved in linear regression model analysis, which confirmed single-SNP associations and revealed three types of SNP networks for marketing weight. The 10 significant SNPs were located within or close to 10 novel genes, which were identified. The qPCR analysis showed significant difference between genotypes of each SNP in seven genes. Developed SLAF-seq and identified genes will enrich growth performance studies, promoting molecular breeding applications to boost the marketing weight of Chinese geese.

Mapping of Quantitative Trait Loci Controlling Egg-Quality and -Production Traits in Japanese Quail (Coturnix japonica) Using Restriction-Site Associated DNA Sequencing

This research was conducted to identify quantitative trait loci (QTL) associated with egg-related traits by constructing a genetic linkage map based on single nucleotide polymorphism (SNP) markers using restriction-site associated DNA sequencing (RAD-seq) in Japanese quail. A total of 138 F₂ females were produced by full-sib mating of F₁ birds derived from an intercross between a male of the large-sized strain with three females of the normal-sized strain. Eggs were investigated at two different stages: the beginning stage of egg-laying and at 12 weeks of age (second stage). Five eggs were analyzed for egg weight, lengths of the long and short axes, egg shell strength and weight, yolk weight and diameter, albumen weight, egg equator thickness, and yolk color (L*, a*, and b* values) at each stage. Moreover, the age at first egg, the cumulative number of eggs laid, and egg production rate were recorded. RAD-seq developed 118 SNP markers and mapped them to 13 linkage groups using the Map Manager QTX b20 software. Markers were spanned on 776.1 cM with an average spacing of 7.4 cM. Nine QTL were identified on chromosomes 2, 4, 6, 10, 12, and Z using the simple interval mapping method in the R/qtl package. The QTL detected affected 10 egg traits of egg weight, lengths of the long and short axes of egg, egg shell strength, yolk diameter and weight, albumen weight, and egg shell weight at the beginning stage, yellowness of the yolk color at the second stage, and age at first egg. This is the first report to perform a quail QTL analysis of egg-related traits using RAD-seq. These results highlight the effectiveness of RAD-seq associated with targeted QTL and the application of marker-assisted selection in the poultry industry, particularly in the Japanese quail.

Hierarchical mixed-model expedites genome-wide longitudinal association analysis

A hierarchical random regression model (Hi-RRM) was extended into a genome-wide association analysis for longitudinal data, which significantly reduced the dimensionality of repeated measurements. The Hi-RRM first modeled the phenotypic trajectory of each individual using a RRM and then associated phenotypic regressions with genetic markers using a multivariate mixed model (mvLMM). By spectral decomposition of genomic relationship and regression covariance matrices, the mvLMM was transformed into a multiple linear regression, which improved computing efficiency while implementing mvLMM associations in efficient mixed-model association expedited (EMMAX). Compared with the existing RRM-based association analyses, the statistical utility of Hi-RRM was demonstrated by simulation experiments. The method proposed here was also applied to find the quantitative trait nucleotides controlling the growth pattern of egg weights in poultry data.

Comparative analysis of hypothalamus transcriptome between laying hens with different egg-laying rates

Egg-laying performance is one of the most important economic traits in the poultry industry. Commercial layers can lay one egg almost every day during their peak-laying period. However, many Chinese indigenous chicken breeds show a relatively low egg-laying rate, even during their peak-laying period. To understand what makes the difference in egg production, we compared the hypothalamus transcriptome profiles of Lushi blue-shelled-egg chickens (LBS), a Chinese indigenous breed with low egg-laying rate and Rhode Island Red chickens (RIR), a commercial layer with relatively high egg-laying rate using RNA-seq. A total of 753 differentially expressed genes (DEGs) were obtained. Of these DEGs, 38 genes were enriched in 2 Gene Ontology (GO) terms, namely reproduction term and the reproductive process term, and 6 KEGG pathways, namely Wnt signaling pathway, Oocyte meiosis, GnRH signaling pathway, Thyroid hormone signaling pathway, Thyroid hormone synthesis and MAPK signaling pathway, which have been long known to be involved in egg production regulation. To further determine the core genes from the 38 DEGs, protein-protein interaction (PPI) network, co-expression network and transcriptional regulatory network analyses were carried out. After integrated analysis and experimental validation, 4 core genes including RAC1, MRE11A, MAP7 and SOX5 were identified as the potential core genes that are responsible for the laying-rate difference between the 2 breeds. These findings paved the way for future investigating the mechanism of egg-laying regulation and enriched the chicken reproductive regulation theory.

Exploring the genetic architecture of feed efficiency traits in chickens

Chicken feed efficiency (FE) traits are the most important economic traits in broiler production. Several studies evaluating genetic factors affecting food consumption in chickens are available. However, most of these studies identified genomic regions containing putative quantitative trait loci for each trait separately. It is still a challenge to find common gene networks related to these traits. Therefore, here, a genome-wide association study (GWAS) was conducted to explore candidate genomic regions responsible for Feed Intake (FI), Body Weight Gain (BWG) and Feed Conversion Ratio (FCR) traits and their gene networks. A total of 1430 broilers from an experimental population was genotyped with the high density Affymetrix 600K SNP array. A total of 119 associated SNPs located in 20 chromosomes were identified, where some of them were common in more than one FE trait. In addition, novel genomic regions were prospected considering the SNPs dominance effects and sex interaction, identifying putative candidate genes only when these effects were fit in the model. Relevant candidate genes such as ATRNL1, PIK3C2A, PTPRN2, SORCS3 and gga-mir-1759 were highlighted in this study helping to elucidate the genomic architecture of feed efficiency traits. These results provide new insights on the mechanisms underlying the consumption and utilization of food in chickens.

Design and evaluation of a custom 50K Infinium SNP array for egg-type chickens

With the development of molecular genetics and high-throughput sequencing technology, genotyping arrays consisting of large numbers of SNP have raised great interest in animal and plant research. However, the application of commercial chicken 600K SNP arrays has varied in different populations of egg-type chickens. Moreover, their genotyping cost is too high for large-scale population applications. Herein, we independently developed a custom Illumina 50K BeadChip, named PhenoixChip-I, for egg-type chickens based on SNP from 479 sequenced individuals in 7 lines. We filtered and selected SNP with stringent criteria, such as high polymorphism, genome coverage, design score, and priorities. Finally, a total of 43,681 effective SNP successfully genotyped were included on our custom array. Approximately 14K SNP were previously reported to be associated with important economic traits in egg-type chickens. Subsequently, we verified the applicability and efficiency of the PhenoixChip-I SNP array from many aspects, including evaluating its use scientific research (population structure analysis and genome-wide association study) and the poultry breeding industry (genomic selection). The findings in our study will play a crucial role in accelerating the genetic improvement of egg-type chickens.

Avian eggshell biomineralization: an update on its structure, mineralogy and protein tool kit

BACKGROUND

The avian eggshell is a natural protective envelope that relies on the phenomenon of biomineralization for its formation. The shell is made of calcium carbonate in the form of calcite, which contains hundreds of proteins that interact with the mineral phase controlling its formation and structural organization, and thus determine the mechanical properties of the mature biomaterial. We describe its mineralogy, structure and the regulatory interactions that integrate the mineral and organic constituents during eggshell biomineralization. Main Body. We underline recent evidence for vesicular transfer of amorphous calcium carbonate (ACC), as a new pathway to ensure the active and continuous supply of the ions necessary for shell mineralization. Currently more than 900 proteins and thousands of upregulated transcripts have been identified during chicken eggshell formation. Bioinformatic predictions address their functionality during the biomineralization process. In addition, we describe matrix protein quantification to understand their role during the key spatially- and temporally- regulated events of shell mineralization. Finally, we propose an updated scheme with a global scenario encompassing the mechanisms of avian eggshell mineralization.

CONCLUSION

With this large dataset at hand, it should now be possible to determine specific motifs, domains or proteins and peptide sequences that perform a critical function during avian eggshell biomineralization. The integration of this insight with genomic data (non-synonymous single nucleotide polymorphisms) and precise phenotyping (shell biomechanical parameters) on pure selected lines will lead to consistently better-quality eggshell characteristics for improved food safety. This information will also address the question of how the evolutionary-optimized chicken eggshell matrix proteins affect and regulate calcium carbonate mineralization as a good example of biomimetic and bio-inspired material design.

Highly elevated base excision repair pathway in primordial germ cells causes low base editing activity in chickens

Base editing technology enables the generation of precisely genome-modified animal models. In this study, we applied base editing to chicken, an important livestock animal in the fields of agriculture, nutrition, and research through primordial germ cell (PGC)-mediated germline transmission. Using this approach, we successfully produced two genome-modified chicken lines harboring mutations in the genes encoding ovotransferrin (TF) and myostatin (MSTN); however, only 55.5% and 35.7% of genome-modified chickens had the desired base substitutions in TF and MSTN, respectively. To explain the low base-editing activity, we performed molecular analysis to compare DNA repair pathways between PGCs and the chicken fibroblast cell line DF-1. The results revealed that base excision repair (BER)-related genes were significantly elevated in PGCs relative to DF-1 cells. Subsequent functional studies confirmed that the editing activity could be regulated by modulating the expression of uracil N-glycosylase (UNG), an upstream gene of the BER pathway. Collectively, our findings indicate that the distinct DNA repair property of chicken PGCs causes low editing activity during genome modification, however, modulation of BER functions could promote the production of genome-modified organisms with the desired genotypes.

Hybrids generated by crossing elite laying chickens exhibited heterosis for clutch and egg quality traits

Crossbreeding advantage in hybrids compared with their parents, termed heterosis, has been exhaustively exploited in chicken breeding over the last century. Reports for crossbreeding of elite laying chickens covering rearing and laying period remain infrequent. In this study, resource populations of Rhode Island Red (RIR) and White Leghorn (WL) pure-bred chickens were reciprocally crossed to generate 4 distinct groups that were evaluated for prelaying growth, egg production, and egg quality. Birds monitored for prelaying growth consists of 105 (RIR), 131 (WL), 207 (RIR × WL) and 229 (WL × RIR), and 30 pullets from each group were evaluated. Egg laying records were collected from 102, 89, 147, and 191 hens in the 4 populations, respectively. In addition, expression of 5 candidate genes for egg production in the ovarian follicles was measured by RT-qPCR. Results showed that BW of hatched chicks in the WL line was higher than the other populations. However, the 2 crossbreds grew faster than WL purebred throughout the prelaying period. Low to medium heterosis was observed for BW and body length before the onset of lay. White Leghorn and the hybrids commenced laying earlier than RIR pullets and egg production traits were favorable in the crossbreds compared with purebreds. Heterosis for egg number and clutch size was moderate in WL × RIR but low in RIR × WL hens. Expression of antimullerian hormone gene was high in WL and RIR × WL hybrids, suggesting WL parent-specific enhancing dominant expression. Shell weight was higher in the crossbreds than purebreds at 52 wk of age, but RIR hens laid eggs with higher shell ratio than the other populations (P < 0.05). Conversely, WL and the hybrids had higher eggshell strength than RIR birds (P < 0.05). Eggshell strength was the only egg quality trait that showed heterosis above 10% in WL × RIR hybrids at 32 and 52 wk of age. White Leghorn × RIR hens demonstrated higher percent heterosis for economic traits than birds of the reciprocal hybrid. This means that RIR breed is a better dam than a sire line for growth, egg laying, and egg quality traits.

Deciphering the mode of action and position of genetic variants impacting on egg number in broiler breeders

Background

Aim of the present study was first to identify genetic variants associated with egg number (EN) in female broilers, second to describe the mode of their gene action (additive and/or dominant) and third to provide a list with implicated candidate genes for the trait. A number of 2586 female broilers genotyped with the high density (~ 600 k) SNP array and with records on EN (mean = 132.4 eggs, SD = 29.8 eggs) were used. Data were analyzed with application of additive and dominant multi-locus mixed models.

Results

A number of 7 additive, 4 dominant and 6 additive plus dominant marker-trait significant associations were detected. A total number of 57 positional candidate genes were detected within 50 kb downstream and upstream flanking regions of the 17 significant markers. Functional enrichment analysis pinpointed two genes (BHLHE40 and CRTC1) to be involved in the ‘entrainment of circadian clock by photoperiod’ biological process. Gene prioritization analysis of the positional candidate genes identified 10 top ranked genes (GDF15, BHLHE40, JUND, GDF3, COMP, ITPR1, ELF3, ELL, CRLF1 and IFI30). Seven prioritized genes (GDF15, BHLHE40, JUND, GDF3, COMP, ELF3, CRTC1) have documented functional relevance to reproduction, while two more prioritized genes (ITPR1 and ELL) are reported to be related to egg quality in chickens.

Conclusions

Present results have shown that detailed exploration of phenotype-marker associations can disclose the mode of action of genetic variants and help in identifying causative genes associated with reproductive traits in the species.

Endocrine and genetic factors affecting egg laying performance in chickens: a review

1. Egg-laying performance reflects the overall reproductive performance of breeding hens. The genetic traits for egg-laying performance have low or medium heritability, and, depending on the period involved, usually ranges from 0.16 to 0.64. Egg-laying in chickens is regulated by a combination of environmental, endocrine and genetic factors. 2. The main endocrine factors that regulate egg-laying are gonadotropin-releasing hormone (GnRH), prolactin (PRL), follicle-stimulating hormone (FSH) and luteinising hormone (LH). 3. In the last three decades, many studies have explored this aspect at a molecular genetic level. Recent studies identified 31 reproductive hormone-based candidate genes that were significantly associated with egg-laying performance. With the development of genome-sequencing technology, 64 new candidate genes and 108 single nucleotide polymorphisms (SNPs) related to egg-laying performance have been found using genome-wide association studies (GWAS), providing novel insights into the molecular genetic mechanisms governing egg production. At the same time, microRNAs that regulate genes responsible for egg-laying in chickens were reviewed. 4. Research on endocrinological and genetic factors affecting egg-laying performance will greatly improve the reproductive performance of chickens and promote the protection, development, and utilisation of poultry. This review summarises studies on the endocrine and genetic factors of egg-laying performance in chickens from 1972 to 2019.

A genome-wide single nucleotide polymorphism scan reveals genetic markers associated with fertility rate in Chinese Jing Hong chicken

The function of the sperm storage tubules is directly correlated with the fertility of laying hens. However, little is known about the molecular mechanisms regulating the fertility traits in chicken. To identify genetic markers associated with reproductive traits, we calculated fertility rate at 61 to 69 wk (51 D) of Jing Hong chickens parent generation as the phenotype and the genotype were detected by the chicken 600K Affymetrix Axiom High Density single nucleotide polymorphisms (SNP)-array. The genome-wide association study using 190 Jing Hong hens showed that the 20 SNP in chromosomes 3 and 13 were significantly associated with fertility rate. To verify these results, a total of 1900 Jing Hong laying hens from 2 populations (P1 and P2) were further genotyped by polymerase chain reaction-restriction fragments length polymorphisms method. The association analysis results revealed that 12 polymorphisms (AX-75769978, AX-76582632, AX-75730546, AX-75730496, AX-75730588, AX-76530282, AX-76530329, AX-76529310, AX-75769906, AX-75755394, AX-80813697 and AX-76582809) out of 20 showed highly significant effects (P < 0.0001) on fertility rate in P1, P2 and P1+P2. Six haplotypes (TTAA, TTGG, TTAG, CTAA, CTGG, and CTAG) were inferred based on significant loci (AX-75730546 and AX-76530282) also showed significant association with fertility rate, where haplotype CTAG was shown to be markedly associated with the significantly highest (P < 0.0001) fertility rate (in P1, 86.42 ± 0.59; P2, 85.98 ± 0.59 and P1+P2, 86.16 ± 0.42) followed by other haplotypes for the irrespective of population studied. Collectively, we report for the first time that 12 SNP in the chromosomes 3 and 13 were significantly associated with fertility rate during the later stage of egg production, which could be used as the potential genetic markers that would be able to facilitate in the selection and improvement of fertility rate through chicken breeding.

Accuracy of genomic prediction of shell quality in a White Leghorn line

Several genomic methods were applied for predicting shell quality traits recorded at 4 different hen ages in a White Leghorn line. The accuracies of genomic prediction of single-step GBLUP and single-trait Bayes B were compared with predictions of breeding values based on pedigree-BLUP under single-trait or multitrait models. Breaking strength (BS) and dynamic stiffness (Kdyn) measurements were collected on 18,524 birds from 3 consecutive generations, of which 4,164 animals also had genotypes from an Affymetrix 50K panel containing 49,591 SNPs after quality control edits. All traits had low to moderate heritability, ranging from 0.17 for BS to 0.34 for Kdyn. The highest accuracies of prediction were obtained for the multitrait single-step model. The use of marker information resulted in higher prediction accuracies than pedigree-based models for almost all traits. A genome-wide association study based on a Bayes B model was conducted to detect regions explaining the largest proportion of genetic variance. Across all 8 shell quality traits analyzed, 7 regions each explaining over 2% of genetic variance and 54 regions each explaining over 1% of genetic variance were identified. The windows explaining a large proportion of genetic variance overlapped with several potential candidate genes with biological functions linked to shell formation. A multitrait repeatability model using a single-step method is recommended for genomic evaluation of shell quality in layer chickens.

Genome-wide association analysis of egg production performance in chickens across the whole laying period

BACKGROUND

Egg production is the most economically-important trait in layers as it directly influences benefits of the poultry industry. To better understand the genetic architecture of egg production, we measured traits including age at first egg (AFE), weekly egg number (EN) from onset of laying eggs to 80 weeks which was divided into five stage (EN1: from onset of laying eggs to 23 weeks, EN2: from 23 to 37 weeks, EN3: from 37 to 50 weeks, EN4: from 50 to 61 weeks, EN5: from 61 to 80 weeks) based on egg production curve and total egg number across the whole laying period (Total-EN). Then we performed genome-wide association studies (GWAS) in 1078 Rhode Island Red hens using a linear mixed model.

RESULTS

Estimates of pedigree and SNP-based genetic parameter showed that AFE and EN1 exhibited high heritability (0.51 ± 0.09, 0.53 ± 0.08), while the h2 for EN in other stages varied from low (0.07 ± 0.04) to moderate (0.24 ± 0.07) magnitude. Subsequently, seven univariate GWAS for AFE and ENs were carried out independently, from which a total of 161 candidate SNPs located on GGA1, GGA2, GGA5, GGA6, GGA9 and GGA24 were identified. Thirteen SNP located on GGA6 were associated with AFE and an interesting gene PRLHR that may affect AFE through regulating oxytocin secretion in chickens. Sixteen genome-wide significant SNPs associated with EN3 were in a strong linkage disequilibrium (LD) region spanning from 117.87 Mb to 118.36 Mb on GGA1 and the most significant SNP (rs315777735) accounted for 3.57% of phenotypic variance. Genes POLA1, PDK3, PRDX4 and APOO identified by annotating sixteen genome-wide significant SNPs can be considered as candidates associated with EN3. Unfortunately, our study did not find any candidate gene for the total egg number.

CONCLUSIONS

Findings in our study could provide promising genes and SNP markers to improve egg production performance based on marker-assisted breeding selection, while further functional validation is still needed in other populations.

Genetic analysis of production, physiological, and egg quality traits in heat-challenged commercial white egg-laying hens using 600k SNP array data

Background

Heat stress negatively affects the welfare and production of chickens. High ambient temperature is considered one of the most ubiquitous abiotic environmental challenges to laying hens around the world. In this study, we recorded several production traits, feed intake, body weight, digestibility, and egg quality of 400 commercial white egg-laying hens before and during a 4-week heat treatment. For the phenotypes that had estimated heritabilities (using 600k SNP chip data) higher than 0, SNP associations were tested using the same 600k genotype data.

Results

Seventeen phenotypes had heritability estimates higher than 0, including measurements at various time points for feed intake, feed efficiency, body weight, albumen weight, egg quality expressed in Haugh units, egg mass, and also for change in egg mass from prior to heat exposure to various time points during the 4-week heat treatment. Quantitative trait loci (QTL) were identified for 10 of these 17 phenotypes. Some of the phenotypes shared QTL including Haugh units before heat exposure and after 4 weeks of heat treatment.

Conclusions

Estimated heritabilities differed from 0 for 17 traits, which indicates that they are under genetic control and that there is potential for improving these traits through selective breeding. The association of different QTL with the same phenotypes before heat exposure and during heat treatment indicates that genomic control of traits under heat stress is distinct from that under thermoneutral conditions. This study contributes to the knowledge on the genomic control of response to heat stress in laying hens.

Electronic supplementary material

The online version of this article (10.1186/s12711-019-0474-6) contains supplementary material, which is available to authorized users.

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 F2 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.

Widespread introgression in Chinese indigenous chicken breeds from commercial broiler

Chinese indigenous chickens (CICs) constitute world-renowned genetic resources due to their excellent traits, including early puberty, good meat quality and strong resistance to disease. Unfortunately, the introduction of a large number of commercial chickens in the past two decades has had an adverse effect on CICs. Using the chicken 60 K single nucleotide polymorphism chip, we assessed the genetic diversity and population structure of 1,187 chickens, representing eight Chinese indigenous chicken breeds, two hybrid chicken breeds, two ancestral chicken breeds, two commercial populations and additional red jungle fowl. By investigating haplotype similarity, we found extensive gene introgression from commercial broiler to almost all CICs. Approximately 15% of the genome, on average, of CICs was introgressed, ranging from 0.64% for Tibetan chicken to 21.52% for Huiyang Bearded chicken. Further analysis revealed signals consistent with positive selection in the introgression loci. For the first time, we systematically mapped and quantified introgression from commercial broiler to CICs at the whole genome level. Our data provided a usable resource for chicken genetic diversity, and our findings indicated a dire need for protecting the genetic resources of CICs.

Genome-wide association study and a post replication analysis revealed a promising genomic region and candidate genes for chicken eggshell blueness

The eggshell blueness is an interesting object for chicken genetic studies and blue-shelled chicken industry, especially after the discovery of the causative mutation of chicken blue eggshell. In the present study, genome wide association study (GWAS) was conducted in Chinese Dongxiang blue-shelled chicken underlying four traits of blue eggshell pigments: quantity of biliverdin (QB), quantity of protoporphyrin (QP), quantity of total pigment (QT), and color density trait (CD). A total of 139 individuals were randomly collected for GWAS. We detected two SNPs in genome-wise significance and 35 in suggestive significance, 24 out of the 37 SNP were located either within intron/exon or near 15 genes in a range of ~1.17 Mb on GGA21. For further confirmation of the identified SNP loci by GWAS, the follow-up replication studies were performed in two populations. A total of 146 individuals of the second generation derived from the former GWAS population, as well as 280 individuals from an alternative independent population were employed for genotyping by MALDI-TOF MS in a genotype-phenotype association study. Eighteen SNPs evenly distributed on the GGA21 significant region were successfully genotyped in the two populations, of which 4 and 6 SNP loci were shown significantly associated with QB, QT and QP in the two repeat populations, respectively. Further, the SNPs were narrowed down to a region of ~ 653.819 Kb on GGA21 that harbors five candidate genes: AJAP1, TNFRSF9, C1ORF174, CAMTA1, and CEP104. Shell gland of chickens laying dark and light blue eggshell was chosen for detection of mRNA expression of the five candidate genes. The results showed differential expression levels of these genes in the two groups. The specific function of these genes has not yet been defined clearly in chickens and further in-depth studies are needed to explore the new functional role in chicken eggshell blueness.

Identification of quantitative trait loci affecting production and biochemical traits in a unique Japanese quail resource population

The objective of the current study was to identify QTL associated with body weight, growth rate, egg quality traits, concentration of selected blood plasma, and yolk lipids as well as concentration of selected macro- and microelements, color, pH, basic chemical composition, and drip loss of breast muscle of Japanese quail (Coturnix japonica). Twenty-two meat-type males (line F33) were crossed with twenty-two laying-type females (line S22) to produce a generation of F1 hybrids. The F2 generation was created by mating 44 randomly chosen F1 hybrids, which were full siblings. The birds were individually weighed from the first to eighth week of age. At the age of 19 wk, 2 to 4 eggs were individually collected from each female and an analysis of the egg quality traits was performed. At slaughter, blood and breast muscles were collected from 324 individuals of the resource population. The basic chemical composition, concentration of chosen macro- and microelements, color, pH, and drip loss were determined in the muscle samples. The concentration of chosen lipids was determined in egg yolk and blood plasma. In total, 30 microsatellite markers located on chromosome 1 and 2 were genotyped. QTL mapping including additive and dominance genetic effects revealed 6 loci on chromosome 1 of the Japanese quail affecting the egg number, egg production rate, egg weight, specific gravity, egg shell weight, concentration of Na in breast muscle. In turn, there were 9 loci on chromosome 2 affecting the body weight in the first, fourth, and sixth week of age, growth rate in the second and seventh week of age, specific gravity, concentration of K and Cu in breast muscle, and the levels of triacylglycerols in blood plasma. In this study, QTL with a potential effect on the Na, K, and Cu content in breast muscles in poultry and on specific gravity in the Japanese quail were mapped for the first time.

Genetic variations for egg quality of chickens at late laying period revealed by genome-wide association study

With the extension of the egg-laying cycle, the rapid decline in egg quality at late laying period has aroused great concern in the poultry industry. Herein, we performed a genome-wide association study (GWAS) to identify genomic variations associated with egg quality, employing chicken 600 K high-density SNP arrays in a population of 1078 hens at 72 and 80 weeks of age. The results indicated that a genomic region spanning from 8.95 to 9.31 Mb (~0.36 Mb) on GGA13 was significantly associated with the albumen height (AH) and the haugh unit (HU), and the two most significant SNPs accounted for 3.12 ~ 5.75% of the phenotypic variance. Two promising genes, MSX2 and DRD1, were mapped to the narrow significant region, which was involved in embryonic and ovary development and found to be related to egg production, respectively. Moreover, three interesting genes, RHOA, SDF4 and TNFRSF4, identified from three significant loci, were considered to be candidate genes for egg shell colour. Findings in our study could provide worthy theoretical basis and technological support to improve late-stage egg quality for breeders.

Genome-Wide Association Analysis of Age-Dependent Egg Weights in Chickens

Egg weight (EW) is an economically-important trait and displays a consecutive increase with the hen's age. Because extremely large eggs cause a range of problems in the poultry industry, we performed a genome-wide association study (GWAS) in order to identify genomic variations that are associated with EW. We utilized the Affymetrix 600 K high density SNP array in a population of 1,078 hens at seven time points from day at first egg to 80 weeks age (EW80). Results reveal that a 90 Kb genomic region (169.42 Mb ~ 169.51 Mb) in GGA1 is significantly associated with EW36 and is also potentially associated with egg weight at 28, 56, and 66 week of age. The leading SNP could account for 3.66% of the phenotypic variation, while two promising genes (DLEU7 and MIR15A) can be mapped to this narrow significant region and may affect EW in a pleiotropic manner. In addition, one gene (CECR2 on GGA1) and two genes (MEIS1 and SPRED2 on GGA3), which involved in the processes of embryogenesis and organogenesis, were also considered to be candidates related to first egg weight (FEW) and EW56, respectively. Findings in our study could provide worthy theoretical basis to generate eggs of ideal size based on marker assisted breeding selection.

RNA-Seq reveals differentially expressed genes affecting polyunsaturated fatty acids percentage in the Huangshan Black chicken population

Fatty acids metabolic products determine meat quality in chickens. Identifying genes associated with fatty acids composition could provide valuable information for the complex genetic networks of genes with underlying variations in fatty acids synthesis. RNA sequencing (RNA-Seq) was conducted to explore the chicken transcriptome from the thigh muscle tissue of 6 Huangshan Black Chickens with 3 extremely high and low phenotypic values for percentage of polyunsaturated fatty acids (PUFAs). In total, we obtained 41,139,108–44,901,729 uniquely mapped reads, which covered 74.15% of the current annotated transcripts including 18964 mRNA transcripts, across all the six thigh muscle tissue samples. Of these, we revealed 274 differentially expressed genes (DEGs) with a highly significant correlation with polyunsaturated fatty acids percentage between the comparison groups based on the ratio of PUFA/SFA. Gene ontology and pathway analysis indicated that the DEGs were enriched in particular biological processes affecting fatty acids metabolism, biosynthesis of unsaturated fatty acids (USFAs), and cell junction-related pathways. Integrated interpretation of differential gene expression and formerly reported quantitative trait loci (QTL) demonstrated that FADS2, DCN, FRZB, OGN, PRKAG3, LHFP, CHCHD10, CYTL1, FBLN5, and ADGRD1 are the most promising candidate genes affecting polyunsaturated fatty acids percentage.

Widespread patterns of sexually dimorphic gene expression in an avian hypothalamic-pituitary-gonadal (HPG) axis

The hypothalamic-pituitary-gonadal (HPG) axis is a key biological system required for reproduction and associated sexual behaviors to occur. In the avian reproductive model of the rock dove (Columba livia), we characterized the transcript community of each tissue of the HPG axis in both sexes, thereby significantly expanding our mechanistic insight into HPG activity. We report greater sex-biased differential expression in the pituitary as compared to the hypothalamus, with multiple genes more highly expressed in the male pituitary being related to secretory function, and multiple genes more highly expressed in the female pituitary being related to reproduction, growth, and development. We report tissue-specific and sex-biased expression in genes commonly investigated when studying reproduction, highlighting the need for sex parity in future studies. In addition, we uncover new targets of investigation in both sexes, which could potentially change our understanding of HPG function.

Genome-wide association study for performance traits in chickens using genotype by sequencing approach

Performance traits are economically important and are targets for selection in breeding programs, especially in the poultry industry. To identify regions on the chicken genome associated with performance traits, different genomic approaches have been applied in the last years. The aim of this study was the application of CornellGBS approach (134,528 SNPs generated from a PstI restriction enzyme) on Genome-Wide Association Studies (GWAS) in an outbred F₂ chicken population. We have validated 91.7% of these 134,528 SNPs after imputation of missed genotypes. Out of those, 20 SNPs were associated with feed conversion, one was associated with body weight at 35 days of age (P < 7.86E-07) and 93 were suggestively associated with a variety of performance traits (P < 1.57E-05). The majority of these SNPs (86.2%) overlapped with previously mapped QTL for the same performance traits and some of the SNPs also showed novel potential QTL regions. The results obtained in this study suggests future searches for candidate genes and QTL refinements as well as potential use of the SNPs described here in breeding programs.

Genetic Mapping of Quantitative Trait Loci for Egg Production and Egg Quality Traits in Chickens: a Review

Chickens display a wide spectrum of phenotypic variations in quantitative traits such as egg-related traits. Quantitative trait locus (QTL) analysis is a statistical method used to understand the relationship between phenotypic (trait measurements) and genotypic data (molecular markers). We have performed QTL analyses for egg-related traits using an original resource population based on the Japanese Large Game (Oh-Shamo) and the White Leghorn breeds of chickens. In this article, we summarize the results of our extensive QTL analyses for 11 and 66 traits for egg production and egg quality, respectively. We reveal that at least 30 QTL regions on 17 different chromosomes affect phenotypic variation in egg-related traits. Each locus had an age-specific effect on traits, and a variety in effects was also apparent, such as additive, dominance, and epistatic-interaction effects. Although genome-wide association study (GWAS) is suitable for gene-level resolution mapping of GWAS loci with additive effects, QTL mapping studies enable us to comprehensively understand genetic control, such as chromosomal regions, genetic contribution to phenotypic variance, mode of inheritance, and age-specificity of both common and rare alleles. QTL analyses also describe the relationship between genotypes and phenotypes in experimental populations. Accumulation of QTL information, including GWAS loci, is also useful for studies of population genomics approached without phenotypic data in order to validate the identified genomic signatures of positive selection. The combination of QTL studies and next-generation sequencing techniques with uncharacterized genetic resources will enhance current understanding of the relationship between genotypes and phenotypes in livestock animals.

The association of very low-density lipoprotein receptor (VLDLR) haplotypes with egg production indicates VLDLR is a candidate gene for modulating egg production

The very low-density lipoprotein receptor (VLDLR) transports egg yolk precursors into oocytes. However, our knowledge of the distribution patterns of VLDLR variants among breeds and their relationship to egg production is still incomplete. In this study, eight single nucleotide polymorphisms (SNPs) that account for 87% of all VLDLR variants were genotyped in Nick Chick (NC, n=91), Lohmann Brown (LohB, n=50) and Lueyang (LY, n=381) chickens, the latter being an Chinese indigenous breed. Egg production by NC and LY chickens was recorded from 17 to 50 weeks. Only four similar haplotypes were found in NC and LohB, of which two accounted for 100% of all NC haplotypes and 92.5% of LohB haplotypes. In contrast, there was considerable haplotypic diversity in LY. Comparison of egg production in LY showed that hens with NC-like haplotypes had a significantly higher production (p < 0.05) than those without the haplotypes. However, VLDLR expression was not significantly different between the haplotypes. These findings indicate a divergence in the distribution of VLDLR haplotypes between selected and non-selected breeds and suggest that the near fixation of VLDLR variants in NC and LohB is compatible with signature of selection. These data also support VLDLR as a candidate gene for modulating egg production.

Genome-wide association study reveals novel variants for growth and egg traits in Dongxiang blue-shelled and White Leghorn chickens

This study was designed to investigate the genetic basis of growth and egg traits in Dongxiang blue-shelled chickens and White Leghorn chickens. In this study, we employed a reduced representation sequencing approach called genotyping by genome reducing and sequencing to detect genome-wide SNPs in 252 Dongxiang blue-shelled chickens and 252 White Leghorn chickens. The Dongxiang blue-shelled chicken breed has many specific traits and is characterized by blue-shelled eggs, black plumage, black skin, black bone and black organs. The White Leghorn chicken is an egg-type breed with high productivity. As multibreed genome-wide association studies (GWASs) can improve precision due to less linkage disequilibrium across breeds, a multibreed GWAS was performed with 156 575 SNPs to identify the associated variants underlying growth and egg traits within the two chicken breeds. The analysis revealed 32 SNPs exhibiting a significant genome-wide association with growth and egg traits. Some of the significant SNPs are located in genes that are known to impact growth and egg traits, but nearly half of the significant SNPs are located in genes with unclear functions in chickens. To our knowledge, this is the first multibreed genome-wide report for the genetics of growth and egg traits in the Dongxiang blue-shelled and White Leghorn chickens.

Quantitative Trait Locus and Genetical Genomics Analysis Identifies Putatively Causal Genes for Fecundity and Brooding in the Chicken

Life history traits such as fecundity are important to evolution because they make up components of lifetime fitness. Due to their polygenic architectures, such traits are difficult to investigate with genetic mapping. Therefore, little is known about their molecular basis. One possible way toward finding the underlying genes is to map intermediary molecular phenotypes, such as gene expression traits. We set out to map candidate quantitative trait genes for egg fecundity in the chicken by combining quantitative trait locus mapping in an advanced intercross of wild by domestic chickens with expression quantitative trait locus mapping in the same birds. We measured individual egg fecundity in 232 intercross chickens in two consecutive trials, the second one aimed at measuring brooding. We found 12 loci for different aspects of egg fecundity. We then combined the genomic confidence intervals of these loci with expression quantitative trait loci from bone and hypothalamus in the same intercross. Overlaps between egg loci and expression loci, and trait–gene expression correlations identify 29 candidates from bone and five from hypothalamus. The candidate quantitative trait genes include fibroblast growth factor 1, and mitochondrial ribosomal proteins L42 and L32. In summary, we found putative quantitative trait genes for egg traits in the chicken that may have been affected by regulatory variants under chicken domestication. These represent, to the best of our knowledge, some of the first candidate genes identified by genome-wide mapping for life history traits in an avian species.

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.