Quantitative Trait Loci Mapping for External Egg Traits in F₂ Chickens

Genome-wide association analysis of eggshell color of an F2 generation population reveals candidate genes in chickens

Eggshell color is an important visual characteristic that affects consumer preferences for eggs. Eggshell color, which has moderate to high heritability, can be effectively enhanced through molecular marker selection. Various studies have been conducted on eggshell color at specific time points. However, few longitudinal data are available on eggshell color. Therefore, the objective of this study was to investigate eggshell color using the Commission International de L'Eclairage L*a*b* system with multiple measurements at different ages (age at the first egg and at 32, 36, 40, 44, 48, 52, 56, 60, 66, and 72 weeks) within the same individuals from an F2 resource population produced by crossing White Leghorn and Dongxiang Blue chicken. Using an Affymetrix 600 single nucleotide polymorphism (SNP) array, we estimated the genetic parameters of the eggshell color trait, performed genome-wide association studies (GWASs), and screened for the potential candidate genes. The results showed that pink-shelled eggs displayed a significant negative correlation between L* values and both a* and b* values. Genetic heritability based on SNPs showed that the heritability of L*, a*, and b* values ranged from 0.32 to 0.82 for pink-shelled eggs, indicating a moderate to high level of genetic control. The genetic correlations at each time point were mostly above 0.5. The major-effect regions affecting the pink eggshell color were identified in the 10.3-13.0 Mb interval on Gallus gallus chromosome 20, and candidate genes were selected, including SLC35C2, PCIF1, and SLC12A5. Minor effect polygenic regions were identified on chromosomes 1, 6, 9, 12, and 15, revealing 11 candidate genes, including MTMR3 and SLC35E4. Members of the solute carrier family play an important role in influencing eggshell color. Overall, our findings provide valuable insights into the phenotypic and genetic aspects underlying the variation in eggshell color. Using GWAS analysis, we identified multiple quantitative trait loci (QTLs) for pink eggshell color, including a major QTL on chromosome 20. Genetic variants associated with eggshell color may be used in genomic breeding programs.

Morphological variation of tail bone among two chicken breeds and their F1 progeny

Fancy breeds of Japanese indigenous chicken display extensive morphological diversity, particularly in tail feathers. Although marked differences in tail and bone traits have been reported between Tosa-jidori (wild type) and Minohikichabo (rich type) breeds, little is known about the pattern of genetic inheritance in cross experiments. Therefore, this study aimed to investigate the strain and sex effects, and inheritance patterns, in the morphometric variation of pygostyle bones among Tosa-jidori, Minohikichabo, and their F1 hybrids. Five morphological traits, angle of the apex of the pygostyle, pygostyle length, margo cranialis length, tail feather number, and body weight, were evaluated at the adult stage. A significant strain difference was detected in all traits, whereas significant sex differences were observed in only three traits, but not in the angle of the apex of the pygostyle and tail feather number. In F1 hybrids, the angle of the apex of the pygostyle was significantly different to that of Tosa-jidori but not that of Minohikichabo, whereas the pygostyle length and tail number of F1 hybrids were significantly different from those of Minohikichabo but not those of Tosa-jidori. A significant heterosis effect was found in the margo cranialis length and body weight. All five traits showed nonadditive inheritance patterns but varied in each trait between partial dominance (angle of the apex of pygostyle), full dominance (pygostyle length and tail feather number), and over-dominance (margo cranialis length and body weight). Interestingly, different patterns of genetic inheritance in the F1 hybrid were observed at different locations, even within the same pygostyle bone. Using the Japanese indigenous chicken model, these results provide a substantial step toward understanding the genetic architecture of morphology in chickens.

Refine localizations of functional variants affecting eggshell color of Lueyang black-boned chicken in the SLCO1B3

Table eggs with color-uniformity shell are visually attractive for consumers. Lueyang black-boned chicken (LBC) lays colorful eggs, which is undesirable for sale of table eggs, but provides a segregating population for mapping functional variants affecting eggshell color. SLCO1B3 was identified as the causative gene for blue eggs in the Dongxiang and Araucana chickens. The aim of this study is to map functional variants associated with chicken eggshell color in the SLCO1B3. Eggshell color of LBC (n = 383) was measured using the L*a*b color space. SLCO1B3 was resequencing using a subset (n = 30) of 383 samples. Linkage disequilibrium among 139 SNP was analyzed. Association of 16 SNP in the SLCO1B3 and 8 in CPOX, ALAS1, and ABCG2 genes with L*a*b were tested by a polygenic model (LMM) and a polygenic/oligogenic mixed model (BSLMM). Chromatin state annotations were retrieved from the UCSC database. Effect of SLCO1B3 variants distributed in mapping and upstream 1.6-kb regions on promoter activities were analyzed using dual-luciferase reporter assay. One hundred and thirty-nine variants maintained low linkage disequilibrium with 80% of r2 less than 0.226. Fifteen SLCO1B3 variants were significantly associated with a*, of which 1B3_SNP108 was showed the strongest association and the largest effect on a*. In the BSLMM, 1B3_SNP108 alone appeared in the Markov chain Monte Carlo as major variants in 100% of posterior inclusion probability. None of variants in CPOX, ALAS1, and ABCG2 were significantly associated with color indexes except that 2 ALAS1 variants were associated with L*. 1B3_SNP108 distributes in the Intron4 where 6 active enhancers and 1 ATAC island were enriched. However, 1B3_SNP108-containing constructs showed negligible activities in the reporter assay. No significant differences of activities between haplotypes were found for five 5'-deleted promoter constructs. The data recognizes 1B3_SNP108 as a valuable marker for breeding of eggshell color. Functional variants are localized in the region adjacent to the 1B3_SNP108 due to low linkage disequilibrium in the LBC. Our findings extend the role of SLCO1B3 from a causative gene for blue eggs to a major regulator driving continuous variation of LBC eggshell color.

Genotype affects free amino acids of egg yolk and albumen in Japanese indigenous breeds and commercial Brown layer chickens

Using a variety of genetic resources, the aim of this study is to see how genetic background affects egg traits in chickens. Three different chicken genotypes (a commercial Brown layer, BOR; 2 Japanese indigenous breeds, NGY and YKD) were investigated effects on genotype in 10 external and internal egg quality traits along with 20 yolk and albumen free amino acid traits. Significant effects on genotype in 10 external and internal egg quality traits and 18 yolk and 17 albumen amino acid traits were found (P < 0.05). In sizes and weights of egg and eggshell redness, there were significant differences among all combinations of genotype (BOR > NGY > YKD). In 14 yolk (Asn, Ser, Gln, Gly, His, Arg, Ala, Pro, Tyr, Val, Met, Leu, Phe, and Lys) and 8 albumen amino acid traits (Gln, Gly, His, Arg, Val, Ile, Leu, and Lys), BOR was significantly higher than NGY and YKD, while the opposite relations were seen in 2 amino acid traits (Cys and GABA). Moreover, phenotypic correlation analyses revealed that positive correlations among amino acid traits within each yolk and albumen were broadly seen (0.30 < r < 0.98, P < 0.05). However, there are almost no phenotypic correlations in amino acids between yolk and albumen in BOR and NGY, but negative correlations in YKD, which implying a potential use of untapped genetic resources for modifying amino acid balance. These results indicate genetic background affects not only sizes and weights of egg but also amino acid contents and their balance of yolk and albumen.

Quantitative trait loci for growth-related traits in Japanese quail (Coturnix japonica) using restriction-site associated DNA sequencing

This study aimed to identify quantitative trait loci (QTLs) for growth-related traits by constructing a genetic linkage map based on single nucleotide polymorphism (SNP) markers in Japanese quail. A QTL mapping population of 277 F₂ birds was obtained from an intercross between a male of a large-sized strain and three females of a normal-sized strain. Body weight (BW) was measured weekly from hatching to 16 weeks of age. Non-linear regression growth models of Weibull, Logistic, Gompertz, Richards, and Brody were analyzed, and growth curve parameters of Richards was selected as the best model to describe the quail growth curve of the F₂ birds. Restriction-site associated DNA sequencing developed 125 SNP markers that were informative between their parental strains. The SNP markers were distributed on 16 linkage groups that spanned 795.9 centiMorgan (cM) with an average marker interval of 7.3 cM. QTL analysis of phenotypic traits revealed four main-effect QTLs. Detected QTLs were located on chromosomes 1 and 3 and were associated with BW from 4 to 16 weeks of age and asymptotic weight of Richards model at genome-wide significant at 1% or 5% level. No QTL was detected for BW from 0 to 3 weeks of age. This is the first report identified QTLs for asymptotic weight of the Richards parameter in Japanese quail. These results highlight that the combination of QTL studies and the RAD-seq method will aid future breeding programs identify genes underlying the QTL and the application of marker-assisted selection in the poultry industry, particularly the Japanese quail.

Untargeted UHPLC-MS metabolic profiling as a valuable tool for the evaluation of eggs quality parameters after dietary supplementation with oregano, thyme, sideritis tea and chamomile on brown laying hens

INTRODUCTION

Bioactive constituents of medicinal-aromatic plants used as feed additives may affect the metabolic profile and oxidative stability of hen eggs.

OBJECTIVES

To determine the effects of dietary supplementation with a mixture of dried oregano, thyme, sideritis tea and chamomile on laying hen performance, egg quality parameters, and oxidative stability in the egg yolk were monitored.

METHODS

In this trial 432 hens were allocated in two treatments (unsupplemented vs. supplemented with the mixture) and fed for 42 days. Eggs were collected at the end of the trial period, egg yolk was separated, extracted, and the total phenolic content (TPC) and oxidative stability was measured. Furthermore, LC-MS metabolic profile of eggs was studied and pathway analysis was elaborated in MetaboAnalyst to facilitate annotation of features.

RESULTS

Overall, egg production and feed conversion ratio were not affected by the supplementation. However, eggs from the supplemented treatment showed improved shell thickness and strength, and yolk resistance to oxidation. Moreover, LC-MS metabolomic analysis of egg yolk of supplemented and unsupplemented layers showed significant variations and tight clustering in unsupervised principal component analysis due to different chemical profiling of egg yolk. LC-MS study showed that secondary metabolites of aromatic plants did not transfer into yolk, nevertheless the feed supplementation impacted the pathway metabolism of tyrosine, phenylalanine, propanate, and the biosynthesis of aminoacyl-tRNA, phenylalanine, tyrosine and tryptophan.

CONCLUSIONS

The dietary supplementation of layers with a mixture of dried medicinal aromatic plants affected shell thickness and strength, the lipid and protein oxidative stability and increased tyrosine and phenylalanine content in eggs.

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.

Breed and feed affect amino acid contents of egg yolk and eggshell color in chickens

Genetic and environmental factors regulate hen egg traits. To demonstrate the possibility of producing designer eggs through genetic and environmental factors, we investigated the effects of breed and feed on egg traits using 2 chicken breeds, Rhode Island Red (RIR) and Australorp (AUS), and 2 feeds, mixed feed and fermented feed. A total of 40 eggs were collected at 33 wk of age (0 mo under mixed feed) and 1, 1.5, and 2 mo after switching to fermented feed. Two-way ANOVA mixed design was used to evaluate 10 egg traits: weight, length of the long axis, length of the short axis, eggshell weight, yolk weight, albumen weight, eggshell thickness, eggshell lightness, redness, and yellowness, and 19 yolk amino acids. The results revealed significant breed effects on eggshell redness and yellowness, with higher values of these traits in RIR eggs compared with AUS eggs. There was a significant effect of feed on eggshell lightness, with a lighter color observed under fermented feed compared with mixed feed. Significant effects of breed and breed × feed were found for yolk cysteine content. Eggs from AUS had a higher yolk cysteine content than those from RIR. The cysteine content in AUS eggs increased gradually after starting fermented feed, although RIR remained relatively constant over time. These findings suggest that it is possible to produce designer eggs with enriched components, including yolk amino acids, by adjusting both genetic and environmental factors. This represents a first step in understanding the mechanisms underlying the production of value-added eggs in chickens.

Metabolomics Approach Reveals the Effects of Breed and Feed on the Composition of Chicken Eggs

Chicken eggs provide essential nutrients to consumers around the world. Although both genetic and environmental factors influence the quality of eggs, it is unclear how these factors affect the egg traits including egg metabolites. In this study, we investigated breed and feed effects on 10 egg traits, using two breeds (Rhode Island Red and Australorp) and two feed conditions (mixed feed and fermented feed). We also used gas chromatography-mass spectrometry (GC-MS/MS) to analyze 138 yolk and 132 albumen metabolites. Significant breed effects were found on yolk weight, eggshell weight, eggshell colors, and one albumen metabolite (ribitol). Three yolk metabolites (erythritol, threitol, and urea) and 12 albumen metabolites (erythritol, threitol, ribitol, linoleic acid, isoleucine, dihydrouracil, 4-hydroxyphenyllactic acid, alanine, glycine, N-butyrylglycine, pyruvic acid, and valine) were significantly altered by feed, and a significant interaction between breed and feed was discovered in one albumen metabolite (N-butyrylglycine). Yolk and albumin had higher levels of sugar alcohols when hens were fed a fermented diet, which indicates that sugar alcohol content can be transferred from diet into eggs. Linoleic acid was also enriched in albumen under fermented feed conditions. This study shows that yolk and albumen metabolites will be affected by breed and feed, which is the first step towards manipulating genetic and environmental factors to create "designer eggs."

Causal phenotypic networks for egg traits in an F2 chicken population

Traditional single-trait genetic analyses, such as quantitative trait locus (QTL) and genome-wide association studies (GWAS), have been used to understand genotype-phenotype relationships for egg traits in chickens. Even though these techniques can detect potential genes of major effect, they cannot reveal cryptic causal relationships among QTLs and phenotypes. Thus, to better understand the relationships involving multiple genes and phenotypes of interest, other data analysis techniques must be used. Here, we utilized a QTL-directed dependency graph (QDG) mapping approach for a joint analysis of chicken egg traits, so that functional relationships and potential causal effects between them could be investigated. The QDG mapping identified a total of 17 QTLs affecting 24 egg traits that formed three independent networks of phenotypic trait groups (eggshell color, egg production, and size and weight of egg components), clearly distinguishing direct and indirect effects of QTLs towards correlated traits. For example, the network of size and weight of egg components contained 13 QTLs and 18 traits that are densely connected to each other. This indicates complex relationships between genotype and phenotype involving both direct and indirect effects of QTLs on the studied traits. Most of the QTLs were commonly identified by both the traditional (single-trait) mapping and the QDG approach. The network analysis, however, offers additional insight regarding the source and characterization of pleiotropy affecting egg traits. As such, the QDG analysis provides a substantial step forward, revealing cryptic relationships among QTLs and phenotypes, especially regarding direct and indirect QTL effects as well as potential causal relationships between traits, which can be used, for example, to optimize management practices and breeding strategies for the improvement of the traits.

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.

A longitudinal quantitative trait locus mapping of chicken growth traits

Since the growth traits of chickens are largely related to the production of meat and eggs, it is definitely important to understand genetic basis of growth traits. Although many quantitative trait loci (QTLs) that affect growth traits have recently been reported in chickens, little is known about genetic architecture of growth traits across all growth stages. Therefore, we conducted a longitudinal QTL study of growth traits measured from 0 to 64 weeks of age using 134 microsatellite DNA markers on 26 autosomes from 406 F₂ females, which resulted from an intercross of Oh-Shamo and White Leghorn chicken breeds. We found 27 and 21 independent main-effect QTLs for body weight and shank length, respectively. Moreover, 15 and 4 pairs of epistatic QTLs were found for body weight and shank length, respectively. Taken together, the present study revealed 48 QTLs for growth traits on 21 different autosomes, and these loci clearly have age-specific effects on phenotypes throughout stages that are important for meat and egg productions. Approximately 60% of Oh-Shamo-derived alleles increased the phenotypic values, corresponding to the fact that Oh-Shamo traits were higher than those of White Leghorn. On the other hand, remaining Oh-Shamo alleles decreased the phenotypic values. Our results clearly indicated that the growth traits of chickens are regulated by several main and epistatic QTLs that are widely distributed in the chicken genome, and that the QTLs have age-dependent manners of controlling the traits. This study implies importance of not only cross-sectional but also longitudinal growth data for further understanding of the complex genetic architecture in animal.

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.