Development of cryopreservation media for the slow-freezing of cultured primordial germ cells in chicken.

Conservation of chicken germplasm is crucial in supporting commercial breeds for sustainable egg and meat production and preserving the genetic diversity of indigenous breeds for future breeding. Cryopreservation of chicken fertilized eggs or embryos is not feasible, owing to the large yolk-laden structure of the eggs. Primordial germ cells (PGCs), the embryonic precursors of gametes, are the best candidates for the cryobanking of chicken germplasm. Effective cryobanking of chicken PGCs requires an optimal cryopreservation protocol. Cryomedia containing dimethyl sulfoxide (DMSO) or DMSO combined with serum have been widely used for the cryopreservation of chicken PGCs. However, as cryoprotectants are yet to be optimized for chicken PGCs, the efficacy of cryomedia can be further improved. Here, we investigated the cryoprotective effects of propylene glycol (PG), an alternative to DMSO, on chicken PGCs. We found that the addition of non-permeable cryoprotectants, such as trehalose or chicken serum, to DMSO or PG cryomedia improved the recovery and survival rates of post-thawed PGCs. We further investigated the cryoprotective effects of trehalose and chicken serum and found that these additives have different cryoprotective actions. Based on these findings, we designed two different cryomedia: DTS, including 5% DMSO, 0.3 M trehalose, and 1% chicken serum, and PTS, including 7.5% PG, 0.1 M trehalose, and 5% chicken serum. Among the different PGC lines and freshly isolated PGCs, the cryomedia showed similar post-thaw recovery rates. Following transplantation, post-thawed male PGCs can colonize gonads and differentiate into functional sperm. We successfully revived the offspring of Kurokashiwa, a rare chicken breed in Japan, with cryopreserved PGCs. In conclusion, we developed two different cryomedia that achieved > 50% recovery of viable PGCs after thawing while maintaining germline competency.

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.

The formation of multiple pituitary pouches from the oral ectoderm causes ectopic lens development in hedgehog signaling-defective avian embryos.

BACKGROUND: Hedgehog signaling has various regulatory functions in tissue morphogenesis and differentiation. To investigate its involvement in anterior pituitary precursor development and the lens precursor potential for anterior pituitary precursors, we investigated Talpid mutant Japanese quail embryos, in which hedgehog signaling is defective. RESULTS: Talpid mutants develop multiple pituitary precursor-like pouches of variable sizes from the oral ectoderm (OE). The ectopic pituitary pouches initially express the pituitary-associated transcription factor (TF) LHX3 similarly to Rathke's pouch, the genuine pituitary precursor. The pouches coexpress the TFs SOX2 and PAX6, a signature of lens developmental potential. Most Talpid mutant pituitary pouches downregulate LHX3 expression and activate the lens-essential TF PROX1, leading to the development of small lens tissue expressing α-, ß-, and δ-crystallins. In contrast, mutant Rathke's pouches express a lower level of LHX3, which is primarily localized in the cytoplasm, and activate the lens developmental pathway. CONCLUSIONS: Hedgehog signaling in normal embryos regulates the development of Rathke's pouch in two steps. First, by confining Rathke's pouch development in a low hedgehog signaling region of the OE. Second, by sustaining LHX3 activity to promote anterior pituitary development, while inhibiting ectopic lens development.

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.

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.

Changes in prolactin receptor homodimer availability may cause late feathering in chickens.

Chicken early (EF) and late feathering (LF) are sex-linked phenotypes conferred by wild-type k+ and dominant K alleles on chromosome Z, respectively. Besides prolactin (PRL) receptor (PRLR) and sperm flagellar 2 (SPEF2) genes, the K allele contains a fusion gene in which partially duplicated PRLR (dPRLR) and SPEF2 (dSPEF2) genes are linked in a tail-to-tail manner. The causative dPRLR gene encodes a C-terminal truncated receptor. LF chickens have short or no primaries at hatching; however, their feather growth rate is higher than that of EF chickens. This study aimed to elucidate the molecular basis of the K allele's biphasic effect on feather development. By 3'RACE and RT-PCR analyses, we demonstrated that dSPEF2 gene transcription occurred beyond all coding exons of the dPRLR gene on the opposite strand and that dPRLR mRNA was less abundant than PRLR mRNA. In addition, a 5'UTR splice variant (SPV) of PRL receptor mRNAs was increased in LF chickens. In vitro expression analysis of 5'UTR linked to the luciferase reporter gene revealed higher translation efficiency of SPV. RT-qPCR showed that the dPRLR mRNA level was higher in embryos; conversely, SPV was higher in hatched chickens, as was dSPEF2 mRNA. These findings suggest that the K allele inhibits feather development at the fetal stage by expressing dPRLR to attenuate PRLR function and promotes feather growth after hatching by increasing PRLR through dSPEF2 mRNA expression. Increased SPV may cause greater feather growth than that in EF chickens by increasing the availability of PRLR homodimers and enhancing PRL signaling.

Chromosome size-correlated and chromosome size-uncorrelated homogenization of centromeric repetitive sequences in New World quails.

Many families of centromeric repetitive DNA sequences isolated from Struthioniformes, Galliformes, Falconiformes, and Passeriformes are localized primarily to microchromosomes. However, it is unclear whether chromosome size-correlated homogenization is a common characteristic of centromeric repetitive sequences in Aves. New World and Old World quails have the typical avian karyotype comprising chromosomes of two distinct sizes, and C-positive heterochromatin is distributed in centromeric regions of most autosomes and the whole W chromosome. We isolated six types of centromeric repetitive sequences from three New World quail species (Colinus virginianus, CVI; Callipepla californica, CCA; and Callipepla squamata, CSQ; Odontophoridae) and one Old World quail species (Alectoris chukar, ACH; Phasianidae), and characterized the sequences by nucleotide sequencing, chromosome in situ hybridization, and filter hybridization. The 385-bp CVI-MspI, 591-bp CCA-BamHI, 582-bp CSQ-BamHI, and 366-bp ACH-Sau3AI fragments exhibited tandem arrays of the monomer unit, and the 224-bp CVI-HaeIII and 135-bp CCA-HaeIII fragments were composed of minisatellite-like and microsatellite-like repeats, respectively. ACH-Sau3AI was a homolog of the chicken nuclear membrane repeat sequence, whose homologs are common in Phasianidae. CVI-MspI, CCA-BamHI, and CSQ-BamHI showed high homology and were specific to the Odontophoridae. CVI-MspI was localized to microchromosomes, whereas CVI-HaeIII, CCA-BamHI, and CSQ-BamHI were mapped to almost all chromosomes. CCA-HaeIII was localized to five pairs of macrochromosomes and most microchromosomes. ACH-Sau3AI was distributed in three pairs of macrochromosomes and all microchromosomes. Centromeric repetitive sequences may be homogenized in chromosome size-correlated and -uncorrelated manners in New World quails, although there may be a mechanism that causes homogenization of centromeric repetitive sequences primarily between microchromosomes, which is commonly observed in phasianid birds.

Quantitative trait loci mapping of innate fear behavior in day-old F2 chickens of Japanese Oh-Shamo and White Leghorn breeds using restriction site-associated DNA sequencing.

Understanding the genetic mechanisms that underlie innate fear behavior is essential for improving the management and performance of the poultry industry. This study aimed to map QTL associated with innate fear responses in open field (OF) and tonic immobility (TI) tests, using an F2 chicken intercross population between 2 behaviorally distinct breeds: the aggressive Japanese Oh-Shamo (OSM) and the docile White Leghorn T-line (WL-T). Genome-wide QTL analysis for the OF and TI traits was conducted using 2,109 single nucleotide polymorphism (SNP) markers obtained through restriction site-associated DNA sequencing (RAD-seq). While several suggestive QTL were identified for TI and OF traits at genome-wide 20% significance threshold levels, the analysis revealed 2 significant QTL for 2 OF traits (total distance and maximum speed) at genome-wide 5% significance threshold levels. These significant QTL were located between 12.34 and 30.49 megabase (Mb) on chromosome 1 and between 40.02 and 63.38 Mb on chromosome 2, explaining 6.75 to 7.40% of the total variances. These findings provide valuable insights for the poultry industry, particularly in refining chicken management strategies and informing targeted breeding efforts.

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.

New Behavioral Handling Test Reveals Temperament Differences in Native Japanese Chickens.

It is well known in the poultry industry that fear and stress experienced during the handling of day-old chicks in commercial hatcheries can have long-lasting effects on their behavior later in life. These hatchery-related stresses are more intense and complex than those encountered in traditional behavioral tests. Consequently, a single behavioral test may not be sufficient to measure hatchery stresses and chicken temperament. In this study, we developed a new behavioral handling test for day-old chickens, which incorporated concepts from established behavioral tests used with both young and adult birds. The new test assessed 10 behavioral traits, including vocalization frequency and responses to human interaction. It was conducted on 96 two-day-old chicks from seven breeds of native Japanese and Western chickens. The results of the principal component analysis classified chicken temperaments into three distinct categories: bustle, aggression, and timidity. Using these categories, the seven breeds were classified into five groups, each with distinct temperaments. This study highlights the reliability and value of the new handling test in characterizing the temperaments of various chicken breeds and provides insights into the complex behaviors of chickens.

5-Aminolevulinic acid improves chicken sperm motility.

OBJECTIVE: This study investigated the effects of 5-aminolevulinic acid (5-ALA) on the motility parameters, mitochondrial membrane depolarization, and ATP levels in chicken sperm. METHODS: The pooled semen from Barred Plymouth Rock males was used. In the first experiment, the semen was diluted 4-times with phosphate-buffered saline (PBS (-)) containing various concentrations (0, 0.01, 0.05, and 0.1 mM) of 5-ALA, and then the sperm motility parameters after incubation were evaluated by computer-assisted sperm analysis (CASA). In the second experiment, the semen was diluted 4-times with PBS (-) containing 0.05 mM 5-ALA, and then sperm mitochondrial membrane depolarization and ATP levels after 1.5 h of incubation were analyzed with the MitoPT® JC-1 Assay and ATP Assay kits, respectively. In the third experiment, the semen was removed from the seminal plasma and resuspended with the mediums of PBS (-), PBS (-) supplemented with CaCl2 and MgCl2 (PBS (+)) + 5-ALA, PBS (+) + caffeine, and PBS (+) + caffeine + 5-ALA. Then, the sperm motility parameters after incubation were evaluated by CASA. In the last experiment, the semen was treated with the mediums of PBS (-), PBS (-) + 5-ALA, 5.7% glucose, 5.7% glucose + 5-ALA after removing the seminal plasma, and then the sperm motility parameters were evaluated by CASA. RESULTS: The addition of 0.05 mM 5-ALA significantly increased the chicken sperm motility, progressive motility, linearity, average path velocity, curvilinear velocity, straight-line velocity, and the wobble. The sperm mitochondrial membrane depolarization was also increased by the 5-ALA treatment. The 5-ALA treatment decreased the sperm ATP levels. Both the caffeine treatment and glucose treatment decreased the sperm motility during incubation period. CONCLUSION: 5-ALA might increase sperm mitochondrial membrane depolarization to utilize the ATP for enhancing sperm movement.

Longer and faster sperm exhibit better fertilization success in Japanese quail.

In birds, sperm storage tubules (SST) located in the utero-vaginal junction are thought to be a site of sperm selection; however, the exact mechanism of sperm selection is poorly understood. Here, we investigated sperm entry into the SST and subsequent fertilization success under a competitive situation created by artificial insemination of a sperm mixture obtained from 2 males. We employed 2 quail strains, a wild-type and a dominant black (DB) type, as this allows easy assessment of paternity by feather coloration. We found paternity of embryos was biased toward DB males when a sperm mix with similar sperm numbers from the 2 males strains was artificially inseminated into females. Our novel sperm staining method with 2 different fluorescent dyes showed that the DB-biased fertilization was because of the better ability of DB sperm to enter the SST. Moreover, we found that DB sperm had a longer flagellum and midpiece. These characteristics probably allow sperm to swim faster in a high viscosity medium, which may be a similar environment to the lumen of the female reproductive tract. Our results indicated that sperm competition occurs to win a place in the SST and that filling the SST with their own spermatozoa is a critical step to achieve better fertilization success for the male Japanese quail.

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.

A Growth Performance and Nonlinear Growth Curve Functions of Large- and Normal-Sized Japanese Quail (Coturnix japonica).

This study aimed to evaluate the differences between the growth patterns of large- and normal-sized Japanese quail strains and their F1 progeny, by fitting their growth parameter values to five nonlinear regression growth models (Weibull, Logistic, Gompertz, Richards, and Brody). The Richards model presented the best fit for both sexes of the large-sized quail strain, whereas the Gompertz model presented the best fit for both sexes of the normal-sized quail strain, based on goodness-of-fit criteria (higher adjusted R2 and lower Akaike and Bayesian information criteria). Both sexes of F1 birds derived from the cross between normal-sized females and large-sized males were best fitted by the Richards model. In contrast, growth parameters of the F1 birds derived from the cross between large-sized females and normal-sized males were best fitted to the Gompertz model. The data could be fitted nearly as well to the Weibull and Logistic models as to the Richards and Gompertz models. The Brody model presented the poorest fit for the growth parameter values. The results indicated that the Richards and Gompertz models could best describe the growth characteristics of both large- and normal-sized quails. Moreover, the observed growth pattern of the F1 birds was likely inherited from the male parental strain. To the best of our knowledge, this is the first study comparing the growth curves of the reciprocal F1 generations with their parental strains in quails.

Geographic Origin and Genetic Characteristics of Japanese Indigenous Chickens Inferred from Mitochondrial D-Loop Region and Microsatellite DNA Markers.

Japanese indigenous chickens have a long breeding history, possibly beginning 2000 years ago. Genetic characterization of Japanese indigenous chickens has been performed using mitochondrial D-loop region and microsatellite DNA markers. Their phylogenetic relationships with chickens worldwide and genetic variation within breeds have not yet been examined. In this study, the genetic characteristics of 38 Japanese indigenous chicken breeds were assessed by phylogenetic analyses of mitochondrial D-loop sequences compared with those of indigenous chicken breeds overseas. To evaluate the genetic relationships among Japanese indigenous chicken breeds, a STRUCTURE analysis was conducted using 27 microsatellite DNA markers. D-loop sequences of Japanese indigenous chickens were classified into five major haplogroups, A-E, among 15 haplogroups found in chickens worldwide. The haplogroup composition suggested that Japanese indigenous chickens originated mainly from China, with some originating from Southeast Asia. The STRUCTURE analyses revealed that Japanese indigenous chickens are genetically differentiated from chickens overseas; Japanese indigenous chicken breeds possess distinctive genetic characteristics, and Jidori breeds, which have been reared in various regions of Japan for a long time, are genetically close to each other. These results provide new insights into the history of chickens around Asia in addition to novel genetic data for the conservation of Japanese indigenous chickens.

Developmental stages of the blue-breasted quail (Coturnix chinensis).

Chickens and Japanese quail (Coturnix japonica) have traditionally been the primary avian models in developmental biology research. Recently, the blue-breasted quail (Coturnix chinesis), the smallest species in the order Galliformes, has been proposed as an excellent candidate model in avian developmental studies owing to its precocious and prolific properties. However, data on the embryonic development of blue-breasted quail are scarce. Here, we developed a normal developmental series for the blue-breasted quail based on developmental features. The blue-breasted quail embryos take 17 days to reach the hatching period at 37.7°C. We documented specific periods of incubation in which significant development occurred, and created a 39-stage developmental series. The developmental series for the blue-breasted quail was almost identical to that for chickens and Japanese quail in the earlier stages of development (stages 1-16). Our staging series is especially useful at later stages of development (stages 34-39) of blue-breasted quail embryos as a major criterion of staging in this phase of development was the weight of embryos and the length of third toes.

Skeletal development in blue-breasted quail embryos.

The blue-breasted quail (Coturnix chinensis), the smallest species of quail with short generation interval and excellent reproductive performance, is a potential avian research model. A normal series of skeletal development of avian embryos could be served as a reference standard in the fields of developmental biology and teratological testing as well as in the investigation of mutation with skeletal abnormalities and in the study of the molecular mechanisms of skeletal development through genome manipulation. Furthermore, ossification sequence shows a species-specific pattern and has potential utility in phylogeny. However, data on the skeletal development of blue-breasted quail embryos are scarce. Here, we established a series of normal stages for the skeletal development of blue-breasted quail embryos. Cartilage and ossified bones of blue-breasted quail embryos were stained blue and red with Alcian blue 8GX and Alizarin red S, respectively. The time and order of chondrification and calcification of their skeletons were documented every 24 hr from 3 to 17 days of incubation, and a 15-stage series of skeletal development was created. Moreover, a comparative study with the Japanese quail (Coturnix japonica) demonstrated that ossification sequence differed significantly between these two species.

Characterization of Growth, Fat Deposition, and Lipid Metabolism-Related Gene Expression in Lean and Obese Meat-Type Chickens.

Excessive fat deposition adversely affects poultry production. In this study, we investigated growth, fat deposition, and hepatic mRNA expression of 13 lipid metabolism-related genes in three unique breeds of meat-type chickens with distinct breed origins and genetic relationships. One was Nagoya (NAG), a native Japanese breed, whereas the others were White Plymouth Rock (WPR) and White Cornish (WC), which have been used worldwide as the parental breeds of common broiler chickens. NAG chickens were phenotypically characterized by slow growth, lean body fat, and high gizzard and liver weights. In contrast, both WC and WPR chickens were characterized by rapid growth but high percentage of subcutaneous fat and abdominal fat weight, resulting from high feed intake. Among the three breeds, WC had the highest percentage of pectoral muscle weight, whereas WPR was the most obese. Among lipid metabolism-related genes, the expression of PPARA, PPARG, and CD36 was mostly associated with obesity. These results provide basic information for quantitative trait locus (QTL) analysis related to growth and fat traits in an F2 population of the lean NAG breed and the obese WPR breed of meat-type chickens in future.

Mapping of Quantitative Trait Loci for Growth and Carcass-Related Traits in Chickens Using a Restriction-Site Associated DNA Sequencing Method.

In the present study, quantitative trait loci (QTLs) analysis was performed to identify the chromosomal positions of growth and carcass-related trait QTLs using 319 F2 chickens obtained from intercrosses of an Oh-Shamo male and four White Plymouth Rock females. Body weight was measured weekly until the birds were 7 weeks old. Carcass-related traits were also measured at this timepoint. A genetic linkage map was constructed using 545 single nucleotide polymorphism (SNP) markers that were developed using a restriction-site associated DNA sequencing method. The linkage map included the 23 autosomes and the Z chromosome. Using simple interval QTL mapping, we were able to identify 10 significant and suggestive main-effect QTLs for growth and carcass-related traits present on chromosomes 1, 2, 3, 5, 8, 19, 24, and Z. These loci explained 5.60-16.52% of the phenotypic variances. The chromosomal positions of the 10 QTLs overlapped with those of previously reported QTLs, whereas the targeted traits varied. Our QTLs will aid future breeding programs in improving growth and meat yield of chickens (e.g., via marker-assisted selection), particularly in the Japanese brand chicken industry.

Quantitative trait loci mapping for the shear force value in breast muscle of F2 chickens.

The shear force value is one of the major traits that determine meat quality. In the present study, we performed QTL analysis for chicken breast muscle shear force value at 7 wk of age using 545 single nucleotide polymorphism (SNP) markers developed via restriction-site associated DNA sequencing (RAD-seq). An F2 resource family was generated by mating Oh-Shamo, a native Japanese chicken breed, and the White Plymouth Rock chicken breed. A total of 215 F2 birds were produced. Simple interval mapping revealed one significant main-effect QTL between 6.28 and 8.10 Mb SNPs on the chromosome Z with a logarithm of odds score of 5.53 at the genome-wide 5% level. At this QTL, the confidence interval, phenotypic variance explained, and additive effect were 26 cM, 12.24%, and -0.31 in males and -0.34 in females, respectively. No QTL with epistatic interaction effects were detected. To our knowledge, this is the first report on a QTL affecting the shear force value in the chicken breast muscle, using SNP markers derived from RAD-seq.