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.

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.

Distinct usage of three C-type lectins by Japanese encephalitis virus: DC-SIGN, DC-SIGNR, and LSECtin.

Infection with West Nile virus and dengue virus, two mosquito-borne flaviviruses, is enhanced by two calcium-dependent lectins: dendritic cell-specific intercellular adhesion molecule-3-grabbing nonintegrin (DC-SIGN), and its related molecule (DC-SIGNR). The present study examined the relationship between Japanese encephalitis virus (JEV) infection and three lectins: DC-SIGN, DC-SIGNR, and liver sinusoidal endothelial cell lectin (LSECtin). Expression of DC-SIGNR resulted in robust JEV proliferation in a lymphoid cell line, Daudi cells, which was otherwise non-permissive to infection. DC-SIGN expression caused moderate JEV proliferation, with effects that varied according to the cells in which JEV was prepared. LSECtin expression had comparatively minor, but consistent, effects, in all cell types used in JEV preparation. While DC-SIGN/DC-SIGNR-mediated JEV infection was inhibited by yeast mannan, LSECtin-mediated infection was inhibited by N-acetylglucosamine ß1-2 mannose. Although involvement of DC-SIGN/DC-SIGNR in infection seems to be a common characteristic, this is the first report on usage of LSECtin in mosquito-borne flavivirus infection.

A changing thermal regime revealed from shallow to deep basalt source melting in the Moon.

Sample return missions have provided the basis for understanding the thermochemical evolution of the Moon. Mare basalt sources are likely to have originated from partial melting of lunar magma ocean cumulates after solidification from an initially molten state. Some of the Apollo mare basalts show evidence for the presence in their source of a late-stage radiogenic heat-producing incompatible element-rich layer, known for its enrichment in potassium, rare-earth elements, and phosphorus (KREEP). Here we show the most depleted lunar meteorite, Asuka-881757, and associated mare basalts, represent ancient (~3.9 Ga) partial melts of KREEP-free Fe-rich mantle. Petrological modeling demonstrates that these basalts were generated at lower temperatures and shallower depths than typical Apollo mare basalts. Calculated mantle potential temperatures of these rocks suggest a relatively cooler mantle source and lower surface heat flow than those associated with later-erupted mare basalts, suggesting a fundamental shift in melting regime in the Moon from ~3.9 to ~3.3 Ga.

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.

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.

The "Extended Brown" Plumage Color Mutant of Blue-Breasted Quail (Coturnix chinensis) is Associated with a Mutation in the Melanocortin 1-Receptor Gene (MC1R).

The mutant plumage color "extended brown (EB)" of the blue-breasted quail was genetically investigated. Mating experiments revealed that the EB plumage is controlled by an autosomal, incompletely dominant allele, for which we propose the symbol Eb. The EB plumage is characterized by dark brown color, and homozygotes for this mutation generally showed darker pigmentation than the heterozygotes. DNA sequencing and PCR-RFLP analyses of the EB mutants showed a rigid association between the EB plumage and a G-to-A nucleotide substitution at position 274 in the melanocortin 1-receptor gene (MC1R), clearly indicating that MC1R is the candidate gene for the EB plumage color in the blue-breasted quail.

Timing and Interval Effects of Repeated Inseminations by Roosters on the Fathering of Chicks.

The present study investigated the effects of timing and intervals between repeated inseminations by different rooster breeds on the fathering of chicks. The semen from Barred Plymouth Rock (BP), Japanese Silkie White (JS), and White Plymouth Rock (WP) males were used. Eighteen hens (7-month-old BP) were divided into four Groups (A-D). In all groups, the hens were first inseminated with the semen from BP males at 3 pm on day 0. The hens in Group A (n=3) were inseminated with the semen from JS and WP males at 3 pm on days 5 and 10, respectively. Those in Group B (n=3) were inseminated with the semen from JS and WP males at 3 pm on days 5 and 15, respectively. The hens in Group C (n=6) were inseminated with the semen from JS and WP males at 6 am on days 5 and 10, respectively. Lastly, those in Group D (n=6) were inseminated with the semen from JS and WP males at 6 am on days 10 and 20, respectively. The chicks obtained were classified on the basis of their phenotype matching with the breeding male phenotype. The majority of chicks (82.4% to 100% in Groups A and B) were fathered by the sperm from the subsequent insemination when repeated insemination was performed in the afternoon. Moreover, the chicks produced by the most recent insemination in the groups that were subjected to morning insemination could be obtained the next day after insemination (Groups C and D). The percentage of chicks fathered by the sperm from the subsequent insemination was 95.2% to 100% when the inter-insemination interval was 10 days (Groups B and D); these percentages decreased when the duration of the interval between inseminations was decreased to 5 days in Groups A, B, and C.