Search Results (7)

Evaluation of semen quality is crucial for predicting fertility success in artificial insemination and eventual rooster selection within poultry breeding programs. However, the multitude of parameters obtained in semen quality analysis makes it challenging for breeders to make informed selection decisions. This study evaluated semen samples from 210 roosters in seven chicken breeds, using a computer-aided sperm analysis (CASA) system. A multivariate approach utilizing factor analysis (FA) was applied to simplify the data. The FA condensed 14 semen quality traits into 3 factors, linearity factor, velocity factor, and quantitative factor, explaining 75.82% of the original variations. The Beijing-You breed was selected to analyze the association between fertility and these semen quality factors, and we found high correlation between fertility and quantitative (r = 0.84) and linearity (r = 0.63) factors, and low correlation with the velocity factor (r = 0.19). Based on individual factor scores, breed clustering revealed distinct profiles with Houdan, Tibetan, and White Leghorn demonstrating lower sperm counts and poor linearity. Columbian Plymouth Rock exhibited high speed with poor linearity while Beijing-You, Rhode Island Red, and Barred Plymouth Rock displayed higher sperm counts with compromised speed and linearity. This study demonstrates that FA effectively consolidates multiple semen quality traits into fewer, biologically relevant factors. These findings provide valuable insights into breed-specific reproductive characteristics and offer actionable information for optimizing breeding in poultry production. Full article

Mortality from Marek’s disease virus (MDV) infection results in economic loss for the poultry industry. It is controlled by vaccination, but the virus mutates and becomes more virulent. Variation within the MHC is well known to impact the outcomes following MDV infection from research performed utilizing the White Leghorn breed, with laboratory strains of the virus. The effect of the MHC haplotype following MDV challenge was determined from six lines of commercial elite (White Plymouth Rock (two), White Leghorn (three), and Rhode Island Red (one)) egg layer lines, challenged with vv+ virus. Mortality was recorded as sire daughter averages at 16–18 weeks of age from 19 generations of data. Sires were genotyped using a set of MHC-specific SNPs, encompassing 210,000 bp. Across all lines, there was a total of 23 unique MHC haplotypes, of which 15 were found at a frequency greater than 5% and used for further analysis. A significant impact on mortality was found for 16 of the haplotypes, with 9 haplotypes associated with decreased mortality and 7 haplotypes with increased mortality. There were three haplotypes identified in more than one line, allowing cross-line comparisons. The effect of these common haplotypes was consistent (either negative, positive or neutral) between lines. Full article

Understanding genetic diversity, runs of homozygosity (ROH), and selection signatures is critical for the conservation and breeding management of native Japanese chickens. In this study, genetic diversity, ROH, and selection signatures in 11 populations of seven native Japanese breeds and three foreign breeds with different genetic and behavioral backgrounds were investigated using 11,493 SNPs identified through restriction-site-associated DNA sequencing. The Oh-Shamo (OSM), an aggressive cockfighting breed, exhibited the highest genetic diversity. Six native Japanese breeds, Ingie (IG), Ryujin-Jidori (RYU), Tosa-Jidori (TJI), Tosa-Kukin (TKU), Nagoya (NAG), and Ukkokei (UK), showed intermediate levels of genetic diversity and ROH. Population analyses grouped the 11 populations into four distinct clusters: (1) five populations comprising three foreign breeds (the Fayoumi inbred line, closed-colony G line of White Leghorn, commercial T line of WL, and White Plymouth Rock) and the IG Japanese breed; (2) OSM and two old Jidori breeds (RYU and TJI); (3) TKU and UK; and (4) the meat-type Nagoya breed. ROH and Fst analyses identified seven SNPs on chromosomes 13, 17, 20, 24, and 26, five of which were candidate genetic variants for fear-related behavior. These findings provide insights into genetic diversity and conserved genomic segments valuable for breeding and conservation in Japanese chicken breeds. Full article

Selection of livestock for disease resistance is challenging due to the difficulty in obtaining reliable phenotypes. Antibodies are immunological molecules that provide direct and indirect defenses against infection and link the activities of both the innate and adaptive compartments of the immune system. As a result, antibodies have been used as a trait in selection for immune defense. The goal of this study was to identify genomic regions associated with natural and induced antibodies in chickens using low-pass sequencing. Enzyme-linked immunosorbent assays were used to quantify innate (natural) antibodies binding KLH, OVA, and PHA and induced (adaptive) antibodies binding IBD, IBV, NDV, and REO. We collected plasma from four White Leghorn (WL), two White Plymouth Rock (WPR), and two Rhode Island Red (RIR) lines. Samples numbers ranged between 198 and 785 per breed. GWAS was performed within breed on data pre-adjusted for Line-Hatch-Sex effects using GCTA. A threshold of p = 10⁻⁶ was used to select genes for downstream annotation and enrichment analysis with SNPEff and Panther. Significant enrichment was found for the defense/immunity protein, immunoglobulin receptor superfamily, and the antimicrobial response protein in RIR; and the immunoglobulin receptor superfamily, defense/immunity protein, and protein modifying enzyme in WL. However, none were present in WPR, but some of the selected SNP were annotated in immune pathways. This study provides new insights regarding the genetics of the antibody response in layer chickens. Full article

Breeding improvements and quantitative trait genetics are essential to the advancement of broiler production. The impact of artificial selection on genomic architecture and the genetic markers sought remains a key area of research. Here, we used whole-genome resequencing data to analyze the genomic architecture, diversity, and selective sweeps in Cornish White (CRW) and Plymouth Rock White (PRW) transboundary breeds selected for meat production and, comparatively, in an aboriginal Russian breed of Ushanka (USH). Reads were aligned to the reference genome bGalGal1.mat.broiler.GRCg7b and filtered to remove PCR duplicates and low-quality reads using BWA-MEM2 and bcftools software; 12,563,892 SNPs were produced for subsequent analyses. Compared to CRW and PRW, USH had a lower diversity and a higher genetic distinctiveness. Selective sweep regions and corresponding candidate genes were examined based on ZF_ST, hapFLK, and ROH assessment procedures. Twenty-seven prioritized chicken genes and the functional projection from human homologs suggest their importance for selection signals in the studied breeds. These genes have a functional relationship with such trait categories as body weight, muscles, fat metabolism and deposition, reproduction, etc., mainly aligned with the QTLs in the sweep regions. This information is pivotal for further executing genomic selection to enhance phenotypic traits. Full article

The basic units of skeletal muscle in all vertebrates are multinucleate myofibers, which are formed from the fusion of mononuclear myoblasts during the embryonic period. In order to understand the regulation of embryonic muscle development, we selected four chicken breeds, namely, Cornish (CN), White Plymouth Rock (WPR), White Leghorn (WL), and Beijing-You Chicken (BYC), for evaluation of their temporal expression patterns of known key regulatory genes (Myomaker, MYOD, and MSTN) during pectoral muscle (PM) and thigh muscle (TM) development. The highest expression level of Myomaker occurred from embryonic days E13 to E15 for all breeds, indicating that it was the crucial stage of myoblast fusion. Interestingly, the fast-growing CN showed the highest gene expression level of Myomaker during the crucial stage. The MYOD gene expression at D1 was much higher, implying that MYOD might have an important role after hatching. Histomorphology of PM and TM suggested that the myofibers was largely complete at E17, which was speculated to have occurred because of the expression increase in MSTN and the expression decrease in Myomaker. Our research contributes to lay a foundation for the study of myofiber development during the embryonic period in different chicken breeds. Full article

Nagoya (NAG), a native Japanese chicken breed, has high quality meat but low meat yield, whereas White Plymouth Rock (WPR), a parental breed of commercial broilers, has rapid growth but high body fat. We previously reported three quantitative trait loci (QTLs) for early postnatal growth in 239 F₂ chickens between NAG and WPR breeds. In this study, using the same F₂ chickens at 4 weeks of age, we performed genome-wide QTL analysis for breast muscle weight, fat weight and serum and liver levels of biochemical parameters. Two significant QTLs for pectoralis minor and/or major weights were revealed on chromosome 2 between 108 Mb and 127 Mb and chromosome 4 between 10 Mb and 68 Mb. However, no QTL for the other traits was detected. The two QTLs explained 7.0–11.1% of the phenotypic variances, and their alleles derived from WPR increased muscle weights. The chromosome 2 QTL may be a novel locus, whereas the chromosome 4 QTL coincided with a known QTL for meat quality. The findings provide information that is beneficial for genetic improvement of meat yield for the lean NAG breed and, furthermore, provide a better understanding of the genetic basis of chicken muscle development. Full article