Research Note: Fine mapping of sequence variants associated with body weight of Lueyang black-boned chicken in the CCKAR gene

Use of GC-IMS and Stoichiometry to Characterize Flavor Volatiles in Different Parts of Lueyang Black Chicken during Slaughtering and Cutting

Chilled and cut chicken is preferred by consumers for its safeness and readiness to cook. To evaluate the quality characteristics of various chilled chicken products, differences in volatile organic components (VOCs) of six different cut parts (breast, back, leg, heart, liver, and gizzard) of Lueyang black chicken were characterized through gas chromatography-ion mobility spectroscopy (GC-IMS) combined with stoichiometry. A total of 54 peaks in the signal of VOCs were detected by GC-IMS, and 43 VOCs were identified by qualitative analysis. There were 22 aldehydes (20.66-54.07%), 8 ketones (25.74-62.87%), 9 alcohols (4.17-14.69%), 1 ether (0.18-2.22%), 2 esters (0.43-1.54%), and 1 furan (0.13-0.52%), in which aldehydes, ketones, and alcohols were the main categories. Among the six cut parts, the relative content of aldehydes (54.07%) was the highest in the gizzard, and the relative content of ketones (62.87%) was the highest in the heart. Meanwhile, the relative content of alcohols (14.69%) was the highest in the liver. Based on a stable and reliable predictive model established by orthogonal partial least squares-discriminant analysis (OPLS-DA), 3-hydroxy-2-butanone (monomer and dimer), acetone, 2-butanone monomer, hexanal (monomer and dimer), isopentyl alcohol monomer, and n-hexanol monomer were picked out as characteristic VOCs based on variable importance in projection (VIP value > 1.0, p < 0.05). Principal component analysis (PCA) and the clustering heatmap indicated that the characteristic VOCs could effectively distinguish the six cut parts of Lueyang black chicken. The specific VOCs responsible for flavor differences among six different cut parts of Lueyang black chicken were hexanal (monomer and dimer) for the gizzard, 2-butanone monomer and hexanal dimer for the breast, hexanal monomer for the back, 3-hydroxy-2-butanone monomer for the leg, 3-hydroxy-2-butanone (monomer and dimer) for the heart, and acetone and isopentyl alcohol monomer for the liver. These findings could reveal references for quality assessment and development of chilled products related to different cut parts of Lueyang black chicken in the future.

Genome-wide investigation to assess copy number variants in the Italian local chicken population

BACKGROUND

Copy number variants (CNV) hold significant functional and evolutionary importance. Numerous ongoing CNV studies aim to elucidate the etiology of human diseases and gain insights into the population structure of livestock. High-density chips have enabled the detection of CNV with increased resolution, leading to the identification of even small CNV. This study aimed to identify CNV in local Italian chicken breeds and investigate their distribution across the genome.

RESULTS

Copy number variants were mainly distributed across the first six chromosomes and primarily associated with loss type CNV. The majority of CNV in the investigated breeds were of types 0 and 1, and the minimum length of CNV was significantly larger than that reported in previous studies. Interestingly, a high proportion of the length of chromosome 16 was covered by copy number variation regions (CNVR), with the major histocompatibility complex being the likely cause. Among the genes identified within CNVR, only those present in at least five animals across breeds (n = 95) were discussed to reduce the focus on redundant CNV. Some of these genes have been associated to functional traits in chickens. Notably, several CNVR on different chromosomes harbor genes related to muscle development, tissue-specific biological processes, heat stress resistance, and immune response. Quantitative trait loci (QTL) were also analyzed to investigate potential overlapping with the identified CNVR: 54 out of the 95 gene-containing regions overlapped with 428 QTL associated to body weight and size, carcass characteristics, egg production, egg components, fat deposition, and feed intake.

CONCLUSIONS

The genomic phenomena reported in this study that can cause changes in the distribution of CNV within the genome over time and the comparison of these differences in CNVR of the local chicken breeds could help in preserving these genetic resources.

Selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds

BACKGROUND

The genomes of worldwide poultry breeds divergently selected for performance and other phenotypic traits may also be affected by, and formed due to, past and current admixture events. Adaptation to diverse environments, including acclimation to harsh climatic conditions, has also left selection footprints in breed genomes.

RESULTS

Using the Chicken 50K_CobbCons SNP chip, we genotyped four divergently selected breeds: two aboriginal, cold tolerant Ushanka and Orloff Mille Fleur, one egg-type Russian White subjected to artificial selection for cold tolerance, and one meat-type White Cornish. Signals of selective sweeps were determined in the studied breeds using three methods: (1) assessment of runs of homozygosity islands, (2) F_ST based population differential analysis, and (3) haplotype differentiation analysis. Genomic regions of true selection signatures were identified by two or more methods or in two or more breeds. In these regions, we detected 540 prioritized candidate genes supplemented them with those that occurred in one breed using one statistic and were suggested in other studies. Amongst them, SOX5, ME3, ZNF536, WWP1, RIPK2, OSGIN2, DECR1, TPO, PPARGC1A, BDNF, MSTN, and beta-keratin genes can be especially mentioned as candidates for cold adaptation. Epigenetic factors may be involved in regulating some of these important genes (e.g., TPO and BDNF).

CONCLUSION

Based on a genome-wide scan, our findings can help dissect the genetic architecture underlying various phenotypic traits in chicken breeds. These include genes representing the sine qua non for adaptation to harsh environments. Cold tolerance in acclimated chicken breeds may be developed following one of few specific gene expression mechanisms or more than one overlapping response known in cold-exposed individuals, and this warrants further investigation.

Identification of the Core Promoter and Variants Regulating Chicken CCKAR Expression

Decreased expression of chicken cholecystokinin A receptor (CCKAR) attenuates satiety, which contributes to increased food intake and growth for modern broilers. The study aims to define the core promoter of CCKAR, and to identify variants associated with expression activity. A 21 kb region around the CCKAR was re-sequenced to detect sequence variants. A series of 5'-deleted promoter plasmids were constructed to define the core promoter of CCKAR. The effects of sequence variants located in promoter (PSNP) and conserved (CSNP) regions on promoter activity were analyzed by comparing luciferase activity between haplotypes. A total of 182 variants were found in the 21 kb region. There were no large structural variants around CCKAR. pNL-328/+183, the one with the shortest insertion, showed the highest activity among the six promoter constructs, implying that the key cis elements regulating CCKAR expression are mainly distributed 328 bp upstream. We detected significant activity differences between high- and low-growth associated haplotypes in four of the six promoter constructs. The high-growth haplotypes of constructs pNL-1646/+183, pNL-799/+183 and pNL-528/+183 showed lower activities than the low-growth haplotypes, which is consistent with decreased expression of CCKAR in high-growth chickens. Lower expression of the high-growth allele was also detected for the CSNP5-containing construct. The data suggest that the core promoter of CCKAR is located the 328 bp region upstream from the transcription start site. Lower expression activities shown by the high-growth haplotypes in the reporter assay suggest that CSNP5 and variants located between 328 bp and 1646 bp upstream form a promising molecular basis for decreased expression of CCKAR and increased growth in chickens.