Integration of whole genome resequencing and transcriptome sequencing to identify candidate genes for tall and short traits in Baicheng Fatty chickens

The tall and short traits of chickens are significant indicators for evaluating their growth and development. Tall chickens have longer growth cycles, allowing them to accumulate sufficient nutrients and resulting in superior meat quality. This study aims to investigate the tall and short traits of Baicheng Fatty chickens and to identify relevant candidate genes. A total of 25 Baicheng Fatty chickens were selected for this research, where whole genome resequencing was performed on all samples to uncover genetic variations influencing tall and short traits. Additionally, transcriptome sequencing was conducted on 15 of these chickens to identify important genes affecting these traits through combined analysis. Using methods such as population genetic structure analysis, principal component analysis (PCA), linkage disequilibrium analysis (LD), runs of homozygosity (ROH) analysis, as well as genetic differentiation index (FST ) and nucleotide diversity (θπ), a total of 1,019 candidate genes were identified through whole genome resequencing analysis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed on these candidates. From the transcriptome data, 253 differentially expressed genes (DEGs) were identified, including 229 upregulated and 24 downregulated genes. GO and KEGG enrichment analyses were conducted on these differential genes, and a protein-protein interaction network for the DEGs was constructed. Through the combined analysis of whole genome resequencing and transcriptome data, six intersecting genes were identified: KLF15, NRXN1, LOC107050638, MHCY11, HAO1, and BORCS6. KEGG enrichment analysis revealed significant involvement in the Glyoxylate and Dicarboxylate Metabolism pathway, Peroxisome pathway, Carbon Metabolism, and Cell Adhesion Molecules (CAMs) pathway. These genes may influence the growth and developmental patterns of skeletal structures, though their regulatory mechanisms require further investigation. This study provides new insights for further research into the genetic mechanisms underlying chicken skeletal development and growth, as well as potential molecular markers for poultry breeding.

The effects of growth rate on leg morphology and tibia breaking strength, mineral density, mineral content, and bone ash in broilers

Fast-growing broilers are especially susceptible to bone abnormalities, causing major problems for broiler producers. The cortical bones of fast-growing broilers are highly porous, which may lead to leg deformities. Leg problems were investigated in 6-wk-old Arkansas randombred broilers. Body weight was measured at hatch and at 6 wk. There were 8 different settings of approximately 450 eggs each. Two subpopulations, slow-growing (SG; bottom quarter, n=511) and fast-growing (FG; top quarter, n=545), were created from a randombred population based on their growth rate from hatch until 6 wk of age. At 6 wk of age, the broilers were processed and chilled at 4°C overnight before deboning. Shank (78.27±8.06 g), drum stick (190.92±16.91 g), and thigh weights (233.88±22.66 g) of FG broilers were higher than those of SG broilers (54.39±6.86, 135.39±15.45, and 168.50±21.13 g, respectivly; P<0.001). Tibia weights (15.36±2.28 g) of FG broilers were also greater than those of SG broilers (11.23±1.81 g; P<0.001). Shank length (81.50±4.71 g) and tibia length (104.34±4.45 mm) of FG broilers were longer than those of SG broilers (71.88±4.66 and 95.98±4.85 mm, respectively; P<0.001). Shank diameter (11.59±1.60 mm) and tibia diameter (8.20±0.62 mm) of FG broilers were wider than those of SG broilers (9.45±1.74, 6.82±0.58 mm, respectively; P<0.001). Tibia breaking strength (28.42±6.37 kg) of FG broilers was higher than those of SG broiler tibia (21.81±5.89 kg; P<0.001). Tibia density and bone mineral content (0.13±0.01 g/cm2 and 1.29±0.23 g, respectively) of FG broilers were higher than those of SG broiler tibia (0.11±0.01 g/cm2 and 0.79±0.1 g; P<0.001). Tibia percentage of ash content (39.76±2.81) of FG broilers was lower than that of SG broilers (39.99±2.67; P=0.173). Fast-growing broiler bones were longer, wider, heavier, stronger, more dense, and contained more ash than SG ones. After all parameters were calculated per unit of final BW at 6 wk, tibia density and bone ash percentage of FG broilers were lower than those of SG broilers.

Computer-generated radiological imagery of the structure of the spongious substance in the postnatal development of the tibiotarsal bones of the Peking domestic duck (Anas platyrhynchos var. domestica)

The evaluation of the structure of the spongious substance of the tibiotarsal (TT) bones of the domestic duck aged 4 to 8 wk was performed using radiological analysis. The Trabecula program (Czerwiński, 1994) used in the study identified a map of radiological trabeculae and calculated the number, average volume, density, and width of trabeculae. It was stated that the number of trabeculae differed significantly (P ≤ 0.05) variant on age, sex, and a unique fragment of the studied bone. Six-week-old hens whose TT bones were most often exposed to deformities and fractures possessed attenuated bone mass. The number of trabeculae per 1 mm(2) during breeding was the lowest (10.34 and 9.54 mm(2) in the proximal and distal epiphyses, respectively). The tibial bones of the 6-wk-old hens also possessed the lowest volume of trabeculae (44.62 and 39.84% for the proximal and distal epiphyses, respectively). Dependant variances between the BW, the number of recognized radiological trabeculae, and the volume, density, and width of trabeculae were calculated using a selected correlation and regression coefficient (r = 0.41; P ≤ 0.05). Results expounded a unique linear relationship between BW and the volume of trabeculae. Indeed, the larger the BW, the more numerous the trabeculae observed. No significant correlation was determined between the BW and the number of recognized trabeculae nor their density and width. A small number of trabeculae and the lowered density may be the cause of fractures and deformities of the TT bones of the domestic duck.