Fermented bamboo powder activates gut odorant receptors, and promotes intestinal health and growth performance of dwarf yellow-feathered broiler chickens

The present study investigated the effects of fermented bamboo powder (FPB) on gut odorant receptors (OR), intestinal health, and growth performance of dwarf yellow-feathered broiler chickens. Six hundred (600) healthy 1-day-old chicks were randomly assigned into 2 groups, with 10 replicates consisting of 30 chicks each. The control group was fed a basal diet. In contrast, the experimental group was fed the basal diet supplemented with 1.0, 2.0, 4.0, and 6.0 g/kg FBP for 4 different phases, namely phase I (1-22 d), phase II (23-45 d), phase III (46-60 d), and phase IV (61-77 d), respectively. The first 2 phases were considered pretreatment (0-45 d), and the remaining were experimental (46-77 d) periods. The tissue samples were collected from phase IV. The chickens in the FBP supplementation group exhibited a significant increment in body weight gain, evisceration yield, breast, thigh, and liver weight, while also experiencing a decrease in the FCR (P < 0.05). Furthermore, the villus height, crypt depth, and villus area exhibited significant increases in the FBP group (P < 0.01). Additionally, the secretion levels of gut hormones such as glucagon-like peptide-1, peptide YY, cholecystokinin, and 5-hydroxytryptamine were significantly elevated in the serum, duodenum, jejunum, and ileum tissues in the FBP group (P < 0.05). The results of qRT-PCR indicated that ORs had responsive expression in the gizzard, proventriculus, and small intestine of chickens when fed with the FBP diet (P < 0.05). Notably, the expression of the COR1, COR2, COR4, COR6, COR8, COR9, OR52R1, OR51M1, OR1F2P, OR5AP2, and OR14J1L112 genes was stronger in the small intestines compared to the gizzard and proventriculus. In conclusion, these results suggest that the FPB plays a crucial role in growth performance, activation of ORs, and gut health and development.

Comprehensive analysis of structural variants in chickens using PacBio sequencing

Structural variants (SVs) are one of the main sources of genetic variants and have a greater impact on phenotype evolution, disease susceptibility, and environmental adaptations than single nucleotide polymorphisms (SNPs). However, SVs remain challenging to accurately type, with several detection methods showing different limitations. Here, we explored SVs from 10 different chickens using PacBio technology and detected 49,501 high-confidence SVs. The results showed that the PacBio long-read detected more SVs than Illumina short-read technology genomes owing to some SV sites on chromosomes, which are related to chicken growth and development. During chicken domestication, some SVs beneficial to the breed or without any effect on the genomic function of the breed were retained, whereas deleterious SVs were generally eliminated. This study could facilitate the analysis of the genetic characteristics of different chickens and provide a better understanding of their phenotypic characteristics at the SV level, based on the long-read sequencing method. This study enriches our knowledge of SVs in chickens and improves our understanding of chicken genomic diversity.

Prenatal and Early Postnatal Behavioural Programming in Laying Hens, With Possible Implications for the Development of Injurious Pecking

Injurious pecking (IP) represents a serious concern for the welfare of laying hens (Gallus gallus domesticus). The risk of IP among hens with intact beaks in cage-free housing prompts a need for solutions based on an understanding of underlying mechanisms. In this review, we explore how behavioural programming via prenatal and early postnatal environmental conditions could influence the development of IP in laying hens. The possible roles of early life adversity and mismatch between early life programming and subsequent environmental conditions are considered. We review the role of maternal stress, egg conditions, incubation settings (temperature, light, sound, odour) and chick brooding conditions on behavioural programming that could be linked to IP. Brain and behavioural development can be programmed by prenatal and postnatal environmental conditions, which if suboptimal could lead to a tendency to develop IP later in life, as we illustrate with a Jenga tower that could fall over if not built solidly. If so, steps taken to optimise the environmental conditions of previous generations and incubation conditions, reduce stress around hatching, and guide the early learning of chicks will aid in prevention of IP in commercial laying hen flocks.

Identification of Copy Number Variation in Domestic Chicken Using Whole-Genome Sequencing Reveals Evidence of Selection in the Genome

Simple Summary

Chickens have been bred for meat and egg production as a source of animal protein. With the increase of productivity as the main purpose of domestication, factors such as metabolism and immunity were boosted, which are detectable signs of selection on the genome. This study focused on copy number variation (CNV) to find evidence of domestication on the genome. CNV was detected from whole-genome sequencing of 65 chickens including Red Jungle Fowl, broilers, and layers. After that, CNV region, the overlapping region of CNV between individuals, was made to identify which genomic regions showed copy number differentiation. The 663 domesticated-specific CNV regions were associated with various functions such as metabolism and organ development. Also, by performing population differentiation analyses such as clustering analysis and ANOVA test, we found that there are a lot of genomic regions with different copy number patterns between broilers and layers. This result indicates that different genetic variations can be found, depending on the purpose of artificial selection and provides considerations for future animal breeding.

Abstract

Copy number variation (CNV) has great significance both functionally and evolutionally. Various CNV studies are in progress to find the cause of human disease and to understand the population structure of livestock. Recent advances in next-generation sequencing (NGS) technology have made CNV detection more reliable and accurate at whole-genome level. However, there is a lack of CNV studies on chickens using NGS. Therefore, we obtained whole-genome sequencing data of 65 chickens including Red Jungle Fowl, Cornish (broiler), Rhode Island Red (hybrid), and White Leghorn (layer) from the public databases for CNV region (CNVR) detection. Using CNVnator, a read-depth based software, a total of 663 domesticated-specific CNVRs were identified across autosomes. Gene ontology analysis of genes annotated in CNVRs showed that mainly enriched terms involved in organ development, metabolism, and immune regulation. Population analysis revealed that CN and RIR are closer to each other than WL, and many genes (LOC772271, OR52R1, RD3, ADH6, TLR2B, PRSS2, TPK1, POPDC3, etc.) with different copy numbers between breeds found. In conclusion, this study has helped to understand the genetic characteristics of domestic chickens at CNV level, which may provide useful information for the development of breeding systems in chickens.