Integrative analysis of long non-coding RNA and mRNA in broilers with valgus-varus deformity

Tang, Hehe; Guo, Yaping; Zhang, Zhenzhen; Li, Zhuanjian; Zhang, Yanhua; Li, Yuanfang; Kang, Xiangtao; Han, Ruili

doi:10.1371/journal.pone.0239450

Cited by 12 publications

(8 citation statements)

References 52 publications

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“…The Hubbard broilers population was described by Guo et al [20]Tang et al [39]. In detail, Hubbard broiler breeds for the commodity generation were reared at a commercial farm in the same environment and feeding management, free access to food and water.…”

Section: Laboratory Animals and Data Collectionmentioning

confidence: 99%

WITHDRAWN: Identification and Genetic Analysis of Major Gene ST3GAL4 Related to Serum Alkaline Phosphatase in Chickens

Tang

et al. 2021

Preprint

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Background: An increasing number of studies have explored disease and growth traits through quantitative trait locus (QTLs) in chickens. Nevertheless, the pathogenic genes underlying the QTL effects remain poorly understood. Alkaline phosphatase (ALP) is a marker of osteoblast maturation and an important indicator of bone metabolism. The change of ALP can reflect the bone metabolism and growth traits of animals to a certain extent. Results: In this study, we identified a SNP site at ST3GAL4 that found by genome-wide association studies (GWAS) in previous studies, and found another 8 SNPs by DNA sequencing. Interestingly, there are 4 SNPs rs475471G>A, rs475533C>T, rs475621A>G, rs475647C>A were completely linked by haplotype analysis, and selected a tag SNP rs475471G>A to analyze the correlation between this SNP and ALP level in Hubbard leg disease population and an F2 chicken resource population produced by Anka and Gushi chickens, and carried out population genetic analysis in 18 chicken breeds. Association analysis showed that this QTL within ST3GAL4 were highly correlated with ALP level, the mutant individuals with genotype AA had the highest ALP level, followed by GA and GG genotypes. The mutant individuals with genotype AA and GA genotype had higher values for body weight (BW), chest width (CW), body slanting length (BSL), pelvis width (PW) at 4-week, the semi-evisceration weight (SEW), evisceration weight (EW) and Leg weight (LW) of AA and GA genotype also higher. The amplification and typing of 4,852 DNA samples from 18 different breeds and the result shown GG genotype mainly existed in egg-type chickens and dual-type chickens, while AA genotype mainly distributed in commercial broilers and F2 resource population. The individuals of AA genotype had the highest ALP and showed better growth performance. This is the first time to report the causal variant of ST3GAL4 gene that located at chromosome 24 related to chicken serum ALP level. Besides, tissue expression analysis used Cobb broiler showed that there were significant differences between different genotypes in spleen and duodenum.Conclusions: This study the first time to determine 9 SNPs within ST3GAL4 were related to ALP in chickens, 4 of them were complete linkage sequence variants, which provide useful information on the mutation of ST3GAL4 and could predict the serum ALP level of chicken early and effectively as a potential molecular breeding marker.

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Section: Laboratory Animals and Data Collectionmentioning

confidence: 99%

WITHDRAWN: Identification and Genetic Analysis of Major Gene ST3GAL4 Related to Serum Alkaline Phosphatase in Chickens

Tang

et al. 2021

Preprint

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“…Leg diseases affect poultry athletic ability, causing lameness and paralysis, and limiting further improvement in poultry performance and the quality of related meat products [ 1 , 2 ]. The improvement of intensive farming and management technology has promoted the muscle growth rate of broilers [ 3 ]. However, excessive muscle growth in broilers results in the inability of broiler leg bones to support body weight, and the problem of leg diseases is becoming increasingly prominent [ 4 ].…”

Section: Introductionmentioning

confidence: 99%

“…It is estimated that approximately 12.5 billion poultry worldwide suffer from various leg injuries each year [ 5 ]. There are several common bone diseases in the poultry industry, including tibial dyschondroplasia (TD), valgus–varus deformity (VVD), femoral head necrosis (FHN), and bacterial chondronecrosis with osteomyelitis (BCO) [ 2 , 3 , 6 , 7 , 8 ]. In the UK, around 27% of morbid broilers have dyskinesia, and 3.3% of them cannot move [ 9 ].…”

Section: Introductionmentioning

confidence: 99%

“…Various approaches have been found to prevent and treat leg diseases in broilers. Several studies found that long-term breeding for leg health can reduce the incidence of leg diseases, although it has a certain impact on body weight [ 3 , 16 , 21 ]. People provide a suitable breeding environment for broilers by strengthening the regulation of environmental indicators such as temperature, air quality, lighting program, stock density, and litter, which is an important measure to alleviate the occurrence and development of broiler leg diseases [ 19 , 22 ].…”

Section: Introductionmentioning

confidence: 99%

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Effects of Probiotics and Gut Microbiota on Bone Metabolism in Chickens: A Review

Chen

Zhang

et al. 2022

Metabolites

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Broiler leg diseases are a common abnormal bone metabolism issue that leads to poor leg health in growing poultry. Bone metabolism is a complicated regulatory process controlled by genetic, nutritional, feeding management, environmental, or other influencing factors. The gut microbiota constitutes the largest micro-ecosystem in animals and is closely related to many metabolic disorders, including bone disease, by affecting the absorption of nutrients and the barrier function of the gastrointestinal tract and regulating the immune system and even the brain–gut–bone axis. Recently, probiotic-based dietary supplementation has emerged as an emerging strategy to improve bone health in chickens by regulating bone metabolism based on the gut–bone axis. This review aims to summarize the regulatory mechanisms of probiotics in the gut microbiota on bone metabolism and to provide new insights for the prevention and treatment of bone diseases in broiler chickens.

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“…Up to now, the precise etiology and pathogenesis of VVD still remain uncertain [3]. The incidence of VVD has been reduced effectively by genetic selection in the UK [10]. The heritability or pseudo heritability of leg disorders range from 0.10 to 0.40 [11,12].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association study identifies SNPs for growth performance and serum indicators in Valgus-varus deformity broilers (Gallus gallus) using ddGBS sequencing

et al. 2022

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Background Valgus-varus deformity (VVD) is a lateral or middle deviation of the tibiotarsus or tarsometatarsus, which is associated with compromised growth, worse bone quality and abnormal changes in serum indicators in broilers. To investigate the genetic basis of VVD, a genome wide association study (GWAS) was performed to identify candidate genes and pathways that are responsible for VVD leg disease, serum indicators and growth performance in broilers. Results In total, VVD phenotype, seven serum indicators and three growth traits were measured for 126 VVD broilers (case group) and 122 sound broilers (control group) based on a high throughput genome wide genotyping-by-sequencing (GBS) method. After quality control 233 samples (113 sound broilers and 120 VVD birds) and 256,599 single nucleotide polymorphisms (SNPs) markers were used for further analysis. As a result, a total of 5 SNPs were detected suggestively significantly associated with VVD and 70 candidate genes were identified that included or adjacent to these significant SNPs. In addition, 43 SNPs located on Chr24 (0.22 Mb - 1.79 Mb) were genome-wide significantly associated with serum alkaline phosphatase (ALP) and 38 candidate genes were identified. Functional enrichment analysis showed that these genes are involved in two Gene Ontology (GO) terms related to bone development (cartilage development and cartilage condensation) and two pathways related to skeletal development (Toll−like receptor signaling pathway and p53 signaling pathway). BARX2 (BARX homeobox 2) and Panx3 (Pannexin 3) related to skeleton diseases and bone quality were obtained according to functional analysis. According to the integration of GWAS with transcriptome analysis, HYLS1 (HYLS1 centriolar and ciliogenesis associated) was an important susceptibility gene. Conclusions The results provide some reference for understanding the relationship between metabolic mechanism of ALP and pathogenesis of VVD, which will provide a theoretical basis for disease-resistant breeding of chicken leg soundness.

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Integrative analysis of long non-coding RNA and mRNA in broilers with valgus-varus deformity

Cited by 12 publications

References 52 publications

WITHDRAWN: Identification and Genetic Analysis of Major Gene ST3GAL4 Related to Serum Alkaline Phosphatase in Chickens

WITHDRAWN: Identification and Genetic Analysis of Major Gene ST3GAL4 Related to Serum Alkaline Phosphatase in Chickens

Effects of Probiotics and Gut Microbiota on Bone Metabolism in Chickens: A Review

Genome-wide association study identifies SNPs for growth performance and serum indicators in Valgus-varus deformity broilers (Gallus gallus) using ddGBS sequencing

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