Chenglong Luo

Genome-wide association study identified a narrow chromosome 1 region associated with chicken growth traits.

Chicken growth traits are important economic traits in broilers. A large number of studies are available on finding genetic factors affecting chicken growth. However, most of these studies identified chromosome regions containing putative quantitative trait loci and finding causal mutations is still a challenge. In this genome-wide association study (GWAS), we identified a narrow 1.5 Mb region (173.5–175 Mb) of chicken (Gallus gallus) chromosome (GGA) 1 to be strongly associated with chicken growth using 47,678 SNPs and 489 F2 chickens. The growth traits included aggregate body weight (BW) at 0–90 d of age measured weekly, biweekly average daily gains (ADG) derived from weekly body weight, and breast muscle weight (BMW), leg muscle weight (LMW) and wing weight (WW) at 90 d of age. Five SNPs in the 1.5 Mb KPNA3-FOXO1A region at GGA1 had the highest significant effects for all growth traits in this study, including a SNP at 8.9 Kb upstream of FOXO1A for BW at 22–48 d and 70 d, a SNP at 1.9 Kb downstream of FOXO1A for WW, a SNP at 20.9 Kb downstream of ENSGALG00000022732 for ADG at 29–42 d, a SNP in INTS6 for BW at 90 d, and a SNP in KPNA3 for BMW and LMW. The 1.5 Mb KPNA3-FOXO1A region contained two microRNA genes that could bind to messenger ribonucleic acid (mRNA) of IGF1, FOXO1A and KPNA3. It was further indicated that the 1.5 Mb GGA1 region had the strongest effects on chicken growth during 22–42 d.

Microbial metabolite butyrate facilitates M2 macrophage polarization and function

Metabolites from intestinal microbes modulate the mucosal immune system by regulating the polarization and expansion of T cells. Whether the microbial metabolites influence macrophage polarization, however, is poorly understood. Here, we show that the large bowel microbial fermentation product, butyrate, facilitates M2 macrophage polarization, in vitro and in vivo. The supernatant from butyrate-treated M2 macrophage increased the migration and enhanced the wound closure rate of MLE-12 cells. Butyrate attenuated intestinal inflammation in mice with dextran sulfate sodium (DSS)-induced colitis, with a significant increase in colonic expression of the M2 macrophage-associated protein, Arg1. M2 macrophage treated with butyrate, had increased activation of the H3K9/STAT6 signaling pathway, suggesting a mechanism for butyrate facilitated M2 macrophage polarization. Collectively, our study indicated that commensal microbe-derived butyrate is a novel activator of STAT6-mediated transcription through H3K9 acetylation driving M2 macrophage polarization, and delineated new insights into the immune interplay underlying inflammatory bowel disease.

Genetic dissection of growth traits in a Chinese indigenous × commercial broiler chicken cross

BackgroundIn China, consumers often prefer indigenous broiler chickens over commercial breeds, as they have characteristic meat qualities requested within traditional culinary customs. However, the growth-rate of these indigenous breeds is slower than that of the commercial broilers, which means they have not yet reached their full economic value. Therefore, combining the valuable meat quality of the native chickens with the efficiency of the commercial broilers is of interest. In this study, we generated an F2 intercross between the slow growing native broiler breed, Huiyang Beard chicken, and the fast growing commercial broiler breed, High Quality chicken Line A, and used it to map loci explaining the difference in growth rate between these breeds.ResultsA genome scan to identify main-effect loci affecting 24 growth-related traits revealed nine distinct QTL on six chromosomes. Many QTL were pleiotropic and conformed to the correlation patterns observed between phenotypes. Most of the mapped QTL were found in locations where growth QTL have been reported in other populations, although the effects were greater in this population. A genome scan for pairs of interacting loci identified a number of additional QTL in 10 other genomic regions. The epistatic pairs explained 6–8% of the residual phenotypic variance. Seven of the 10 epistatic QTL mapped in regions containing candidate genes in the ubiquitin mediated proteolysis pathway, suggesting the importance of this pathway in the regulation of growth in this chicken population.ConclusionsThe main-effect QTL detected using a standard one-dimensional genome scan accounted for a significant fraction of the observed phenotypic variance in this population. Furthermore, genes in known pathways present interesting candidates for further exploration. This study has thus located several QTL regions as promising candidates for further study, which will increase our understanding of the genetic mechanisms underlying growth-related traits in chickens.

Polymorphisms of the IGF1R gene and their genetic effects on chicken early growth and carcass traits

BackgroundThe insulin-like growth factor I receptor (IGF1R) has an important effect on growth, carcass, and meat quality traits in many species. However, few studies on associations of the IGF1R gene with growth and carcass traits have been reported in chickens. The objectives of the present study were to study the associations of the IGF1R gene with chicken early growth and carcass traits using a neutral test, variation scan of the gene, genetic diversity, linkage disequilibrium and association analyses.ResultsThe tree generated from the amino acid sequences of 15 species showed that the IGF1R gene was conservative in the whole evolution among the mammalian animals and chickens. In a total of 10,818 bp of sequence, 70 single nucleotide polymorphisms were identified in the chicken IGF1R gene. The allelic and genotypic frequency distribution, genetic diversity and linkage disequilibrium of 18 single nucleotide polymorphisms (SNPs) in the Xinghua and White Recessive Rock chickens showed that six of them were possibly associated with growth traits. Association analyses showed that the A17299834G SNP was significantly associated with chicken carcass body weight, eviscerated weight with giblets, eviscerated weight, body weights at 28, 35, and 56 d of age, leg length at 56 d of age, and daily weight gain at 0–4 weeks. The haplotypes of the A17307750G and A17307494G were associated with early growth traits. The haplotypes of the A17299834G and C17293932T were significantly associated with most of the early growth traits and carcass traits.ConclusionThere were rich polymorphisms in the chicken IGF1R gene. Several SNPs associated with chicken early growth traits and carcass traits were identified in the IGF1R gene by genetic diversity, linkage disequilibrium, and association analyses in the present study.

Genome-wide association study of antibody response to Newcastle disease virus in chicken

BackgroundSince the first outbreak in Indonesia in 1926, Newcastle disease has become one of the most common and contagious bird diseases throughout the world. To date, enhancing host antibody response by vaccination remains the most efficient strategy to control outbreaks of Newcastle disease. Antibody response plays an important role in host resistance to Newcastle disease, and selection for antibody response can effectively improve disease resistance in chickens. However, the molecular basis of the variation in antibody response to Newcastle disease virus (NDV) is not clear. The aim of this study was to detect genes modulating antibody response to NDV by a genome-wide association study (GWAS) in chickens.ResultsTo identify genes or chromosomal regions associated with antibody response to NDV after immunization, a GWAS was performed using 39,833 SNP markers in a chicken F2 resource population derived from a cross between two broiler lines that differed in their resistance. Two SNP effects reached 5% Bonferroni genome-wide significance (P<1.26×10-6). These two SNPs, rs15354805 and rs15355555, were both on chicken (Gallus gallus) chromosome 1 and spanned approximately 600 Kb, from 100.4 Mb to 101.0 Mb. Rs15354805 is in intron 7 of the chicken Roundabout, axon guidance receptor, homolog 2 (ROBO2) gene, and rs15355555 is located about 243 Kb upstream of ROBO2. Rs15354805 explained 5% of the phenotypic variation in antibody response to NDV, post immunization, in chickens. Rs15355555 had a similar effect as rs15354805 because of its linkage disequilibrium with rs15354805 (r2=0.98).ConclusionThe region at about 100 Mb from the proximal end of chicken chromosome 1, including the ROBO1 and ROBO2 genes, has a strong effect on the antibody response to the NDV in chickens. This study paves the way for further research on the host immune response to NDV.

Genetic effects of polymorphisms in candidate genes and the QTL region on chicken age at first egg

BackgroundThe age at first egg (AFE), an important indicator for sexual maturation in female chickens, is controlled by polygenes. Based on our knowledge of reproductive physiology, 6 genes including gonadotrophin releasing hormone-I (GnRH-I), neuropeptide Y (NPY), dopamine D2 receptor (DRD2), vasoactive intestinal polypeptide (VIP), VIP receptor-1 (VIPR-1), and prolactin (PRL), were selected as candidates for influencing AFE. Additionally, the region between ADL0201 and MCW0241 of chromosome Z was chosen as the candidate QTL region according to some QTL databases. The objective of the present study was to investigate the effects of mutations in candidate genes and the QTL region on chicken AFE.ResultsMarker-trait association analysis of 8 mutations in those 6 genes in a Chinese native population found a highly significant association (P < 0.01) between G840327C of the GnRH-I gene with AFE, and it remained significant even with Bonferroni correction. Based on the results of the 2-tailed χ2 test, mutations T32742394C, T32742468C, G32742603A, and C33379782T in the candidate QTL region of chromosome Z were selected for marker-trait association analysis. The haplotypes of T32742394C and T32742468C were significantly associated (P < 0.05) with AFE. Bioinformatics analysis indicated that T32742394C and T32742468C were located in the intron region of the SH3-domain GRB2-like 2 (SH3GL2) gene, which appeared to be associated in the endocytosis and development of the oocyte.ConclusionThis study found that G840327C of the GnRH-I gene and the haplotypes of T32742394C-T32742468C of the SH3GL2 gene were associated with the chicken AFE.

The dopamine D2 receptor gene polymorphisms associated with chicken broodiness

Chicken broodiness is a polygenic trait controlled by autosomal genes. Prolactin gene is a candidate of great interest in molecular studies of broodiness. However, another candidate dopamine D2 receptor (DRD2) gene has not been studied extensively. The objective of this study was to analyze the genetic effects of the DRD2 gene on chicken broodiness through linkage disequilibrium analyses, tag SNP selection, genetic diversity observation, 2-tailed test, and association analyses. In this study, we assayed 27 variations of this gene in 456 individuals from 6 chicken populations to observe linkage disequilibrium pattern, the tag SNP, and genetic diversity. Among the 6 populations, Taihe Silkies exhibited no characteristic between the square of the correlation coefficient of gene frequencies (r(2)) and physical distance. The other populations including Red Jungle Fowls, Xinghua chickens, Ningdu Sanhuang chickens (NDH), Baier Huang chickens, and Leghorn layers exhibited conspicuous characteristic of decreasing r(2) value over physical distance. Linkage disequilibrium decayed more rapidly in Red Jungle Fowls, Xinghua, and NDH than in Baier Huang and Leghorn layers. Allelic frequencies and genotype distributions in the 5 populations showed that A-38600G, I-38463D, T-32751C, A-16105G, A-6543G, C-6539T, and A+2794G were possibly associated with broodiness. Besides the above 7 sites, another 2 sites that might be associated with broodiness were screened by 2-tailed test. All 9 sites were used for association analyses with broodiness in 644 NDH chickens. A significant association (P < 0.05) was found between A-16105G and broody frequency (%), and the T+619C in intron 1 was significantly associated with duration of broodiness (P < 0.05). These findings suggested that the DRD2 gene should be included in future genetic studies of chicken broodiness and 2 SNP of A-16105G and T+619C might be markers for breeding against broodiness.

Effects of the thyroid hormone responsive spot 14α gene on chicken growth and fat traits

The thyroid hormone responsive spot 14alpha (THRSPalpha) gene plays important roles in chicken growth and fat deposition. The aim of this study was to identify new variations in the gene to determine their effects on growth and fat traits in chicken and to observe the effects of the THRSPalpha gene on chicken lipid profile and lipoprotein and glucose and triiodothyronine effects on the THRSPalpha expression in liver and fat cells. Two new variations, namely A197835978G and G197836086A, and a reported 9-bp insertion-deletion (indel) of the THRSPalpha gene were genotyped by single-stranded conformational polymorphism in a Xinghua x White Recessive Rock F(2) full-sib resource population. The results showed that the A197835978G was significantly associated with hatch weight and BW at 28 d of age and breast muscle weight at 90 d of age in chickens (P < 0.05). The G197836086A was significantly associated with cingular fat width (P = 0.0349) and breast muscle crude fat content (P = 0.0349). The indel was significantly associated with abdominal fat weight (P = 0.0445). The above new THRSPalpha polymorphisms were also significantly associated with the total cholesterol and low-density lipoprotein, in which the THRSPalpha GA/AG genotype was associated with lipid and lipoprotein and the THRSPalpha BB indel genotype was significantly associated with liver weight in chicken breeds. The mRNA expression analysis in vivo and in vitro culture studies suggested that the THRSPalpha gene is more responsive to glucose than triiodothyronine. In conclusion, the 3 variations of the chicken THRSPalpha gene were associated with both growth and fat traits in this study. Such effects of the THRSPalpha gene were further supported from the data of observations in association analysis of the gene with phenotypic records and plasma lipid profiles, in the THRSPalpha gene expression in chicken development, and in vivo and in vitro cell culture observation of liver and abdominal fat tissues.

Associations between polymorphisms in the chicken VIP gene, egg production and broody traits

1. In this study, the vasoactive intestinal peptide (VIP) gene was screened for variations by cloning and sequencing to analyse the association with chicken egg production and broodiness traits. 2. Sequencing revealed that 69 polymorphisms were found in a 9305-bp length of the chicken VIP gene, of which 39 were located in introns, 28 in 5′ regulatory region, 1 in exon 6 (synonymous) and 1 in 3′-UTR. The nucleotide diversity corrected for sample size was 1·96 × 10−3. 3. Five polymorphisms, C-3134T, “AGG” indel at −2648 to −2650, C + 338T, G + 780T and A + 4691G, were genotyped in 644 individuals of Ningdu Sanhuang chickens to evaluate their effects on egg production and broodiness traits. Marker-trait association analyses showed that the “AGG” indel was associated with total number of eggs from 90 to 300 d of age and total number of qualified eggs from 90 to 300 d of age. In contrast, C + 338T was associated with duration of broodiness.

SNP mapping of QTL affecting growth and fatness on chicken GGA1

An F2 chicken population was established from a crossbreeding between a Xinghua line and a White Recessive Rock line. A total of 502 F2 chickens in 17 full-sib families from six hatches was obtained, and phenotypic data of 488 individuals were available for analysis. A total of 46 SNP on GGA1 was initially selected based on the average physical distance using the dbSNP database of NCBI. After the polymorphism levels in all F0 individuals (26 individuals) and part of the F1 individuals (22 individuals) were verified, 30 informative SNP were potentially available to genotype all F2 individuals. The linkage map was constructed using Cri-Map. Interval mapping QTL analyses were carried out. QTL for body weight (BW) of 35 d and 42 d, 49 d and 70 d were identified on GGA1 at 351–353 cM and 360 cM, respectively. QTL for abdominal fat weight was on GGA1 at 205 cM, and for abdominal fat rate at 221 cM. Two novel QTL for fat thickness under skin and fat width were detected at 265 cM and 72 cM, respectively.