Association of IGF1 and KDM5A polymorphisms with performance, fatness and carcass traits in chickens

Co-expression analysis of long non-coding RNAs and mRNAs involved in intramuscular fat deposition in Muchuan black-bone chicken

The intramuscular fat (IMF) content in meat products is positively correlated with meat quality, making it an important consumer trait. Long non-coding RNAs (lncRNAs) play central roles in regulating various biological processes, but little is currently known about the mechanisms by which they regulate IMF deposition in chickens. This study sampled the breast muscles of chickens with high (H) and low (L) IMF content and constructed six small RNA libraries. High-throughput sequencing technology was used to profile the breast muscle transcriptome (lncRNA and mRNA) and to identify the differentially expressed lncRNAs (DELs) and mRNAs (DEGs) between the H and L groups. In total, 263 DELs (118 up-regulated and 145 down-regulated lncRNAs) and 443 DEGs (203 up-regulated and 240 down-regulated genes) were identified between the two groups. To analyse the DELs-DEGs interaction network, co-expression analysis was conducted to identify lncRNA-mRNA pairs. In total, 19,270 lncRNA/mRNA pairs were identified, including 16,398 significant correlation pairs that presented as positive and 2872 pairs that presented as negative. The lncRNA-mRNA network comprised 263 lncRNA nodes and 440 mRNA nodes. Pathway analysis, using the Kyoto Encyclopedia of Genes and Genomes, indicated that pathways associated with fat deposition and lipid metabolism such as the MAPK, PPAR, GnRH, ErbB and calcium signalling pathways, fatty acid elongation and fatty acid metabolism. Overall, the study identified potential candidate lncRNAs, genes and regulatory networks associated with chicken IMF deposition. These findings provide new insights to help clarify the regulatory mechanisms of IMF deposition in chickens which can be used to improve the IMF content in poultry.

Performance, Blood Lipid Profile, and the Expression of Growth Hormone Receptor (GHR) and Insulin-like Growth Factor-1 (IGF-1) Genes in Purebred and Crossbred Quail Lines

The aim was to evaluate the performance, blood lipid profile, and the relative expression of growth-related genes in purebred white and brown quail lines and their crossbred lines. A total of 240 one-day-old Japanese quail chicks of white and brown line, their crossbred line (WBQ: male white × female brown), and reciprocal crossbred line (BWQ: male brown × female white) were divided into four equal groups (60 birds each). The white quail line showed significantly higher final body weight, daily gain, and feed intake compared with the other quail lines (p < 0.001). Meanwhile, both crossbred quail lines (WBQ and BWQ) showed significantly lower FCR compared with both purebred quail lines (p = 0.001). Both crossbred quail lines showed greater dressing percentages compared with both purebred quail lines (p = 0.038). The brown quail line showed significantly (p = 0.05) higher levels of serum triglycerides and VLDL compared with the white and BWQ lines. The WBQ crossbred line exhibited significantly higher mRNA expression of GHR and IGF-1 genes compared with other quail lines (p < 0.001). Both crossbred lines (WBQ and BWQ) exhibited negative heterosis percentages for body weight (−4.39 and −3.90%, respectively) and feed intake (−10.87 and −14.59%, respectively). Meanwhile, heterosis percentages for FCR (−6.46 and −9.25%, respectively) and dressing percentage (7.54 and 6.38%, respectively) were improved in both crossbred lines. The WBQ line showed high heterosis percentages for the expression of GHR and IGF-1 genes (52.28 and 88.81%, respectively). In conclusion, the WBQ line exhibited significantly greater dressing percentage and better FCR, as well as higher mRNA expression of GHR and IGF-1 genes. These results may be helpful to improve breeding programs and to develop commercial lines of meat-type Japanese quail.

Beneficial impact of dietary methyl methionine sulfonium chloride and/or L-carnitine supplementation on growth performance, feed efficiency, and serum biochemical parameters in broiler chicken: role of IGF-1 and MSTN genes

The purpose of this study was to examine the effect of dietary supplementation with methyl methionine sulfonium chloride (MMSC), and L-carnitine (L-CAR) alone or in combination on the growth performance of broilers through their impact on the expression of IGF-1 and MSTN genes associated with growth in broilers. One-day-old female Ross 308 broiler chicks were allocated into four groups, each of which received a broiler starter diet and water daily ad libitum. The control group (group 1) was given drinking water without any additives. Group 2 received 0.25 g L-carnitine per liter of drinking water, group 3 received 0.25 g MMSC per liter of drinking water, and group 4 received 0.25 g of both L-carnitine and MMSC per liter of drinking water. Birds were given a starter diet to 21 days after which they received a broiler grower diet to 35 days when the experiment ended. There were five replicate groups of 12 birds per treatment. Body weights and feed intake were recorded weekly. Compared to the control group of birds, supplementation with MMSC either alone or in combination with L-carnitine resulted in an increase in growth rate or feed utilization efficiency; L-carnitine by itself had no effect. MMSC supplementation, again either alone or in combination with L-carnitine, increased jejunal and ileal villi height, increased serum total proteins and globulins, downregulated myostatin (MSTN) mRNA, and upregulated insulin growth factor-1 (IGF-1) mRNA expression. Supplementation with L-carnitine alone showed none of these effects. We conclude that MMSC supplementation improved growth performance through the upregulation of IGF-1 mRNA expression and downregulation of MSTN mRNA expression.

TSG Targeting KDM5A Affects Osteogenic Differentiation of Bone Mesenchymal Stem Cells Induced by Bone Morphogenetic Protein 2

Objectives. To investigate the effect of 2,3,5,4′-tetrahydroxystilbene-2-O-β-D-glucoside (TSG) on the osteogenic differentiation of bone marrow mesenchymal stem cells (BMSCs) and its molecular mechanism. Methods. After TSG treatment of rBMSCs, alkaline phosphatase (ALP) activity was compared between the drug treatment group and the control group. The effects of TSG on alkaline phosphatase positive cloning and mineralized nodule formation were also detected. Total mRNA and protein were extracted, and the effects of TSG on the expression levels of osteopontin (OPN), osteocalcin (OCN), Runt-related transcription factor 2 (Runx2), Osterix, and Col1a1 were detected by real-time fluorescence quantitative PCR. Western blotting was used to detect the inhibitory effect of TSG on KDM5A. BMSCs were transfected with small interfering RNA (siRNA) targeting KDM5A (si-KMD5A) and pcDNA3.1 KMD5A. Results. TSG significantly increased the activity of ALP, the number of alkaline phosphatase clones, and calcified nodule formation. The OPN, OCN, Runx2, and Osterix expression levels were significantly increased among the osteoblasts after TSG treatment. A mechanistic study showed that the effect of TSG is realized by inhibiting KDM5A. Conclusions. KDM5A signaling may be involved in the regulation of osteogenic differentiation of rBMSCs. TSG can promote osteogenic differentiation and maturation of rBMSCs at 0.1–50 μmol/L. The mechanism of action was realized by inhibiting the expression of KDM5A.

A Missense Mutation in the MYBPH Gene Is Associated With Abdominal Fat Traits in Meat-Type Chickens

Chicken is an important source of protein for human nutrition and a model system for growth and developmental biology. Although the genetic architecture of quantitative traits in meat-type chickens has been the subject of ongoing investigation, the identification of mutations associated with carcass traits of economic interest remains challenging. Therefore, our aim was to identify predicted deleterious mutation, which potentially affects protein function, and test if they were associated with carcass traits in chickens. For that, we performed a genome-wide association analysis (GWAS) for breast, thigh and drumstick traits in meat-type chickens and detected 19 unique quantitative trait loci (QTL). We then used: (1) the identified windows; (2) QTL for abdominal fat detected in a previous study with the same population and (3) previously obtained whole genome sequence data, to identify 18 predicted deleterious single nucleotide polymorphisms (SNPs) in those QTL for further association with breast, thigh, drumstick and abdominal fat traits. Using the additive model, a predicted deleterious SNP c.482C > T (SIFT score of 0.4) was associated (p-value < 0.05) with abdominal fat weight and percentage. This SNP is in the second exon of the MYBPH gene, and its allele frequency deviates from Hardy–Weinberg equilibrium. In conclusion, our study provides evidence that the c.482C > T SNP in the MYBPH gene is a putative causal mutation for fat deposition in meat-type chickens.

Association of growth hormone and insulin-like growth factor I genotype with body weight, dominance of body weight, and mRNA expression in Korat slow-growing chickens

Objective

Growth hormone (GH) and insulin-like growth factor I (IGF-I) play a critical role in animal growth rates. We aimed to investigate the effect of GH and IGF-I genotypes on body weight (BW), dominance, and gene expression in slow-growing chickens at different ages.

Methods

A total of 613 Korat chickens (KRs) were bred and divided into three groups by genotype – A1A1, A1A3, and A3A3 for GH and AA, AC, and CC for IGF-I. Chickens were weighed every two weeks, and liver and breast muscle tissues were collected at 10 weeks of age. Genetic parameters of KRs were estimated using ASReml software. The GH and IGF-I mRNA levels were measured by quantitative polymerase chain reaction. Significant differences between traits were analyzed using the generalized linear model.

Results

A significant effect of GH genotypes on BW was found at most ages, and the A1A1 genotype had the highest value of BW. Compared with the A3A3 genotype, the A1A1 and A1A3 genotypes showed a higher dominance effect at 0 and 2 weeks, and genotype A1A1 had the highest value of dominance at 8 weeks of age. A difference in GH mRNA levels between genotypes was detected in breast muscle at 6 weeks and in the liver tissue at 2 weeks. In the case of IGF-I gene, the AA genotype had the highest BW at the beginning of life. Significant differences in BW dominance were found at 2 weeks. However, IGF-I mRNA levels were not different among genotypes in both breast muscles and liver tissues.

Conclusion

Our results revealed that GH and IGF-I influence growth, but may not be involved in heterosis. GH can be used as a marker gene in selection programs for growth because the homozygous genotype (A1A1) had the highest BW at all ages. The IGF-I is not a useful marker gene for selection programs.

Genome-wide association scan for QTL and their positional candidate genes associated with internal organ traits in chickens

Background

Poultry breeding programs have been focused on improvement of growth and carcass traits, however, this has resulted in correlated changes in internal organ weights and increased incidence of metabolic disorders. These disorders can affect feed efficiency or even cause death. We used a high density SNP array (600 K, Affymetrix) to estimate genomic heritability, perform genome-wide association analysis, and identify genomic regions and positional candidate genes (PCGs) associated with internal organ traits in an F2 chicken population. We integrated knowledge of haplotype blocks, selection signature regions and sequencing data to refine the list of PCGs.

Results

Estimated genomic heritability for internal organ traits in chickens ranged from low (LUNGWT, 0.06) to high (GIZZWT, 0.45). A total of 20 unique 1 Mb windows identified on GGA1, 2, 4, 7, 12, 15, 18, 19, 21, 27 and 28 were significantly associated with intestine length, and weights or percentages of liver, gizzard or lungs. Within these windows, 14 PCGs were identified based on their biological functions: TNFSF11, GTF2F2, SPERT, KCTD4, HTR2A, RB1, PCDH7, LCORL, LDB2, NR4A2, GPD2, PTPN11, ITGB4 and SLC6A4. From those genes, two were located within haplotype blocks and three overlapped with selection signature regions. A total of 13,748 annotated sequence SNPs were in the 14 PCGs, including 156 SNPs in coding regions (124 synonymous, 26 non-synonymous, and 6 splice variants). Seven deleterious SNPs were identified in TNFSF11, NR4A2 or ITGB4 genes.

Conclusions

The results from this study provide novel insights to understand the genetic architecture of internal organ traits in chickens. The QTL detection performed using a high density SNP array covered the whole genome allowing the discovery of novel QTL associated with organ traits. We identified PCGs within the QTL involved in biological processes that may regulate internal organ growth and development. Potential functional genetic variations were identified generating crucial information that, after validation, might be used in poultry breeding programs to reduce the occurrence of metabolic disorders.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-6040-3) contains supplementary material, which is available to authorized users.

Across-breed validation study confirms and identifies new loci associated with sexual precocity in Brahman and Nellore cattle

The aim of this study was to identify candidate regions associated with sexual precocity in Bos indicus. Nellore and Brahman were set as validation and discovery populations, respectively. SNP selected in Brahman to validate in Nellore were from gene regions affecting reproductive traits (G1) and significant SNP (p ≤ 10^-3 ) from a meta-analysis (G2). In the validation population, early pregnancy (EP) and scrotal circumference (SC) were evaluated. To perform GWAS in validation population, we used regression and Bayes C. SNP with p ≤ 10^-3 in regression and Bayes factor ≥3 in Bayes C were deemed significant. Significant SNP (for EP or SC) or SNP in their ±250 Kb vicinity region, which were in at least one discovery set (G1 or G2), were considered validated. SNP identified in both G1 and G2 were considered candidate. For EP, 145 SNP were validated in G1 and 41 in G2, and for SC, these numbers were 14 and 2. For EP, 21 candidate SNP were detected (G1 and G2). For SC, no candidate SNP were identified. Validated SNP and their vicinity region were located close to quantitative trait loci or genes related to reproductive traits and were enriched in gene ontology terms related to reproductive success. These are therefore strong candidate regions for sexual precocity in Nellore and Brahman.

IGF2 enhanced the osteo-/dentinogenic and neurogenic differentiation potentials of stem cells from apical papilla

OBJECTIVES

In dental tissue engineering, niche is important for maintaining stem cell function and regenerating the dental tissues. However, there is limited knowledge for the growth factors in niche to maintain the function of stem cells. In this study, we investigated the effect of IGF2, a growth factor in stem cells from apical papilla (SCAPs) niche, on differentiation and proliferation potentials of SCAPs.

MATERIALS AND METHODS

Recombinant human IGF2 protein (rhIGF2) was used. Cell counting kit-8 assay, Carboxyfluorescein succinimidyl ester assay, alkaline phosphatase (ALP) activity, Alizarin Red staining, quantitative calcium analysis, immunofluorescence staining and real-time RT-PCR were performed to investigate the cell proliferation and differentiation potentials of SCAPs. And proteomic analysis was used to identify the differential secreted proteins.

RESULTS

By ALP activity assay, we found that 5 ng/mL rhIGF2 might be the optimal concentration for treatment. Then, Alizarin Red staining, quantitative calcium analysis and osteogenesis-related gene expression results showed that 5 ng/mL rhIGF2 could enhance the osteo-/dentinogenic differentiation potentials in SCAPs. Immunofluorescence staining and real-time RT-PCR results showed that neurogenic markers were significantly induced by 5 ng/mL rhIGF2 in SCAPs. Then, CCK-8 assay and CFSE assay results showed that 5 ng/mL rhIGF2 could enhance the cell proliferation in SCAPs. Furthermore, proteomic analysis showed that IGF2 could induce some secreted proteins which function related to the osteogenesis, neurogenesis and cell proliferation.

CONCLUSIONS

Our results identified that IGF2 might be the potential mediator in niche to promote SCAP function and dental tissue regeneration.

Oral administration of Lactobacillus reuteri expressing a 3D8 single-chain variable fragment (scFv) enhances chicken growth and conserves immune homeostasis

The present study was aimed to investigate the effects of 3D8 scFv-secreting Probiotic Lactobacillus reuteri (L. reuteri) on growth performance, inflammatory responses, and intestinal microbial flora in chickens. To this end, a total of 14 healthy wild-type chickens were divided into two experimental groups. Each group was orally administrated with a daily dose of 10⁹ colony-forming units (CFU) of 3D8 scFv-producing L. reuteri or wild-type (WT) for 35 days. Administration of L. reuteri/3D8 scFv significantly improved the body weight of chickens when compared to L. reuteri/WT group. The bacterial taxonomic composition of the fecal microbiota was determined by pyrosequencing of 16S rRNA gene amplicons. Firmicutes, Actinobacteria, and Proteobacteria were dominant phyla in two experimental groups. However, in 3D8 L. reuteri treatment groups at genus level, the Lactobacillus was highly abundant, being represented by 18.12%. In addition, serum levels of primary cytokines such as IL-6, IL-8, TNF-α, IFN-γ, IL-4, and IGF1 were markedly reduced in the probiotic L. reuteri 3D8 group. In summary, our results indicate that the administration of L. reuteri expressing 3D8 scFv has a modulatory effect on inflammatory responses, improves weight gain while not affecting the common microbial composition of the chicken intestine.

Genome-wide association studies targeting the yield of extraembryonic fluid and production traits in Russian White chickens

Background

The Russian White is a gene pool breed, registered in 1953 after crossing White Leghorns with local populations and, for 50 years, selected for cold tolerance and high egg production (EL). The breed has great potential in meeting demands of local food producers, commercial farmers and biotechnology sector of specific pathogen-free (SPF) eggs, the former valuing the breed for its egg weight (EW), EL, age at first egg (AFE), body weight (BW), and the latter for its yield of extraembryonic fluid (YEF) in 12.5-day embryos, ratio of extraembryonic fluid to egg weight, and embryo mass. Moreover, its cold tolerance has been presumably associated with day-old chick down colour (DOCDC) – white rather than yellow, the genetic basis of these traits being however poorly understood.

Results

We undertook genome-wide association studies (GWASs) for eight performance traits using single nucleotide polymorphism (SNP) genotyping of 146 birds and an Illumina 60KBeadChip. Several suggestive associations (p < 5.16*10^− 5) were found for YEF, AFE, BW and EW. Moreover, on chromosome 2, an association with the white DOCDC was found where there is an linkage disequilibrium block of SNPs including genes that are responsible not for colour, but for immune resistance.

Conclusions

The obtained GWAS data can be used to explore the genetics of immunity and carry out selection for increasing YEF for SPF eggs production.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5605-5) contains supplementary material, which is available to authorized users.

Integration of genome wide association studies and whole genome sequencing provides novel insights into fat deposition in chicken

Excessive fat deposition is a negative factor for poultry production because it reduces feed efficiency, increases the cost of meat production and is a health concern for consumers. We genotyped 497 birds from a Brazilian F₂ Chicken Resource Population, using a high-density SNP array (600 K), to estimate the genomic heritability of fat deposition related traits and to identify genomic regions and positional candidate genes (PCGs) associated with these traits. Selection signature regions, haplotype blocks and SNP data from a previous whole genome sequencing study in the founders of this chicken F2 population were used to refine the list of PCGs and to identify potential causative SNPs. We obtained high genomic heritabilities (0.43-0.56) and identified 22 unique QTLs for abdominal fat and carcass fat content traits. These QTLs harbored 26 PCGs involved in biological processes such as fat cell differentiation, insulin and triglyceride levels, and lipid biosynthetic process. Three of these 26 PCGs were located within haplotype blocks there were associated with fat traits, five overlapped with selection signature regions, and 12 contained predicted deleterious variants. The identified QTLs, PCGs and potentially causative SNPs provide new insights into the genetic control of fat deposition and can lead to improved accuracy of selection to reduce excessive fat deposition in chickens.

Insulinlike Growth Factor 1 Gene Variation in Vertebrates

IGF1-a small, single-chain, secreted peptide in mammals-is essential for normal somatic growth and is involved in a variety of other physiological and pathophysiological processes. IGF1 expression appears to be controlled by several different signaling mechanisms in mammals, with GH playing a key role by activating an inducible transcriptional pathway via the Jak2 protein kinase and the Stat5b transcription factor. Here, to understand aspects of Igf1 gene regulation over a substantially longer timeline than is discernible in mammals, Igf1 genes have been examined in 21 different nonmammalian vertebrates representing five different classes and ranging over ∼500 million years of evolutionary history. Parts of vertebrate Igf1 genes resemble components found in mammals. Conserved exons encoding the mature IGF1 protein are detected in all 21 species studied and are separated by a large intron, as seen in mammals; the single promoter contains putative regulatory elements that are similar to those functionally mapped in human IGF1 promoter 1. In contrast, GH-activated Stat5b-binding enhancers found in mammalian IGF1 loci are completely absent, there is no homolog of promoter 2 or exon 2 in any nonmammalian vertebrate, and different types of "extra" exons not present in mammals are found in birds, reptiles, and teleosts. These data collectively define properties of Igf1 genes and IGF1 proteins that were likely present in the earliest vertebrates and support the contention that common structural and regulatory features in Igf1 genes have a long evolutionary history.

Association of growth rate with hormone levels and myogenic gene expression profile in broilers

Background

The growth rate often varies among individual broilers of the same breed under a common management condition. To investigate whether a variation in the growth rate is associated with a difference in hormone levels and myogenic gene expression profile in broilers, a feeding trial was conducted with 10,000 newly hatched Ross 308 chicks in a commercial production facility under standard management. At 38 d of age, 30 fast-, 30 medium-, and 30 slow-growing broilers were selected among 600 healthy male individuals. The levels of insulin-like growth factor-1 (IGF-1), triiodothyronine (T3), thyroxine (T4), and growth hormone in the serum or breast muscle were assayed by ELISA or RIA kits, and the expression levels of several representative pro- and anti-myogenic genes in the breast muscle were also measured by real-time PCR.

Results

Results showed that both absolute and relative weights of the breast muscle were in linear positive correlations with the body weight of broilers (P < 0.001). Fast-growing broilers had higher concentrations of IGF-1 than slow-growing broilers (P < 0.05) in both the serum and breast muscle. The serum concentration of T3 was significantly higher in fast-growing birds than in slow-growing birds (P < 0.05). However, no difference was observed in growth hormone or T4 concentration among three groups of birds. Additionally, a decreased expression of an anti-myogenic gene (myostatin) and increased expressions of pro-myogenic genes such as myogenic differentiation factor 1, myogenin, muscle regulatory factor 4, myogenic factor 5, IGF-1, and myocyte enhancer factor 2B, C, and D were observed in fast-growing broilers (P < 0.05), relative to slow-growing broilers.

Conclusions

Collectively, these findings suggested that the growth rate is linked to the hormone and myogenic gene expression levels in broiler chickens. Some of these parameters such as serum concentrations of IGF-1 and T3 could be employed to breed for enhanced growth.

Association of a Cac8I polymorphism in the IGF1 gene with growth traits in Indian goats

The Insulin-like Growth Factor 1 (IGF1) gene is a member of somatotropic axis and plays a key role in proliferation of cells, mitosis, myogenesis, meiosis, differentiation in foetal development and post natal growth. The objectives of this study were to verify the single nucleotide polymorphisms (SNPs) in IGF1 gene and their association with growth traits in two indigenous native goat genetic groups of Kerala, viz., Malabari and Attappady Black. A total of 277 goats were genotyped using a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) using the restriction enzyme Cac8I. One SNP, A224G was detected in the 5′ non-coding region of the IGF1 gene, and accordingly two genotypes were revealed, GG and AG. This SNP was significantly associated with growth traits in Attappady Black goats, which is maintained as meat breed in Kerala. Results from this study demonstrated higher performance of GG animals for growth traits. The association of IGF1 gene with these traits emphasizes the importance of caprine IGF1 as a candidate gene for growth traits in goat breeding.

Genome-wide association study for performance traits in chickens using genotype by sequencing approach

Performance traits are economically important and are targets for selection in breeding programs, especially in the poultry industry. To identify regions on the chicken genome associated with performance traits, different genomic approaches have been applied in the last years. The aim of this study was the application of CornellGBS approach (134,528 SNPs generated from a PstI restriction enzyme) on Genome-Wide Association Studies (GWAS) in an outbred F₂ chicken population. We have validated 91.7% of these 134,528 SNPs after imputation of missed genotypes. Out of those, 20 SNPs were associated with feed conversion, one was associated with body weight at 35 days of age (P < 7.86E-07) and 93 were suggestively associated with a variety of performance traits (P < 1.57E-05). The majority of these SNPs (86.2%) overlapped with previously mapped QTL for the same performance traits and some of the SNPs also showed novel potential QTL regions. The results obtained in this study suggests future searches for candidate genes and QTL refinements as well as potential use of the SNPs described here in breeding programs.

An ultra-high density linkage map and QTL mapping for sex and growth-related traits of common carp (Cyprinus carpio)

High density genetic linkage maps are essential for QTL fine mapping, comparative genomics and high quality genome sequence assembly. In this study, we constructed a high-density and high-resolution genetic linkage map with 28,194 SNP markers on 14,146 distinct loci for common carp based on high-throughput genotyping with the carp 250 K single nucleotide polymorphism (SNP) array in a mapping family. The genetic length of the consensus map was 10,595.94 cM with an average locus interval of 0.75 cM and an average marker interval of 0.38 cM. Comparative genomic analysis revealed high level of conserved syntenies between common carp and the closely related model species zebrafish and medaka. The genome scaffolds were anchored to the high-density linkage map, spanning 1,357 Mb of common carp reference genome. QTL mapping and association analysis identified 22 QTLs for growth-related traits and 7 QTLs for sex dimorphism. Candidate genes underlying growth-related traits were identified, including important regulators such as KISS2, IGF1, SMTLB, NPFFR1 and CPE. Candidate genes associated with sex dimorphism were also identified including 3KSR and DMRT2b. The high-density and high-resolution genetic linkage map provides an important tool for QTL fine mapping and positional cloning of economically important traits, and improving common carp genome assembly.

Quantitative trait loci identified for blood chemistry components of an advanced intercross line of chickens under heat stress

BACKGROUND

Heat stress in poultry results in considerable economic losses and is a concern for both animal health and welfare. Physiological changes occur during periods of heat stress, including changes in blood chemistry components. A highly advanced intercross line, created from a broiler (heat susceptible) by Fayoumi (heat resistant) cross, was exposed to daily heat cycles for seven days starting at 22 days of age. Blood components measured pre-heat treatment and on the seventh day of heat treatment included pH, pCO2, pO2, base excess, HCO3, TCO2, K, Na, ionized Ca, hematocrit, hemoglobin, sO2, and glucose. A genome-wide association study (GWAS) for these traits and their calculated changes was conducted to identify quantitative trait loci (QTL) using a 600 K SNP panel.

RESULTS

There were significant increases in pH, base excess, HCO3, TCO2, ionized Ca, hematocrit, hemoglobin, and sO2, and significant decreases in pCO2 and glucose after 7 days of heat treatment. Heritabilities ranged from 0.01-0.21 for pre-heat measurements, 0.01-0.23 for measurements taken during heat, and 0.00-0.10 for the calculated change due to heat treatment. All blood components were highly correlated within measurement days, but not correlated between measurement days. The GWAS revealed 61 QTL for all traits, located on GGA (Gallus gallus chromosome) 1, 3, 6, 9, 10, 12-14, 17, 18, 21-28, and Z. A functional analysis of the genes in these QTL regions identified the Angiopoietin pathway as significant. The QTL that co-localized for three or more traits were on GGA10, 22, 26, 28, and Z and revealed candidate genes for birds' response to heat stress.

CONCLUSIONS

The results of this study contribute to our knowledge of levels and heritabilities of several blood components of chickens under thermoneutral and heat stress conditions. Most components responded to heat treatment. Mapped QTL may serve as markers for genomic selection to enhance heat tolerance in poultry. The Angiopoietin pathway is likely involved in the response to heat stress in chickens. Several candidate genes were identified, giving additional insight into potential mechanisms of physiologic response to high ambient temperatures.

Association of Chicken Growth Hormones and Insulin-like Growth Factor Gene Polymorphisms with Growth Performance and Carcass Traits in Thai Broilers

Molecular marker selection has been an acceptable tool in the acceleration of the genetic response of desired traits to improve production performance in chickens. The crossbreds from commercial parent stock (PS) broilers with four Thai synthetic breeds; Kaen Thong (KT), Khai Mook Esarn (KM), Soi Nin (SN), and Soi Pet (SP) were used to study the association among chicken growth hormones (cGH) and the insulin-like growth factor (IGF-I) genes for growth and carcass traits; for the purpose of developing a suitable terminal breeding program for Thai broilers. A total of 408 chickens of four Thai broiler lines were genotyped, using polymerase chain reaction-restriction fragment length polymorphism methods. The cGH gene was significantly associated with body weight at hatching; at 4, 6, 8, 10 weeks of age and with average daily gain (ADG); during 2 to 4, 4 to 6, 0 to 6, 0 to 8, and 0 to 10 weeks of age in PS×KM chickens. For PS×KT populations, cGH gene showed significant association with body weight at hatching, and ADG; during 8 to 10 weeks of age. The single nucleotide polymorphism variant confirmed that allele G has positive effects for body weight and ADG. Within carcass traits, cGH revealed a tentative association within the dressing percentage. For the IGF-I gene polymorphism, there were significant associations with body weight at hatching; at 2, 4, and 6 weeks of age and ADG; during 0 to 2, 4 to 6, and 0 to 6 weeks of age; in all of four Thai broiler populations. There were tentative associations of the IGF-I gene within the percentages of breast muscles and wings. Thus, cGH gene may be used as a candidate gene, to improve growth traits of Thai broilers.