D. F. Li

A Genome-Wide SNP Scan Reveals Novel Loci for Egg Production and Quality Traits in White Leghorn and Brown-Egg Dwarf Layers

Availability of the complete genome sequence as well as high-density SNP genotyping platforms allows genome-wide association studies (GWAS) in chickens. A high-density SNP array containing 57,636 markers was employed herein to identify associated variants underlying egg production and quality traits within two lines of chickens, i.e., White Leghorn and brown-egg dwarf layers. For each individual, age at first egg (AFE), first egg weight (FEW), and number of eggs (EN) from 21 to 56 weeks of age were recorded, and egg quality traits including egg weight (EW), eggshell weight (ESW), yolk weight (YW), eggshell thickness (EST), eggshell strength (ESS), albumen height(AH) and Haugh unit(HU) were measured at 40 and 60 weeks of age. A total of 385 White Leghorn females and 361 brown-egg dwarf dams were selected to be genotyped. The genome-wide scan revealed 8 SNPs showing genome-wise significant (P<1.51E-06, Bonferroni correction) association with egg production and quality traits under the Fishers combined probability method. Some significant SNPs are located in known genes including GRB14 and GALNT1 that can impact development and function of ovary, but more are located in genes with unclear functions in layers, and need to be studied further. Many chromosome-wise significant SNPs were also detected in this study and some of them are located in previously reported QTL regions. Most of loci detected in this study are novel and the follow-up replication studies may be needed to further confirm the functional significance for these newly identified SNPs.

Copy number variations identified in the chicken using a 60K SNP BeadChip

Copy number variation (CNV) is considered an important genetic variation, contributing to many economically important traits in the chicken. Although CNVs can be detected using a comparative genomic hybridization array, the high-density SNP array has provided an alternative way to identify CNVs in the chicken. In the current study, a chicken 60K SNP BeadChip was used to identify CNVs in two distinct chicken genetic lines (White Leghorn and dwarf) using the PENNCNV program. A total of 209 CNV regions were identified, distributing on chromosomes 1-22 and 24-28 and encompassing 13.55 Mb (1.42%) of chicken autosomal genome area. Three of seven selected CNVs (73.2% individuals) were completely validated by quantitative PCR. To our knowledge, this is the first report in the chicken identifying CNVs using a SNP array. Identification of 190 new identified CNVs illustrates the feasibility of the chicken 60K SNP BeadChip to detect CNVs in the chicken, which lays a solid foundation for future analyses of associations of CNVs with economically important phenotypes in chickens.

Effects of chitosan on growth performance and energy and protein utilisation in broiler chickens

1. Two experiments were conducted to investigate the effects of dietary chitosan on growth performance, energy availability and protein retention in broilers. 2. Experiment 1 was a 42-d growth assay, in which 294 1-d-old male broilers were given one of 7 dietary treatments. A control feed was supplemented with 5 levels of chitosan (0·2, 0·5, 1·0, 3·0 and 5·0u2009g/kg) or 50u2009mg/kg chlortetracycline (CTC). 3. Increasing chitosan inclusion gave a nonlinear increase (Pu2009<u20090·001) in feed conversion efficiency (FCE). Optimal growth and feed conversion were obtained with 0·5–1·0u2009g/kg chitosan. 4. In experiment 2, 42 1-d-old male broilers (6/treatment) were individually housed but fed on the same diets as in experiment 1. Excreta were collected from d 19–21 and d 40–42. 5. The addition of 0·5–1·0u2009g/kg chitosan increased nitrogen retention compared with the control group (Pu2009<u20090·01), while apparent metabolisable energy in the diets was not altered.

A genome-wide SNP scan reveals two loci associated with the chicken resistance to Marek's disease.

Mareks disease (MD) is a neoplastic disease in chickens, caused by the Mareks disease virus (MDV). To investigate host genetic resistance to MD, we conducted a genome-wide association study (GWAS) on 67 MDV-infected chickens based on a case and control design, including 57 susceptible chickens in the case group and 10 resistant chickens as controls. After searching 38xa0655 valid genomic markers, two SNPs were found to be associated with host resistance to MD. One SNP, rs14527240, reaching chromosome-wide significance level (Pxa0<xa00.01) was located in the SPARC-related modular calcium-binding 1 (SMOC1) gene on GGA5. The other one, GGaluGA156129, reaching genome-wide significance (Pxa0<xa00.05), was located in the protein tyrosine phosphatase, non-receptor type 3 (PTPN3) gene on GGA2. In addition, expression patterns of these two genes in spleens were detected by qPCR. The expression of SMOC1 was significantly up-regulated (Pxa0<xa00.05), whereas the expression of PTNP3 did not show significance when the case group was compared with the control group. Up-regulation of SMOC1 in susceptible spleens suggests its important roles in MD tumorigenesis. This is the first study to investigate MD-resistant loci, and it demonstrates the power of GWASs for mapping genes associated with MD resistance.

Effect of stachyose supplementation on growth performance, nutrient digestibility and caecal fermentation characteristics in broilers.

1.u2003The objective of this study was to evaluate whether the oligosaccharide stachyose enhances gastrointestinal tract health by fermentation and proliferation of desirable bacteria species and thus affects growth performance and nutrient digestibility in broilers. 2.u2003A total of 432 1-d-old male Arbor Acres (AA) broilers were randomly allocated to one of 6 treatments, with 12 replicate pens per treatment and 6 birds per pen. Chicks were fed a maize–hamlet protein 300 (HP300) basal diet with 0, 4·0, 8·0, 12·0 or 16·0u2009g/kg stachyose. A sixth diet contained no HP300 but soybean meal (SBM) and provided 8·7u2009g/kg stachyose and 3·1u2009g/kg raffinose. The duration of the study was 42u2009d. 3.u2003Stachyose contents above 12·0u2009g/kg depressed group body weights, average daily gain and feed/gain but not feed intake during the whole experimental period. Broiler growth decreased linearly and quadratically with increasing stachyose content. No differences were detected between diets supplemented with 12·0u2009g/kg stachyose and SBM. 4.u2003Nutrient digestibility tended to decrease but not significantly with increasing stachyose. 5.u2003Stachyose content had no significant positive effects on caecal pH, microflora population and the resulting short-chain fatty acid (SCFA) metabolites during the 42u2009d experiment, with only butyrate differing significantly in the initial period.

Whole-genome scan for signatures of recent selection reveals loci associated with important traits in White Leghorn chickens

Chicken is considered to be an excellent model for genetic studies of phenotypic and genomic evolution, with large effective population size, specialized commercial lines, and strong human-driven selection. High-density chicken SNP chips can help to achieve a better understanding of the selection mechanisms in artificially selected populations. We performed the genome-wide tests for the selection signature in 385 White Leghorn hens and mapped positively selected regions to the genome annotations. Ten QTL related to egg production, egg quality, growth, and disease resistance traits were selected for extended haplotype homozygosity tests to give a brief overview of recent selection signatures in chicken QTL. We also reported 185 candidate genes/CDSs showing top P-values and slower decay of haplotype homozygosities. Some of these genes seemed to have significant effects on important economical traits, and most of them have not been reported in chickens. The current study provides a genome-wide map of linkage disequilibrium extents and distributions and selection footprints in the chicken genome. A panel of genes, including PRL, NCKX1, NRF1, LHX2, and SFRP1 associated with egg production, metabolism traits, and response to illumination were identified. In addition, there were more genes identified that have not yet been reported in chickens, and our results provide new clues for further study.

A genome-wide association study identifies novel single nucleotide polymorphisms associated with dermal shank pigmentation in chickens

Shank color of domestic chickens varies from black to blue, green, yellow, or white, which is controlled by the combination of melanin and xanthophylls in dermis and epidermis. Dermal shank pigmentation of chickens is determined by sex-linked inhibitor of dermal melanin (Id), which is located on the distal end of the long arm of Z chromosome, through controlling dermal melanin pigmentation. Although previous studies have focused on the identification of Id and the linear relationship with barring and recessive white skin, no causal mutations have yet been identified in relation to the mutant dermal pigment inhibiting allele at the Id locus. In this study, we first used the 600K Affymetrix Axiom HD genotyping array, which includes ~580,961 SNP of which 26,642 SNP were on the Z chromosome to perform a genome-wide association study on pure lines of 19 Tibetan hens with dermal pigmentation shank and 21 Tibetan hens with yellow shank to refine the Id location. Association analysis was conducted by the PLINK software using the standard chi-squared test, and then Bonferroni correction was used to adjust multiple testing. The genome-wide study revealed that 3 SNP located at 78.5 to 79.2 Mb on the Z chromosome in the current assembly of chicken genome (galGal4) were significantly associated with dermal shank pigmentation of chickens, but none of them were located in known genes. The interval we refined was partly converged with previous results, suggesting that the Id gene is in or near our refined genome region. However, the genomic context of this region was complex. There were only 15 SNP markers developed by the genotyping array within the interval region, in which only 1 SNP marker passed quality control. Additionally, there were about 5.8-Mb gaps on both sides of the refined interval. The follow-up replication studies may be needed to further confirm the functional significance for these newly identified SNP.