Genome-wide association studies for feed intake and efficiency in two laying periods of chickens.

BACKGROUND: Feed contributes to over 60 % of the total production costs in the poultry industry. Increasing feed costs prompt geneticists to include feed intake and efficiency as selection goals in breeding programs. In the present study, we used an F2 chicken population in a genome-wide association study (GWAS) to detect potential genetic variants and candidate genes associated with daily feed intake (FI) and feed efficiency, including residual feed intake (RFI) and feed conversion ratio (FCR). METHODS: A total of 1534 F2 hens from a White Leghorn and Dongxiang reciprocal cross were phenotyped for feed intake and efficiency between 37 and 40 weeks (FI1, RFI1, and FCR1) and between 57 and 60 weeks (FI2, RFI2, and FCR2), and genotyped using the chicken 600 K single nucleotide polymorphism (SNP) genotyping array. Univariate, bivariate, and conditional genome-wide association studies (GWAS) were performed with GEMMA, a genome-wide efficient mixed model association algorithm. The statistical significance threshold for association was inferred by the simpleM method. RESULTS: We identified eight genomic regions that each contained at least one genetic variant that showed a significant association with FI. Genomic regions on Gallus gallus (GGA) chromosome 4 coincided with known quantitative trait loci (QTL) that affect feed intake of layers. Of particular interest, eight SNPs on GGA1 in the region between 169.23 and 171.55 Mb were consistently associated with FI in both univariate and bivariate GWAS, which explained 3.72 and 2.57 % of the phenotypic variance of FI1 and FI2, respectively. The CAB39L gene can be considered as a promising candidate for FI1. For RFI, a haplotype block on GGA27 harbored a significant SNP associated with RFI2. The major allele of rs315135692 was favorable for a lower RFI, with a phenotypic difference of 3.35 g/day between opposite homozygous genotypes. Strong signals on GGA1 were detected in the bivariate GWAS for FCR. CONCLUSIONS: The results demonstrated the polygenic nature of feed intake. GWAS identified novel variants and confirmed a QTL that was previously reported for feed intake in chickens. Genetic variants associated with feed efficiency may be used in genomic breeding programs to select more efficient layers.

De novo transcriptome assembly and identification of genes associated with feed conversion ratio and breast muscle yield in domestic ducks.

Breast muscle yield and feed conversion efficiency are the major breeding aims in duck breeding. Understanding the role of specific transcripts in the muscle and small intestine might lead to the elucidation of interrelated biological processes. In this study, we obtained jejunum and breast muscle samples from two strains of Peking ducks that were sorted by feed conversion ratio (FCR) and breast muscle percentage into two-tailed populations. Ten RNA-Seq libraries were developed from the pooled samples and sequenced using the Hiseq2000 platform. We created a reference duck transcript database using de novo assembly methods, which included 16 663 irredundant contigs with an N50 length of 1530 bp. This new duck reference cDNA dataset significantly improved the mapping rate for RNA-Seq data, from 50% to 70%. Mapping and annotation were followed by Gene Ontology analysis, which showed that numerous genes were differentially expressed between the low and high FCR groups. The differentially expressed genes in the jejunum were enriched in biological processes related to immune response and immune response activation, whereas those in the breast muscle were significantly enriched in biological processes related to muscle cell differentiation and organ development. We identified new candidate genes, that is, PCK1, for improving the FCR and breast muscle yield of ducks and obtained much better reference duck transcripts. This study suggested that de novo assembly is essential when applying transcriptome analysis to a species with an incomplete genome.

PTEN regulated by gga-miR-20a-5p is involved in chicken macrophages inflammatory response to APEC infection via autophagy.

Colibacillosis, a bacterial disease caused by avian pathogenic E. coli (APEC), is a prevalent condition in the poultry industry, resulting in substantial economic losses annually. Previously, we identified PTEN as a crucial candidate gene that may play a significant role in chicken's immune response to APEC infection. Bioinformatics analysis indicated that the PTEN protein was unstable, hydrophilic and nuclear localization, with multiple putative phosphorylation sites and a high degree of similarity to duck and goose PTEN. Moreover, PTEN exhibited high expression levels in various tissues such as the stomach, cecum, small intestine, spleen, thymus, harderian gland, muscle, cerebrum, cerebellum, lung, and liver in comparison to heart tissue. Overexpression of PTEN resulted in a significant promotion of the expression level of pro-apoptosis genes and inflammatory mediators, as well as the production of NO, with or without APEC infection, which led to cellular injury. Furthermore, overexpression of PTEN was found to regulate the expression levels of autophagy related genes, regardless of APEC infection. Additionally, PTEN was a target gene of gga-miR-20a-5p and regulated by gga-miR-20a-5p upon APEC infection. Taken together, these findings establish a foundation for investigating the biological function of chicken PTEN, providing a potential target for future treatments against APEC infection as well as the breeding of genetically resistant poultry.

[Detection of chicken dominant white gene PMEL17 mutation site by a pooling method].

Dominant white locus is one of the major loci affecting feather color in the domestic chicken and its dominant allele I can inhibit the synthesis of the melanin. Therefore, the homozygotes (I/I) or heterozygotes (I/i) show a white phenotype. It has been confirmed that the Dominant white locus encodes PMEL17 protein which is a specific protein and plays a key role in the development of melanocytes, thus PMEL17 gene is identified as a positional candidate gene for the dominant white phenotype in chicken. In our present study, we created an economic and efficient pooling method for detecting PMEL17 mutations in large populations, known as PCR product pooling method, and the steps are as follows: firstly, PMEL17 segments containing the mutation site from individual genomic DNA samples were amplified by PCR; secondly, 10 PCR products were mixed in a pool, and then the pooled PCR samples were separated on non-denatured PAGE gels; and finally, the mutation profile of PMEL17 in certain populations were analyzed. In addition, a comparative study between the genomic DNA pooling and the PCR product pooling method was performed, and the mutation of PMEL17 was also ana-lyzed in our experimental population. In conclusion, the PCR product pooling method proved to be appropriate power to test gene mutations.

[Analysis of genetic relationship of egg-type chickens using microsatellite markers].

Twenty microsatellite markers were used to analyse the genetic relationship among four package lines (A, B, C, D) of egg-type chickens introduced in 2001 an 2002. The genetic heterozygosity, polymorphism information content (PIC), effective allele number, and genetic distance among lines were calculated and dendrogram was constructed to evaluate the genetic variability within line and genetic relations among lines. In total, 65 alleles in 20 microsatellite markers were detected. Average allele number for microsatellite markers is 3.250, and average effective allele number for those markers is 2.395. The PIC of microsatellite markers averaged at 0.454, ranging from 0.102 to 0.729. The heterozygosity of microsatellite markers ranged from 0.108 to 0.765. The heterozygosity of A2001 (0.390) was lowest, and that of D2001 (0.452) highest. The genetic distances among A and B lines were 0.005-0.016, while those among C and D lines were 0.094-0.119. Genetic resemble coefficients among A and B lines were above 0.984, while those among C and D lines around 0.900. The results proved, on the molecular level, that A and B are identical or two lines but very closed in genetic background while C and D are two different lines.

[Conservation efficiency of local chicken breeds in different farms as revealed by microsatellite markers].

Twenty-eight microsatellite markers were used to analyze the conservation efficiency of two local chicken breeds (Dagu Chicken and Beijing Fatty Chicken) in different farms. Genotypes were detected in 125 samples. The genetic variations among and within the populations were calculated by the number of alleles, gene frequency, genetic heterozygosity (H), PIC, F-statistics, Nei's genetic distance and UPGMA. High polymorphism was found in the four populations, and H and PIC values of each population were more than 0. 5. All loci detected in the study showed polymorphism and the number of alleles ranged from 2 to 22 in total population. Most of these loci were at Hardy-Weinberg equilibrium except two loci (LE110194, MCW0032). The four conservation farms for the two breeds were shown to have retained substantial biodiversity, indicating that the conservation programs are efficient. However, differences between the farms of the same breeds were observed.

[Comparison of denatured and non-denatured PAGE-silver-staining detection of PCR product of microsatellites].

The genomic DNAs from six chicken breeds in China were amplified using two microsatellite primers. The PCR products were detected by non-denatured and denatured PAGE gels respectively, and the gels were dyed by silver. There were distinct differences between the two kinds of gel. In non-denatured gels. There were many nonspecific bands while clear purposed bands were showed in denatured gels.

[Genetic diversity in Tibetan chicken].

Morphological traits and living habit of Tibetan chicken, which is an aboriginal chicken breed on plateau with its own characteristic populational genetic features, are in great common with the Red Jungle Fowl, the assumed ancestry of domestic chicken. To fully exploit this chicken resource, Multiplex PCR with semi-automated polyacrilamide gel electrophoresis (PAGE) using fluorescently labeled microsatellite primers was used to detect the polymorphism at 20 microsatellite loci. At the same time, we randomly test the individual morphology and performance. It showed that numbers of polymorphic alleles were 4 approximately 10, with mean value 7.25 per locus. Polymorphism Information Content (C(PI)) and Heterozygosity (H) had mean values 0.67 and 0.74, respectively. Macrochromosomes had relatively higher polymorphism than microchromosomes(P > 0.05). In all, high polymorphisms at microsatellite loci related to the uneven production performance and morphological discrepancy of population genetic characteristics in Tibetan chicken.