R.L. Han

Association study of polymorphisms inside the miR-1657 seed region with chicken growth and meat traits.

1. Polymorphisms occurring in the seed region of microRNAs (miRNAs) could influence their target gene and lead to phenotypic variation. The purpose of the research was to explore the genetic effects of the rs14934924 (Gu2009>u2009A) mutation resident in the conserved seed region of miR-1657 on growth and meat traits of the Gushi-Anka F2 resource population. 2. The NdeI polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method and association analysis were used to analyse the polymorphism. 3. The mutation was associated with body weight at 8 weeks of age, shank girth at 12 weeks of age, breast bone length at 12 weeks of age, pelvis breadth at 4 weeks of age and subcutaneous fat thickness (Pu2009<u20090·05) and was associated with body weight at 4, 6, 10 and 12 weeks of age (Pu2009<u20090·01). 4. Our results will be a useful resource for a subsequent study in miRNA function, and provide a basis for molecular techniques in chicken breeding.

Effect of γ-aminobutyric acid on growth performance and immune function in chicks under beak trimming stress

This experiment was undertaken to examine the effect of beak trimming stress on the growth performance and immune system, and to consider possible roles of γ-aminobutyric acid (GABA) in this stress response. Results showed that body weight, feed intake and relative spleen weight were significantly increased by GABA at 80 mg/kg (P < 0.05) under beak trimming stress, whereas the relative organ weights of the bursa of fabricius and thymus were not significantly affected (P > 0.05). Adrenocorticotropic hormone concentration in serum was highest for chicks fed the GABA-deficient water and was significantly decreased by the supplement of GABA at days 1, 3 and 5 after beak trimming (P < 0.05). The supplement of GABA significantly increased the proportions of CD4(+) and CD8(+) lymphocytes, especially at the dose of 60 mg/kg (P < 0.05). The levels of interleukin (IL)-1β, lipopolysaccharide-induced tumor necrosis factor-α and IL-6 in serum were significantly decreased by GABA at 80 mg/kg (P < 0.05). All the three cytokines expressed in the spleen were significantly decreased by GABA at 80 mg/kg when birds were under beak trimming stress (P < 0.05). It is concluded that beak trimming suppressed the immune response of chicks, whereas the immune response of chicks could be improved by GABA supplementation.

MicroRNAs-1614-3p gene seed region polymorphisms and association analysis with chicken production traits

In the present study, a total of 860 chickens from a Gushi–Anka F2 resource population were used to evaluate the genetic effect of the gga-miR-1614-3p gene. A novel, silent, single nucleotide polymorphism (SNP, +5 C>T) was detected in the gga-miR-1614-3p gene seed region through AvaII polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) and PCR products sequencing methods. Associations between the SNP and chicken growth, meat quality and carcass traits were performed by association analysis. The results showed that the SNP was significantly associated with breast muscle shear force and leg muscle water loss rate, wing weight, liver weight and heart weight (pu2009<u20090.05), and highly significantly associated with the weight of the abdominal fat (pu2009<u20090.01). The secondary structure of gga-miR-1614 and the free energy were altered due to the variation predicted by the M-fold program.

Polymorphisms of the pro-opiomelanocortin and agouti-related protein genes and their association with chicken production traits.

Pro-opiomelanocortin (POMC) and agouti-related protein (AGRP) are hypothalamic neuropeptides that play a central role in the regulation of food intake and energy expenditure and for this reason the variations in the POMC and AGRP genes in chicken were examined by screening the DNA pools. Two silent cSNPs mutations in POMC gene and one silent cSNP mutation in AGRP gene were identified. PCR-restriction fragment length polymorphism (RFLP) was used to test the cSNPs c. C495T in the POMC and c. C9T in the AGRP gene in the F2 resource population of Gushi chicken crossed with Anak broiler. The association analysis on the polymorphisms of POMC, AGRP gene and production traits showed that the c. C495T mutation in the POMC gene was significantly linked to the pelvis breadth at 4xa0weeks of age (Pxa0=xa00.035), body weight at 2xa0weeks of age (Pxa0=xa00.013) and was highly significantly linked to the chest depth at 12xa0weeks of age (Pxa0=xa00.006). The c. T9T genotype in the AGRP gene was associated with a low breast muscle water loss rate (Pxa0=xa00.025), increased chest width at 12xa0weeks of age (Pxa0=xa00.005) and body weight at 2xa0weeks of age (Pxa0=xa00.036), a high slaughter rate (Pxa0=xa00.049) and semi-evisceration weight (Pxa0=xa00.019). These findings may have important implications for the molecular aspects of chicken breeding.

A novel 31-bp indel in the paired box 7 (PAX7) gene is associated with chicken performance traits

Abstract 1. A novel 31-bp indel polymorphism in intron 3 of the chicken paired box 7 (PAX7) gene was identified and genotyped in an F2 resource population of Gushi chicken crossed with Anka broiler to analyse its associations with chicken growth, carcass and meat quality traits. 2. Results showed that the 31-bp indel was significantly associated with body weight at 4, 6, 8, 10, 12 weeks of age and body size indices including shank length, shank girth, body slanting length at 8 and 12 weeks of age. Significant associations were found for carcass weight, semi-evisceration weight, evisceration weight, breast muscle fibre diameter, leg muscle fibre diameter, breast muscle fibre density, while no significant association with leg muscle fibre density was observed. 3. It was concluded that the 31-bp indel in intron 3 of the PAX7 gene was associated with chicken growth, carcass and meat quality traits where the 31-bp deletion had a negative effect on chicken growth and carcass traits and positive effect on meat quality traits.

A novel 2-bp indel within Krüppel-like factor 15 gene (KLF15) and its associations with chicken growth and carcass traits

Abstract 1. The Krüppel-like factor (KLF) family of zinc-finger transcription factors plays a critical role in cell differentiation, phenotypic modulation and physiologic function. KLF15 has been proposed to regulate adipogenesis and gluconeogenesis. The objective of this study was to establish the association between KLF15 gene polymorphism and chicken growth and carcass traits. 2. An F2resource population of Gushi chickens crossed with Anka broilers was used to investigate the genetic effects of the chicken KLF15 gene. A 2-bp indel mutation (G13781_13782del/insAG) within intron 2 was detected, and a polymerase chain reaction–restriction fragment length polymorphism method was developed to genotype the F2 individuals. 3. Association analysis showed that the Single Nucleotide Polymorphisms (SNP) was significantly associated with chicken growth and carcass traits. The chickens with the insAG/insAG genotype generally had a significantly higher body weight and size than other genotypes. Gene expression for each genotype showed that birds carrying insAG/insAG had a higher expression level than the other genotypes. 4. The results suggested that this polymorphic site may serve as a useful target for marker assisted selection of chicken growth and carcass traits.

Polymorphisms of the interleukin-15 gene and their associations with fatness and muscle fiber traits in chickens

Interleukin-15 (IL-15) is a cytokine that has been proposed to modulate skeletal muscle and adipose tissue mass. In the present study, an F2 resource population of Gushi chickens crossed with Anka broilers was used to investigate the genetic effects of the chicken IL-15 gene. Two single nucleotide polymorphisms (SNPs) (g.31224G>A and g.31266T>G) were identified in exon 5 of the IL-15 gene by means of polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) and DNA sequencing. Associations between the two SNPs and chicken fatness and muscle fiber traits were determined using linkage disequilibrium, haplotype construction, and association analysis. Both of the SNPs were associated with abdominal fat weight, leg muscle fiber diameter, and leg muscle fiber density (pu2009<u20090.05). Haplotypes of the two linked SNPs were associated with abdominal fat weight, fat thickness under the skin, and leg muscle fiber diameter (pu2009<u20090.05). The results suggested that the IL-15 gene might be associated with the causative mutation or the quantitative trait locus (QTL) controlling the fatness traits and muscle fiber traits in chickens.

Cloning of TPO gene and associations of polymorphisms with chicken growth and carcass traits

Thyroid peroxidase (TPO), which located on the apical membrane surface of thyrocytes, is the key enzyme involved in thyroid hormone synthesis, mainly catalyses the iodination of tyrosine residues and the coupling of iodotyrosines on thyroglobulin to form thyroxine and triiodothyronine. The objectives of this study were to identify genetic polymorphisms of the chicken TPO gene and to analyze potential association between single nucleotide polymorphisms (SNPs) and growth and carcass traits in chicken. Partial sequences of TPO gene were cloned firstly. The nucleotide sequence was found to have 72xa0% identity with that of humans. The chicken TPO amino acid sequence was 71xa0%. Through polymerase chain reaction-restriction fragment length polymorphism and DNA sequencing methods, three novel mutations of the chicken TPO gene were detected in the F2 resource population from Gushi chickens and Anka broilers. The association analysis indicated that all of the three SNPs showed association with chicken growth at different periods. The g.29996C>T polymorphisms was significantly associated with body weight, breast bone length, pectoral angle at 12xa0weeks, claw weight and leg muscle weight (Pxa0<xa00.05). In addition, individuals with the TT genotype had higher value for almost all the traits than CC and CT genotype. Meanwhile for CLW, the additive effects were significant (Pxa0<xa00.05). Hence, we suggest that genotype TT can be regarded as a potential molecular marker for later growth and carcass traits in chicken.

Genetic diversity of mtDNA D-loop sequences in four native Chinese chicken breeds

ABSTRACT 1. To explore the genetic diversity of Chinese indigenous chicken breeds, a 585 bp fragment of the mitochondrial DNA (mtDNA) region was sequenced in 102 birds from the Xichuan black-bone chicken, Yunyang black-bone chicken and Lushi chicken. In addition, 30 mtDNA D-loop sequences of Silkie fowls were downloaded from NCBI. The mtDNA D-loop sequence polymorphism and maternal origin of 4 chicken breeds were analysed in this study. 2. The results showed that a total of 33 mutation sites and 28 haplotypes were detected in the 4 chicken breeds. The haplotype diversity and nucleotide diversity of these 4 native breeds were 0.916 ± 0.014 and 0.012 ± 0.002, respectively. Three clusters were formed in 4 Chinese native chickens and 12 reference breeds. Both the Xichuan black-bone chicken and Yunyang black-bone chicken were grouped into one cluster. Four haplogroups (A, B, C and E) emerged in the median-joining network in these breeds. 3. It was concluded that these 4 Chinese chicken breeds had high genetic diversity. The phylogenetic tree and median network profiles showed that Chinese native chickens and its neighbouring countries had at least two maternal origins, one from Yunnan, China and another from Southeast Asia or its surrounding area.

Promoter analysis and tissue expression of the chicken ASB15 gene

ABSTRACT 1. This study was conducted to explore the promoter region of the chicken ASB15 gene by detecting the activities of the dual luciferase reporter gene and to assess expression profiles of the ASB15 gene in 10 different tissues from Gushi chickens. 2. Five dual luciferase reporter gene vectors were constructed and transfected into DF1 cells. The activities of recombined plasmids were measured and the core promoter was confirmed by bioinformatic analysis. Total RNA was extracted and the relative expression of the ASB15 gene was examined. 3. Data analysis indicated that the promoter was located from −955 to −212 bp. Results showed that the chicken ASB15 gene was expressed in heart, breast muscle and leg muscle. 4. This study has confirmed the promoter region and the expression profile of the chicken ASB15 gene, which provides a foundation for further exploring its transcriptional regulation and function.