Muhammad Cahyadi

Quantitative trait loci and candidate genes for the economic traits in meat-type chicken

Recent progress has been achieved in the identification of quantitative trait loci (QTLs) and candidate genes, and they have been found to be very important for the production of chickens with more desirable meat characteristics. The major economic traits of chicken meat production were divided into two major categories, namely growth and carcass condition. In this paper, the QTL locations and candidate genes for the above mentioned traits are reviewed. The results presented here will provide guidelines for the selection of high quality and highly productive chickens through the marker assisted selection (MAS), which should be extensively used by poultry breeders and companies.

Association of SNPs in ODC and PRDM16 with Body Weight Traits in Korean Native Chicken

Both ODC and PRDM16 genes were known to be associated with body weight traits in chicken. These two genes were located on GGA3 and GGA21, respectively, where the QTLs of body weights are located. Therefore, the objectives of this study were to identify the SNPs in these two genes and their associations with body weight traits in Korean native chicken. Fluidigm Dynamic Array integrated fluidic circuits (IFCs) assay was used to genotype 7 SNPs consisting g.-353C>T, g.2136A>G, g.2524T>C, g.3607C>T SNPs of the ODC gene, and g.182216C>T, g.182290A>T, g.182491A>T SNPs of the PRDM16 gene. Statistical analysis showed that g.2136A>G SNP of the ODC was associated with body weight at 20 weeks of age and slaughter weight, and g.3607C>T SNP of the ODC was associated with body weight at 2 weeks of age. Association between g.182216C>T SNP of the PRDM16 and body weight at 12 weeks of age has also been revealed. In addition, g.182491A>T SNP of PRDM16 has significant correlation with body weight (BW) at 8 weeks, BW at 10 weeks and BW at 14 weeks of age. These results suggested that both ODC and PRDM16 could be strong candidate genes for body weight traits in Korean native chicken.

Genetic Parameters for Growth-Related Traits in Korean Native Chicken

Body and carcass weights are always being main focus in poultry industry. The aim of current study was to estimate the heritability, genetic and phenotypic correlations of growth-related traits in Korean native chicken. A total of 596 chickens representing five lines of Korean native chicken (Black, Gray-Brown, Red-Brown, White, and Yellow-Brown) were reared under the standard breeding procedures in the National Institute of Animal Science (NIAS), Korea. Their body weights were observed every two weeks from hatched to 20 weeks of age. In addition, shank length and carcass weight were also measured before and after slaughter, respectively. The ASReml-R program was used to compute genetic parameters. The body weight traits were moderate to high heritability values (ranged 0.29∼0.63). The heritablilites of carcass weight (h 2 =0.20) and shank length (h 2 =0.20) were categorized as moderate. Moreover, both genetic and phenotypic correlations were ranged form 0.62 to 0.99 and ranged from 0.42 to 0.98, respectively. These findings can be useful information for quantitative genetic studies and breeding plan of Korean native chicken.

Variance Component Quantitative Trait Locus Analysis for Body Weight Traits in Purebred Korean Native Chicken

Quantitative trait locus (QTL) is a particular region of the genome containing one or more genes associated with economically important quantitative traits. This study was conducted to identify QTL regions for body weight and growth traits in purebred Korean native chicken (KNC). F1 samples (n = 595) were genotyped using 127 microsatellite markers and 8 single nucleotide polymorphisms that covered 2,616.1 centi Morgan (cM) of map length for 26 autosomal linkage groups. Body weight traits were measured every 2 weeks from hatch to 20 weeks of age. Weight of half carcass was also collected together with growth rate. A multipoint variance component linkage approach was used to identify QTLs for the body weight traits. Two significant QTLs for growth were identified on chicken chromosome 3 (GGA3) for growth 16 to18 weeks (logarithm of the odds [LOD] = 3.24, Nominal p value = 0.0001) and GGA4 for growth 6 to 8 weeks (LOD = 2.88, Nominal p value = 0.0003). Additionally, one significant QTL and three suggestive QTLs were detected for body weight traits in KNC; significant QTL for body weight at 4 weeks (LOD = 2.52, nominal p value = 0.0007) and suggestive QTL for 8 weeks (LOD = 1.96, Nominal p value = 0.0027) were detected on GGA4; QTLs were also detected for two different body weight traits: body weight at 16 weeks on GGA3 and body weight at 18 weeks on GGA19. Additionally, two suggestive QTLs for carcass weight were detected at 0 and 70 cM on GGA19. In conclusion, the current study identified several significant and suggestive QTLs that affect growth related traits in a unique resource pedigree in purebred KNC. This information will contribute to improving the body weight traits in native chicken breeds, especially for the Asian native chicken breeds.

FABP3 and FABP4 Genes Are the Potential Candidates for Body Weights in Korean Native Chicken

FABPs, 15 kDa organic substances, are small intracellular proteins which have a primary role to regulate fatty acid uptake and intracellular transport. This study was conducted to identify SNPs in the two FABP family genes and their associations with the body weight traits in Korean native chicken (KNC). Two SNPs, namely g.508C>T of FABP3 gene and g.285C>T of FABP4 gene, have been genotyped by using PCR-RFLP method. The results showed that FABP3 was significantly associated with body weight at birth, body weights at 12 to 20 weeks, and also slaughter weight. Moreover, the g.285C>T SNP of FABP4 gene was not associated with any body weight traits. These results suggested that the g.508C>T SNP of FABP3 genes can be used as molecular markers to select KNC having desirable body weights.

Identification of quantitative trait loci for the fatty acid composition in Korean native chicken

Objective Fatty acid composition is one of the most important meat quality traits because it can contribute to functional, sensorial, and nutritional factors. In this study, quantitative trait locus (QTL) analyses for fatty acid composition traits were investigated in thigh and breast meat of Korean native chicken (KNC). Methods In total, 18 fatty acid composition traits were investigated from each meat sample using 83 parents, and 595 F1 chicks of 20 week old. Genotype assessment was performed using 171 informative DNA markers on 26 autosomes. The KNC linkage map was constructed by CRI-MAP software, which calculated genetic distances, with map orders between markers. The half-sib and full-sib QTL analyses were performed using GridQTL and SOLAR programs, respectively. Results In total, 30 QTLs (12 in the thigh and 18 in the breast meat) were detected by the half-sib analysis and 7 QTLs (3 in the thigh and 4 in the breast meat) were identified by the full-sib analysis. Conclusion With further verification of the QTL regions using additional markers and positional candidate gene studies, these results can provide valuable information for determining causative mutations affecting the fatty acid composition of KNC meat. Moreover, these findings may aid in the selection of birds with favorable fatty acid composition traits.

Association of SNPs from iNOS and TLR-4 Genes with Economic Trait in Chicken

Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 305-764, KoreaABSTRACT iNOS (Inducible nitric oxide synthase) and TLR-4 (Toll-like Receptor-4) play crucial roles in innate immunity of poultry. iNOS has been mapped to chicken chromosome 14 and implicated in a variety of chicken diseases. iNOS possesses potent antimicrobial activity, including the inhibition of microbes replication in vitro. TLR-4 is a pathogen associated molecular- pattern receptor for bacterial product, such as LPS (lipopolysaccharides) found in Gram negative bacteria, that triggers pro-inflammatory cytokine expression after engagement with ligands. In the previous studies, genetic analysis of iNOS and TLR-4 revealed the possible association of mutation in these genes with the intestinal microflora of cecum when infected with Salmonella spp. This study was aimed to augment previous findings, which show the association of iNOS (C14513T) and TLR-4 (G4409T) polymorphisms with economic traits in Korean Native Black (KNB), Rhode Island Red (RIR) and Cornish chickens. Investigation in the effect of SNPs on economic traits (layday, layw, layno, bw150, bw270, layw270) was conducted. iNOS (C14513T) had a significant effect on the average body weight at 270 days of age (p 0.05). The results obtained from using the candidate genes can be useful for the genetic improvement of body weight in both KNB and RIR breeds.(Key words : chicken, Korea Native Chicken, Cornish, Rhode Island Red, iNOS, TLR-4)