Identification and association of the single nucleotide polymorphisms in calpain3 (CAPN3) gene with carcass traits in chickens

Genetic polymorphisms of calpain1 and calpain3 genes and their effects on growth, carcass, and meat quality traits in Betong chicken (KU line)

Betong chicken (KU line) is a slow-growing Thai native chicken used for meat production. The objectives of this study were to identify polymorphisms of the calpain1 (CAPN1) and calpain3 (CAPN3) genes and to investigate their effects on growth, carcass, and meat quality traits in Betong chickens (KU line). A sample of 252 Betong chickens (KU line) was screened for CAPN1 and CAPN3 polymorphisms. The polymorphisms of CAPN1 were detected using gel electrophoresis and DNA sequencing, whereas the polymorphisms of CAPN3 were identified using restriction fragment length polymorphism. Polymorphisms were detected in both CAPN1 (AA, AB, and BB genotypes) and CAPN3 (CC, CT, and TT genotypes). The frequency of the B allele was higher than for the A allele (0.78 and 0.22, respectively) in CAPN1, while the C allelic frequency was higher than for the T allele (0.54 and 0.46, respectively) in CAPN3. The CAPN1 genotype and the combination of the CAPN1 and CAPN3 genotypes could be used as genetic markers for meat lightness. The CAPN3 could be useful for increasing body weight, live weight, and breast meat weight in Betong chickens (KU line).

Evaluation of dietary metabolizable energy concentrations on meat quality and lipid metabolism-related gene expression in yellow-feathered chickens

This study evaluated the effects of different dietary metabolizable energy (ME) concentrations on the meat quality, carcass traits, volatile flavour and lipid metabolism-related gene expression levels in yellow-feathered chickens. In total, 600 Huxu female chickens aged 90 days were randomly assigned to six dietary treatments, each with 10 replicates of 10 birds. During the finisher phase, the birds were fed diets containing 2880 (low), 2940, 3000, 3060, 3120 and 3180 (high) kcal ME/kg. The results showed that the average daily gain of chickens increased as the dietary ME concentration increased, while the feed to gain improved (p < 0.05), and the intramuscular fat content of breast muscle increased (p < 0.05). The energy concentration had no effect on the breast muscle pH (45 min and 24 h), colour parameter (L*) or percentage of drip loss (p > 0.05), but the shear force values decreased significantly (p < 0.05). The diameter and area of the breast muscle fiber decreased and the muscle fibre density increased as the dietary ME concentration increased (p < 0.05). The highest ME concentration (3180 kcal) increased the percentages of aldehydes (hexanal, heptanal, 2,4-nonadienal, octanal, nonanal and 2-decenal), alcohols (2-nonen-1-ol, trans-2-undecen-1-ol, 7-hexadecenal, 2-hexyl-1-decanoal and n-nonadecanol-1,3,7,11-trimethyl-1-dodecanol), alkanes (2,6-dimethyl-heptadecane) and carboxylic acids (9-hexadecenoic acid), but reduced the percentages of octadecanal, octadecane, heneicosane and tetradecanal (p < 0.05). In addition, the mRNA gene expression levels of fatty acid-binding protein 3 and apolipoprotein B were significantly upregulated in the liver, whereas that of cholesteryl ester transfer protein was significantly downregulated. In conclusion, increasing the ME diet to 3180 kcal/kg significantly improved the quality and flavour of the meat from yellow-feathered broilers. our finding may help poultry producers to improve the taste of meat by regulating genes related to lipid metabolism, thereby achieving the flavour and taste characteristics preferred by consumers.

Genome-wide comparative analyses reveal selection signatures underlying adaptation and production in Tibetan and Poll Dorset sheep

The identification of genome-wide selection signatures can provide insights on the mechanisms of natural and/or artificial selection and uncover genes related to biological functions and/or phenotypes. Tibetan sheep are an important livestock in Tibet, providing meat and wool for Tibetans who are renown for breeding livestock that adapt well to high altitudes. Using whole-genome sequences with an effective sequencing depth of 5×, we investigated the genomic diversity and structure and, identified selection signatures of White Tibetan, Oula and Poll Dorset sheep. We obtained 30,163,679 Single Nucleotide Polymorphisms (SNPs) and 5,388,372 indels benchmarked against the ovine Oar_v4.0 genome assembly. Next, using F_ST, ZHp and XP-EHH approaches, we identified selection signatures spanning a set of candidate genes, including HIF1A, CAPN3, PRKAA1, RXFP2, TRHR and HOXA10 that are associated with pathways and GO categories putatively related to hypoxia responses, meat traits and disease resistance. Candidate genes and GO terms associated with coat color were also identified. Finally, quantification of blood physiological parameters, revealed higher levels of mean corpuscular hemoglobin measurement and mean corpuscular hemoglobin concentration in Tibetan sheep compared with Poll Dorset, suggesting a greater oxygen-carrying capacity in the Tibetan sheep and thus better adaptation to high-altitude hypoxia. In conclusion, this study provides a greater understanding of genome diversity and variations associated with adaptive and production traits in sheep.

Molecular genetic characterisation and expression profiling of calpain 3 transcripts in red sea bream (Pagrus major)

Calpains (CAPNs) belong to the papain superfamily of cysteine proteases, and they are calcium-dependent cytoplasmic cysteine proteases that regulate a variety of physiological processes. We obtained the sequence of CAPN3 from an NGS-based analysis of Pagrus major (PmCAPN3) and confirmed the conserved molecular biological properties in the predicted amino acid sequence. The amino acid sequence and predicted domains of CAPN3 were found to be highly conserved in all of the examined species, and one catalytic domain and four calcium binding sites were identified. In healthy P. major, the PmCAPN3 mRNA was most abundantly expressed in the muscle and skin, and ubiquitously expressed in the other tissues used in the experiment. After artificial infections with fish pathogens, significant changes in its expression levels were found in immune-related tissues, most of showed upregulation. In particular, the highest level of expression was found in the liver, a tissue associated with protease activity. Taken together, these results suggest a physiological activity for PmCAPN3 in P. major and reveal functional possibilities that have not yet been reported in the immune system.

Genotype frequency distributions of 28 SNP markers in two commercial lines and five Chinese native chicken populations

Background

Modern breeding in the poultry industry mainly aims to produce high-performance poultry lines and breeds in two main directions of productivity, meat and eggs. To understand more about the productive potential of lowly selected Chinese native chicken populations, we selected 14 representative SNP markers strongly associated with growth traits or carcass traits and 14 SNP markers strongly associated with egg laying traits through previous reports. By using the MassArray technology, we detected the genotype frequency distributions of these 28 SNP markers in seven populations including four lowly selected as well as one moderately selected Sichuan native chicken populations, one commercial broiler line and one commercial layer line.

Results

Based on the genotype frequency distributions of these 28 SNP markers in 5 native chicken populations and 2 commercial lines, the results suggested that these Chinese indigenous chicken populations have a relatively close relationship with the commercial broiler line but a marked distinction from the commercial layer line. Two native chicken breeds, Shimian Caoke Chicken and Daheng Broilers, share similar genetic structure with the broiler line.

Conclusions

Our observations may help us to better select and breed superior domestic chickens and provide new clues for further study of breeding programs in local chicken populations.

Association of single nucleotide polymorphism in NLRC3, NLRC5, HIP1, and LRP8 genes with fecal egg counts in goats naturally infected with Haemonchus contortus

Haemonchus contortus is a common, intractably pathogenic and economically important gastrointestinal nematode for goat producers worldwide, especially in tropical and subtropical regions. The objective of this study is to identify single nucleotide polymorphisms (SNPs) of 12 candidate goat genes mainly related to the innate immune response associated with fecal egg counts (FECs) of Haemonchus contortus in goat as an indicator of the level of parasite infection. Phenotypic data including FEC and blood traits were recorded in 189 native goats from China and 191 ones from Bangladesh, respectively. Bangladeshi goats had significantly (P < 0.01) lower FEC compared to that of Chinese goats, suggesting higher susceptible and infection rates in Chinese goat populations. FEC was significantly positive correlated with body weight (r = 0.64, P < 0.01) and hemoglobin (r = 0.49, P < 0.01) value, but negative with pack cell volume (r = - 0.63, P < 0.05) in goats. Genotyping of SNPs was performed using a matrix-assisted laser desorption ionization time of flight mass spectrometry assay and a generalized linear model was used to evaluate the association between each SNP and goat FEC trait. Eleven novel SNPs in the NLRC3, NLRC5, HIP1, and LRP8, out of 46 variants from these 12 genes, were significantly associated with FEC of goats with a nominal significance level of P < 0.05. Of these 11 SNPs, linkage disequilibrium were revealed among SNPs in LRP8 (r² = 0.87 to 1), between SNPs in NLRC3, NLRC5, and HIP1 (r² = 0.96 to 0.99), respectively. Further, haplotypes within NLRC3, NLRC5, and HIP1 were significantly associated (P < 0.001) with FEC. In artificial challenge trail, quantitative real-time PCR exposed that the relative expression of mRNA was higher in the resistant group for NLRC3 (P < 0.01), LRP8 and HIP1 (P < 0.001) but lower in the resistant group for NLRC5 (P < 0.0001), compared to the susceptible group. The possible SNP markers and genes identified in this study could be potentially used in marker-assisted selection for breeding local goats breeds resistant to gastrointestinal nematode parasite particularly for Haemonchus contortus, and then for improving health and productivity of goat.

Whole-genome resequencing analysis of Pengxian Yellow Chicken to identify genome-wide SNPs and signatures of selection

Chinese indigenous chickens have experienced strong selective pressure in genes or genomic regions controlling critical agricultural traits. To exploit the genetic features that may be useful in agriculture and are caused by artificial selection, we performed whole-genome sequencing of six Pengxian Yellow Chickens and downloaded the sequence data of five Red Jungle fowls from the NCBI. Through selective sweep analysis, we detected several regions with strong selection signals, containing 497 protein-coding genes. These genes were involved in developmental processes, metabolic processes, the response to external stimuli and other biological processes including digestion (ABCG5, ABCG8 and ADRB1), muscle development and growth (SMPD3, NELL1, and BICC1) and reduced immune function (CD86 and MTA3). Interestingly, we identified several genes with extremely strong selection signals associated with the loss of visual capability of domestic chickens relative to their wild ancestors. Amongst them, we propose that CTNND2 is involved in the evolutionary changes of domestic chickens toward reduced visual ability through the diopter system. VAT1 was also likely to contribute to these processes through its regulation of mitochondrial fusion. In summary, these data illustrate the patterns of genetic changes in Pengxian yellow chickens during domestication and provide valuable genetic resources that facilitate the utilization of chickens in agricultural production.

Single nucleotide polymorphisms in candidate genes are significantly associated with resistance to Haemonchus contortus infection in goats

BACKGROUND

Haemonchosis is a major economic problem in goat production in humid, tropical and subtropical regions. The disease is caused by an abomasal nematode, Haemonchus contortus, which is highly pathogenic in small ruminants. The aim of this study was to identifying single-nucleotide polymorphisms (SNP) that were associated with fecal egg counts (FEC) and could be used as markers to identify resistance to H. contortus in goats.

RESULTS

Ten novel variants in the CIITA, ATP2A3, HSPA8, STAT5B, ESYT1, and SERPING1 genes were associated with FEC in goats with a nominal significance level of P < 0.05. Two missense mutation in the exon region of the caprine CIITA gene resulted in replacement of arginine with cysteine at position 9473550 (R9473550C) and aspartic acid with glutamic acid at position 9473870 (D9473870E). Chinese goat breeds had significantly higher FEC than Bangladeshi goat breeds within their respective genotypes. Polymorphism information content (PIC), effective allele number (Ne), and heterozygosity (He) were greatest for the STAT5B_197_A > G SNP locus in all goat breeds. Pairwise coefficients of linkage disequilibrium (D´, r 2) revealed complete LD (r 2 = 1) between significant SNP polymorphisms in CIITA and SERPING1 and strong LD (r 2 = 0.93 and 0.98) between polymorphisms in HSPA8 and ATP2A3, respectively. Correlation coefficient (r) between FEC and body weight (BW) was significantly positive (r = 0.56***, P < 0.001) but that between FEC and packed cell volume (PCV) was negatively significant (r = - 0.47**, P < 0.01) in the total population of goats. On the other hand, correlation coefficient (r) between BW and PCV was not significant in total population of goats. Association analysis revealed that haplotypes within ATP2A3, HSPA8, and SERPING1 were significantly associated with FEC. Quantitative real-time PCR revealed that the relative expression of mRNA was higher (P < 0.001) for resistant, compared to susceptible, groups of goats for all candidate genes except CIITA.

CONCLUSIONS

This study identified SNP markers that can potentially be used in marker-assisted selection programs to develop goat breeds that are resistant to H. contortus.

Characterization of the Goose CAPN3 Gene and its Expression Pattern in Muscle Tissues of Sichuan White Geese at Different Growth Stages

Calpain 3 (CAPN3), also known as p94, is associated with multiple production traits in domestic animals. However, the molecular characteristics of the CAPN3 gene and its expression profile in goose tissues have not been reported. In this study, CAPN3 cDNA of the Sichuan white goose was cloned, sequenced, and characterized. The CAPN3 full-length cDNA sequence consists of a 2,316-bp coding sequence (CDS) that encodes 771 amino acids with a molecular mass of 89,019 kDa. The protein was predicted to have no signal peptide, but several N-glycosylation, O-glycosylation, and phosphorylation sites. The secondary structure of CAPN3 was predicted to be 38.65% α-helical. Sequence alignment showed that CAPN3 of Sichuan white goose shared more than 90% amino acid sequence similarity with those of Japanese quail, turkey, helmeted guineafowl, duck, pigeon, and chicken. Phylogenetic tree analysis showed that goose CAPN3 has a close genetic relationship and small evolutionary distance with those of the birds. qRT-PCR analysis showed that in 15-day-old animals, the expression level of CAPN3 was significantly higher in breast muscle than in thigh tissues. These results serve as a foundation for further investigations of the function of the goose CAPN3 gene.

Investigation of biochemical changes of the ovine calpain 3 exon-10 polymorphism

Calpain 3 (CAPN3) is a tissue specific calpain, and its mRNA is the most expressed calpain isoform in skeletal muscles. Many mutations and polymorphisms within the human CAPN3 gene have been reported and related to limb-girdle muscular dystrophy. Several reports link CAPN3 polymorphisms and meat quality. An association between three allele variants in exon-10 of ovine CAPN3 and the yield of fat trimmed meat cuts has been reported. This research investigated the biochemical significance of polymorphic variation in CAPN3. CAPN3 mRNA sequences were obtained from muscle samples collected from lambs which were homozygous for each of the three alleles. Four single base substitutions were found besides those in exon-10, but none of them, including the variations within exon-10, caused a change in amino acid sequence. The expression of CAPN3 mRNA and the amounts of CAPN3 protein were also compared among genotypes, and no significant differences were found. These results suggest that the reported association of specific allele variants within CAPN3 exon-10 to phenotype variations were not direct effects of CAPN3 polymorphisms. Interspecies analyses of the CAPN3 sequences indicated that the sequence reported here is more likely to be the correct common ovine CAPN3 sequence than the reference sequence.

Association between Motilin Receptor Gene Haplotypes and Growth Traits in Japanese Hinai-dori Crossbred Chickens

We previously identified quantitative trait loci (QTL) for body weight and average daily gain in a common region between ADL0198 (chr 1: 171.7 Mb) and ABR0287 (chr 1: 173.4 Mb) on chicken chromosome 1 in an F₂ resource population produced by crossing low- and high-growth lines of the Hinai-dori breed. Motilin receptor (MLNR) is a candidate gene affecting growth traits in the region. In this study, we genotyped polymorphisms of the MLNR gene and investigated its association with growth traits in a Hinai-dori F₂ intercross population. All the exons of the MLNR gene in the parental population were subjected to PCR amplification, nucleotide sequenced and haplotypes identified. To distinguish resultant diplotype individuals in the F₂ population, a mismatch amplification mutation assay was performed. Three haplotypes (Haplotypes 1–3) were accordingly identified. Six genotypes produced by the combination of three haplotypes (Haplotype 1, 2, and 3) were examined in order to identify associations between MLNR haplotypes and growth traits. The data showed that Haplotype 1 was superior to Haplotype 2 and 3 in body weight at 10 and 14 weeks of age, average daily gain between 4 and 10 weeks, 10 and 14 weeks, and 0 and 14 weeks of age in female in F₂ females. It was concluded that MLNR is a useful marker of growth traits and could be used to develop strategies for improving growth traits in the Hinai-dori breed.

A New Insight into the Role of Calpains in Post-mortem Meat Tenderization in Domestic Animals: A review

Tenderness is the most important meat quality trait, which is determined by intracellular environment and extracellular matrix. Particularly, specific protein degradation and protein modification can disrupt the architecture and integrity of muscle cells so that improves the meat tenderness. Endogenous proteolytic systems are responsible for modifying proteinases as well as the meat tenderization. Abundant evidence has testified that calpains (CAPNs) including calpain I (CAPN1) and calpastatin (CAST) have the closest relationship with tenderness in livestock. They are involved in a wide range of physiological processes including muscle growth and differentiation, pathological conditions and post-mortem meat aging. Whereas, Calpain3 (CAPN3) has been established as an important activating enzyme specifically expressed in livestock's skeletal muscle, but its role in domestic animals meat tenderization remains controversial. In this review, we summarize the role of CAPN1, calpain II (CAPN2) and CAST in post-mortem meat tenderization, and analyse the relationship between CAPN3 and tenderness in domestic animals. Besides, the possible mechanism affecting post-mortem meat aging and improving meat tenderization, and current possible causes responsible for divergence (whether CAPN3 contributes to animal meat tenderization or not) are inferred. Only the possible mechanism of CAPN3 in meat tenderization has been confirmed, while its exact role still needs to be studied further.

Titanium dioxide nanoparticles affect the growth and microRNA expression of tobacco (Nicotiana tabacum)

Titanium dioxide (TiO(2)) is one of the most widely used pigments in the world. Due to its heavy use in industry and daily life, such as food additives, cosmetics, pharmaceuticals, and paints, many residues are released into the environment and currently TiO(2) nanoparticles are considered an emerging environmental contaminant. Although several studies have shown the effect of TiO(2) nanoparticles on a wide range of organisms including bacteria, algae, plankton, fish, mice, and rats, little research has been performed on land plants. In this study, we investigated the effect of TiO(2) nanoparticles on the growth, development, and gene expression of tobacco, an important economic and agricultural crop in the southeastern USA as well as around the world. We found that TiO(2) nanoparticles significantly inhibited the germination rates, root lengths, and biomasses of tobacco seedlings after 3 weeks of exposure to 0.1, 1, 2.5, and 5 % TiO(2) nanoparticles and that overall growth and development of the tobacco seedlings significantly decreased as TiO(2) nanoparticle concentrations increased. Overall, tobacco roots were the most sensitive to TiO(2) nanoparticle exposure. Nano-TiO(2) also significantly influenced the expression profiles of microRNAs (miRNAs), a recently discovered class of small endogenous noncoding RNAs (∼20-22 nt) that are considered important gene regulators and have been shown to play an important role in plant development as well as plant tolerance to abiotic stresses such as drought, salinity, cold, and heavy metal. Low concentrations (0.1 and 1 %) of TiO(2) nanoparticles dramatically induced miRNA expression in tobacco seedlings with miR395 and miR399 exhibiting the greatest fold changes of 285-fold and 143-fold, respectively. The results of this study show that TiO(2) nanoparticles have a negative impact on tobacco growth and development and that miRNAs may play an important role in tobacco response to heavy metals/nanoparticles by regulating gene expression.

Dietary lysine affects chickens from local Chinese pure lines and their reciprocal crosses

The objective of this experiment was to evaluate the effect of dietary lysine concentration on meat quality and carcass traits in 2 chicken lines, SD02 and SD03, and their crosses, both originating from a Chinese native breed, the Erlang Mountainous chicken. The lines were selected for 4 generations by Sichuan Agricultural University (Ya'an, China); for the present study, chickens from the 2 lines and their crosses were randomly assigned at hatch to 1 of 2 dietary groups. One group was offered diets containing 1, 0.85, and 0.70% total lysine, whereas the other was offered diets with 1.15, 1, and 0.85% total lysine from d 1 to 28, d 29 to 49, and d 50 to 70, respectively. In total, 252 chickens were commercially processed at 70 d old. Traits measured included live BW, subcutaneous fat thickness, weight of carcass, eviscerated carcass, semi-eviscerated carcass, breast muscle (left pectoralis major and minor), leg muscle (boneless left drum plus thigh), heart, gizzard, proventriculus, spleen, liver, comb, and abdominal fat, color parameters lightness, redness, or yellowness (L*, a*, and b*), pH, and breast muscle intramuscular fat content. The results indicated that, although dietary lysine concentration did not affect subcutaneous fat thickness, color parameters, pH, intramuscular fat content, and organ weights, there were effects on feed conversion and muscle and BW (P < 0.05). Males and females displayed major differences in feed conversion, BW, muscle growth, and organ weight. The Line SD02 chickens grew faster and displayed less fat deposition and superior feed conversion compared with Line SD03 and the reciprocal crosses. In conclusion, performance of the chicken stocks evaluated in this study differs substantially in muscle weight and carcass weight.

Characterization of small RNAs and their target genes in wheat seedlings using sequencing-based approaches

Wheat is the most highly cultivated plant species for its grain production throughout the world. Because small RNA-dependent gene regulation is critical for successful completion of plant life cycle including its productivity, identification of not only miRNAs but also confirming their targets in wheat is important. To identify small RNAs including novel miRNAs as well as miRNA targets in wheat, we constructed small RNA and degradome libraries from wheat seedlings. Small RNA analysis resulted in identification of most conserved miRNAs including novel miRNAs that can be grouped into 32 miRNA families. The sequence analysis also led to the characterization of two abundantly expressed rRNA-derived small RNAs. To identify miRNA targets, degradome library was sequenced and the bioinformatic analysis confirmed 53 genes as targets for miRNAs and Tas3-siRNAs. Degradome analysis also confirmed a conserved fine-tuning mechanism of Tas3-siRNA abundance by siRNA-mediated silencing of TAS3 transcripts in diverse plant species. These findings added additional information to the small RNA knowledge-base in wheat.

Identification and association of polymorphisms in CAPN1 and CAPN3 candidate genes related to performance and meat quality traits in chickens

Meat quality is an important feature for the poultry industry and is associated with consumer satisfaction. The calpain 1 (CAPN1) gene is related to the tenderness process of meat post- mortem, and the calpain 3 (CAPN3) gene plays an important role in myofibrillar organization and growth. The objective of the present study was to identify polymorphisms in these genes and to determine the association between these polymorphisms and traits of economic interest in poultry. Eleven animals (F₁) from an experimental poultry population at Embrapa Swine and Poultry were used to identify the polymorphisms. Four single nucleotide polymorphisms (SNPs) were found in the CAPN1 gene, and one SNP was found in the CAPN3 gene. A polymorphism from each gene was selected for genotyping in 152 chickens from the Embrapa F₂ experimental population and 311 chickens from a commercial population. Polymorphism g.2554T>C (CAPN1) was associated with body weight at 35 to 42 days, thigh weight, breast weight, carcass weight, and meat lightness content. SNP g.15486C>T (CAPN3) was associated with thigh yield, thawing-cooking loss, and shear force. Results suggest the possibility of using molecular markers in CAPN1 and CAPN3 genes as a tool for performance and meat quality traits in poultry breeding programs.

Association between cholecystokinin type A receptor haplotypes and growth traits in Japanese Hinai-dori crossbred chickens

We previously identified quantitative trait loci for body weight and average daily gain in a common region between MCW0240 (chr 4: 69.9 Mb) and ABR0622 (chr 4: 86.3 Mb) on chicken chromosome 4 in an F(2) resource population produced by crossing low- and high-growth lines of the Hinai-dori breed. Cholecystokinin type A receptor (CCKAR) is a candidate gene affecting growth traits in the region. In this study, we genotyped polymorphisms of the CCKAR gene and investigated its association with growth traits in a Hinai-dori F(2) intercross population. All the exons of the CCKAR gene in the parental population were subjected to PCR amplification, nucleotide sequenced and haplotypes identified. To distinguish resultant diplotype individuals in the F(2) population, a mismatch amplification mutation assay was performed. Five haplotypes (Haplotypes 1-5) were accordingly identified. Six genotypes produced by the combination of three haplotypes (Haplotype 1, 3, and 4) were examined in order to identify associations between CCKAR haplotypes and growth traits. The data indicate that Haplotype 1 was superior to Haplotype 3 and 4 in body weight at 10 and 14 weeks of age, average daily gain between 4 and 10 weeks, 10 and 14 weeks, and 0 and 14 weeks of age. It was concluded that CCKAR is a useful marker of growth traits and could be used to develop strategies for improving growth traits in the Hinai-dori breed.

Characterization of the expression profile of calpain-3 (CAPN3) gene in chicken

Calpain-3 is a skeletal muscle-specific protease and participates in the regulation of myogenesis. In this study, we quantified the expression of calpain-3 (CAPN3) mRNA in a Chinese local chicken breed (Sichuan Mountainous Black-boned chicken [MB]), to discern the tissue and ontogenic expression pattern. Meanwhile, we compared the CAPN3 mRNA expression pattern in MB chicken at 10 weeks with a commercial meat type chicken line (S01) of the same age to identify the unique expression pattern under different genetic background. A real time quantitative PCR (qRT-PCR) assay was developed for an accurate measurement of its expression in various tissues from chickens at different ages (0, 2, 4, 6, 8, 10, and 12 weeks). Expression of the CAPN3 mRNA was detected in the selected tissues, regardless of age. The breast muscle and leg muscle tissues had a significantly higher expression than the other tissues from the same individual (P < 0.01). Overall, the CAPN3 mRNA level exhibited a "rise-decline" developmental change in detected tissues except for brain. The S01 chicken had a higher expression of the CAPN3 mRNA in detected tissues than the MB chicken at 10 weeks. The present expression data of chicken CAPN3 gene may provide some information to shed light on the tissue and ontogenic expression pattern during chicken development.

Gene expression profiling of skeletal muscle of nursing piglets

To gain insight into the regulation mechanism associated with the rapid gain in skeletal muscle during neonatal period, gene expression profiles of skeletal muscle of nursing pigs was investigated using Affymetrix Porcine GeneChip. A total of 1094 transcripts were detected as differential expression over time course tested (p<0.01, q<0.05). With combinative use of partitioning around medoid and hierarchical clustering, three clusters of transcripts with distinct temporal expression were defined. Gene functional categories and pathways, particularly involved in cell signaling, cell cycle, cell adhesion, ECM-receptor interaction, glycolysis, protein synthesis and degradation, and intracellular transport, were identified. Moreover, we showed 49 of the differentially expressed genes within published QTL regions or with marked deletion effects. Our study demonstrates previously uncharacterized changes in transcription accompanying early postnatal growth of skeletal muscle of pigs. It has highlighted potential cascades and important candidates for further investigation on controlling of postnatal muscle growth.

Association of FATP1 gene polymorphisms with chicken carcass traits in Chinese meat-type quality chicken populations

In this study, we aimed to detect the single nucleotide polymorphisms (SNPs) of the chicken FATP1 gene and discern the potential association between FATP1 SNPs and chicken carcass traits. A total of 620 meat-type quality chickens from six commercial pure lines (S01, S02, S03, S05, S06 and D99) and two cross lines (S05 × S01 and S06 × S01) were screened by using the single-strand conformational polymorphism analysis (SSCP) and DNA sequencing. Five SNPs [g.49360G > A, g.48195G > A, g.46847A > G, g.46818A > G, and g.46555A > G] were identified in chicken FATP1 gene. SNP g.46818 A > G was a rare variant and was not considered in the subsequent analysis. Sixteen haplotypes were reconstructed on the basis of the other four SNPs. The linear regression model analysis indicated that there were significant associations of certain diplotypes with part of carcass traits, such as live weight (LW), carcass weight (CW), and semi-eviscerated weight (SEW) (P < 0.05). In particular, diplotype H2H4 had a negative effect on LW, CW, SEW, and abdominal fat weight (AW); diplotype H6H10 had the highest reducing effect on subcutaneous fat thickness (SFT). Our results suggested that FATP1 gene polymorphisms were associated with chicken carcass traits or was linked with the major gene. The SNPs in this gene may be utilized as potential markers for marker-assisted selection (MAS) during chicken breeding.