Effect of single nucleotide polymorphisms of CAPN1 and CAST genes on meat traits in Nellore beef cattle (Bos indicus) and in their crosses with Bos taurus

The objectives of this work were to study the segregation of single nucleotide polymorphisms of the calpain 1, large subunit ( CAPN1 ) and calpastatin ( CAST ) genes in Nellore ( Bos indicus ) and Nellore × Bos taurus beef cattle, as well as to evaluate their effects on meat traits. For this, 300 animals, including 114 Nellore, 67 Angus × Nellore, 44 Rubia Gallega × Nellore, 41 Canchim, 19 Brangus three-way crosses and 15 Braunvieh three-way crosses, were genotyped for the CAPN4751 [AF_248054.2:g.6545C>T (GenBank accession AF248054.2 )] and CAST/DdeI [AF_159246.1:g.2959A>G (GenBank accession AF159246.1 )] polymorphisms and phenotyped for Ribeye Area, Backfat Thickness, Intramuscular Fat, Shear Force (SF) and Myofibrillar Fragmentation Index (MFI). In relation to the CAPN4751 polymorphism, a frequency of 10.5% was observed for the C allele in the Nellore breed. In the total sample of studied animals, a significant association was found between genotypes and meat tenderness, assessed by SF ( P  = 0.005) and MFI ( P  = 0.008), with genotype CT being more favourable than TT. For the CAST/DdeI polymorphism, a frequency of 55.7% was found for the A allele in the Nellore breed. In the total sample, a significant association was observed between genotypes and meat tenderness – SF ( P  = 0.004) and MFI ( P  = 0.006), with genotype AA being more favourable than AG. The relationship between genotypes and aged meat tenderness in confluence with the distribution of favourable alleles shows great potential for application of the CAPN4751 and CAST/DdeI polymorphisms in the genetic improvement of the Nellore breed, whilst contributing to the validation, in this breed and in its crosses with B. taurus , of the association results previously described in the literature.     

Association analysis of adiponectin and somatostatin polymorphisms on BTA1 with growth and carcass traits in Angus cattle

This study tested positional candidate genes adiponectin (ADIPOQ) and somatostatin (SST) for effects on carcass traits in a commercially relevant cattle population. Both genes are located within a region of BTA1 previously reported to harbour quantitative trait loci (QTL) that affect marbling, quality grade, yield grade, ribeye area and weaning weight in Bos taurus x Bos indicus crosses. Except for the first intron of ADIPOQ, both genes, including over 2 kb upstream of the promoters, were sequenced in five registered Angus sires to identify polymorphisms. A variable copy duplication and three single nucleotide polymorphisms (SNPs) in ADIPOQ and one SNP in SST were genotyped and tested for association with 19 traits in a 14-generation pedigree of 1697 registered Angus artificial insemination sires representing all the major USA lineages of the breed. Linear models that parameterized predicted genetic merits in terms of allele substitution effects were fit by weighted least squares, and goodness-of-fit tests were employed to differentiate causal mutations or polymorphisms in strong linkage disequilibrium (LD) with causal mutations from markers in weak LD with QTL. We confirmed the presence of QTL affecting marbling, ribeye muscle area and fat thickness in the vicinity of SST and ADIPOQ on BTA1 in Angus; excluded SST as underlying the ribeye muscle area QTL; and excluded ADIPOQ as underlying the marbling score QTL. However, association analysis provides very limited information about QTL location and has little intrinsic value when performed in the absence of linkage or LD analysis using flanking marker data to localize the QTL effect relative to positional candidate genes.     

Association between JY-1 gene polymorphisms and reproductive traits in beef cattle

Reproductive traits have a high economic value and it is interesting to include them in the selection objectives of an animal breeding program. These traits generally show low heritability and molecular markers may therefore be used in genetic evaluations to improve the accuracy of predictions. The JY-1 gene is expressed in the oocyte and it is associated with folliculogenesis and early embryo development. It has been suggested to affect reproductive traits. In this study, exons 1 and 2 of the JY-1 gene were studied in 385 Nellore females by PCR-sequencing. Seventeen polymorphisms were identified. After analysis of linkage disequilibrium, association tests were performed between eight SNPs and the occurrence of early pregnancy, age at first calving, days to calving, and reconception of primiparous heifers. Seven SNPs were significant for three traits. The most significant was chr29:12,999 T/A (p = 0.003) which was associated with the occurrence of early pregnancy. This SNP might be involved in protein translation inhibition since it affects the initial methionine codon. The JY-1, an oocyte specific gene, influences reproductive traits; further studies investigating other regions of the gene or other genes expressed in tissues of the female reproductive system would be interesting to be performed.     

Association among growth, food consumption-related traits and amylase gene polymorphism in the Pacific oyster Crassostrea gigas

To examine further a previously reported association between amylase gene polymorphism and growth in the Pacific oyster Crassostrea gigas, ecophysiological parameters and biochemical and molecular expression levels of alpha-amylase were studied in Pacific oysters of different amylase genotypes. Genotypes that previously displayed significantly different growth were found to be significantly different for ingestion and absorption efficiency. These estimated parameters, used in a dynamic energy budget model, showed that observed ingestion rates (unlike absorption efficiencies) allowed an accurate prediction of growth potential in these genotypes. The observed association between growth and amylase gene polymorphism is therefore more likely to be related to ingestion than to absorption efficiency. Additionally, relative mRNA levels of the two amylase cDNAs were also strongly associated with amylase gene polymorphism, possibly reflecting variation in an undefined regulatory region, although no corresponding variation was observed in specific amylase activity. Amylase gene sequences were determined for each genotype, showing the existence of only synonymous or functionally equivalent non-synonymous polymorphisms. The observed associations among growth, food consumption-related traits and amylase gene polymorphism are therefore more likely to be related to variation in the level of amylase gene expression than to functional enzymatic variants.     

Association of an insulin-like growth factor 1 gene microsatellite with phenotypic variation and estimated breeding values of growth traits in Canchim cattle

A population of 1398 Canchim (CA) cattle was genotyped to assess the association of an insulin-like growth factor 1 (IGF1) gene microsatellite with phenotypic variation and estimated breeding values of pre-weaning, weaning and post-weaning growth traits. After an initial analysis, the IGF1 genotype only had a significant effect (P < 0.05) on birth weight (BW) and weaning weight adjusted to 240 days (WW240). For these two traits, direct and maternal breeding values were estimated using the restricted maximum likelihood (reml). Two analyses were carried out. In the first (Model I), all fixed effects were fitted. In the second (Model II), the fixed effect of the IGF1 genotype was omitted. The estimated genetic and phenotypic components of variance were similar for every trait in both models. For Model I, estimated direct and maternal heritabilities were 0.26 and 0.16 for BW and 0.23 and 0.14 for WW240 respectively. The genetic and phenotypic correlations between BW and WW240 were 0.38 and 0.38 (Model I) and 0.19 and 0.38 (Model II) respectively. Fifty animals were classified according to their direct and maternal breeding values for both traits. Spearman rank-order correlation between animal rankings in the two models was used to assess the effect of including the IGF1 genotype in the model. Non-significant values from this correlation were indicative of a difference in breeding value rankings between the two approaches. The IGF1 gene was found to be associated with phenotypic variation and breeding values in the early phase of growth.     

Restriction fragment length polymorphisms in dairy and beef cattle at the growth hormone and prolactin loci

Two bovine populations, a Holstein-Friesian dairy stock and a synthetic (Baladi X Hereford X Simmental X Charolais) beef stock, were screened for restriction fragment length polymorphisms (RFLPs) at the growth hormone and prolactin genes. Most RFLPs at the growth hormone gene are apparently the consequence of an insertion/deletion event which was localized to a region downstream of the structural gene. The restriction map for the genomic region including the growth hormone gene was extended. Two HindIII RFLPs at the growth hormone locus, as well as several RFLPs at the prolactin gene, seemed to be the consequence of a series of point mutations. The results are discussed in terms of the possibility that minor genomic variability underlies quantitative genetic variation.     

Effects of polymorphic microsatellites in the regulatory region of IGF1 and GHR on growth and carcass traits in beef cattle

Growth hormone (GH), insulin-like growth factors 1 and 2 (IGF1 and IGF2) and their associated binding proteins and transmembrane receptors (GHR, IGF1R and IGF2R) play an important role in the physiology of mammalian growth. The objectives of the present study were to estimate the allele and genotype frequencies of microsatellite markers located in the 5'-regulatory region of the IGF1 and GHR genes in beef cattle belonging to different genetic groups and to determine effects of these markers on growth and carcass traits in these animals under an intensive production system. For this purpose, genotyping was performed on 384 bulls including 79 Nellore, 30 Canchim (5/8 Charolais + 3/8 Zebu) and 275 crossbred animals originating from crosses of Simmental (1/2 Simmental, n = 30) and Angus (1/2 Angus, n = 245) sires with Nellore females. The effects of substituting L allele for S allele of GHR microsatellite across Nellore, Canchim and 1/2 Angus were significant for weight gain and body weight (P < 0.05). The IGF1 microsatellite allele substitutions of 229 for 225 within Nellore group and of 225 for 229 within 1/2 Angus were not significant for any of the traits.     

Breed variation and genetic parameters for growth and body development in diverse beef cattle genotypes

Conformation scores can account for more than 20% of cattle price variation at Australian livestock sales. However, there are limited available references which define genetic factors relating objective live developmental traits to carcass composition. Weaning and post-weaning weight, height, length, girth, muscle (ratio of stifle to hip width) and fat depth of 1202 progeny from mature Hereford cows (637) mated to seven sire breeds (Jersey, Wagyu, Angus, Hereford, South Devon, Limousin and Belgian Blue) were examined for growth and development across ages. Crossbred Wagyu and Jersey were both lighter in weight and smaller in size (height, length and girth) than purebred Hereford and crossbred Angus, South Devon, Limousin and Belgian Blue. Within the five larger crossbreds, there were significant changes in relative weight from weaning to 600 days. Sire breeds differed in fat depth, with Angus being the fattest (9% on average fatter than Hereford and Wagyu), and Jersey 5% less fat than Hereford, followed by South Devon and Limousin (19% lower than Hereford) and Belgian Blue (39% lower than Hereford). Direct heritability ranged from 19 to 42% and was higher than the proportion of total phenotypic variance accounted for by maternal effects (which ranged from 0 to 17%) for most body measurement traits except for weight (38 v. 18%) and girth (36 v. 9%) traits at weaning, an indication of maternal effect on some body conformation traits at early ages. Muscularity (19 to 44%) and fat depth (26 to 43%) were moderately to highly heritable across ages. There were large differences for growth and the objective measures of body development between crossbreds with a degree of overlap among the progeny of the seven sire breeds. The variation between genetic (positive) and environmental (negative) correlations for dry versus wet season average daily gains in weight and fat, suggested the potential use of live-animal conformation traits for within breed selection of genetically superior animal in these traits across seasons.     

Relationship between an indel mutation within the SIRT4 gene and growth traits in Chinese cattle

Abstract

Growth traits are mainly determined by genetic factors. SIRT4, a class II sirtuin, predominantly acts as an ADP-ribosyltransferase and inhibits fatty acid oxidation. In this study, a total of 1005 cattle belonging to five indigenous Chinese breeds were used to evaluate the relationship between the potential insertions/deletions (indels) within the SIRT4 gene and growth traits. The results revealed that only one intronic variation was present, which showed Hardy–Weinberg equilibrium (p?>?0.05) in all the populations. The relationship analyses indicated that this indel was significantly associated with growth traits (p?<?0.05), implying that SIRT4 significantly affects the growth traits. Therefore, the deletion mutation within the SIRT4 gene could be considered as a molecular marker to screen for growth traits in the cattle industry.     

Research on association between variants and haplotypes of TRPV1 and TRPA1 genes with growth traits in three cattle breeds

The objective of this study was to examine the association of transient receptor potential vanilloid 1 (TRPV1) and transient receptor potential ankyrin 1 (TRPA1) genes polymorphisms with growth traits in three Chinese cattle breeds (Jiaxian red cattle, Qinchuan cattle and Luxi cattle). Through experiments we identified three single nucleotide polymorphisms (SNPs) in these three cattle breeds TRPV1 and TRPA1 genes using PCR-SSCP, (forced) PCR-RFLP methods. Three of these polymorphisms are all synonymous mutation which includes (NW_003104493.1: 30327 C?>?T), (NW_003104493.1: 33394 A?>?G) and (NW_003104493.1: 38471?G?>?A) are in exons. The other three polymorphisms are located at 3'UTR. Furthermore, we evaluated the haplotype frequency and the statistical analyses indicated that these SNPs of TRPV1 and TRPA1 genes were associated with bovine body height, body length, waist angle width, hucklebone width, cross ministry height, chest qingwidth (p?<?0.05) and recommendation height, cannon circumference (p?<?0.01) of Qingchuan cattle; body length, waist angle width (p?<?0.05) of Jiaxian red cattle; body weight, Body length, cannon circumference, chest circumference (p?<?0.05) and body height (p?<?0.01) of Luxi cattle. Our result confirms the polymorphisms in the TRPV1 and TRPA1 genes are associated with growth traits that may be used for marker-assisted selection (MAS) in three beef breeds programs.     

Quantitative trait loci for chemical body composition traits in pigs and their positional associations with body tissues, growth and feed intake

In this study, quantitative trait loci (QTL) for chemical and physical body composition, growth and feed intake in pigs were identified in a three-generation full-sib population, developed by crossing Pietrain sires with a commercial dam line. Phenotypic data from 315 F₂ animals were available for protein and lipid deposition measured in live animals by the deuterium dilution technique at 30-, 60-, 90-, 120- and 140-kg body weight. At 140-kg body weight, carcass characteristics were measured by the AutoFOM grading system and after dissection. Three hundred and eighty-six animals from 49 families were genotyped for 51 molecular markers covering chromosomes SSC2, SSC4, SSC8, SSC9, SSC10 and SSC14. Novel QTL for protein (lipid) content at 60-kg body weight and protein (lipid) accretion from 120 to 140 kg were detected on SSC9 near several previously detected QTL for lean and fat tissue in neck, shoulder and ham cuts. Another QTL for lipid accretion was found on SSC8, closely associated with a QTL for intramuscular fat content. QTL for daily feed intake were detected on SSC2 and SSC10. The favourable allele of a QTL for food conversion ratio (FCR) on SSC2 was associated with alleles for increased lean tissue and decreased fat tissue. Because no QTL for growth rate were found in the region, the QTL for FCR is most likely due to a change in body composition. These QTL provide insights into the genomic regulation of chemical or physical body composition and its association with feed intake, feed efficiency and growth.     

Synergism between altered cortical polarity and the PI3K/TOR pathway in the suppression of tumour growth

Loss of function of pins (partner of inscuteable) partially disrupts neuroblast (NB) polarity and asymmetric division, results in fewer and smaller NBs and inhibits Drosophila larval brain growth. Food deprivation also inhibits growth. However, we find that the combination of loss of function of pins and dietary restriction results in loss of NB asymmetry, overproliferation of Miranda-expressing cells, brain overgrowth and increased frequency of tumour growth on allograft transplantation. The same effects are observed in well-fed pins larvae that are mutant for pi3k (phosphatidylinositol 3-kinase) or exposed to the TOR inhibitor rapamycin. Thus, pathways that are sensitive to food deprivation and dependent on PI3K and TOR are essential to suppress tumour growth in Drosophila larval brains with compromised pins function. These results highlight an unexpected crosstalk whereby the normally growth-promoting, nutrient-sensing PI3K/TOR pathway suppresses tumour formation in neural stem cells with compromised cell polarity.