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Comparative transcriptome analysis of Qinchuan and Wagyu cattle reveals lnc11599 as a negative regulator of intramuscular fat deposition.

BACKGROUND: Intramuscular fat (IMF) content is a critical factor determining beef quality, influenced by various factors including breed and age. However, the regulatory role of long non-coding RNAs (lncRNAs) in IMF deposition remains unclear. METHODS: This study investigated IMF deposition in the longissimus dorsi muscle of one- and two-year-old Qinchuan and Wagyu cattle through histological examination and fat content measurement. Based on transcriptome sequencing data of intramuscular fat tissue, differential expression analysis and weighted gene co-expression network analysis (WGCNA) were performed to identify lncRNAs associated with IMF deposition. The effects of a key candidate lncRNA on the adipogenic differentiation of cattle intramuscular preadipocytes were further examined. RESULTS: Results showed that Wagyu cattle exhibited stronger IMF deposition capacity than Qinchuan cattle across all age groups, with IMF content increasing with age in both breeds. We identified 7,910 lncRNAs from intramuscular fat tissue transcriptome data, including 6,455 novel lncRNAs. Through integrated differential expression analysis and WGCNA, 88 lncRNAs closely associated with IMF deposition were screened from two-year-old Qinchuan and Wagyu cattle. Notably, lnc11599 was significantly upregulated in Qinchuan cattle intramuscular fat tissue, but its expression decreased during intramuscular preadipocyte differentiation. Functional experiments demonstrated that lnc11599 knockdown enhanced adipogenic differentiation capacity, manifested as a highly significant increase in lipid accumulation, upregulation of key adipogenic genes at the mRNA level, together with increases in total fatty acid content and unsaturated fatty acid proportion. CONCLUSIONS: This study established the lncRNA expression profiles in intramuscular fat tissue of Qinchuan and Wagyu cattle across different developmental stages, and demonstrated that lnc11599 acts as a negative regulator of intramuscular fat deposition. These findings provide new directions for elucidating the mechanisms of cattle IMF deposition and offer potential targets for genetic improvement of beef quality.

Animals↗

Quantitative trait loci analysis for growth and carcass traits in a half-sib family of purebred Japanese Black (Wagyu) cattle.

We used a half-sib family of purebred Japanese Black (Wagyu) cattle to locate economically important quantitative trait loci. The family was composed of 348 fattened steers, 236 of which were genotyped for 342 microsatellite markers spanning 2,664 cM of 29 bovine autosomes. The genome scan revealed evidence of 15 significant QTL (<5% chromosome-wise level) affecting growth and carcass traits. Of the 15 QTL, six QTL were significant at the 5% experiment-wise level and were located in bovine chromosomes (BTA) 4, 5, and 14. We analyzed these three chromosomes in more detail in the 348 steers, with an average marker interval of 1.2 cM. The second scan revealed that the same haplotype of the BTA 4 region (52 to 67 cM) positively affected LM area and marbling. We confirmed the QTL for carcass yield estimate on BTA 5 in the region of 45 to 54 cM. Five growth-related QTL located on BTA 14, including slaughter and carcass weights, were positively affected by the same region of the haplotype of BTA 14 (29-51 cM). These data should provide a useful reference for further marker-assisted selection in the family and positional cloning research. The research indicates that progeny design with moderate genotyping efforts is a powerful method for detecting QTL in a purebred half-sib family.

Animals↗

Chediak-Higashi syndrome mutation and genetic testing in Japanese black cattle (Wagyu).

Chediak-Higashi Syndrome (CHS) is an autosomal recessive disorder that affects several species including mice, humans, and cattle. Evidence based on clinical characteristics and somatic cell genetics suggests that mutations in a common gene cause CHS in the three species. The CHS locus on human chromosome 1 and mouse chromosome 13 encodes a lysosomal trafficking regulator formerly known as LYST, now known as CHS1, and is defective in CHS patients and beige mice, respectively. We have mapped the CHS locus to the proximal region of bovine chromosome 28 by linkage analysis using microsatellite markers previously mapped to this chromosome. Furthermore, we have identified a missense A:T-->G:C mutation that results in replacement of a histidine with an arginine residue at codon 2015 of the CHS1 gene. This mutation is the most likely cause of CHS in Wagyu cattle. In addition, we describe quick, inexpensive, PCR based tests that will permit elimination of the CHS mutation from Wagyu breeding herds.

Alleles↗

Relationship of fatty acid composition to intramuscular fat content in beef from crossbred Wagyu cattle.

The deposition of i.m. fat, or marbling, in cattle is recognized as a desirable carcass trait in North American beef grading schemes. In order to investigate the relationship between degree of marbling and fatty acid composition of whole bovine muscle, we extracted the total lipid from pars costalis diaphragmatis (PCD) (n = 23) and longissimus (n = 36) muscles from Wagyu crossbred cattle that were assigned Canadian Grading Agency marbling scores ranging from 1 to 8 on an inverse 10-point scale (i.e., a score of 1 indicated "very abundant" marbling and a score of 10 would be assigned to a carcass "devoid" of marbling). Fatty acid methyl esters (FAME) of the total lipid and triacylglycerol fractions were resolved and quantified through GLC. Marbling scores were negatively associated with total lipid from both PCD (r = -.57, P < .01) and longissimus (r = -.80, P < .001). Differences between PCD and longissimus were found for almost all FAME studied from both lipid fractions, but no differences (P > .05) were seen when the monounsaturated:saturated fatty acid (MUFA/SFA) ratios were compared. Heifers had higher (P < .05) oleic acid content and lower (P < .05) palmitic acid content in lipid extracted from both muscles, resulting in higher (P < .05) MUFA/SFA ratios than those for steers. The relative amount of myristic acid increased as the lipid content (total lipid and triacylglycerol) increased in either longissimus (r values from .48 to .55; n = 36; P < .01) or PCD muscles (r from .67 to .76; n = 23; P < .001). The relative amount of linoleic acid (cis-9, cis-12 isomer) from total lipid was negatively associated with all chemical measurements of lipid from the longissimus (r from -.52 to -.64; n = 36; P < .001) and PCD muscles (r from -.75 to -.85; n = 23; P < .001). This association was not significant (P > .1) for either muscle when linoleic acid from the triacylglycerol fraction was examined, suggesting the negative association between this fatty acid and lipid content was due to a dilution of membrane phospholipids with increasing triacylglycerol. Indices of fatty acid elongase activity, calculated from FAME data, implicated the balance between this enzyme activity and fatty acid synthase as a source of variation between animals displaying various degrees of marbling and worthy of further investigation to better understand the process of marbling fat deposition in beef cattle.

Adipose Tissue↗

Mapping of quantitative trait loci for carcass traits in a Japanese Black (Wagyu) cattle population.

To detect quantitative trait loci (QTL) that influence economically important traits in a purebred Japanese Black cattle population, we performed a preliminary genome-wide scan using 187 microsatellite markers across a paternal half-sib family composed of 258 offspring. We located six QTL at the 1% chromosome-wise level on bovine chromosomes (BTA) 4, 6, 13, 14 and 21. A second screen of these six QTL regions using 138 additional paternal offspring half-sib from the same sire, provided further support for five QTL: carcass weight on BTA14 (22-39 cM), one for rib thickness on BTA6 (27-58 cM) and three for beef marbling score (BMS) on BTA4 (59-67 cM), BTA6 (68-89 cM) and BTA21 (75-84 cM). The location of QTL for subcutaneous fat thickness on BTA13 was not supported by the second screen (P > 0.05). We determined that the combined contribution of the three QTLs for BMS was 10.1% of the total variance. The combined phenotypic average of these three Q was significantly different (P < 0.001) from those of other allele combinations. Analysis of additional half-sib families will be necessary to confirm these QTL.

Animals↗

Genetic and economic evaluation of Japanese Black (Wagyu) cattle breeding schemes.

Deterministic simulation was used to evaluate 10 breeding schemes for genetic gain and profitability and in the context of maximizing returns from investment in Japanese Black cattle breeding. A breeding objective that integrated the cow-calf and feedlot segments was considered. Ten breeding schemes that differed in the records available for use as selection criteria were defined. The schemes ranged from one that used carcass traits currently available to Japanese Black cattle breeders (Scheme 1) to one that also included linear measurements and male and female reproduction traits (Scheme 10). The latter scheme represented the highest level of performance recording. In all breeding schemes, sires were chosen from the proportion selected during the first selection stage (performance testing), modeling a two-stage selection process. The effect on genetic gain and profitability of varying test capacity and number of progeny per sire and of ultrasound scanning of live animals was examined for all breeding schemes. Breeding schemes that selected young bulls during performance testing based on additional individual traits and information on carcass traits from their relatives generated additional genetic gain and profitability. Increasing test capacity resulted in an increase in genetic gain in all schemes. Profitability was optimal in Scheme 2 (a scheme similar to Scheme 1, but selection of young bulls also was based on information on carcass traits from their relatives) to 10 when 900 to 1,000 places were available for performance testing. Similarly, as the number of progeny used in the selection of sires increased, genetic gain first increased sharply and then gradually in all schemes. Profit was optimal across all breeding schemes when sires were selected based on information from 150 to 200 progeny. Additional genetic gain and profitability were generated in each breeding scheme with ultrasound scanning of live animals for carcass traits. Ultrasound scanning of live animals was more important than the addition of any other traits in the selection criteria. These results may be used to provide guidance to Japanese Black cattle breeders.

Animals↗

Genetic mapping of a locus associated with bovine chronic interstitial nephritis to chromosome 1.

Chronic interstitial nephritis with diffuse zonal fibrosis (CINF) occurs in Japanese Black cattle (Wagyu) as an autosomal recessive disorder leading to death prior to puberty, first six months or a year of life. We performed a genome-wide scan using microsatellite markers in a Wagyu pedigree segregating for CINF and mapped the CINF locus to bovine chromosome 1. CINF was closest to microsatellites BM9019 and INRA49 (Z score = 12.0; P < 3.4 x 10(-10)).

Animals↗

Characterization of 42 highly polymorphic bovine microsatellite markers.

We have isolated 42 highly polymorphic microsatellite (GT/CA)n markers from Japanese black cattle Wagyu (Bos taurus). Forty-one of the markers were assigned to bovine autosomes with lod scores > 6, through linkage analyses performed on the International Bovine Reference Family Panel (IBRP). The remaining marker showed X-linked inheritance. These markers exhibited an average heterozygosity value of 0.67 with between four and 17 alleles on the IBRP.

Alleles↗

Clinical features of renal tubular dysplasia, a new hereditary disease in Japanese Black cattle.

A new hereditary disease characterised by renal failure, poor growth and long hooves in Japanese Black cattle (wagyu) has been recognised in a region of central Japan since 1990. The number of calves affected has increased gradually, with the incidence reaching 17 of 485 (3.51 per cent) in 1995. Almost all the calves were slightly undersized at birth, and repeatedly had diarrhoea during the neonatal period. They began to show signs of growth retardation with proportional body and elongation of the hooves from about two to five months of age, but they had an almost normal or only slightly decreased appetite. The concentrations of urea nitrogen, creatinine and inorganic phosphorus in serum were high, and the affected calves excreted diluted urine frequently. Among 25 cases, the urine of 21 contained occult blood, 24 contained protein and two contained glucose. In 29 calves observed for 30 to 130 days, the course of the disease varied; in 21 of them it remained unchanged, six became gradually worse and two became severely debilitated and died. The disease was diagnosed as renal tubular dysplasia by histopathological examination.

Animals↗

A new deletion mutation in bovine Claudin-16 (CL-16) deficiency and diagnosis.

Bovine claudin-16/paracellin-1 (CL-16/PCLN-1) deficiency is an autosomal recessive disorder caused by a 37-kb deletion mutation containing the first four exons of the CL-16 gene, which leads to the absence of the CL-16 transcript (type-1 mutation). A PCR-based DNA test for the CL-16 mutation (type-1) was used to screen a herd of Wagyu cattle. A recent report suggested that affected cattle can be bred by dams diagnosed as normal, suggesting the presence of a new mutation in the CL-16 locus. We identified the new mutation as a 56-kb deletion containing exon-1 to -4 and 21-bp of exon-5 of CL-16, and refer to this as a type-2 mutation. A DNA test for specific for this mutation was then established.

Animals↗

Genetic effects on fatty acid composition of carcass fat of Japanese Black Wagyu steers.

Two hundred ninety-three Japanese Black Wagyu steers derived from 34 sires were used to investigate genetic effects on the fatty acid composition of carcass fat. All steers were fed identical diets for 365 d and slaughtered at similar ages. If the percentage of genetic contribution of sire A, B, or C was not lower than 25%, steers were classified into groups A, B, and C, respectively. Fatty acid compositions differed depending on deposit sites. Mean percentage of monounsaturated fatty acids (MUFA) tended to be higher in the outer parts than in the inner parts of the body. Percentage of MUFA in carcass fat was negatively correlated with withers height and BW and positively correlated with meat quality score and marbling score. Fatty acid compositions of the 34 sire groups varied, and mean percentages of MUFA in i.m. fat ranged from 47.71 to 54.77%. Steers in the C group grew larger than those in the A or B group. Mean percentages of MUFA for i.m. fat in the A, B, and C groups (52.83, 51.88, and 50.33%, respectively) differed (P < 0.05) from each other. Steers in the C group had higher (P < 0.05) percentages of saturated fatty acids than those in the A or B groups. Percentages of genetic contribution of sires B (P < 0.05) and C (P < 0.001) were negatively correlated with percentage of MUFA in i.m. fat. These results suggested that genetic factors affected fatty acid composition of carcass fat in Japanese Black Wagyu cattle and that some sires had potent genetic factors affecting this composition.

Adipose Tissue↗

Relationship among GeneSTAR marbling marker, intramuscular fat deposition, and expected progeny differences in early weaned Simmental steers.

Research has demonstrated that triiodothyronine and thyroxin are correlated with marbling (MARB) deposition in Wagyu cattle. Polymorphisms in the 5' region of the thyroglobulin gene have been associated with an improvement in overall fattening and could be used as a gene marker for MARB. The commercially available GeneSTAR MARB test measures the specific thyroglobulin gene polymorphism and identifies cattle as having 0, 1, or 2 copies of the allele; these are identified as 0-STAR, 1-STAR, or 2-STAR, respectfully. Early weaned Simmental steers (n = 192) of known genetics were individually fed over a repeated 4-yr trial period to determine the correlations between GeneSTAR MARB test [Genetic Solutions/Bovigen Pty. Ltd. (Australia) in conjunction with Frontier Beef Systems, LLC (Louisville, CO)] results and intramuscular fat (IMF) deposition. Yearling weight, MARB, percent retail cuts, and carcass weight EPD were calculated for each steer. Steers were weaned at 88.0 +/- 1.1 d, pen-fed a high-concentrate diet for 84.5 +/- 0.4 d before allotment, and subsequently individually fed a 90% concentrate diet composed primarily of cracked corn and corn silage for 249.7 +/- 0.7 d. Steers were slaughtered at 423.3 +/- 1.4 d. Deoxyribonucleic acid samples were used by Genetic Solutions/Bovigen (Australia) for GeneSTAR MARB analysis. Steers with allele types of 0-STAR (n = 47), 1-STAR (n = 95), and 2-STAR (n = 33) had no effect (P > 0.10) on MARB score, chemically determined IMF percentage, quality grade, or percent low Choice and better. There were no differences (P > 0.10) in performance or other carcass parameters among the allele types. GeneSTAR results were not associated with MARB (P > 0.10). Conversely, MARB EPD was correlated (P < 0.01) with MARB score (r = 0.44) and IMF percentage (r = 0.27). Thus, in this management system, MARB EPD is an accurate predictor of IMF deposition. These data suggest that the GeneSTAR MARB marker was not an efficacious predictor of IMF deposition in early weaned Simmental steers fed a high-energy diet.

Adipose Tissue↗

Effects of biological type and dietary fat treatment on factors associated with tenderness: I. Measurements on beef longissimus muscle.

The objective was to evaluate chemical, mechanical, and sensory attributes associated with tenderness in divergent cattle breeds--Wagyu (W; n = 12), Limousin (L; n = 12) and F1-cross (WxL; n = 12)--fed two dietary treatments (0 or 6% sunflower oil (DM basis)). A randomized complete block repeated measures design in a 3 x 2 factorial arrangement of treatments was used, and effects of breed, diet, block, and associated interactions were tested. Cattle were fed barley-based diets for an average of 259 d. Twenty-four hours postmortem (PM), steaks from the longissimus muscle (LM) were sliced, vacuum-packaged, aged (1, 3, 7, 14, 28, and 56 d PM) at 2 degrees C, and frozen (-40 degrees C) until analyzed. Wagyu steaks had lower (P < 0.05) Warner-Bratzler shear force (WBSF) values than L steaks across all aging times. At 1 d PM, W steaks required slightly more (P > 0.05) force to shear than WxL or L (0.30 and 0.11 kg, respectively); however, by d 14 PM, W steaks required 0.77 kg less (P < 0.05) force to shear than L. Wagyu steaks received higher (P < 0.05) sensory panel sustained tenderness scores at d 14 PM than L. The pH decline was slower (P < 0.05), and temperature decline more (P < 0.05) rapid, in W carcasses than L or WxL carcasses. Breed and diet did not affect (P > 0.10) free calcium levels (FCL) over time (0, 1, 3, 7, and 14 d PM), 0-h calpastatin activity (CA), d-1 percent collagen (OH-PRO), or d-1 collagen cross-linking (HP). Western blot analysis for the presence of the troponin-T (TNT) 30-kDa fragment, conducted only on samples from steers fed the 0% sunflower oil diet, demonstrated more proteolysis by d 3 PM in L than W or WxL. Overall, breed differences in mechanical and sensory measures of tenderness were not explained by FCL, CA, OH-Pro, and HP. Even though the initial appearance of the TNT 30-kDa fragment was greater in L, linear slopes for appearance of TNT degradation product across aging time were greater for W and WxL (P < 0.01 and P = 0.056, respectively) than for L, suggesting that tenderness differences due to breed may have been facilitated by more-rapid proteolytic degradation over time.

Animals↗

Comparison of enzyme activities in plasma and leukocytes in dairy and beef cattle.

Concentrations of plasma glucose, immunoreactive insulin (IRI) and free fatty acid (FFA) and activities of enzymes related to energy metabolism and lactate dehydrogenase (LDH) isoenzyme pattern in plasma and leukocytes were investigated in lactating Holstein cows (dairy cattle) and fattening Japanese Black Wagyu x Holstein steers (beef cattle). IRI concentrations and LDH and malate dehydrogenase (MDH) activities in the plasma of beef cattle were significantly higher than those in dairy cattle. The cytosolic ratio of MDH/LDH activity in the leukocytes of beef cattle was significantly higher than that of dairy cattle. These findings might be associated with the different energy metabolism between dairy and beef cattle.

Animals↗

Craniometrical estimation of the native Japanese Mishima cattle, using multivariate analysis.

The present study on measurement of the skull of Mishima cattle, which has been postulated as the only pure representative breed of native Japanese cattle, was performed using craniometrical multivariate analysis. The data of the skull of Mishima cattle was compared with 17 breeds of cattle, i.e. Korean cattle (Hamhung, Pyongyang, Chinju Suwon, and Kwangju), Mongolian cattle, Hainan Tao cattle, northeastern Chinese cattle (Shuangliao, Shenyang, Tongliao, Lüta, and Chilin), Astatic Water Buffalo, Yak, Bos Banteng, American Bison, and Holstein-Friesian. The Mishima cattle was included in the group of Korean breeds, especially it was closed on the group of Pyongyang and Chinju breeds. The distance on the craniometrical multivariate analyzing co-ordinate between Mishima cattle and Hainan Tao breed of Zebu cattle was larger than the distance between Mishima cattle and Korean breeds. While result, as a above the present study was very important for the origin of "Wagyu" (native Japanese cattle). Since the northern route theory of the origin of Mishima cattle has been reported on the type of serum enzymes and hemotypes. It was suggested that the craniometrical multivariate analysis supported to the northern route theory of the origin of Mishima cattle.

Animals↗

Evaluation of candidate gene effects for beef backfat via Bayesian model selection.

Candidate gene approaches provide tools for exploring and localizing causative genes affecting quantitative traits and the underlying variation may be better understood by determining the relative magnitudes of effects of their polymorphisms. Diacyglycerol O-acyltransferase 1 (DGAT1), fatty acid binding protein (heart) 3 (FABP3), growth hormone 1 (GH1), leptin (LEP) and thyroglobulin (TG) have been previously identified as genes contributing to genetic control of subcutaneous fat thickness (SFT) in beef cattle. In the present research, Bayesian model selection was used to evaluate effects of these five candidate genes by comparing competing non-nested models and treating candidate gene effects as either random or fixed. The analyses were implemented in SAS to simplify the programming and computation. Phenotypic data were gathered from a F(2) population of Wagyu x Limousin cattle. The five candidate genes had significant but varied effects on SFT in this population. Bayesian model selection identified the DGAT1 model as the one with the greatest model probability, whether candidate gene effects were considered random or fixed, and DGAT1 had the greatest additive effect on SFT. The SAS codes developed in the study are freely available and can be downloaded at: http://www.ansci.wsu.edu/programs/.

Adiposity↗

Relationship between fatty acid-binding protein activity and marbling scores in bovine longissimus muscle.

Studies were conducted in an attempt to establish a relationship between fatty acid-binding protein (FABP) activity and marbling score in bovine longissimus muscle. Longissimus muscle was obtained from four 20-mo-old Charolais-Hereford crossbred heifers, three 16-mo-old Angus steers, and four 18-mo-old Angus steers. Immediately after slaughter, longissimus muscles were removed for the extraction of FABP. Supernatant (S104) fractions containing 41.3 to 144 mg of protein (depending on animal group) were eluted over Sephadex columns, and elution fractions were analyzed for the binding of radiolabeled palmitoyl-coenzyme A (CoA). Specific activities of FABP were 23, 32, and 101 nmol palmitoyl-CoA bound/mg protein for the Charolais-Hereford, 16-mo-old Angus, and 18-mo-old Angus cattle, respectively. These preliminary results suggested that longissimus muscle FABP activity was positively correlated with marbling score. To test specifically for this possibility, longissimus muscle was obtained at slaughter from each of four Wagyu steers, Angus heifers and Braford heifers. Marbling scores taken at the 12th-13th rib junction were Sm45, Sm43, and SI50 for the Wagyu, Angus, and Braford cattle, respectively. Interfascicular adipose tissue was exhaustively removed from sections of the 5th to 8th thoracic region of the longissimus muscle to eliminate any contribution of adipose tissue to FABP activity. For each animal, 300 mg of the S104 were eluted over Sephadex columns. Specific activities for the Wagyu, Angus, and Braford longissimus muscle FABP were 3.1, 3.8, and 3.9 pmol palmitoyl-CoA bound/mg protein, respectively, and were not different (P greater than .05) among the three animal groups.(ABSTRACT TRUNCATED AT 250 WORDS)

Adipose Tissue↗

Postweaning growth and carcass traits in crossbred cattle from Hereford, Angus, Norwegian Red, Swedish Red and White, Friesian, and Wagyu maternal grandsires.

The objective of this study was to characterize breeds representing diverse biological types for postweaning growth and carcass composition traits in terminal crossbred cattle. Postweaning growth and carcass traits were analyzed on 434 steers and 373 heifers obtained by mating F1 cows to Charolais sires. Maternal grandsires represented Hereford, Angus, and MARC III (1/4 Hereford, 1/4 Angus, 1/4 Pinzgauer, and 1/4 Red Poll) dams to Hereford or Angus (British Breeds), Norwegian Red, Swedish Red and White, Wagyu, or Friesian breeds. Breed groups were slaughtered serially in each of 2 yr (2002 and 2003). Postweaning ADG, slaughter weight, hot carcass weight, dressing percentage, percentage Choice, LM area, marbling score, USDA yield grade, fat thickness, retail product yield (percentage), retail product weight, fat yield (percentage), fat weight, bone yield (percentage), and bone weight were analyzed. Maternal grandsire breed was significant (P < 0.05) for all traits except dressing percentage, percentage Choice, and LM area. Marbling score for animals with Norwegian Red, Wagyu, Swedish Red and White, British Breeds, and Friesian inheritance was 550, 544, 532, 530, and 515, respectively (SEM = 8). Retail product weight for these animals was 224, 211, 227, 223, and 223 kg, respectively (SEM = 2 kg). Maternal granddam breed was not significant for any of the traits analyzed. Grandsire breed effects can be optimized by selection and use of appropriate crossbreeding systems.

Adipose Tissue↗