Identification of quantitative trait loci for growth and carcass composition in cattle

A genomic screening to detect quantitative trait loci (QTL) affecting growth, carcass composition and meat quality traits was pursued. Two hundred nineteen microsatellite markers were genotyped on 176 of 620 (28%) progeny from a Brahman x Angus sire mated to mostly MARC III dams. Selective genotyping, based on retail product yield (%) and fat yield (%), was used to select individuals to be genotyped. Traits included in the study were birth weight (kg), hot carcass weight (kg), retail product yield, fat yield, marbling score (400 = slight00 and 500 = small00), USDA yield grade, and estimated kidney, heart and pelvic fat (%). The QTL were classified as significant when the expected number of false positives (ENFP) was less than 0.05 (F-statistic greater than 17.3), and suggestive when the ENFP was <1 (F-statistic between 10.2 and 17.3). A significant QTL (F = 19; ENFP = 0.02) was detected for marbling score at centimorgan (cM) 54 on chromosome 2. Suggestive QTL were detected for fat yield at 50 cM, for retail product yield at 53 cM, and for USDA yield grade at 63 cM on chromosome 1, for marbling score at 56 cM, for retail product yield at 70 cM, and for estimated kidney, heart and pelvic fat at 79 cM on chromosome 3, for marbling score at 44 cM, for hot carcass weight at 49 cM, and for estimated kidney, heart and pelvic fat at 62 cM on chromosome 16, and for fat yield at 35 cM on chromosome 17. Two suggestive QTL for birth weight were identified, one at 12 cM on chromosome 20 and the other at 56 cM on chromosome 21. An additional suggestive QTL was detected for retail product yield, for fat yield, and for USDA yield grade at 26 cM on chromosome 26. Results presented here represent the initial search for quantitative trait loci in this family. Validation of detected QTL in other populations will be necessary.     

雷琼牛GH基因第五外显子遗传多样性及其分化

对16头雷琼牛GH基因第5外显子序列进行分析,发现了1个变异位点,定义了2种单倍型。引用巴州牦牛2个个体GH基因同源区序列并结合GenBank中牛属普通牛、其它瘤牛和牦牛3个种群与水牛1个远缘种GH基因同源区序列,分别采用邻接（NJ）法和最大简约（MP）法构建分子系统发育树,得到基本一致的拓扑结构,结果显示GH基因的分化早于雷琼牛（瘤牛）、其它瘤牛、普通牛、牦牛和水牛的分化,瘤牛物种内存在多型,同时证实了GH基因第5外显子区有着较高的突变率。     

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.     

Porcine skeletal muscle differentially expressed gene CMYA1: isolation, characterization, mapping, expression and association analysis with carcass traits

To investigate the differences in gene expression between some obese and lean pig breeds, differential display of mRNA was employed in our previous research. One differentially expressed EST ( BI596262 ) was further identified as the porcine cardiomyopathy associated 1 ( CMYA1 ) gene because of its homology to the human CMYA1 gene. The full-length DNA of the porcine CMYA1 gene encompasses 9379 bp, including a complete open reading frame encoding 1839 amino acid residues, a 158-bp 5'-untranslated region and a 630-bp 3'-untranslated region. The porcine CMYA1 gene was assigned to chromosome 13 by the radiation hybrid panel (IMpRH). The porcine CMYA1 gene was expressed only in the striated muscle. Single nucleotide polymorphism (SNP) scanning in the coding region identified one synonymous mutation (c.1053C>T) and three missense mutations, c.1394A>G (p.His465Arg), c.1751A>G (p.Asp582Gly) and c.3290C>A (p.Thr1097Asp). The allele frequencies were tested among about 200 unrelated pigs from several pig breeds. Linkage mapping was further conducted with the SNP c.1751A>G (p.Asp582Gly) in a Berkshire × Yorkshire resource family and this confirmed that porcine CMYA1 is closely linked with Sw344 (distance  =  2 cM, LOD score is 129.47), an interesting region harbouring a QTL for back fat thickness. Association analysis in our experimental pig population showed that different genotypes of CMYA1 gene were associated with different back fat thicknesses ( P  <   0.05). Our results suggest that the porcine CMYA1 gene has effects on porcine back fat deposition and further investigation will be necessary to illustrate the underlying mechanisms.     

Restriction fragment length polymorphism analysis of the kappa-casein locus in cattle

The two common genetic variants (A and B) of bovine kappa-casein originate from two point mutations in the codons for the aminoacids in position 136 and 148. These mutations give rise to polymorphic sites for the restriction endonucleases Hin dIII, AluI, HinfI, Mbo II and TaqI. We have examined DNAs of several Italian Friesian cows and bulls of known and unknown genotype by Southern analyses using kappa-casein cDNA probes. Restriction fragment length polymorphisms (RFLPs) specific for the A and B alleles were identified for each of the above enzymes, except for AluI, which has a non-polymorphic site 12bp away from the polymorphic one. We have also found two new polymorphic sites for MboII and TaqI in the non-coding regions. These sites differentiate the A allele into two new variants, named A1 and A2. The RFLP analysis permits the characterization of kappa-casein alleles even in the absence of their expression. This should facilitate selective breeding programmes aimed at increasing the frequency of the kappa-casein B allele whose product improves the cheesemaking properties of milk.     

A genome scan for quantitative trait loci influencing carcass,post‐natal growth and reproductive traits in commercial Angus cattle

To gain insight into the number of loci of large effect that underlie variation in cattle, a quantitative trait locus (QTL) scan for 14 economically important traits was performed in two commercial Angus populations using 390 microsatellites, 11 single nucleotide polymorphisms (SNPs) and one duplication loci. The first population comprised 1769 registered Angus bulls born between 1955 and 2003, with Expected Progeny Differences computed by the American Angus Association. The second comprised 38 half‐sib families containing 1622 steers with six post‐natal growth and carcass phenotypes. Linkage analysis was performed by half‐sib least squares regression with gridqtl or Bayesian Markov chain Monte Carlo analysis of complex pedigrees with loki . Of the 673 detected QTL, only 118 have previously been reported, reflecting both the conservative approach to QTL reporting in the literature, and the more liberal approach taken in this study. From 33 to 71% of the genetic variance and 35 to 56% of the phenotypic variance in each trait was explained by the detected QTL. To analyse the effects of 11 SNPs and one duplication locus within candidate genes on each trait, a single marker analysis was performed by fitting an additive allele substitution model in both mapping populations. There were 53 associations detected between the SNP/duplication loci and traits with ?log₁₀P_nominal≥ 4.0, where each association explained 0.92% to 4.4% of the genetic variance and 0.01% to 1.86% of the phenotypic variance. Of these associations, only six SNP/duplication loci were located within 8 cM of a QTL peak for the trait, with two being located at the QTL peak: SST_DG156121:c.362A>G for ribeye muscle area and TG_X05380:c.422C>T for calving ease. Strong associations between several SNP/duplication loci and trait variation were obtained in the absence of any detected linked QTL. However, we reject the causality of several commercialized DNA tests, including an association between TG_X05380:c.422C>T and marbling in Angus cattle.     

Evaluation of growth hormone production from GH1 cells in vitro: Effect of culture media and time in culture

Summary Growth hormone production by a rat pituitary tumor cell line (GH1) was measured during lag, exponential, and plateau phases of growth in different culture media. Growth hormone secretion was low during lag and early exponential phase; it increased late in the exponential phase and continued to increase during the plateau phase. This biphasic pattern of growth hormone production was observed in all media and sera utilized. Both the doubling time and growth hormone production were influenced by the choice of media and sera. In addition, the length of time in culture affected the growth fraction with passage level 40 GH1 cells having a 79% growth fraction, whereas the growth fraction of passage level 100 cells was 95%. Using the population doubling time as a criterion for a choice of medium, F-10 medium supplemented with 20% fetal bovine serum consistently yielded the most rapid doubling time (32 hr), whereas Dulbecco's MEM supplemented with 15% horse serum and 2.5% fetal bovine serum yielded the greatest plateau cell density. Growth hormone secretion and the population doubling times were directly related to culture conditions including length of time in culture, choice of tissue culture media, choice of sera, and the phase of cell growth (lag, exponential or plateau).     

Assignment of the gene for porcine insulin-like growth factor 1 (IGF1) to chromosome 5 by linkage mapping

Investigation of published sequence data from the porcine insulin-like growth factor 1 (IGF1) gene, resulted in the detection of a microsatellite in the first intron of the gene. Polymerase chain reaction (PCR) primers flanking the (CA)₁₉ repeat were constructed. Polymorphism and Mendelian segregation were documented in a three-generation pedigree and allele frequencies were determined in 74 unrelated animals from four different breeds. Seven alleles were encountered. Linkage analysis was performed in a large pedigree established for gene mapping. Linkage between the IGF1 microsatellite and an anonymous microsatellite marker, S0005, was detected. Furthermore, IGF1 and S0005 was found to be linked to the porcine submaxillary gland mucin (MUC) gene, previously assigned to chromosome 5. The results presented here extend the linkage group on pig chromosome 5 and are in accordance with conserved synteny between human chromosome 12, cattle chromosome 5, mouse chromosome 10 and pig chromosome 5.     

东方(鱼屯)生长激素基因内含子2的克隆与多态性分析

以暗纹东方鲀(Takifugu obscurus)、红鳍东方鲀(Takifugu rubripes)、星点东方鲀(Takifugu niphobles)共82个个体为对象,运用PCR产物电泳检测、单链构向多态性(SSCP)技术和克隆测序技术检测到生长激素(Growth Hormone, GH)基因内含子2的长度和序列多态性。结果表明,3个群体中GH基因内含子2存在9种长度类型,分别为A、B、C、D、E、F、G、H、I,变异频率达到24.22％。对这9种序列进行比对分析,(1)发现9种长度类型A、G、T、C的平均百分比为17.15％、20.77％、37.38％、24.70％,其中G+C(45.47％)含量与A+T(54.53%)的含量差异不显著;(2)9种序列分别长351 bp、327 bp、319 bp、303 bp、295 bp、291 bp、287 bp、283 bp和271 bp,引起长度变化的主要原因是短串联序列TCTG的重复 (重复次数从20到40不等); (3)发现4个突变位点,其中3个转换位点为83(C→T),101(A→G)296(G→A),一处颠换位点103(C→A)。用UPGMA法构建分子系统树,发现DD与II首先聚为一类,然后依次与GG、AA聚为一大类,BB与CC,EE与HH分别聚为一类,最后再与FF聚为一大类,由此可见GH基因内含子2在品种间的差异远大于品种内差异。     

伴性矮小型鸡GH、GHR和IGF-1基因的表达变化

采用荧光实时定量PCR的方法, 从转录水平上分析了伴性矮小型鸡和普通鸡肝脏中GH、GHR和IGF-1基因的表达变化趋势。结果表明：伴性矮小型鸡和普通鸡肝脏组织中GH的mRNA表达量没有明显差异, 而GHR在矮小鸡中的表达量明显比普通鸡的高3倍多, 但IGF-1基因在矮小鸡肝脏中的表达量却远远低于普通鸡, 差异达到2个数量级。这表明, 伴性矮小型鸡GHR外显子10 和3′非翻译区的长片断缺失并没有降低GHR基因的表达, 相反有所增高, 这一过程中可能存在相应的功能代偿机制。与此同时, 在伴性矮小型鸡肝脏中几乎观察不到IGF-1基因的表达, 证明正是由于GHR基因的缺陷影响了GH生理效应的发挥。实验结果印证了伴性矮小表型与GH和GHR的转录水平无关, 而可能是GHR编码产物异常阻碍了GH-GHR-IGF信号通路, 导致IGF-1表达受阻, 不能发挥正常的生理功能。     

水稻生长发育多效基因DDF1的遗传分析与基因定位

植物中存在许多多效性基因,它们在调控植物的营养生长与生殖发育过程中起着关键性作用。文章在籼稻育种材料中发现了一个植株显著矮化且花器官明显变异的突变体ddf1(dwarf and deformed flower 1)。遗传分析表明,该突变体由单基因隐性突变所致,这说明该基因是一个同时控制营养生长和生殖发育的多效性基因,暂命名为DDF1。为了定位该基因,将ddf1杂合体与热带粳稻品种DZ60杂交,建立了F2定位群体,利用水稻RM系列微卫星标记,通过混合分离分析(BSA)和小群体连锁分析,将DDF1初步定位在水稻第6号染色体RM588和RM587标记之间,与两标记的遗传距离分别为3.8 cM和2.4 cM。进一步利用已经公布的水稻基因组序列,在初步定位的区间内开发新的SSR标记,将DDF1定位在165 kb的区间内。该结果为克隆DDF1奠定了基础。     

A genome‐wide scan for signatures of recent selection in Holstein cattle

The data from the newly available 50 K SNP chip was used for tagging the genome‐wide footprints of positive selection in Holstein–Friesian cattle. For this purpose, we employed the recently described Extended Haplotype Homozygosity test, which detects selection by measuring the characteristics of haplotypes within a single population. To assess formally the significance of these results, we compared the combination of frequency and the Relative Extended Haplotype Homozygosity value of each core haplotype with equally frequent haplotypes across the genome. A subset of the putative regions showing the highest significance in the genome‐wide EHH tests was mapped. We annotated genes to identify possible influence they have in beneficial traits by using the Gene Ontology database. A panel of genes, including FABP3, CLPN3, SPERT, HTR2A5, ABCE1, BMP4 and PTGER2, was detected, which overlapped with the most extreme P‐values. This panel comprises some interesting candidate genes and QTL, representing a broad range of economically important traits such as milk yield and composition, as well as reproductive and behavioural traits. We also report high values of linkage disequilibrium and a slower decay of haplotype homozygosity for some candidate regions harbouring major genes related to dairy quality. The results of this study provide a genome‐wide map of selection footprints in the Holstein genome, and can be used to better understand the mechanisms of selection in dairy cattle breeding.     

Effect of compensatory growth on performance, carcass composition and plasma IGF-1 in grower finisher pigs

A total of 48 female pigs (Large White × Landrace × Duroc cross) were used to determine whether a compensatory feed regime influenced performance, carcass composition and the level of plasma IGF-1. Pigs of initial age 73 days were fed a commercial diet at 0.70 of ad libitum (R) for 40 days followed by a return to ad libitum feeding for a further 42 days. The control group was fed ad libitum (A) throughout. Groups of animals on R and A feed regimes were slaughtered at the end of restriction period (SL1), 2 days after refeeding ad libitum (SL2) to establish the more immediate effects of refeeding on IGF levels, and after 42 days refeeding (SL3; n = 8 for each group). As expected, during the restriction period, average daily live weight gain in all the slaughter groups of R pigs was significantly lower than A pigs (P < 0.01); there was no significant difference in feed conversion ratios. In the re-alimentation period of SL3, R pigs grew 12.9% faster (P = 0.033), indicating compensatory growth. At SL1, there was a trend for carcass weight (P = 0.108) of A pigs to be higher than R pigs, but at SL2 live weight and carcass weight of A pigs were significantly heavier than R pigs (P < 0.05), but not at SL3. For killing-out percentage, there was no difference in SL1. After refeeding for 2 days (SL2) and 42 days (SL3), R pigs had significantly lower killing-out percentage than A pigs (P < 0.05). As a proportion of live weight, R pigs had smaller heart, kidney and liver (P < 0.05) than A pigs at SL1. At SL2, only the kidney was smaller in the restricted group (P < 0.05) and there were no significant differences in SL3. As a proportion of carcass weight, Longissimus dorsi was heavier in the R pigs at SL1 (P = 0.108) and SL2 (P < 0.05), but not at SL3. At SL1, there was a trend for intramuscular fat of A pigs to be higher than R pigs. The plasma IGF-1 level was lower in R pigs than A pigs (P = 0.010) at SL1, and slightly lower at SL2 (P = 0.110), with no significant differences at SL3. Dietary restriction period influenced plasma IGF-1 levels, which returned to the ad libitum group levels when animals were refed, as did live weight and carcass weight. It appears that the internal organs and possibly fat, but not muscles, underwent a compensatory response when animals were refed.     

The analysis of genetic diversity and differentiation of six Chinese cattle populations using microsatellite markers

A total of 321 individuals from six cattle populations of four species in a bovine subfamily in China were studied using 12 pairs of microsatellite markers. The genetic diversities within and between populations were calculated. The phylogenetic trees were constructed by （δμ）^2 and DA distances, and the divergence times between populations were estimated by （δμ）^2. Altogether, 144 microsatellite alleles were detected including 24 private alleles and nine shared alleles. Chinese Holstein had the largest number of private alleles （10）, whereas Bohai black and Buffalo had the smallest number of private alleles （2）. Chinese Holstein showed the highest genetic variability. Its observed number of alleles （Na）, mean effective number of alleles （MNA）, and mean heterozygosity （He） were 7.7500, 4.9722, and 0.7719, respectively, whereas, the Buffalo and Yak showed low genetic variability. In the phylogenetic trees, Luxi and Holstein grouped first, followed by Bohai and Minnan. Yak branched next and buffalo emerged as the most divergent population from other cattle populations. Luxi and Bohai were estimated to have diverged 0.039-0.105 million years ago （MYA）, however, buffalo and Holstein diverged 0.501-1.337 MYA. The divergence time of Yak versus Minnan, Holstein and buffalo was 0.136-0.363, 0.273-0.729, and 0.326-0.600 MYA, respectively.