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1.
Continued validation of genetic markers for economically important traits is crucial to establishing marker-assisted selection as a tool in the cattle industry. The objective of the current study was to evaluate the association of a SNP (T(9)/T(10)) in the osteopontin gene (SPP1) with growth rate in a large cattle population spanning multiple generations and representing alleles from 12 founding breeds. This population has been maintained at the US Meat Animal Research Center since 1981 and subjected to selection for twinning rate. Phenotypic records for this population included twinning rate and ovulation rate, providing an opportunity to examine the potential effects of SPP1 genotype on reproductive traits. A set of 2,701 animals was geno-typed for the T(9)/T(10) polymorphism at SPP1. The geno-typic data, including previously genotyped markers on chromosome 6 (BTA6), were used in conjunction with pedigree information to estimate genotypic probabilities for all 14,714 animals with phenotypic records. The genotypic probabilities for females were used to calculate independent variables for regressions of additive, dominance, and imprinting effects. Genotypic regressions were fit as fixed effects in a mixed model analysis, in which each trait was analyzed in a 2-trait model where single births were treated as a separate trait from twin births. The association of the SPP1 marker with birth weight (P < 0.006), weaning weight (P < 0.007), and yearling weight (P < 0.003) was consistent with the previously reported effects of SPP1 genotype on yearling weight. Our data supports the conclusion that the SNP successfully tracks functional alleles affecting growth in cattle. The previously undetected effect of the SNP on birth and weaning weight suggests this particular SPP1 marker may explain a portion of the phenotypic variance explained by QTL for birth and HCW on BTA6.  相似文献   

2.
Twinning in cattle is a complex trait that is associated with economic loss and health issues such as abortion, dystocia, and reduced calf survival. Twinning-rate QTL have been detected previously on BTA5 in the North American Holstein and Norwegian dairy cattle populations and in a USDA herd selected for high twinning rate. In previous work with the North American Holstein population, the strongest evidence for a QTL was obtained from analysis of an extended, multiple-generation family. Using additional animals, an increased density of SNP marker association tests, and a combined linkage and linkage disequilibrium mapping method, we refined the position of this QTL in the North American Holstein population. Two sets of twinning-rate predicted transmitting abilities estimated during 2 different time periods in the North American dairy cattle population were used to provide validation of results. A total of 106 SNP and 3 microsatellites were used to scan the genomic region between 5 and 80 Mb on BTA5. Combined linkage-linkage disequilibrium analysis identified significant evidence for QTL within the 25- to 35-Mb and 64- to 70-Mb regions of BTA5. The IGF-1 gene (IGF1) was examined as a positional candidate gene and an SNP in intron 2 of IGF1 was significantly associated with twinning rate by using both data sets (P = 0.003 and P = 1.05 x 10(-6)). Replication of this association in other cattle populations will be required to examine the extent of linkage disequilibrium with the underlying quantitative trait nucleotide across breeds.  相似文献   

3.
The genetics of reproduction is poorly understood because the heritabilities of traits currently recorded are low. To elucidate the genetics underlying reproduction in beef cattle, we performed a genome-wide association study using the bovine SNP50 chip in 2 tropically adapted beef cattle breeds, Brahman and Tropical Composite. Here we present the results for 3 female reproduction traits: 1) age at puberty, defined as age in days at first observed corpus luteum (CL) after frequent ovarian ultrasound scans (AGECL); 2) the postpartum anestrous interval, measured as the number of days from calving to first ovulation postpartum (first rebreeding interval, PPAI); and 3) the occurrence of the first postpartum ovulation before weaning in the first rebreeding period (PW), defined from PPAI. In addition, correlated traits such as BW, height, serum IGF1 concentration, condition score, and fatness were also examined. In the Brahman and Tropical Composite cattle, 169 [false positive rate (FPR) = 0.262] and 84 (FPR = 0.581) SNP, respectively, were significant (P < 0.001) for AGECL. In Brahman, 41% of these significant markers mapped to a single chromosomal region on BTA14. In Tropical Composites, 16% of these significant markers were located on BTA5. For PPAI, 66 (FPR = 0.67) and 113 (FPR = 0.432) SNP were significant (P < 0.001) in Brahman and Tropical Composite, respectively, whereas for PW, 68 (FPR = 0.64) and 113 (FPR = 0.432) SNP were significant (P < 0.01). In Tropical Composites, the largest concentration of PPAI markers were located on BTA5 [19% (PPAI) and 23% (PW)], and BTA16 [17% (PPAI) and 18% (PW)]. In Brahman cattle, the largest concentration of markers for postpartum anestrus was located on BTA3 (14% for PPAI and PW) and BTA14 (17% PPAI). Very few of the significant markers for female reproduction traits for the Brahman and Tropical Composite breeds were located in the same chromosomal regions. However, fatness and BW traits as well as serum IGF1 concentration were found to be associated with similar genome regions within and between breeds. Clusters of SNP associated with multiple traits were located on BTA14 in Brahman and BTA5 in Tropical Composites.  相似文献   

4.
A genetic correlation near unity between ovulation rate in heifers and later twinning frequency led to consideration of using measures of ovulation rate in heifers for each estrous cycle, beginning at puberty, to increase accuracy of selection for twinning rate. An initial evaluation with a multiple trait animal model for predicting breeding values included six genetic groups: 1) selected Scandinavian bulls, 2) transfers from other populations at the Research Center to a twinning project, 3) early-purchased Holsteins, 4) late-purchased Holsteins, 5) early purchases-other breeds, and 6) late purchases-other breeds. For ovulation and twin measures, heritabilities of .100 and .070 and repeatabilities of .120 and .092 were assumed. Assumed phenotypic correlation between ovulation and twin measures of .08 was accounted for by genetic correlation of .89 and permanent environmental correlation of .19. The number of animals evaluated was 1,745; 6,912 estrous cycles were measured for ovulation rate on 840 heifers and 1,929 parturitions were observed for occurrence of twinning on 851 cows, of which 346 had ovulation rate measured as heifers. The remaining 400 animals were foundation animals that created relationships among those with records or were sires of animals with records. The Scandinavian genetic group effect was substantially greater than that of the others. Joint evaluations were compared to evaluations using only twinning measures. For animals with twin evaluations based only on parents but with ovulation rates measured, the multiple trait evaluation increased accuracy of evaluation from .62 (twin information only) to .81.(ABSTRACT TRUNCATED AT 250 WORDS)  相似文献   

5.
Repeated measures of ovulation rate on puberal heifers should be an effective way to select for increased twinning rate. A reliable estimate of the genetic correlation between ovulation and twinning rates is needed to implement such selection and to predict its efficiency. Restricted maximum likelihood was used to estimate genetic correlations from subsets of data collected from the twinning project at the Roman L. Hruska U.S. Meat Animal Research Center. The animal model included numerator relationships among the animals and fixed effects of year-season of measurement, age at measurement, and birth group. Genetic correlations between averages of ovulation rates for three, four, five, six, seven, and eight estrous cycles and the occurrence of twins were, respectively, .62, .76, 1.00, 1.00, 1.00, and .98 based on observations on 200 to 325 puberal heifers. Corresponding phenotypic correlations ranged from .06 to .26. Genetic correlations between ovulation rate in a single estrous cycle and occurrence of twins were .38, .98, and .98, respectively, for 323, 430, and 283 cows with ovulation rate measured after measurement of twinning, in the same season as measurement of twinning, and more than 1 yr before measurement of twinning. Phenotypic correlations were .00, .07, and .00. Genetic and phenotypic correlations among ovulation rates at six consecutive estrous cycles averaged, respectively, .66 and .12 for 610 heifers. Heritabilities for ovulation rates in individual cycles averaged .16. No evidence of negative environmental covariance between ovulation rates in adjacent cycles was found. These results support the approach of indirectly selecting for twinning rate by measuring ovulation rates in estrous cycles of puberal heifers.  相似文献   

6.
The objective of this study was to identify genomic regions associated with fat‐related traits using a Japanese Black cattle population in Hyogo. From 1836 animals, those with high or low values were selected on the basis of corrected phenotype and then pooled into high and low groups (n = 100 each), respectively. DNA pool‐based genome‐wide association study (GWAS) was performed using Illumina BovineSNP50 BeadChip v2 with three replicate assays for each pooled sample. GWAS detected that two single nucleotide polymorphisms (SNPs) on BTA7 (ARS‐BFGL‐NGS‐35463 and Hapmap23838‐BTA‐163815) and one SNP on BTA12 (ARS‐BFGL‐NGS‐2915) significantly affected fat percentage (FAR). The significance of ARS‐BFGL‐NGS‐35463 on BTA7 was confirmed by individual genotyping in all pooled samples. Moreover, association analysis between SNP and FAR in 803 Japanese Black cattle revealed a significant effect of SNP on FAR. Thus, further investigation of these regions is required to identify FAR‐associated genes and mutations, which can lead to the development of DNA markers for marker‐assisted selection for the genetic improvement of beef quality.  相似文献   

7.
A genome wide-association study for production traits in cattle was carried out using genotype data from the 10K Affymetrix (Santa Clara, CA) and the 50K Illumina (San Diego, CA) SNP chips. The results for residual feed intake (RFI), BW, and hip height in 3 beef breed types (Bos indicus, Bos taurus, and B. indicus × B. taurus), and for stature in dairy cattle, are presented. The aims were to discover SNP associated with all traits studied, but especially RFI, and further to test the consistency of SNP effects across different cattle populations and breed types. The data were analyzed within data sets and within breed types by using a mixed model and fitting 1 SNP at a time. In each case, the number of significant SNP was more than expected by chance alone. A total of 75 SNP from the reference population with 50K chip data were significant (P < 0.001) for RFI, with a false discovery rate of 68%. These 75 SNP were mapped on 24 different BTA. Of the 75 SNP, the 9 most significant SNP were detected on BTA 3, 5, 7, and 8, with P ≤ 6.0 × 10(-5). In a population of Angus cattle divergently selected for high and low RFI and 10K chip data, 111 SNP were significantly (P < 0.001) associated with RFI, with a false discovery rate of 7%. Approximately 103 of these SNP were therefore likely to represent true positives. Because of the small number of SNP common to both the 10K and 50K SNP chips, only 27 SNP were significantly (P < 0.05) associated with RFI in the 2 populations. However, other chromosome regions were found that contained SNP significantly associated with RFI in both data sets, although no SNP within the region showed a consistent effect on RFI. The SNP effects were consistent between data sets only when estimated within the same breed type.  相似文献   

8.
Genomic scans were conducted with 273 markers on 181 sires from a cattle population selected for increased twinning rate to identify chromosomal regions containing genes that influence ovulation rate. Criteria used for selecting markers were number of alleles, ease of scoring, and relative position within linkage group. Markers were multiplexed or multiple-loaded on the gels to reduce the costs and labor required to obtain genotypic data. This approach reduced the number of gels by 45% when compared with running each marker independently. Male animals selected for the genomic scan sired the majority of the population. A modified interval analysis was used in a granddaughter design to compare effects of each allele within sire for 10 different sire families. The midparent deviation of the son's estimated breeding value for ovulation rate was used as the phenotype. Forty-one potential peaks were identified with a nominal significance level < or = 0.05. The 10 peaks with the highest significance levels (P < 0.02) were selected for further analysis. Markers were genotyped across daughters of the sire where nominal significance was found for each of the 10 peaks. One peak (BTA5, relative position 40 cM) was found to be nominally significant in the daughters. The nominal significance levels were P = 0.01 for the sons (n = 32) and P = 0.02 for the daughters (n = 94) of sire 784403. A combined genomewide significance value (P = 0.07) was calculated that accounted for the 10 analyses with sons and the 10 analyses with daughters. These results strongly suggest that this region contains a gene(s) that is involved in the follicular recruitment and development process.  相似文献   

9.
Background: Recent technological advances in genomics have allowed the genotyping of cattle through single nucleotide polymorphism(SNP) panels. High-density SNP panels possess greater genome coverage and are useful for the identification of conserved regions of the genome due to selection, known as selection signatures(SS). The SS are detectable by different methods, such as the extended haplotype homozygosity(EHH); and the integrated haplotype score(i HS), which is derived from the EHH. The aim of this study was to identify SS regions in Canchim cattle(composite breed), genotyped with high-density SNP panel.Results: A total of 687,655 SNP markers and 396 samples remained for SS analysis after the genotype quality control. The i HS statistic for each marker was transformed into pi HS for better interpretation of the results.Chromosomes BTA5 and BTA14 showed pi HS 5, with 39 and nine statistically significant SNPs(P 0.00001),respectively. For the candidate selection regions, i HS values were computed across the genome and averaged within non-overlapping windows of 500 Kb. We have identified genes that play an important role in metabolism,melanin biosynthesis(pigmentation), and embryonic and bone development.Conclusions: The observation of SS indicates that the selection processes performed in Canchim, as well as in the founder breeds(i.e. Charolais), are maintaining specific genomic regions, particularly on BTA5 and BTA14. These selection signatures regions could be associated with Canchim characterization.  相似文献   

10.
Twinning in dairy cattle is an unavoidable outcome of reproduction and is undesirable because it reduces the overall profitability of a dairy operation through negative effects on cows calving twins as well as on calves born as twins. Cows calving twins are at greater risk for many periparturient reproductive and metabolic disorders than nontwinning herdmates, and incidences of abortion, stillbirth, neonatal calf mortality, and reduced birth weight are greater among twin compared with singleton calves. Twinning is a complex trait with multiple causative factors, and empirical evidence supports a role for both genetic and environmental risk factors in cattle. Risk factors for twinning include genetics, season, parity, ovulation rate, and milk production. The observation that twinning has increased in the dairy cattle population over time suggests a concurrent change in one or more of these causative factors during this same period. At present, dairy farmers and their consultants are ill prepared to make sound-management decisions to mitigate the negative effects of twinning on their operations because of a lack of applied scientific data on management strategies for periparturient dairy cows carrying twin fetuses. A clear understanding of the factors responsible for twinning is essential for future development of strategies to manage twinning in dairy operations.  相似文献   

11.
Dairy cows with increased rectal temperature experience lower milk yield and fertility. Rectal temperature during heat stress is heritable, so genetic selection for body temperature regulation could reduce effects of heat stress on production. One aim of the study was to validate the relationship between genotype and heat tolerance for single nucleotide polymorphisms (SNPs) previously associated with resistance to heat stress. A second aim was to identify new SNPs associated with heat stress resistance. Thermotolerance was assessed in lactating Holsteins during the summer by measuring rectal temperature (a direct measurement of body temperature regulation; n = 435), respiration rate (an indirect measurement of body temperature regulation, n = 450) and sweating rate (the major evaporative cooling mechanism in cattle, n = 455). The association between genotype and thermotolerance was evaluated for 19 SNPs previously associated with rectal temperature from a genomewide analysis study (GWAS), four SNPs previously associated with change in milk yield during heat stress from GWAS, 2 candidate gene SNPs previously associated with rectal temperature and respiration rate during heat stress (ATPA1A and HSP70A) and 66 SNPs in genes previously shown to be associated with reproduction, production or health traits in Holsteins. For SNPs previously associated with heat tolerance, regions of BTA4, BTA6 and BTA24 were associated with rectal temperature; regions of BTA6 and BTA24 were associated with respiration rate; and regions of BTA5, BTA26 and BTA29 were associated with sweating rate. New SNPs were identified for rectal temperature (n = 12), respiration rate (n = 8) and sweating rate (n = 3) from among those previously associated with production, reproduction or health traits. The SNP that explained the most variation were PGR and ASL for rectal temperature, ACAT2 and HSD17B7 for respiration rate, and ARL6IP1 and SERPINE2 for sweating rate. ARL6IP1 was associated with all three thermotolerance traits. In conclusion, specific genetic markers responsible for genetic variation in thermoregulation during heat stress in Holsteins were identified. These markers may prove useful in genetic selection for heat tolerance in Holstein cattle.  相似文献   

12.
Genomic imprinting should be considered in animal breeding systems to avoid lead in bias in genetic parameter estimation. The objective of this study was to clarify the effects of pedigree information on imprinting variances for carcass traits and fatty acid composition in Japanese Black cattle. Carcass records [carcass weight, rib eye area, rib thickness (RT), subcutaneous fat thickness and beef marbling score (BMS)] and fatty acid composition were obtained for 11,855 Japanese Black feedlot cattle. To estimate and compare the imprinting variances for the traits, two imprinting models with different pedigree information [the sire–dam gametic relationship matrix (Model 1) and the sire–maternal grandsire (MGS) numerator relationship matrix (Model 2)] were fitted. The ratio of the imprinting variance to the total additive genetic variance for RT (6.33%) and BMS (19.00%) was significant in Model 1, but only that for BMS (21.09%) was significant in Model 2. This study revealed that fitting the sire–MGS model could be useful in estimating imprinting variance under certain conditions, such as when restricted pedigree information is available. Furthermore, the present result suggested that the maternal gametic effects on BMS should be included in breeding programmes for Japanese Black cattle to avoid selection bias caused by imprinting effects.  相似文献   

13.
前期研究通过荷斯坦公牛全基因组重测序鉴定到17个奶牛产奶性状候选功能基因,其中,肽基脯氨酸顺反异构酶基因(PIN1)参与甘油三酯代谢、甘油磷脂代谢以及mTOR信号通路,且位于产奶量和乳蛋白量性状QTL区间。为进一步系统分析PIN1基因是否对奶牛产奶性状具有遗传效应,本实验基于40头公牛的基因组DNA混池,采用PCR产物直接测序法对PIN1基因的全部编码区以及上下游调控区2000 bp进行扫描,在内含子2检测到1个SNP位点7:g.14432394G>A,A、G等位基因频率分别为0.4797和0.5203。采用靶向测序基因型技术对北京地区987头中国荷斯坦母牛进行个体基因型检测,对SNP位点7:g.14432394G>A与5个产奶性状进行关联分析。结果表明:在第1泌乳期,SNP 7:g.14432394G>A与产奶量、乳脂量、乳蛋白量和乳蛋白率呈显著或极显著关联(P=0.0001~0.0493);在第2泌乳期,SNP与产奶量、乳脂量、乳脂率和乳蛋白量呈显著或极显著关联(P=0.0001~0.0104);SNP位点7:g.14432394G>A对产奶量、乳脂量、乳蛋白量和乳蛋白率的加性效应或等位基因替代效应均达到显著或极显著。综上,PIN1基因对中国荷斯坦牛的产奶量和乳蛋白、乳脂性状具有显著遗传效应,可作为遗传标记用于基因组选择,以加快遗传进展。  相似文献   

14.
Genomic selection using high‐density single nucleotide polymorphism (SNP) genotype data may accelerate genetic improvements in livestock animals. In this study, we attempted to estimate the variance components of six carcass traits in fattened Japanese Black steers using SNP genotype data. Six hundred and seventy‐three steers were genotyped using an Illumina Bovine SNP50 BeadChip and phenotyped for cold carcass weight, ribeye area, rib thickness, subcutaneous fat thickness, estimated yield percent and marbling score. Additive polygenic variance and the variance attributable to a set of SNPs that had statistically significant effects on the trait were estimated via Gibbs sampling with two models: (i) a model with the chosen SNPs and the additive polygenic effects; and (ii) a model with the polygenic effects alone. The proportion of the estimated variance attributable to the SNPs became higher as the number of SNP effects that fit increased. High correlations between breeding values estimated with the model containing the polygenic effect alone and those estimated by chosen SNPs were obtained. No fraction of the total genetic variance was explained by SNPs associated with the trait at P ≥ 0.1. Our results suggest that for the carcass traits of Japanese Black cattle, a maximum of half of the total additive genetic variance may be explained by SNPs between 100 several tens to several 100s.  相似文献   

15.
Foundation cows were selected using prior records from one of two sources, private herds or other projects at the Research Center. Comparing twinning rates before and after selection, the repeatability was lower for those from the first (.08) than for those from the second (.16) source with a combined value of .12. Realized heritability of single-parity twinning rate estimated from selection of parents and response in daughters of foundation females was .06. Paternal half-sib estimate of heritability of twinning rate was .02 +/- .07. Estimates of repeatability computed from calving records of females born in the project indicate that permanent environmental effects on twinning rate in cattle are small. Mean calving rate of females born in the project was 1.11 in the data set that included all data and 1.09 in the data set that excluded females from highly selected parents. Twinning rate was greater (P less than .05) in fall than in spring calving (1.13 vs 1.06). Data on twinning rate of a sample of the Swedish Friesian breed were summarized. Mean twinning rate of the Swedish Friesian breed is 2.57%. Age adjusted mean twinning rate of daughters of 32 half-sib sons of one particular Swedish Frieisan sire averaged 5.4% and ranged from .9% to 13.6%. There was no indication of a bimodal distribution, which would be expected if a single gene with a major effect on twinning rate were segregating. The estimated genetic standard deviation (sigma-xn) for mean twinning rates of the 32 sire progeny groups was 1.8%. Observed range among son progenies was .127 or 7.2 sigma-xn, in reasonable agreement with the hypothesis that twinning rate in this population is inherited as a quantitative trait.  相似文献   

16.
牛双胎的研究与应用   总被引：6，自引：0，他引：6  
牛双胎可显著的提高生产效率，对母牛和犊牛没有明显的不良影响，不利之处是异性双胎造成母犊不孕、。双胎是可以遗传的，双亲的影响较大；不同品种间的双胎率差异显著；另外胎次、季节、营养均影响双胎率。目前常用的提高双胎率的方法是通过遗传选择、激素诱导、激素免疫、胚胎移植等方法。但如果结合标记辅助选择法（MAS）、性别控制、及转基因与克隆技术将有助于快速提高双胎率，提高生产效益。  相似文献   

17.
Multiple genomic scans have identified QTL for backfat deposition across the porcine genome. The objective of this study was to detect SNP and genomic regions associated with ultrasonic backfat. A total of 74 SNP across 5 chromosomes (SSC 1, 3, 7, 8, and 10) were selected based on their proximity to backfat QTL or to QTL for other traits of interest in the experimental population. Gilts were also genotyped for a SNP thought to influence backfat in the thyroxine-binding globulin gene (TBG) on SSC X. Genotypic data were collected on 298 gilts, divided between the F8 and F10 generations of the US Meat Animal Research Center Meishan resource population (composition, one-quarter Meishan). Backfat depths were recorded by ultrasound from 3 locations along the back at approximately 210 and 235 d of age in the F8 and F10 generations, respectively. Ultrasound measures were averaged for association analyses. Regressors for additive, dominant, and parent-of-origin effects of each SNP were calculated using genotypic probabilities computed by allelic peeling algorithms in GenoProb. The association model included the fixed effects of scan date and TBG genotype, the covariates of weight and SNP regressors, and random additive polygenic effects to account for genetic similarities between animals not explained by known genotypes. Variance components for polygenic effects and error were estimated using MTDFREML. Initially, each SNP was fitted (once with and once without parent-of-origin effects) separately due to potential multi-collinearity between regressions of closely linked markers. To form a final model, all significant SNP across chromosomes were included in a common model and were individually removed in successive iterations based on their significance. Across all analyses, TBG was significant, with an additive effect of approximately 1.2 to 1.6 mm of backfat. Three SNP on SSC3 remained in the final model even though few studies have identified QTL for backfat on this chromosome. Two of these SNP exhibited irregular parent-of-origin effects and may not have been detected in other genome scans. One significant SNP on SSC7 remained in the final, backward-selected model; the estimated effect of this marker was similar in magnitude and direction to previously identified QTL. This SNP can potentially be used to introgress the leaner Meishan allele into commercial swine populations.  相似文献   

18.
The identification of genomic regions including signatures of selection produced by domestication and its subsequent artificial selection processes allows the understanding of the evolution of bovine breeds. Although several studies describe the genomic variability among meat or milk production cattle breeds, there are limited studies orientated towards bovine behavioural features. This study is focused on mapping genomic signatures of selection which may provide insights of differentiation between neutral and selected polymorphisms. Their effects are studied in the Lidia cattle traditionally selected for agonistic behaviour compared with Spanish breeds showing tamed behaviour. Two different approaches, BayeScan and SelEstim, were applied using genotypic 50K SNP BeadChip data. Both procedures detected two genomic regions bearing genes previously related to behavioural traits. The frequencies of the selected allele in these two regions in Lidia breed were opposite to those found in the tamed breeds. In these genomic regions, several putative genes associated with enriched metabolic pathways related to the behavioural development were identified, as neurochondrin gene (NCDN) or glutamate ionotropic receptor kainate type subunit 3 (GRIK3) both located at BTA3 or leucine‐rich repeat and Ig domain containing 2 (LINGO2) and phospholipase A2‐activating protein (PLAA) at BTA8.  相似文献   

19.
Identification of quantitative trait loci affecting reproduction in pigs   总被引：14，自引：0，他引：14  
The objective of this research was to identify chromosomal regions harboring QTL affecting reproduction in pigs. A three-generation resource population was developed by crossing low-indexing pigs from a randomly selected control line (C) with high-indexing pigs of a line selected for increased index of ovulation rate and embryonic survival (I). Differences between Lines I and C at Generation 10 were 6.7 ova and 3.3 fetuses at 50 d of gestation and 3.1 fully formed and 1.6 live pigs at birth. Phenotypic data were collected on F2 females, born in three replicates, for ovulation rate (n = 423), age at puberty (n = 295), litter size (n = 370), and number of nipples (n = 428). Litter-size data included number of fully formed, live, stillborn, and mummified pigs. Grandparent, F1, and F2 animals were genotyped for 151 microsatellite markers distributed across all 18 autosomes and the X chromosome. Genotypic data were available on 423 F2 females. Average spacing between markers was 19.3 Kosambi centimorgans. Calculations of logarithms of odds (LOD) scores were by least squares, and fixed effects for sire-dam combination and replicate were included in the models. Genome-wide significance level thresholds of 5% and 10% were calculated using a permutation approach. There was evidence (P < 0.05) for QTL affecting ovulation rate on SSC9, age at puberty on SSC7 and SSC8, number of nipples on SSC8 and SSC11, number of stillborn pigs on SSC5 and SSC13, and number of fully formed pigs on SSC11. There was evidence (P < 0.10) for additional QTL affecting age at puberty on SSC7, SSC8, and SSC12, number born live on SSC11, and number of nipples on SSC1, SSC6, and SSC7. Litter size is lowly heritable and sex-limited. Therefore, accuracy of selection for litter size may be enhanced by marker-assisted selection. Ovulation rate and age at puberty are laborious to measure, and thus marker-assisted selection may provide a practical and efficient method of selection.  相似文献   

20.
The benefit of using genomic breeding values (GEBV) in predicting ADG, DMI, and residual feed intake for an admixed population was investigated. Phenotypic data consisting of individual daily feed intake measurements for 721 beef cattle steers tested over 5 yr was available for analysis. The animals used were an admixed population of spring-born steers, progeny of a cross between 3 sire breeds and a composite dam line. Training and validation data sets were defined by randomly splitting the data into training and testing data sets based on sire family so that there was no overlap of sires in the 2 sets. The random split was replicated to obtain 5 separate data sets. Two methods (BayesB and random regression BLUP) were used to estimate marker effects and to define marker panels and ultimately the GEBV. The accuracy of prediction (the correlation between the phenotypes and GEBV) was compared between SNP panels. Accuracy for all traits was low, ranging from 0.223 to 0.479 for marker panels with 200 SNP, and 0.114 to 0.246 for marker panels with 37,959 SNP, depending on the genomic selection method used. This was less than accuracies observed for polygenic EBV accuracies, which ranged from 0.504 to 0.602. The results obtained from this study demonstrate that the utility of genetic markers for genomic prediction of residual feed intake in beef cattle may be suboptimal. Differences in accuracy were observed between sire breeds when the random regression BLUP method was used, which may imply that the correlations obtained by this method were confounded by the ability of the selected SNP to trace breed differences. This may also suggest that prediction equations derived from such an admixed population may be useful only in populations of similar composition. Given the sample size used in this study, there is a need for increased feed intake testing if substantially greater accuracies are to be achieved.  相似文献   

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