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1.
Genetic marker data are likely to be obtained from a relatively small proportion of the individuals in many livestock populations. Information from genetic markers can be extrapolated to related individuals without marker data by computing genotype probabilities using an algorithm referred to as peeling. However, genetic markers may have many alleles and the number of computations in traditional peeling algorithms is proportional to the number of alleles raised to the sixth or eighth power, depending on pedigree structure. An alternative algorithm for computing genotype probabilities of marker loci with many alleles in large, nonlooped pedigrees with incomplete marker data is presented. The algorithm is based on recursive computations depending on alleles instead of genotypes, as in traditional peeling algorithms. The number of computations in the allelic peeling algorithm presented here is proportional to the square of the number of alleles, which makes this algorithm more computationally efficient than traditional peeling for loci with many alleles. Memory requirements are roughly proportional to the number of individuals in the pedigree and the number of alleles. The recursive allelic peeling algorithm cannot be applied to pedigrees that include full sibs or loops. However, it is a preliminary step toward a more complex and encompassing iterative approach to be described in a companion paper. 相似文献
2.
Casas E Shackelford SD Keele JW Koohmaraie M Smith TP Stone RT 《Journal of animal science》2003,81(12):2976-2983
The objective of the present study was to detect quantitative trait loci for economically important traits in a family from a Bos indicus x Bos taurus sire. A Brahman x Hereford sire was used to develop a half-sib family (n = 547). The sire was mated to Bos taurus cows. Traits analyzed were birth (kg) and weaning weights (kg); hot carcass weight (kg); marbling score; longissimus area (cm2); USDA yield grade; estimated kidney, pelvic, and heart fat (%); fat thickness (cm); fat yield (%); and retail product yield (%). Meat tenderness was measured as Warner-Bratzler shear force (kg) at 3 and 14 d postmortem. Two hundred and thirty-eight markers were genotyped in 185 offspring. One hundred and thirty markers were used to genotype the remaining 362 offspring. A total of 312 markers were used in the final analysis. Seventy-four markers were common to both groups. Significant QTL (expected number of false-positives < 0.05) were observed for birth weight and longissimus area on chromosome 5, for longissimus area on chromosome 6, for retail product yield on chromosome 9, for birth weight on chromosome 21, and for marbling score on chromosome 23. Evidence suggesting (expected number of false-positives < 1) the presence of QTL was detected for several traits. Putative QTL for birth weight were detected on chromosomes 1, 2, and 3, and for weaning weight on chromosome 29. For hot carcass weight, QTL were detected on chromosomes 10, 18, and 29. Four QTL for yield grade were identified on chromosomes 2, 11, 14, and 19. Three QTL for fat thickness were detected on chromosomes 2, 3, 7, and 14. For marbling score, QTL were identified on chromosomes 3, 10, 14, and 27. Four QTL were identified for retail product yield on chromosomes 12, 18, 19, and 29. A QTL for estimated kidney, pelvic, and heart fat was detected on chromosome 15, and a QTL for meat tenderness measured as Warner-Bratzler shear force at 3 d postmortem was identified on chromosome 20. Two QTL were detected for meat tenderness measured as Warner-Bratzler shear force at 14 d postmortem on chromosomes 20 and 29. These results present a complete scan in all available progeny in this family. Regions underlying QTL need to be assessed in other populations. 相似文献
3.
Evaluation of single-nucleotide polymorphisms in CAPN1 for association with meat tenderness in cattle 总被引：24，自引：0，他引：24
Page BT Casas E Heaton MP Cullen NG Hyndman DL Morris CA Crawford AM Wheeler TL Koohmaraie M Keele JW Smith TP 《Journal of animal science》2002,80(12):3077-3085
Micromolar calcium activated neutral protease (CAPN1) was evaluated as a candidate gene for a quantitative trait locus (QTL) on BTA29 affecting meat tenderness by characterization of nucleotide sequence variation in the gene. Single-nucleotide polymorphisms (SNP) were identified by sequencing all 22 exons and 19 of the 21 introns in two sires (Piedmontese x Angus located at the U.S. Meat Animal Research Center in Clay Center, NE; Jersey x Limousin located at AgResearch in New Zealand) of independent resource populations previously shown to be segregating meat tenderness QTL on BTA29. The majority of the 38 SNP were found in introns or were synonymous substitutions in the coding regions, with two exceptions. Exons 14 and 9 contained SNP that were predicted to alter the protein sequence by the substitution of isoleucine for valine in Domain III of the protein, and alanine for glycine in Domain II of the protein. The resource populations were genotyped for these two SNP in addition to six intronic polymorphisms and two silent substitutions. Analysis of genotypes and shear force values in both populations revealed a difference between paternal CAPN1 alleles in which the allele encoding isoleucine at position 530 and glycine at position 316 associated with decreased meat tenderness (increased shear force values) relative to the allele encoding valine at position 530 and alanine at position 316 (P < 0.05). The association of maternal alleles with meat tenderness phenotypes is consistent with the hypothesis of CAPN1 as the gene underlying the QTL effect in two independent resource populations and presents the possibility of using these markers for selective breeding to reduce the numbers of animals with unfavorable meat tenderness traits. 相似文献
4.
Initial results of genomic scans for ovulation rate in a cattle population selected for increased twinning rate 总被引：2，自引：0，他引：2
Kappes SM Bennett GL Keele JW Echternkamp SE Gregory KE Thallman RM 《Journal of animal science》2000,78(12):3053-3059
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
5.
Bovine CAPN1 maps to a region of BTA29 containing a quantitative trait locus for meat tenderness 总被引：21，自引：0，他引：21
Micromolar calcium activated neural protease (CAPN1) was investigated as a potential candidate gene for a quantitative trait locus (QTL) on BTA29 affecting meat tenderness. A 2,948-bp bovine cDNA containing the entire coding region of the gene was obtained, showing 91% identity to human CAPN1. The 716 AA protein predicted from this sequence shows 97% similarity (95% identity) to the 714 AA human protein. Analysis of the gene structure revealed that CAPN1 mRNA is encoded by at least 19 exons, and 11,055 bp of the gene were sequenced, including 17 introns. Two single nucleotide polymorphisms (SNP) were detected in intron 12 and were used to map bovine CAPN1 to the telomeric end of the BTA29 linkage group. This approximately coincides with the position of the QTL, demonstrating that CAPN1 protease is a positional candidate gene potentially affecting variation in meat tenderness in a bovine resource mapping population. 相似文献
6.
7.
White SN Casas E Allan MF Keele JW Snelling WM Wheeler TL Shackelford SD Koohmaraie M Smith TP 《Journal of animal science》2007,85(1):1-10
The objectives of this study were to 1) estimate the allelic frequencies in US beef cattle of 6 DNA markers reported to be associated with variation in dairy production traits; and 2) evaluate the association of these markers with beef production traits. Several genetic markers have been associated with milk yield or composition, including polymorphisms in secreted phosphoprotein 1 (SPP1; also called osteopontin), growth hormone receptor (GHR), casein S1 (CSN1S1), diacylglycerol O-acyltransferase 1 (DGAT1), peroxisome proliferator-activated receptor gamma co-activator-1alpha (PPARGC1A), and ATP-binding cassette subfamily G (white) member 2 (ABCG2). Allelic frequencies for these 6 markers, and their association with 21 phenotypes, were evaluated in 2 crossbred beef cattle populations that sample influential industry sires. Five of 6 markers were segregating in beef cattle populations; the exception was ABCG2. The SPP1 marker was associated with yearling weight (P = 0.025), live weight at slaughter (P = 0.016), postweaning ADG (P = 0.007), and HCW (P = 0.007) in a large, multisire population representing the 7 most populous beef breeds in the United States. Postweaning growth trait associations were confirmed in an independent population of similar construction, including sires from tropically adapted breeds. The SPP1 marker was associated with yearling weight (P = 0.034), live weight at slaughter (P = 0.011), and postweaning ADG (P = 0.015) and showed a trend toward association with HCW (P = 0.083) in this population. Whereas DGAT1, GHR, and CSN1S1 polymorphisms showed association with some traits in individual populations, the lack of consistent predictive merit between populations indicates they may not be suited for beef cattle selection. No significant associations were observed for the PPARGC1A marker and any of 21 recorded traits, indicating this marker had no apparent value in selection for the beef cattle traits tested in these populations. The SPP1 marker had consistent associations and effect sizes (10.5 to 11.5 kg of live weight at slaughter) in both populations, providing strong evidence for utility of the SPP1 marker for postweaning growth in beef cattle. 相似文献
8.
White SN Casas E Wheeler TL Shackelford SD Koohmaraie M Riley DG Chase CC Johnson DD Keele JW Smith TP 《Journal of animal science》2005,83(9):2001-2008
The three objectives of this study were to 1) test for the existence of beef tenderness markers in the CAPN1 gene segregating in Brahman cattle; 2) test existing CAPN1 tenderness markers in indicus-influenced crossbred cattle; and 3) produce a revised marker system for use in cattle of all subspecies backgrounds. Previously, two SNP in the CAPN1 gene have been described that could be used to guide selection in Bos taurus cattle (designated Markers 316 and 530), but neither marker segregates at high frequency in Brahman cattle. In this study, we examined three additional SNP in CAPN1 to determine whether variation in this gene could be associated with tenderness in a large, multisire American Brahman population. One marker (termed 4751) was associated with shear force on postmortem d 7 (P < 0.01), 14 (P = 0.015), and 21 (P < 0.001) in this population, demonstrating that genetic variation important for tenderness segregates in Bos indicus cattle at or near CAPN1. Marker 4751 also was associated with shear force (P < 0.01) in the same large, multisire population of cattle of strictly Bos taurus descent that was used to develop the previously reported SNP (referred to as the Germplasm Evaluation [GPE] Cycle 7 population), indicating the possibility that one marker could have wide applicability in cattle of all subspecies backgrounds. To test this hypothesis, Marker 4751 was tested in a third large, multisire cattle population of crossbred subspecies descent (including sire breeds of Brangus, Beefmaster, Bonsmara, Romosinuano, Hereford, and Angus referred to as the GPE Cycle 8 population). The highly significant association of Marker 4751 with shear force in this population (P < 0.001) confirms the usefulness of Marker 4751 in cattle of all subspecies backgrounds, including Bos taurus, Bos indicus, and crossbred descent. This wide applicability adds substantial value over previously released Markers 316 and 530. However, Marker 316, which had previously been shown to be associated with tenderness in the GPE Cycle 7 population, also was highly associated with shear force in the GPE Cycle 8 animals (P < 0.001). Thus, Marker 316 may continue to be useful in a variety of populations with a high percentage of Bos taurus backgrounds. An optimal marker strategy for CAPN1 in many cases will be to use both Markers 316 and 4751. 相似文献
9.
Association of markers in the bovine CAPN1 gene with meat tenderness in large crossbred populations that sample influential industry sires 总被引：1，自引：0，他引：1
Page BT Casas E Quaas RL Thallman RM Wheeler TL Shackelford SD Koohmaraie M White SN Bennett GL Keele JW Dikeman ME Smith TP 《Journal of animal science》2004,82(12):3474-3481
Two previously identified single-nucleotide polymorphism markers located within the micromolar calcium-activated neutral protease gene (CAPN1) were evaluated for their association with variation in meat tenderness using one commercial sample of Simmental x Angus crossbred calves and one multibreed, crossbred research herd. The commercial sample included 362 animals sired by 23 registered Simmental bulls bred to unregistered Angus cows and represented current industry animals in which to test the predictive merit of the markers. The second sample was a research herd including 564 steers from the Germplasm Evaluation Cycle VII population at the U.S. Meat Animal Research Center, produced with semen from popular sires of the seven Bos taurus beef breeds with the most registrations in the United States (Angus, Charolais, Gelbvieh, Hereford, Limousin, Red Angus, and Simmental) on Angus, Hereford, and MARC III cows. These animals form a relatively outbred population that constituted a stringent test of the predictive merit of the genetic markers, although small groups were half-sibs. Warner-Bratzler shear force measurements were used to determine tenderness phenotypes for all animals. The populations were genotyped for two markers that predict variation at amino acid positions 316 and 530 of the mu-calpain polypeptide, produced by the CAPN1 gene. Minor allele frequencies for markers 316 and 530 in the commercial sample were 0.17 and 0.37, respectively, and in the Cycle VII animals, were 0.20 and 0.28, respectively. Both markers showed association with shear force in the commercial sample (P = 0.04) and the Cycle VII population (P = 0.02), supporting the hypothesis that they represent potential markers to aid selection for improved meat tenderness in commercial populations of beef cattle in the United States. 相似文献
10.
B A Freking J W Keele S D Shackelford T L Wheeler M Koohmaraie M K Nielsen K A Leymaster 《Journal of animal science》1999,77(9):2336-2344
A resource flock of 362 F2 lambs provided phenotypic and genotypic data to estimate effects of callipyge (CLPG) genotypes (NN, NC, CN, and CC) on meat quality traits. The mutant allele is represented as C, the normal allele(s) as N, and the paternal allele of a genotype is given first. Lambs of each genotype born in 1994 and 1995 were serially slaughtered in six groups at 3-wk intervals starting at 23 wk of age. Warner-Bratzler shear force and subjective evaluation of marbling were collected during both years from longissimus. Calpastatin activity was measured on longissimus from the 1994 group, and ELISA quantification of calpastatin protein was obtained from the 1995 group. Significant additive and paternal polar overdominance effects on meat quality traits were detected. This is in contrast to previous research that detected only polar overdominance effects on slaughter and carcass traits in this population. The magnitude of genotypic effects on shear force differed significantly between years; however, additive (P < .01), paternal polar overdominance (P < .001), and maternal dominance (P < .01) effects adjusted for variation in carcass weight were detected within each year. Shear force data adjusted to the mean slaughter age or carcass weight indicated that the means and variances of CN and CC genotypes were greater than values of NC and NN. Shear force values were greatest for CN and were intermediate for CC. The difference in shear force (adjusted for variation in slaughter age) between homozygous genotypes (additive effect) was supported by calpastatin activity data with 2-df F-tests of 3.66 (P < .05) and 11.84 (P < .001) at d 0 and 7 postmortem, respectively. Corresponding values for the paternal polar overdominance effects on calpastatin activity were 53.80 (P < .001) and 87.43 (P < .001). Calpastatin ELISA data (d 0, adjusted for slaughter age) exhibited a paternal polar overdominance effect exclusively with a 2-df F-test of 57.63 (P < .001). Additive and paternal polar overdominance effects on marbling adjusted for slaughter age had F-tests of 6.41 (P < .01) and 93.29 (P < .001), respectively. Consequences of increased longissimus shear force must be addressed if the advantages of CN lambs for dressing percentage and carcass composition are to be realized. Further research is needed to establish whether selection targeted at changing the background genome can mitigate the negative effects of the C allele on meat tenderness. 相似文献