Mark Allan - Academia.edu (original) (raw)
Papers by Mark Allan
Developments in biologicals, 2008
The Germplasm Evaluation (GPE) Project at the US Meat Animal Research Center (USMARC) is planned ... more The Germplasm Evaluation (GPE) Project at the US Meat Animal Research Center (USMARC) is planned to produce about 3,000 calves per year in support of the following objectives: identification and validation of genetic polymorphisms related to economically relevant traits (ERT), estimation of breed and heterosis effects among 16 breeds for ERT, and estimation of genetic correlations among ERT and physiological indicator traits (PIT). Opportunities exist for collaboration in the development and collection of PIT phenotypes for disease resistance. Other areas of potential collaboration include detailed diagnosis (identification of disease causing organisms, etc.) of treated animals, collaborative development of epidemiological statistical models that would extract more information from the records of diagnoses and treatments, or pharmacogenetics. Concentrating a variety of different phenotypes and research approaches on the same population makes each component much more valuable than it...
Molecular and cellular biology, 1990
We have identified a short, highly repetitive element within intron -1 of the human c-Ha-ras gene... more We have identified a short, highly repetitive element within intron -1 of the human c-Ha-ras gene. This element was found to be transcribed in both orientations and to be homologous to heterogeneous nonpolyadenylated transcripts. The repetitive element blocked transcriptional readthrough from a strong upstream viral promoter but allowed unimpaired readthrough from the c-Has-ras promoter. We suggest that it may serve to prevent excessive transcription into the coding region of the gene under such circumstances as viral insertion.
PloS one, 2009
The success of genome-wide association (GWA) studies for the detection of sequence variation affe... more The success of genome-wide association (GWA) studies for the detection of sequence variation affecting complex traits in human has spurred interest in the use of large-scale high-density single nucleotide polymorphism (SNP) genotyping for the identification of quantitative trait loci (QTL) and for marker-assisted selection in model and agricultural species. A cost-effective and efficient approach for the development of a custom genotyping assay interrogating 54,001 SNP loci to support GWA applications in cattle is described. A novel algorithm for achieving a compressed inter-marker interval distribution proved remarkably successful, with median interval of 37 kb and maximum predicted gap of <350 kb. The assay was tested on a panel of 576 animals from 21 cattle breeds and six outgroup species and revealed that from 39,765 to 46,492 SNP are polymorphic within individual breeds (average minor allele frequency (MAF) ranging from 0.24 to 0.27). The assay also identified 79 putative co...
Meat Science, 2008
Substantial improvements in production efficiency and quality of beef and dairy products have bee... more Substantial improvements in production efficiency and quality of beef and dairy products have been made possible through manipulation of bovine genetics. The advent of modern breeds in the last two centuries, the institution of phenotypic selection practices and quantitative genetics, even the process of domestication in the distant past, have all represented means to make use of naturally occurring variation in the genome to tailor the animal for a desired outcome. We discuss the history of genome research in cattle and recent technological advances that promise a leap forward in the use of DNA sequence to facilitate selection, in which a detailed genome-level view for individual animals may provide comprehensive and relatively accurate assessment of the consequences, both desired and unintended, of genetic selection for livestock production.
Journal of Animal Science, 2009
Depletion of the ovarian reserve is associated with reproductive senescence in mammalian females,... more Depletion of the ovarian reserve is associated with reproductive senescence in mammalian females, and there is a positive relationship between the size of the ovarian reserve and the number of antral follicles on the surface of the ovary. Therefore, we conducted a series of experiments to investigate the influence of stage of the estrous cycle, age, and birth weight on antral follicle counts (AFC) in beef cows and heifers. Pairs of ovaries were collected from crossbred beef cows at slaughter (n = 72) or at necropsy (n = 333; 0 to 11 yr of age); all visible antral follicles were counted, the ovaries were weighed, and stage of the estrous cycle was estimated based on ovarian morphology. There was no influence of estimated stage of the estrous cycle on AFC (P = 0.36). There was a small but positive effect of birth weight on AFC [AFC = -1.7 + 0.31(birth weight); P = 0.007, r(2) = 0.05]. When antral follicle counts were regressed on age, there was a quadratic effect of age such that AFC increased until 5 yr of age and decreased thereafter [AFC = 12.9 + 9.0(yr) - 0.86(yr(2)); P < 0.001, r(2) = 0.22]. In a third experiment, crossbred beef heifers (n = 406; 353 to 463 d of age) at 3 locations were subjected to ovarian ultrasonography on unknown day of the estrous cycle. Heifers were classified as low AFC (<15 follicle, n = 84) or high AFC (>24 follicles, n = 178). Whereas estimated stage of the estrous cycle did not influence AFC (P = 0.62), heifers classified as low AFC had smaller ovaries (P = 0.001), decreased birth weight (P = 0.003), and a decreased heifer pregnancy rate (P = 0.05) compared with heifers in the high AFC group. From these results, we conclude that AFC in beef cows and heifers is influenced by birth weight and age but not by stage of the estrous cycle. In beef cows, the number of antral follicles increases to 5 yr of age and then begins to decline. This may indicate that a decrease in fertility due to decline of the ovarian reserve may begin earlier than previously thought in beef cows.
Journal of Animal Science, 2008
polymorphism map for twinning and ovulation rate on bovine chromosome 5 Confirmation of quantitat... more polymorphism map for twinning and ovulation rate on bovine chromosome 5 Confirmation of quantitative trait loci using a low-density single nucleotide
Journal of Animal Science, 2007
Effects of ovulation rate and of fetal number and distribution within the uterus on pregnancy rat... more Effects of ovulation rate and of fetal number and distribution within the uterus on pregnancy rate and fetal survival were evaluated in nulliparous (n = 1,331) and parous (n = 3,517) cattle selected for twinning. Cattle were divided into a spring (70 d) and fall (60 d) breeding season and bred by a combination of AI and natural service. Ovulation rate, pregnancy status, and fetal number and distribution were determined by transrectal, real-time ultrasonography of the uterus and both ovaries at the end of the breeding season. Pregnancy was reconfirmed by rectal palpation at 75 to 135 d of gestation. For heifers and cows combined, ovulation rate increased (P &amp;lt; 0.01) from 1.46 +/- 0.4 in 1994 to 1.89 +/- 0.4 in 2004; number of calves per parturition increased (P &amp;lt; 0.01) from 1.34 +/- 0.3 to 1.56 +/- 0.3, respectively, which included an increase in triplet and quadruplet ovulations and triplet births. Bilateral twin ovulations yielded proportionately more (P &amp;lt; 0.01) twin births than unilateral twin ovulations. Ovulation rate was greater (P &amp;lt; 0.01) in the fall than spring breeding season. Pregnancy rate at ultrasound diagnosis did not differ among females with 1, 2, or 3 ovulations (89.1 +/- 0.7, 91.2 +/- 0.7, or 91.5 +/- 2.8%, respectively), but rates at calving decreased (P &amp;lt; 0.01) with increasing ovulation rate (85.1 +/- 0.6, 82.7 +/- 0.6, or 64.2 +/- 2.7%, respectively). Pregnancy rate was less (P &amp;lt; 0.01) after twin or triplet births than single births. For dams birthing twins or triplets, pregnancy rate was less in the fall vs. spring, but rates were similar between seasons for dams with a single birth (type of birth x season, P &amp;lt; 0.05). Cows &amp;lt;/= 50 d postpartum had a decreased (P &amp;lt; 0.01) pregnancy rate compared with cows &amp;gt; 60 d, regardless of type of birth. Maintenance of pregnancy to term differed (P &amp;lt; 0.01) among females diagnosed with 1, 2, or 3 fetuses (95.7 +/- 0.6, 87.8 +/- 0.8, and 54.9 +/- 2.3%, respectively). The reduced survival of twin and triplet fetuses in heifers had occurred (P &amp;lt; 0.01) by d 75 to 135 of gestation, and fetal losses were greater (P &amp;lt; 0.01) for unilateral than bilateral twins or triplets, whereas loss of twin or triplet fetuses in cows occurred later in gestation, and losses were not affected by uterine location. Thus, increased calf production from selecting for increased ovulation rate in beef cattle is tempered by increased fetal mortality, partially associated with the crowding of 2 or 3 fetuses within 1 uterine horn, especially in heifers.
Journal of Animal Science, 2012
Journal of Animal Science, 2007
The effects of increasing fetal numbers and their distribution between the left and right uterine... more The effects of increasing fetal numbers and their distribution between the left and right uterine horns on calf survival, calf BW at birth and weaning, gestation length, dystocia, and calf sex ratio were evaluated for single (n = 1,587), twin (n = 2,440), and triplet calves (n = 147) born to primiparous and multiparous females in the Twinner population at the US Meat Animal Research Center between 1994 and 2004. Cattle were distributed equally between the spring and fall breeding seasons. Fetal number and distribution in utero were determined by real-time ultrasonography at 40 to 70 d postbreeding. For cows and heifers combined, number of calves per parturition increased from 1.34 in 1994 to 1.56 in 2004. Gestation length was 6.8 d shorter (P &amp;lt; 0.01) for twins compared with singles (277.5 +/- 0.2 vs. 284.3 +/- 0.2 d) and 12.7 d shorter for triplets (271.6 +/- 0.8 d). Survival and BW of individual calves at birth decreased (P &amp;lt; 0.01) but total calf BW per dam increased (P &amp;lt; 0.01) as fetal number increased from single to triplet births. Twins resulting from bilateral twin ovulations had increased (P &amp;lt; 0.01) survival and BW at birth, a longer (P &amp;lt; 0.01) gestation length, and less (P &amp;lt; 0.01) dystocia than twins resulting from unilateral twin ovulations. Calf survival and BW at birth were 97.2 +/- 0.3% and 48.0 +/- 0.1 kg for singles, 92.0 +/- 0.4% and 39.0 +/- 0.2 kg for bilateral twins, 83.2 +/- 0.4% and 36.7 +/- 0.2 kg for unilateral twins, 73.8 +/- 1.4% and 30.6 +/- 0.7 kg for bilateral triplets, and 51.9 +/- 3.2% and 31.7 +/- 1.6 kg for unilateral triplets. Birth weight of single calves increased by 0.51 kg/d for each additional day of gestation length vs. 0.38 kg/d for individual twins. Calf BW at birth increased (P &amp;lt; 0.01) with age of dam from 2 to 4 yr. Twin and triplet births had a greater (P &amp;lt; 0.01) incidence of dystocia than single births. The ratio of male:female calves (0.52:0.48) at birth was not affected by type of birth. Postnatal calf survival was similar for all 3 types of birth. Total progeny BW at weaning for single, twin, and triplet births was 217.7 +/- 2.5, 328.3 +/- 3.2, and 378.4 +/- 15.0 kg, respectively (P &amp;lt; 0.01). Although most bovine females have the uterine capacity to gestate twin calves, decreased survival and BW of unilateral twins and of all triplets indicate that their growth and development may have been compromised by uterine crowding.
Journal of Animal Science, 2007
Journal of Animal Science, 2011
The effects of individual SNP and the variation explained by sets of SNP associated with DMI, met... more The effects of individual SNP and the variation explained by sets of SNP associated with DMI, metabolic midtest BW, BW gain, and feed efficiency, expressed as phenotypic and genetic residual feed intake, were estimated from BW and the individual feed intake of 1,159 steers on dry lot offered a 3.0 Mcal/kg ration for at least 119 d before slaughter. Parents of these F(1) × F(1) (F(1)(2)) steers were AI-sired F(1) progeny of Angus, Charolais, Gelbvieh, Hereford, Limousin, Red Angus, and Simmental bulls mated to US Meat Animal Research Center Angus, Hereford, and MARC III composite females. Steers were genotyped with the BovineSNP50 BeadChip assay (Illumina Inc., San Diego, CA). Effects of 44,163 SNP having minor allele frequencies &amp;amp;amp;gt;0.05 in the F(1)(2) generation were estimated with a mixed model that included genotype, breed composition, heterosis, age of dam, and slaughter date contemporary groups as fixed effects, and a random additive genetic effect with recorded pedigree relationships among animals. Variance in this population attributable to sets of SNP was estimated with models that partitioned the additive genetic effect into a polygenic component attributable to pedigree relationships and a genotypic component attributable to genotypic relationships. The sets of SNP evaluated were the full set of 44,163 SNP and subsets containing 6 to 40,000 SNP selected according to association with phenotype. Ninety SNP were strongly associated (P &amp;amp;amp;lt; 0.0001) with at least 1 efficiency or component trait; these 90 accounted for 28 to 46% of the total additive genetic variance of each trait. Trait-specific sets containing 96 SNP having the strongest associations with each trait explained 50 to 87% of additive variance for that trait. Expected accuracy of steer breeding values predicted with pedigree and genotypic relationships exceeded the accuracy of their sires predicted without genotypic information, although gains in accuracy were not sufficient to encourage that performance testing be replaced by genotyping and genomic evaluations.
Journal of Animal Science, 2010
Chromosomal regions harboring variation affecting cattle birth weight and BW gain to 1 yr of age ... more Chromosomal regions harboring variation affecting cattle birth weight and BW gain to 1 yr of age were identified by marker association using the highly parallel BovineSNP50 BeadChip (50K) assay composed of 54,001 individual SNP. Genotypes were obtained from progeny (F(1); 590 steers) and 2-, 3-, and 4-breed cross grandprogeny (F(1)(2) = F(1) x F(1); 1,306 steers and 707 females) of 150 AI sires representing 7 breeds (22 sires per breed; Angus, Charolais, Gelbvieh, Hereford, Limousin, Red Angus, and Simmental). Genotypes and birth, weaning, and yearling BW records were used in whole-genome association analyses to estimate effects of individual SNP on growth. Traits analyzed included growth component traits: birth weight (BWT), 205-d adjusted birth to weaning BW gain (WG), 160-d adjusted postweaning BW gain (PWG); cumulative traits: 205-d adjusted weaning weight (WW = BWT + WG) and 365-d adjusted yearling weight (YW = BWT + WG + PWG); and indexes of relative differences between postnatal growth and birth weight. Modeled fixed effects included additive effects of calf and dam SNP genotype, year-sex-management contemporary groups, and covariates for calf and dam breed composition and heterosis. Direct and maternal additive polygenic effects and maternal permanent environment effects were random. Missing genotypes, including 50K genotypes of most dams, were approximated with a single-locus BLUP procedure from pedigree relationships and known 50K genotypes. Various association criteria were applied: stringent tests to account for multiple testing but with limited power to detect associations with small effects, and relaxed nominal P that may detect SNP associated with small effects but include excessive false positive associations. Genomic locations of the 231 SNP meeting stringent criteria generally coincided with described previously QTL affecting growth traits. The 12,425 SNP satisfying relaxed tests were located throughout the genome. Most SNP associated with BWT and postnatal growth affected components in the same direction, although detection of SNP associated with one component independent of others presents a possible opportunity for SNP-assisted selection to increase postnatal growth relative to BWT.
Journal of Animal Breeding and Genetics, 2000
... different set of sires was used to represent the sire breeds although some sires were repeate... more ... different set of sires was used to represent the sire breeds although some sires were repeated, especially in Limousin, Simmental and South Devon breeds (Smith et al., 1976b). Thus significance of breed of sire by year interactions may be due to differences in sets of sires as ...
This is the assignment for week 1
Developments in biologicals, 2008
The Germplasm Evaluation (GPE) Project at the US Meat Animal Research Center (USMARC) is planned ... more The Germplasm Evaluation (GPE) Project at the US Meat Animal Research Center (USMARC) is planned to produce about 3,000 calves per year in support of the following objectives: identification and validation of genetic polymorphisms related to economically relevant traits (ERT), estimation of breed and heterosis effects among 16 breeds for ERT, and estimation of genetic correlations among ERT and physiological indicator traits (PIT). Opportunities exist for collaboration in the development and collection of PIT phenotypes for disease resistance. Other areas of potential collaboration include detailed diagnosis (identification of disease causing organisms, etc.) of treated animals, collaborative development of epidemiological statistical models that would extract more information from the records of diagnoses and treatments, or pharmacogenetics. Concentrating a variety of different phenotypes and research approaches on the same population makes each component much more valuable than it...
Molecular and cellular biology, 1990
We have identified a short, highly repetitive element within intron -1 of the human c-Ha-ras gene... more We have identified a short, highly repetitive element within intron -1 of the human c-Ha-ras gene. This element was found to be transcribed in both orientations and to be homologous to heterogeneous nonpolyadenylated transcripts. The repetitive element blocked transcriptional readthrough from a strong upstream viral promoter but allowed unimpaired readthrough from the c-Has-ras promoter. We suggest that it may serve to prevent excessive transcription into the coding region of the gene under such circumstances as viral insertion.
PloS one, 2009
The success of genome-wide association (GWA) studies for the detection of sequence variation affe... more The success of genome-wide association (GWA) studies for the detection of sequence variation affecting complex traits in human has spurred interest in the use of large-scale high-density single nucleotide polymorphism (SNP) genotyping for the identification of quantitative trait loci (QTL) and for marker-assisted selection in model and agricultural species. A cost-effective and efficient approach for the development of a custom genotyping assay interrogating 54,001 SNP loci to support GWA applications in cattle is described. A novel algorithm for achieving a compressed inter-marker interval distribution proved remarkably successful, with median interval of 37 kb and maximum predicted gap of <350 kb. The assay was tested on a panel of 576 animals from 21 cattle breeds and six outgroup species and revealed that from 39,765 to 46,492 SNP are polymorphic within individual breeds (average minor allele frequency (MAF) ranging from 0.24 to 0.27). The assay also identified 79 putative co...
Meat Science, 2008
Substantial improvements in production efficiency and quality of beef and dairy products have bee... more Substantial improvements in production efficiency and quality of beef and dairy products have been made possible through manipulation of bovine genetics. The advent of modern breeds in the last two centuries, the institution of phenotypic selection practices and quantitative genetics, even the process of domestication in the distant past, have all represented means to make use of naturally occurring variation in the genome to tailor the animal for a desired outcome. We discuss the history of genome research in cattle and recent technological advances that promise a leap forward in the use of DNA sequence to facilitate selection, in which a detailed genome-level view for individual animals may provide comprehensive and relatively accurate assessment of the consequences, both desired and unintended, of genetic selection for livestock production.
Journal of Animal Science, 2009
Depletion of the ovarian reserve is associated with reproductive senescence in mammalian females,... more Depletion of the ovarian reserve is associated with reproductive senescence in mammalian females, and there is a positive relationship between the size of the ovarian reserve and the number of antral follicles on the surface of the ovary. Therefore, we conducted a series of experiments to investigate the influence of stage of the estrous cycle, age, and birth weight on antral follicle counts (AFC) in beef cows and heifers. Pairs of ovaries were collected from crossbred beef cows at slaughter (n = 72) or at necropsy (n = 333; 0 to 11 yr of age); all visible antral follicles were counted, the ovaries were weighed, and stage of the estrous cycle was estimated based on ovarian morphology. There was no influence of estimated stage of the estrous cycle on AFC (P = 0.36). There was a small but positive effect of birth weight on AFC [AFC = -1.7 + 0.31(birth weight); P = 0.007, r(2) = 0.05]. When antral follicle counts were regressed on age, there was a quadratic effect of age such that AFC increased until 5 yr of age and decreased thereafter [AFC = 12.9 + 9.0(yr) - 0.86(yr(2)); P < 0.001, r(2) = 0.22]. In a third experiment, crossbred beef heifers (n = 406; 353 to 463 d of age) at 3 locations were subjected to ovarian ultrasonography on unknown day of the estrous cycle. Heifers were classified as low AFC (<15 follicle, n = 84) or high AFC (>24 follicles, n = 178). Whereas estimated stage of the estrous cycle did not influence AFC (P = 0.62), heifers classified as low AFC had smaller ovaries (P = 0.001), decreased birth weight (P = 0.003), and a decreased heifer pregnancy rate (P = 0.05) compared with heifers in the high AFC group. From these results, we conclude that AFC in beef cows and heifers is influenced by birth weight and age but not by stage of the estrous cycle. In beef cows, the number of antral follicles increases to 5 yr of age and then begins to decline. This may indicate that a decrease in fertility due to decline of the ovarian reserve may begin earlier than previously thought in beef cows.
Journal of Animal Science, 2008
polymorphism map for twinning and ovulation rate on bovine chromosome 5 Confirmation of quantitat... more polymorphism map for twinning and ovulation rate on bovine chromosome 5 Confirmation of quantitative trait loci using a low-density single nucleotide
Journal of Animal Science, 2007
Effects of ovulation rate and of fetal number and distribution within the uterus on pregnancy rat... more Effects of ovulation rate and of fetal number and distribution within the uterus on pregnancy rate and fetal survival were evaluated in nulliparous (n = 1,331) and parous (n = 3,517) cattle selected for twinning. Cattle were divided into a spring (70 d) and fall (60 d) breeding season and bred by a combination of AI and natural service. Ovulation rate, pregnancy status, and fetal number and distribution were determined by transrectal, real-time ultrasonography of the uterus and both ovaries at the end of the breeding season. Pregnancy was reconfirmed by rectal palpation at 75 to 135 d of gestation. For heifers and cows combined, ovulation rate increased (P &amp;lt; 0.01) from 1.46 +/- 0.4 in 1994 to 1.89 +/- 0.4 in 2004; number of calves per parturition increased (P &amp;lt; 0.01) from 1.34 +/- 0.3 to 1.56 +/- 0.3, respectively, which included an increase in triplet and quadruplet ovulations and triplet births. Bilateral twin ovulations yielded proportionately more (P &amp;lt; 0.01) twin births than unilateral twin ovulations. Ovulation rate was greater (P &amp;lt; 0.01) in the fall than spring breeding season. Pregnancy rate at ultrasound diagnosis did not differ among females with 1, 2, or 3 ovulations (89.1 +/- 0.7, 91.2 +/- 0.7, or 91.5 +/- 2.8%, respectively), but rates at calving decreased (P &amp;lt; 0.01) with increasing ovulation rate (85.1 +/- 0.6, 82.7 +/- 0.6, or 64.2 +/- 2.7%, respectively). Pregnancy rate was less (P &amp;lt; 0.01) after twin or triplet births than single births. For dams birthing twins or triplets, pregnancy rate was less in the fall vs. spring, but rates were similar between seasons for dams with a single birth (type of birth x season, P &amp;lt; 0.05). Cows &amp;lt;/= 50 d postpartum had a decreased (P &amp;lt; 0.01) pregnancy rate compared with cows &amp;gt; 60 d, regardless of type of birth. Maintenance of pregnancy to term differed (P &amp;lt; 0.01) among females diagnosed with 1, 2, or 3 fetuses (95.7 +/- 0.6, 87.8 +/- 0.8, and 54.9 +/- 2.3%, respectively). The reduced survival of twin and triplet fetuses in heifers had occurred (P &amp;lt; 0.01) by d 75 to 135 of gestation, and fetal losses were greater (P &amp;lt; 0.01) for unilateral than bilateral twins or triplets, whereas loss of twin or triplet fetuses in cows occurred later in gestation, and losses were not affected by uterine location. Thus, increased calf production from selecting for increased ovulation rate in beef cattle is tempered by increased fetal mortality, partially associated with the crowding of 2 or 3 fetuses within 1 uterine horn, especially in heifers.
Journal of Animal Science, 2012
Journal of Animal Science, 2007
The effects of increasing fetal numbers and their distribution between the left and right uterine... more The effects of increasing fetal numbers and their distribution between the left and right uterine horns on calf survival, calf BW at birth and weaning, gestation length, dystocia, and calf sex ratio were evaluated for single (n = 1,587), twin (n = 2,440), and triplet calves (n = 147) born to primiparous and multiparous females in the Twinner population at the US Meat Animal Research Center between 1994 and 2004. Cattle were distributed equally between the spring and fall breeding seasons. Fetal number and distribution in utero were determined by real-time ultrasonography at 40 to 70 d postbreeding. For cows and heifers combined, number of calves per parturition increased from 1.34 in 1994 to 1.56 in 2004. Gestation length was 6.8 d shorter (P &amp;lt; 0.01) for twins compared with singles (277.5 +/- 0.2 vs. 284.3 +/- 0.2 d) and 12.7 d shorter for triplets (271.6 +/- 0.8 d). Survival and BW of individual calves at birth decreased (P &amp;lt; 0.01) but total calf BW per dam increased (P &amp;lt; 0.01) as fetal number increased from single to triplet births. Twins resulting from bilateral twin ovulations had increased (P &amp;lt; 0.01) survival and BW at birth, a longer (P &amp;lt; 0.01) gestation length, and less (P &amp;lt; 0.01) dystocia than twins resulting from unilateral twin ovulations. Calf survival and BW at birth were 97.2 +/- 0.3% and 48.0 +/- 0.1 kg for singles, 92.0 +/- 0.4% and 39.0 +/- 0.2 kg for bilateral twins, 83.2 +/- 0.4% and 36.7 +/- 0.2 kg for unilateral twins, 73.8 +/- 1.4% and 30.6 +/- 0.7 kg for bilateral triplets, and 51.9 +/- 3.2% and 31.7 +/- 1.6 kg for unilateral triplets. Birth weight of single calves increased by 0.51 kg/d for each additional day of gestation length vs. 0.38 kg/d for individual twins. Calf BW at birth increased (P &amp;lt; 0.01) with age of dam from 2 to 4 yr. Twin and triplet births had a greater (P &amp;lt; 0.01) incidence of dystocia than single births. The ratio of male:female calves (0.52:0.48) at birth was not affected by type of birth. Postnatal calf survival was similar for all 3 types of birth. Total progeny BW at weaning for single, twin, and triplet births was 217.7 +/- 2.5, 328.3 +/- 3.2, and 378.4 +/- 15.0 kg, respectively (P &amp;lt; 0.01). Although most bovine females have the uterine capacity to gestate twin calves, decreased survival and BW of unilateral twins and of all triplets indicate that their growth and development may have been compromised by uterine crowding.
Journal of Animal Science, 2007
Journal of Animal Science, 2011
The effects of individual SNP and the variation explained by sets of SNP associated with DMI, met... more The effects of individual SNP and the variation explained by sets of SNP associated with DMI, metabolic midtest BW, BW gain, and feed efficiency, expressed as phenotypic and genetic residual feed intake, were estimated from BW and the individual feed intake of 1,159 steers on dry lot offered a 3.0 Mcal/kg ration for at least 119 d before slaughter. Parents of these F(1) × F(1) (F(1)(2)) steers were AI-sired F(1) progeny of Angus, Charolais, Gelbvieh, Hereford, Limousin, Red Angus, and Simmental bulls mated to US Meat Animal Research Center Angus, Hereford, and MARC III composite females. Steers were genotyped with the BovineSNP50 BeadChip assay (Illumina Inc., San Diego, CA). Effects of 44,163 SNP having minor allele frequencies &amp;amp;amp;gt;0.05 in the F(1)(2) generation were estimated with a mixed model that included genotype, breed composition, heterosis, age of dam, and slaughter date contemporary groups as fixed effects, and a random additive genetic effect with recorded pedigree relationships among animals. Variance in this population attributable to sets of SNP was estimated with models that partitioned the additive genetic effect into a polygenic component attributable to pedigree relationships and a genotypic component attributable to genotypic relationships. The sets of SNP evaluated were the full set of 44,163 SNP and subsets containing 6 to 40,000 SNP selected according to association with phenotype. Ninety SNP were strongly associated (P &amp;amp;amp;lt; 0.0001) with at least 1 efficiency or component trait; these 90 accounted for 28 to 46% of the total additive genetic variance of each trait. Trait-specific sets containing 96 SNP having the strongest associations with each trait explained 50 to 87% of additive variance for that trait. Expected accuracy of steer breeding values predicted with pedigree and genotypic relationships exceeded the accuracy of their sires predicted without genotypic information, although gains in accuracy were not sufficient to encourage that performance testing be replaced by genotyping and genomic evaluations.
Journal of Animal Science, 2010
Chromosomal regions harboring variation affecting cattle birth weight and BW gain to 1 yr of age ... more Chromosomal regions harboring variation affecting cattle birth weight and BW gain to 1 yr of age were identified by marker association using the highly parallel BovineSNP50 BeadChip (50K) assay composed of 54,001 individual SNP. Genotypes were obtained from progeny (F(1); 590 steers) and 2-, 3-, and 4-breed cross grandprogeny (F(1)(2) = F(1) x F(1); 1,306 steers and 707 females) of 150 AI sires representing 7 breeds (22 sires per breed; Angus, Charolais, Gelbvieh, Hereford, Limousin, Red Angus, and Simmental). Genotypes and birth, weaning, and yearling BW records were used in whole-genome association analyses to estimate effects of individual SNP on growth. Traits analyzed included growth component traits: birth weight (BWT), 205-d adjusted birth to weaning BW gain (WG), 160-d adjusted postweaning BW gain (PWG); cumulative traits: 205-d adjusted weaning weight (WW = BWT + WG) and 365-d adjusted yearling weight (YW = BWT + WG + PWG); and indexes of relative differences between postnatal growth and birth weight. Modeled fixed effects included additive effects of calf and dam SNP genotype, year-sex-management contemporary groups, and covariates for calf and dam breed composition and heterosis. Direct and maternal additive polygenic effects and maternal permanent environment effects were random. Missing genotypes, including 50K genotypes of most dams, were approximated with a single-locus BLUP procedure from pedigree relationships and known 50K genotypes. Various association criteria were applied: stringent tests to account for multiple testing but with limited power to detect associations with small effects, and relaxed nominal P that may detect SNP associated with small effects but include excessive false positive associations. Genomic locations of the 231 SNP meeting stringent criteria generally coincided with described previously QTL affecting growth traits. The 12,425 SNP satisfying relaxed tests were located throughout the genome. Most SNP associated with BWT and postnatal growth affected components in the same direction, although detection of SNP associated with one component independent of others presents a possible opportunity for SNP-assisted selection to increase postnatal growth relative to BWT.
Journal of Animal Breeding and Genetics, 2000
... different set of sires was used to represent the sire breeds although some sires were repeate... more ... different set of sires was used to represent the sire breeds although some sires were repeated, especially in Limousin, Simmental and South Devon breeds (Smith et al., 1976b). Thus significance of breed of sire by year interactions may be due to differences in sets of sires as ...
This is the assignment for week 1