Influence of Miles City Line 1 on the United States Hereford population1,2,3

Leesburg, V. L. Reisenauer; MacNeil, M. D.; Neser, F.W.C.

doi:10.2527/jas.2013-6890

Cited by 9 publications

(9 citation statements)

References 15 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Within the US the breed is widely distributed across varying climatic zones. Although comparable levels of observed and expected heterozygosity have been reported for Hereford [41] and other Bos taurus breeds [42], high average genetic relationships have been observed in Herefords, suggesting genetic diversity maybe more limiting than in other breeds [29, 33]. …”

Section: Discussionmentioning

confidence: 63%

“…The inbred population Line 1 has had a significant effect on the Hereford breed and it has been estimated that 79% of the Herefords registered from 2006 to 2008 have some proportion of Line 1 in their pedigree [33]. Due to the large number of Line 1 animals sampled in the “2,000 Bull Project” and Line 1’s general influence among the Hereford breed a second series of analyses were performed to remove the excessive population bias from the dataset.…”

Section: Methodsmentioning

confidence: 99%

“…Due to the large number of Line 1 animals sampled in the “2000 Bull Project” and Line 1’s general influence among the Hereford breed a series of preliminary analyses were performed to evaluate the impact of Line 1. This included evaluating the coefficient of relationships and deleting animals with a high coefficient of relationship, and using proportional assignments made by STRUCTURE [33] to identify and delete animals that had a large genetic relationships to Line 1 (posterior probability of > 0.37). In addition to the attention paid to Line 1 animals raised outside CA we eliminated non-Line 1 animals with high coefficient genetic relationships (> 0.40) with animals from different ecoregions.…”

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

A fine structure genetic analysis evaluating ecoregional adaptability of a Bos taurus breed (Hereford)

et al. 2017

View full text Add to dashboard Cite

Ecoregional differences contribute to genetic environmental interactions and impact animal performance. These differences may become more important under climate change scenarios. Utilizing genetic diversity within a species to address such problems has not been fully explored. In this study Hereford cattle were genotyped with 50K Bead Chip or 770K Bovine Bead Chip to test the existence of genetic structure in five U.S. ecoregions characterized by precipitation, temperature and humidity and designated: cool arid (CA), cool humid (CH), transition zone (TZ), warm arid (WA), and warm humid (WH). SNP data were analyzed in three sequential analyses. Broad genetic structure was evaluated with STRUCTURE, and ADMIXTURE software using 14,312 SNPs after passing quality control variables. The second analysis was performed using principal coordinate analysis with 66 Tag SNPs associated in the literature with various aspects of environmental stressors (e.g., heat tolerance) or production (e.g., milk production). In the third analysis TreeSelect was used with the 66 SNPs to evaluate if ecoregional allelic frequencies deviated from a central frequency and by so doing are indicative of directional selection. The three analyses suggested subpopulation structures associated with ecoregions from where animals were derived. ADMIXTURE and PCA results illustrated the importance of temperature and humidity and confirm subpopulation assignments. Comparisons of allele frequencies with TreeSelect showed ecoregion differences, in particular the divergence between arid and humid regions. Patterns of genetic variability obtained by medium and high density SNP chips can be used to acclimatize a temperately derived breed to various ecoregions. As climate change becomes an important factor in cattle production, this study should be used as a proof of concept to review future breeding and conservation schemes aimed at adaptation to climatic events.

show abstract

Section: Discussionmentioning

confidence: 63%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

A fine structure genetic analysis evaluating ecoregional adaptability of a Bos taurus breed (Hereford)

et al. 2017

View full text Add to dashboard Cite

show abstract

“…Data used in this study were from line 1 Hereford cattle at USDA-ARS, Fort Keogh Livestock and Range Research Laboratory, Miles City, MT (Knapp et al, 1951;MacNeil, 2009;Leesburg et al, 2014). A historical review of the formation and management of this herd is provided by MacNeil (2009).…”

Section: Animals Genotypes and Phenotypesmentioning

confidence: 99%

Inbreeding depression in line 1 Hereford cattle population using pedigree and genomic information1

Sumreddee

Toghiani

Hay

et al. 2018

Journal of Animal Science

View full text Add to dashboard Cite

This study aimed at assessing inbreeding and its effect on growth and fertility traits using the longtime closed line 1 Hereford cattle population. Inbreeding was estimated based on pedigree (F PED) and genomic information. For the latter, three estimates were derived based on the diagonal elements of the genomic relationship matrix using estimated (F GRM) or fixed (F GRM0.5) minor allele frequencies or runs of homozygosity (ROH) (F ROH). A pedigree containing 10,186 animals was used to calculate F PED. Genomic inbreeding was evaluated using 785 animals genotyped for 30,810 SNP. Traits analyzed were birth weight (BWT), weaning weight (WWT), yearling weight (YWT), ADG, and age at first calving (AFC). The number of ROH per animal ranged between 6 and 119 segments with an average of 83. The shortest and longest segments were 1.36 and 64.86 Mb long, respectively, reflecting both ancient and recent inbreeding occurring in the last 30 to 40 generations. The average inbreeding was 29.2%, 16.1%, 30.2%, and 22.9% for F PED , F GRM , F GRM0.5 , and F ROH , respectively. F ROH provided the highest correlations with F PED (r = 0.66). Across paternal half-sib families, with minimal variation in F PED , there were substantial variations in their genomic inbreeding. Inbreeding depression analyses showed that a 1% increase in an animal's F PED resulted in a decrease of 1.20 kg, 2.03 kg, and 0.004 kg/d in WWT, YWT, and ADG, respectively. Maternal inbreeding showed significantly negative effects on progeny growth performance. AFC increased by 1.4 and 0.8 d for each 1% increase in F PED of the cow and her dam, respectively. Using genomic inbreeding, similar impact on growth traits was observed although the magnitude of the effect varied between methods. Across all genomic measures, WWT, YWT, and ADG decreased by 0.21 to 0.53 kg, 0.46 to 1.13 kg, and 0.002 to 0.006 kg/d for each 1% increase in genomic inbreeding, respectively. Four chromosomes (9, 12, 17, and 27) were identified to have a significant association between their homozygosity (F ROH-CHR) and growth traits. Variability in genomic inbreeding could be useful when deciding between full and half-sib selection candidates. Despite the high level of inbreeding in this study, its negative impact on growth performance was not as severe as expected, which may be attributed to the purging of the deleterious alleles due to natural or artificial selection over time.

show abstract

“…Pedigree analysis for the Herefords within each subpopulation indicated that the subpopulations comprised animals from the highly inbred USDA Miles City Line 1 Hereford population (L1) and other individuals representing broader U.S. Hereford pedigrees. Since the founding of the L1 Herefords, the migration of germplasm has been unidirectional from L1 into the broader U.S. industry, as the L1 population has been closed since its founding [18]. L1 Herefords do not segregate for recessive dwarfism, which has been a threat to Hereford breeders since the 1950s, and this has led to L1 cattle becoming popular in the process of purging herds of the defect [19].…”

Section: Resultsmentioning

confidence: 99%

CRUMBLER: A tool for the prediction of ancestry in cattle

et al. 2019

View full text Add to dashboard Cite

In many beef and some dairy production systems, crossbreeding is used to take advantage of breed complementarity and heterosis. Admixed animals are frequently identified by their coat color and body conformation phenotypes, however, without pedigree information it is not possible to identify the expected breed composition of an admixed animal and in the presence of selection, the actual composition may differ from expectation. As the roles of DNA and genotype data become more pervasive in animal agriculture, a systematic method for estimating the breed composition (the proportions of an animal’s genome originating from ancestral pure breeds) has utility for a variety of downstream analyses including the estimation of genomic breeding values for crossbred animals, the estimation of quantitative trait locus effects, and heterosis and heterosis retention in advanced generation composite animals. Currently, there is no automated or semi-automated ancestry estimation platform for cattle and the objective of this study was to evaluate the utility of extant public software for ancestry estimation and determine the effects of reference population size and composition and number of utilized single nucleotide polymorphism loci on ancestry estimation. We also sought to develop an analysis pipeline that would simplify this process for members of the livestock genomics research community. We developed and tested a tool, “CRUMBLER”, to estimate the global ancestry of cattle using ADMIXTURE and SNPweights based on a defined reference panel. CRUMBLER, was developed and evaluated in cattle, but is a species agnostic pipeline that facilitates the streamlined estimation of breed composition for individuals with potentially complex ancestries using publicly available global ancestry software and a specified reference population SNP dataset. We developed the reference panel from a large cattle genotype data set and breed association pedigree information using iterative analyses to identify purebred individuals that were representative of each breed. We also evaluated the numbers of markers necessary for breed composition estimation and simulated genotypes for advanced generation composite animals to evaluate the precision of the developed tool. The developed CRUMBLER pipeline extracts a specified subset of genotypes that is common to all current commercially available genotyping platforms, processes these into the file formats required for the analysis software, and predicts admixture proportions using the specified reference population allele frequencies.

show abstract

Influence of Miles City Line 1 on the United States Hereford population1,2,3

Cited by 9 publications

References 15 publications

A fine structure genetic analysis evaluating ecoregional adaptability of a Bos taurus breed (Hereford)

A fine structure genetic analysis evaluating ecoregional adaptability of a Bos taurus breed (Hereford)

Inbreeding depression in line 1 Hereford cattle population using pedigree and genomic information1

CRUMBLER: A tool for the prediction of ancestry in cattle

Contact Info

Product

Resources

About