scholarly journals 30 Inbreeding in American Angus cattle before and after the implementation of genomic selection

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 14-14
Author(s):  
Emmanuel A Lozada-Soto ◽  
Francesco Tiezzi ◽  
Duc Lu ◽  
Stephen P Miller ◽  
John B Cole ◽  
...  
Keyword(s):  
Genomic Selection ◽  
Effective Population ◽  
Generation Interval ◽  
Inbreeding Coefficients ◽  
Angus Cattle ◽  
Before And After ◽  
Population Sizes ◽  
The Mean ◽  
Time Periods ◽  
Genomic Inbreeding

Abstract The aim of this study was to characterize the American Angus cattle population in terms of changes to the inbreeding rate (ΔF) and effective population size (Ne) before and after the implementation of genomic selection (GS). Genomic information (89,206 SNPs) was obtained for 25,960 bulls and 134,962 cows born between the years 2000 and 2017. Bulls and cows were independently grouped into two groups based on year of birth, pre-GS (2000–2009), and post-GS (2010–2017). Genomic inbreeding (FGRM) was calculated assuming fixed allele frequencies (0.5). Inbreeding based on runs of homozygosity (FROH) was calculated using software SNP1101 (Sargolzaei, 2014). The yearly ΔF for each group was estimated by regressing the inbreeding coefficients on year of birth. The generation intervals (L) were calculated for each of the four pathways of selection at both time periods (pre-GS and post-GS), where the mean of the sires of sires and dams of sires pathways was taken to be the generation interval for the bulls and the mean of the sires of dams and dams of dams pathways was taken to be the generation interval for the cows. The L and ΔF of the three inbreeding coefficients were used to estimate the Ne. Estimates of ΔF and Ne for both sexes at the two time periods can be found in table 1. In both sexes, ΔFROH decreased and NeROH increased from pre-GS to post-GS. For bulls, ΔFGRM and NeGRM did not change, and for cows, ΔFGRM decreased and NeGRM increased from pre-GS to post-GS. These results suggest that the implementation of genomic selection in Angus cattle has not caused the increased inbreeding rates and reduced effective population sizes seen in other species, but instead has been beneficial for the preservation of genetic diversity.

scholarly journals Trends in genetic diversity and the effect of inbreeding in American Angus cattle under genomic selection

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Emmanuel A. Lozada-Soto ◽  
Christian Maltecca ◽  
Duc Lu ◽  
Stephen Miller ◽  
John B. Cole ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Beef Cattle ◽  
Genomic Selection ◽  
Inbreeding Depression ◽  
Growth Traits ◽  
Effective Population ◽  
Angus Cattle ◽  
Genomic Inbreeding ◽  
Chromosome Segments ◽  
The Impact

Abstract Background While the adoption of genomic evaluations in livestock has increased genetic gain rates, its effects on genetic diversity and accumulation of inbreeding have raised concerns in cattle populations. Increased inbreeding may affect fitness and decrease the mean performance for economically important traits, such as fertility and growth in beef cattle, with the age of inbreeding having a possible effect on the magnitude of inbreeding depression. The purpose of this study was to determine changes in genetic diversity as a result of the implementation of genomic selection in Angus cattle and quantify potential inbreeding depression effects of total pedigree and genomic inbreeding, and also to investigate the impact of recent and ancient inbreeding. Results We found that the yearly rate of inbreeding accumulation remained similar in sires and decreased significantly in dams since the implementation of genomic selection. Other measures such as effective population size and the effective number of chromosome segments show little evidence of a detrimental effect of using genomic selection strategies on the genetic diversity of beef cattle. We also quantified pedigree and genomic inbreeding depression for fertility and growth. While inbreeding did not affect fertility, an increase in pedigree or genomic inbreeding was associated with decreased birth weight, weaning weight, and post-weaning gain in both sexes. We also measured the impact of the age of inbreeding and found that recent inbreeding had a larger depressive effect on growth than ancient inbreeding. Conclusions In this study, we sought to quantify and understand the possible consequences of genomic selection on the genetic diversity of American Angus cattle. In both sires and dams, we found that, generally, genomic selection resulted in decreased rates of pedigree and genomic inbreeding accumulation and increased or sustained effective population sizes and number of independently segregating chromosome segments. We also found significant depressive effects of inbreeding accumulation on economically important growth traits, particularly with genomic and recent inbreeding.

scholarly journals Population structure of Czech cold-blooded breeds of horses

2011 ◽  
Vol 54 (1) ◽  
pp. 1-9
Author(s):  
L. Vostrý ◽  
Z. Čapková ◽  
J. Přibyl ◽  
B. Hofmanová ◽  
H. Vostrá Vydrová ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Variability ◽  
Population Size ◽  
Effective Population Size ◽  
Inbreeding Coefficient ◽  
Effective Population ◽  
The Czech Republic ◽  
Generation Interval ◽  
Average Value ◽  
Inbreeding Coefficients

Abstract. In order to estimate effective population size, generation interval and the development of inbreeding coefficients (Fx) in three original breeds of cold-blooded horses kept in the Czech Republic: Silesian Noriker (SN), Noriker (N) and Czech-Moravian Belgian horse (CMB) all animals of the particular breeds born from 1990 to 2007 were analysed. The average values of generation interval between parents and their offspring were: 8.53 in SN, 8.88 in N and 8.56 in CMB. Average values of effective population size were estimated to be: 86.3 in SN, 162.3 in N and 104.4 in CMB. The average values of inbreeding coefficient were 3.13 % in SN stallions and 3.39 % in SN mares, in the N breed 1.76 % and 1.26 % and in the CMB breed 3.84 % and 3.26 % respectively. Overall averages of Fx were: 3.23 %, 1.51 % and 3.55 % for the breeds SN, N and CMB. The average value of inbreeding coefficient Fx increased by 1.22 % in SN, by 0.35 % in N and by 1.01 % in CMB, respectively. This may lead to a reduction in genetic variability. Reduction in genetic variability could be either controlled in cooperation with corresponding populations of cold-blooded breeds in other European countries or controlled by number of sires used in population

scholarly journals Inbreeding in a Population of Polish Holstein-Friesian Young Bulls Before and After Genomic Selection

2020 ◽  
Vol 20 (1) ◽  
pp. 71-83
Author(s):  
Piotr Topolski ◽  
Wojciech Jagusiak
Keyword(s):  
Genomic Selection ◽  
Linear Trend ◽  
Pedigree Analysis ◽  
Breeding Programme ◽  
Black And White ◽  
Holstein Friesian ◽  
Before And After ◽  
Breeding Programmes ◽  
Dynamics Of Population ◽  
The Mean

AbstractInbreeding was analysed in a population of 14,144 Polish Black-and-White Holstein-Friesian (PBWHF) young bulls born between 1994 and 2017 and bred under both conventional and genomic breeding programmes. The inbreeding coefficients were computed using a model with genetic groups, according to the algorithm given by VanRaden. It was found that in the analysed population all bulls are inbred (100% of the population), with the mean coefficient of inbreeding ranging from 0.09% to 26.95%. Pedigree analysis also showed a relationship between the changing number of bulls over the years and the dynamics of population inbreeding. These trends are connected with changes in the breeding scheme, related to the implementation of genomic selection in the breeding programme for PBWHF cattle in 2014. The increasing number of weaned young bulls in Poland was paralleled by a fairly consistent increase in the mean inbreeding, but the inbreeding dynamics were relatively small. A reverse trend was observed in the group of young bulls born after 2013. As the number of bulls very rapidly decreased in successive birth years, the mean inbreeding for successive birth-year groups very rapidly increased. As a result, the estimated linear trend was equal to 0.02% inbreeding per year of birth in the group of bulls raised before genomic selection (~20 birth-year) whereas in the group of bulls raised after genomic selection (~4 birth-year) the trend was much higher and amounted to 0.56% inbreeding per year of birth. The high mean inbreeding found in the group of the genomically selected young bulls may translate into higher inbreeding in the whole population of PBWHF cattle, because these bulls are now intensively used as sires. The results of our study also show that the implementation of genomic selection in the breeding programme caused a very rapid increase in the inbreeding rate per birth-year in young bulls.

Population structure of the Sahiwal breed in Pakistan

1995 ◽  
Vol 60 (2) ◽  
pp. 163-168 ◽  
Author(s):  
A. Dahlin ◽  
U. N. Khan ◽  
A. H. Zafar ◽  
M. Saleem ◽  
M. A. Chaudhry ◽  
...  
Keyword(s):  
Population Structure ◽  
Population Size ◽  
Effective Population Size ◽  
Breeding Population ◽  
Effective Population ◽  
Data Set ◽  
Inbreeding Coefficients ◽  
Sahiwal Cows ◽  
The Mean ◽  
Average Population Size

AbstractThe present study was undertaken to assist conservation and improvement schemes in the Sahiwal breed of cattle in Pakistan. A data set, consisting of records of 244 pure Sahiwal breeding bulls and 5247 cows, the latter representing about 80% of all recorded Sahiwal cows in Pakistan born during a period covering about 20 years, was analysed with regard to inbreeding, additive relationships, effective population size and generation intervals. Average inbreeding coefficients of 1224 cows and 49 bulls, for which at least the grandparents and great-grandsires were known, were 0·043 and 0·046, respectively. About two-thirds of the inbreeding was due to matings between animals with parents or grandparents in common. The mean additive relationship among the cows was 0·062, with within-herd averages ranging from 0·087 to 0·358. The average population size in a subdata set of recorded Sahiwal cattle from 1980 to 1984 was 1612, whereas the most likely estimate of the effective population size was about 30 animals for the same active breeding population. The study indicated the immediate need for an active conservation programme whereby the Sahiwal subpopulations of India and Kenya also should be involved.

Genetics of reintroduced populations of the narrowly endemic thistle, Cirsium pitcheri (Asteraceae)

Botany ◽  
2013 ◽  
Vol 91 (5) ◽  
pp. 301-308 ◽  
Author(s):  
Jeremie B. Fant ◽  
Andrea Kramer ◽  
Eileen Sirkin ◽  
Kayri Havens
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Empirical Studies ◽  
Small Population ◽  
Native Plant ◽  
Effective Population ◽  
Term Survival ◽  
Inbreeding Coefficients ◽  
Native Populations ◽  
Population Sizes

The aim of any reintroduction is to provide sufficient genetic variability to buffer against changing selection pressures and ensure long-term survival. To date, few empirical studies have compared levels of genetic diversity in reintroduced and native plant populations. Using microsatellite markers, we measured the genetic diversity within reintroduced and native populations of the threatened Cirsium pitcher (Eaton) Torrey and Gray. We found that the use of local mixed source was successful in establishing populations with significantly higher genetic diversity (P < 0.005) than the native populations (allelic richness is 3.39 in reintroduced and 1.84 in native populations). However, the reintroduced populations had significantly higher inbreeding coefficients (P < 0.002) (FIS is 0.405 and 0.213 in reintroduced and in native populations, respectively), despite having multiple genetic founders, population sizes equivalent to native populations and a positive growth rate. These results may be due to inbreeding or the Wahlund effect, driven by genetic substructuring. This suggests that the small population size of these reintroduced populations may lead to genetic issues in the future, given the low number of flowering individuals each year. This highlights the importance of considering not only the number of source individuals but the effective population size of the reintroduction.

scholarly journals Evaluation of Linkage Disequilibrium, Effective Population Size and Haplotype Block Structure in Chinese Cattle

Animals ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 83 ◽  
Author(s):  
Lei Xu ◽  
Bo Zhu ◽  
Zezhao Wang ◽  
Ling Xu ◽  
Ying Liu ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Genomic Selection ◽  
Haplotype Block ◽  
Block Structure ◽  
Effective Population ◽  
Chinese Cattle ◽  
Genome Wide ◽  
Population Sizes ◽  
Haplotype Block Structure ◽  
Selection For

Understanding the linkage disequilibrium (LD) across the genome, haplotype structure, and persistence of phase between breeds can enable us to appropriately design and implement the genome-wide association (GWAS) and genomic selection (GS) in beef cattle. We estimated the extent of genome-wide LD, haplotype block structure, and the persistence of phase in 10 Chinese cattle population using high density BovinHD BeadChip. The overall LD measured by r2 between adjacent SNPs were 0.60, 0.67, 0.58, 0.73, and 0.71 for South Chinese cattle (SCHC), North Chinese cattle (NCC), Southwest Chinese cattle (SWC), Simmental (SIM), and Wagyu (WAG). The highest correlation (0.53) for persistence of phase across groups was observed for SCHC vs. SWC at distances of 0–50 kb, while the lowest correlation was 0.13 for SIM vs. SCHC at the same distances. In addition, the estimated current effective population sizes were 27, 14, 31, 34, and 43 for SCHC, NCC, SWC, SIM, and WAG, respectively. Our result showed that 58K, 87K, 95K, 52K, and 52K markers were required for implementation of GWAS and GS in SCHC, NCC, SWC, SIM, and WAG, respectively. Also, our findings suggested that the implication of genomic selection for multipopulation with high persistence of phase is feasible for Chinese cattle.

scholarly journals Estimation of universal and taxon-specific parameters of prokaryotic genome evolution

2017 ◽  
Author(s):  
Itamar Sela ◽  
Yuri I. Wolf ◽  
Eugene V. Koonin
Keyword(s):  
Genome Evolution ◽  
Ad Hoc ◽  
Prokaryotic Genome ◽  
Microbial Genome ◽  
Selection Coefficient ◽  
Effective Population ◽  
Weak Selection ◽  
Gene Acquisition ◽  
Population Sizes ◽  
The Mean

AbstractOur recent study on mathematical modeling of microbial genome evolution indicated that, on average, genomes of bacteria and archaea evolve in the regime of mutation-selection balance defined by positive selection coefficients associated with gene acquisition that is counter-acted by the intrinsic deletion bias. This analysis was based on the strong assumption that parameters of genome evolution are universal across the diversity of bacteria and archaea, and yielded extremely low values of the selection coefficient. Here we further refine the modeling approach by taking into account evolutionary factors specific for individual groups of microbes using two independent fitting strategies, an ad hoc hard fitting scheme and an hierarchical Bayesian model. The resulting estimate of the mean selection coefficient of s∼10-10 associated with the gain of one gene implies that, on average, acquisition of a gene is beneficial, and that microbial genomes typically evolve under a weak selection regime that might transition to strong selection in highly abundant organisms with large effective population sizes. The apparent selective pressure towards larger genomes is balanced by the deletion bias, which is estimated to be consistently greater than unity for all analyzed groups of microbes. The estimated values of s are more realistic than the lower values obtained previously, indicating that global and group-specific evolutionary factors synergistically affect microbial genome evolution that seems to be driven primarily by adaptation to existence in diverse niches.

scholarly journals Pedigree structure of American bison (Bison bison) population

2018 ◽  
Vol 63 (No. 12) ◽  
pp. 507-517 ◽  
Author(s):  
E. Skotarczak ◽  
P. Ćwiertnia ◽  
T. Szwaczkowski
Keyword(s):  
Mean Value ◽  
Bison Bison ◽  
Pedigree Information ◽  
Effective Population ◽  
Pedigree Structure ◽  
Breeding Programs ◽  
Inbreeding Coefficients ◽  
Animal Populations ◽  
The Mean ◽  
Inbreeding Level

An effective realization of breeding programs in zoos is strongly determined by completeness of animal pedigree information. The knowledge of pedigree structure allows to maintain optimal genetic variability of a given population. The aim of this study was to estimate the parameters describing the pedigree structure of American bison housed in zoos in the context of further management of the population. Finally, 4269 American bison were analysed (1883 males, 2217 females, and 169 with unknown sex). The registered animals were born between years 1874 and 2013. The following pedigree parameters were estimated: number of fully traced generations, number of complete generations equivalent, index of pedigree completeness, individual inbreeding coefficients, increase of inbreeding for each individual, effective population size, and genetic diversity. The maximum number of fully traced generations was 3 (the mean value is 0.693). The mean inbreeding coefficient for the population studied was 3.26%, whereas individual increase in inbreeding ranged from 0 to 25.12%. Although the pedigree parameters (including the inbreeding level) in the American bison obtained in the present study seem to be acceptable (from the perspective of other wild animal populations), they can be over/underestimated due to incomplete pedigree.

scholarly journals Biodiversity of Russian Local Sheep Breeds Based on Pattern of Runs of Homozygosity

Diversity ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 360
Author(s):  
Tatiana Deniskova ◽  
Arsen Dotsev ◽  
Marina Selionova ◽  
Gottfried Brem ◽  
Natalia Zinovieva
Keyword(s):  
Genetic Diversity ◽  
Biodiversity Loss ◽  
Inbreeding Coefficient ◽  
Loss Estimation ◽  
Runs Of Homozygosity ◽  
Sheep Breeds ◽  
Snp Data ◽  
Population Sizes ◽  
The Mean ◽  
Genomic Inbreeding

Russian sheep breeds traditionally raised in specific environments are valuable parts of sociocultural heritage and economic component of the regions. However, the import of commercial breeds negatively influences the population sizes of local sheep populations and might lead to biodiversity loss. Estimation of the runs of homozygosity (ROH) in local sheep genomes is an informative tool to address their current genetic state. In this work, we aimed to address the ROH distribution and to estimate genome inbreeding based on SNP data to evaluate genetic diversity in Russian local sheep breeds. Materials for this study included SNP-genotypes from twenty-seven Russian local sheep breeds which were generated using the Illumina OvineSNP50 BeadChip (n = 391) or the Illumina Ovine Infinium HD BeadChip (n = 315). A consecutive runs method was used to calculate ROH which were estimated for each animal and then categorized in the ROH length classes. The ROH were found in all breeds. The mean ROH length varied from 86 to 280 Mb, while the ROH number ranged from 37 to 123. The genomic inbreeding coefficient varied from 0.033 to 0.106. Our findings provide evidence of low to moderate genomic inbreeding in major local sheep populations.

scholarly journals Efficient use of genomic information for sustainable genetic improvement in small cattle populations

2019 ◽  
Author(s):  
J. Obšteter ◽  
J. Jenko ◽  
J. M. Hickey ◽  
G. Gorjanc
Keyword(s):  
Genetic Variation ◽  
Genomic Selection ◽  
Conversion Efficiency ◽  
Genetic Gain ◽  
Progeny Testing ◽  
Effective Population ◽  
Generation Interval ◽  
Truncation Selection ◽  
Selection Accuracy ◽  
Sire Selection

ABSTRACTThis paper compares genetic gain, genetic variation, and the efficiency of converting variation into gain under different genomic selection scenarios with truncation or optimum contribution selection in a small dairy population by simulation. Breeding programs have to maximize genetic gain but also ensure sustainability by maintaining genetic variation. Numerous studies showed that genomic selection increases genetic gain. Although genomic selection is a well-established method, small populations still struggle with choosing the most sustainable strategy to adopt this type of selection. We developed a simulator of a dairy population and simulated a model after the Slovenian Brown Swiss population with ~10,500 cows. We compared different truncation selection scenarios by varying i) the method of sire selection and their use on cows or bull-dams, and ii) selection intensity and the number of years a sire is in use. Furthermore, we compared different optimum contribution selection scenarios with optimization of sire selection and their usage. We compared the scenarios in terms of genetic gain, selection accuracy, generation interval, genetic and genic variance, the rate of coancestry, effective population size, and the conversion efficiency. The results show that early use of genomically tested sires increased genetic gain compared to progeny testing as expected from changes in selection accuracy and generation interval. A faster turnover of sires from year to year and higher intensity increased the genetic gain even further but increased the loss of genetic variation per year. While maximizing intensity gave the lowest conversion efficiency, a faster turn-over of sires gave an intermediate conversion efficiency. The largest conversion efficiency was achieved with the simultaneous use of genomically and progeny tested sires that were used over several years. Compared to truncation selection optimizing sire selection and their usage increased the conversion efficiency by either achieving comparable genetic gain for a smaller loss of genetic variation or achieving higher genetic gain for a comparable loss of genetic variation. Our results will help breeding organizations to implement sustainable genomic selection.

Sign in / Sign up

Export Citation Format

Share Document