Genetic Diversity and the Impact of the Breed Proportions of US Brown Swiss in German Brown Cattle

Increase of inbreeding and loss of genetic diversity have large impact on farm animal genetic resources. Therefore, the aims of the present study were to analyse measures of genetic diversity as well as recent and ancestral inbreeding using pedigree data of the German Brown population, and to identify causes for loss of genetic diversity. The reference population included 922,333 German Brown animals born from 1990 to 2014. Pedigree depth and completeness reached an average number of complete equivalent generations of 6.24. Estimated effective population size for the German Brown reference population was about 112 with a declining trend from 141 to 95 for the birth years. Individual inbreeding coefficients increased from 0.013 to 0.036. Effective number of founders, ancestors and founder genomes of 63.6, 36.23 and 20.34 indicated unequal contributions to the reference population. Thirteen ancestors explained 50% of the genetic diversity. Higher breed proportions of US Brown Swiss were associated with higher levels of individual inbreeding. Ancestral inbreeding coefficients, which are indicative for exposure of ancestors to identical-by-descent alleles, increased with birth years but recent individual inbreeding was higher than ancestral inbreeding. Given the increase of inbreeding and decline of effective population size, measures to decrease rate of inbreeding and increase effective population size through employment of a larger number of sires are advisable.

Download Full-text

Analysis of genetic diversity in four Canadian swine breeds using pedigree data

Canadian Journal of Animal Science ◽

10.4141/cjas10002 ◽

2010 ◽

Vol 90 (3) ◽

pp. 331-340 ◽

Cited By ~ 11

Author(s):

M G Melka ◽

F. Schenkel

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Effective Population Size ◽

Genetic Drift ◽

Relative Proportion ◽

Random Genetic Drift ◽

Pedigree Data ◽

Effective Population ◽

Animal Genetic Resources ◽

Loss Of Genetic Diversity

Conservation of animal genetic resources entails judicious assessment of genetic diversity as a first step. The objective of this study was to analyze the trend of within-breed genetic diversity and identify major causes of loss of genetic diversity in four swine breeds based on pedigree data. Pedigree files from Duroc (DC), Hampshire (HP), Lacombe (LC) and Landrace (LR) containing 480 191, 114 871, 51 397 and 1 080 144 records, respectively, were analyzed. Pedigree completeness, quality and depth were determined. Several parameters derived from the in-depth pedigree analyses were used to measure trends and current levels of genetic diversity. Pedigree completeness indexes of the four breeds were 90.4, 52.7, 89.6 and 96.1%, respectively. The estimated percentage of genetic diversity lost within each breed over the last three decades was approximately 3, 22, 12 and 2%, respectively. The relative proportion of genetic diversity lost due to random genetic drift in DC, HP, LC and LR was 74.5, 63.6, 72.9 and 60.0%, respectively. The estimated current effective population size for DC, HP, LC and LR was 72, 14, 36 and 125, respectively. Therefore, HP and LC have been found to have lost considerable genetic diversity, demanding priority for conservation. Key words: Genetic drift, effective population size

Download Full-text

Genetic Variability in Polish Lowland Sheepdogs Assessed by Pedigree and Genomic Data

Animals ◽

10.3390/ani10091520 ◽

2020 ◽

Vol 10 (9) ◽

pp. 1520

Author(s):

Paula Wiebke Michels ◽

Ottmar Distl

Keyword(s):

Genetic Variability ◽

Population Size ◽

Effective Population Size ◽

Ductus Arteriosus ◽

Genomic Data ◽

Reference Population ◽

Pedigree Data ◽

Effective Population ◽

Inbreeding Coefficients ◽

Candidate Loci

Genetic variability of Polish Lowland Sheepdog (PON) population was evaluated using both pedigree and genomic data. The analyzed pedigree encompassed 8628 PONs, including 153 individuals genotyped on the Illumina CanineHD BeadChip. Runs of homozygosity (ROH) were defined for homozygous stretches extending over 60 to 4300 kb. The inbreeding coefficients FPed based on pedigree data and FROH50 based on ROHs were at 0.18 and 0.31. The correlation between both was 0.41 but 0.52 when excluding animals with less than seven complete generations. The realized effective population size (Ne¯) was 22.2 with an increasing trend over years. Five PONs explained 79% of the genetic diversity of the reference population. The effective population size derived from linkage disequilibrium measured by r² was 36. PANTHER analysis of genes in ROHs shared by ≥50% of the PONs revealed four highly over- or underrepresented biological processes. One among those is the 7.35 fold enriched “forelimb morphogenesis”. Candidate loci for hip dysplasia and patent ductus arteriosus were discovered in frequently shared ROHs. In conclusion, the inbreeding measures of the PONs were high and the genetic variability small compared to various dog breeds. Regarding Ne¯, PON population was minimally endangered according to the European Association for Animal Production.

Download Full-text

Genetic diversity, viability and conservation value of the global captive population of the Moroccan Royal lions

PLoS ONE ◽

10.1371/journal.pone.0258714 ◽

2021 ◽

Vol 16 (12) ◽

pp. e0258714

Author(s):

Kristina Lehocká ◽

Simon A. Black ◽

Adrian Harland ◽

Ondrej Kadlečík ◽

Radovan Kasarda ◽

...

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Effective Population Size ◽

North Africa ◽

Reference Population ◽

Captive Population ◽

Effective Number ◽

Pedigree Data ◽

Effective Population ◽

Loss Of Diversity

This study evaluates the diversity of the so-called ‘Moroccan Royal lions’ using genealogical information. Lions are no longer extant in North Africa, but the previous wild population was an important element of the now-recognised northern subspecies (Panthera leo leo) that ranged across West Africa, North Africa and the Middle East into India. The remaining captive population of ‘Moroccan Royal lions’ seems to be significantly endangered by the loss of diversity due to the effective population size decrease. The pedigree file of this captive lion population consisted of 454 individuals, while the reference population included 98 animals (47 males and 51 females). The completeness of the pedigree data significantly decreased with an increasing number of generations. The highest percentage of pedigree completeness (over 70%) was achieved in the first generation of the reference population. Pedigree-based parameters derived from the common ancestor and gene origin were used to estimate the state of diversity. In the reference population, the average inbreeding coefficient was 2.14%, while the individual increase in inbreeding over generations was 2.31%. Overall, the reference population showed lower average inbreeding and average relatedness compared with the pedigree file. The number of founders (47), the effective number of founders (24) and the effective number of ancestors (22) were estimated in the reference population. The effective population size of 14.02 individuals confirms the critically endangered status of the population and rapid loss of diversity in the future. Thus, continuous monitoring of the genetic diversity of the ‘Moroccan Royal lion’ group is required, especially for long-term conservation management purposes, as it would be an important captive group should further DNA studies establish an affinity to P. leo leo.

Download Full-text

SNP-based analysis reveals unexpected features of genetic diversity, parental contributions and pollen contamination in a white spruce breeding program

Scientific Reports ◽

10.1038/s41598-021-84566-2 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Esteban Galeano ◽

Jean Bousquet ◽

Barb R. Thomas

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Effective Population Size ◽

White Spruce ◽

Seed Orchard ◽

Pedigree Reconstruction ◽

Effective Population ◽

Pollen Contamination ◽

Contamination Levels ◽

The Impact

AbstractAccurate monitoring of genetic diversity levels of seedlots and mating patterns of parents from seed orchards are crucial to ensure that tree breeding programs are long-lasting and will deliver anticipated genetic gains. We used SNP genotyping to characterize founder trees, five bulk seed orchard seedlots, and trees from progeny trials to assess pollen contamination and the impact of severe roguing on genetic diversity and parental contributions in a first-generation open-pollinated white spruce clonal seed orchard. After severe roguing (eliminating 65% of the seed orchard trees), we found a slight reduction in the Shannon Index and a slightly negative inbreeding coefficient, but a sharp decrease in effective population size (eightfold) concomitant with sharp increase in coancestry (eightfold). Pedigree reconstruction showed unequal parental contributions across years with pollen contamination levels between 12 and 51% (average 27%) among seedlots, and 7–68% (average 30%) among individual genotypes within a seedlot. These contamination levels were not correlated with estimates obtained using pollen flight traps. Levels of pollen contamination also showed a Pearson’s correlation of 0.92 with wind direction, likely from a pollen source 1 km away from the orchard under study. The achievement of 5% genetic gain in height at rotation through eliminating two-thirds of the orchard thus generated a loss in genetic diversity as determined by the reduction in effective population size. The use of genomic profiles revealed the considerable impact of roguing on genetic diversity, and pedigree reconstruction of full-sib families showed the unanticipated impact of pollen contamination from a previously unconsidered source.

Download Full-text

Impact of fertility variation on genetic diversity and phenotypic traits in second generation seed production areas and clonal seed orchards of Eucalyptus camaldulensis

Silvae Genetica ◽

10.2478/sg-2019-0006 ◽

2019 ◽

Vol 68 (1) ◽

pp. 29-40

Author(s):

P.G. Suraj ◽

K. Nagabhushana ◽

R. Kamalakannan ◽

M. Varghese

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Effective Population Size ◽

Second Generation ◽

Gene Diversity ◽

Eucalyptus Camaldulensis ◽

Phenotypic Traits ◽

Effective Population ◽

Fertility Variation ◽

The Impact

Abstract Fertility and gene diversity were estimated in three second generation (F2) seed stands (SPA 1-3) and two clone trials (CSO 1&2) of Eucalyptus camaldulensis to assess the impact on seed crop. F2 seedlots were evaluated in comparison to native provenances, ten commercial clones and interspecific hybrids at diverse sites. SPA 1&2 were genetic gain trials of five first generation (F1) orchard seedlots, SPA 3 a plantation of one F1 orchard seedlot, and CSOs were clone trials of 21 commercial clones established at two contrasting sites. Fertility variation, as indicated by sibling coefficient, was high (Ψ, 9-14) in the SPAs as only about 26 % trees were fertile compared to 81 % trees in CSOs. Effective population size was higher in SPA 1 and 2 (Ns, 95 and 74, respectively) than SPA 3 (Ns = 39). Fertility was highly skewed in CSO 2 resulting in low effective population size (Ns = 2) compared to CSO 1 (Ns = 11). Constant seed collection enabled 3-fold increase in relative population size and 22 % higher predicted gene diversity in CSO 2. Genetic diversity (He) estimated using SSR markers was higher in SPA 1&2 and native provenances (NAT), compared to SPA 3 and CSO 1, whereas CSO 2 and clones had lower values. There was a high positive correlation between estimated He and predicted gene diversity values of SPAs and CSOs. He was positively correlated to mean field survival and negatively correlated to kraft pulp yield (KPY), evaluated at three years in progeny trials across three locations. Number of alleles per locus was higher in SPAs and native provenances compared to CSOs and clones. Discriminant principal component analysis clustered CSO, NAT and SPA seedlots in different groups while commercial E. camaldulensis clones clustered close to NAT. Multilocus outcrossing rate was generally high (tm, 91-100 %), though selfing was observed in two families of SPA 3 and CSO 2. Selected interspecific hybrid families of commercial E. camaldulensis clones (with E. urophylla and E. pellita) evaluated at two of the sites had higher He and KPY than clones at three years.

Download Full-text

Population Structure and Genetic Diversity of Italian Beef Breeds as a Tool for Planning Conservation and Selection Strategies

Animals ◽

10.3390/ani9110880 ◽

2019 ◽

Vol 9 (11) ◽

pp. 880 ◽

Cited By ~ 5

Author(s):

Maria Chiara Fabbri ◽

Marcos Paulo Gonçalves de Rezende ◽

Christos Dadousis ◽

Stefano Biffani ◽

Riccardo Negrini ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Population Size ◽

Effective Population Size ◽

Breeding Strategies ◽

Effective Population ◽

Breeding Programs ◽

Inbreeding Coefficients ◽

Selection Strategies ◽

Conservation Measures

The aim was to investigate the population structure of eight beef breeds: three local Tuscan breeds under extinction, Calvana (CAL), Mucca Pisana (MUP), and Pontremolese (PON); three local unselected breeds reared in Sardinia, Sarda (SAR), Sardo Bruna (SAB), and Sardo Modicana (SAM); and two cosmopolitan breeds, Charolais (CHA) and Limousine (LIM), reared in the same regions. An effective population size ranges between 14.62 (PON) to 39.79 (SAM) in local breeds, 90.29 for CHA, and 135.65 for LIM. The average inbreeding coefficients were higher in Tuscan breeds (7.25%, 5.10%, and 3.64% for MUP, CAL, and PON, respectively) compared to the Sardinian breeds (1.23%, 1.66%, and 1.90% in SAB, SAM, and SAR, respectively), while for CHA and LIM they were <1%. The highest rates of mating between half-siblings were observed for CAL and MUP (~9% and 6.5%, respectively), while the highest rate of parent–offspring mating was ~8% for MUP. Our findings describe the urgent situation of the three Tuscan breeds and support the application of conservation measures and/or the development of breeding programs. Development of breeding strategies is suggested for the Sardinian breeds.

Download Full-text

Fluctuating fortunes: genomes and habitat reconstructions reveal global climate-mediated changes in bats' genetic diversity

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2019.0304 ◽

2019 ◽

Vol 286 (1911) ◽

pp. 20190304 ◽

Cited By ~ 3

Author(s):

Balaji Chattopadhyay ◽

Kritika M. Garg ◽

Rajasri Ray ◽

Frank E. Rheindt

Keyword(s):

Climate Change ◽

Genetic Diversity ◽

Population Size ◽

Effective Population Size ◽

Global Climate ◽

Future Climate Change ◽

Effective Population ◽

Population Sizes ◽

Earth’S Climate ◽

The Impact

Over the last approximately 2.6 Myr, Earth's climate has been dominated by cyclical ice ages that have profoundly affected species' population sizes, but the impact of impending anthropogenic climate change on species’ extinction potential remains a worrying problem. We investigated 11 bat species from different taxonomic, ecological and geographical backgrounds using combined information from palaeoclimatic habitat reconstructions and genomes to analyse biotic impacts of historic climate change. We discover tightly correlated fluctuations between species' historic distribution and effective population size, identify frugivores as particularly susceptible to global warming, pinpoint large insectivores as having overall low effective population size and flag the onset of the Holocene (approx. 10–12 000 years ago) as the period with the generally lowest effective population sizes across the last approximately 1 Myr. Our study shows that combining genomic and palaeoclimatological approaches reveals effects of climatic shifts on genetic diversity and may help predict impacts of future climate change.

Download Full-text

Population Structure Analysis of the Border Collie Dog Breed in Hungary

Animals ◽

10.3390/ani9050250 ◽

2019 ◽

Vol 9 (5) ◽

pp. 250 ◽

Cited By ~ 5

Author(s):

Virág Ács ◽

Árpád Bokor ◽

István Nagy

Keyword(s):

Genetic Diversity ◽

Reference Population ◽

Inbreeding Coefficient ◽

Pedigree Data ◽

Effective Population ◽

Inbreeding Coefficients ◽

Population Structure Analysis ◽

Dog Breed ◽

Fixation Indices ◽

Mixed Line

Pedigree data of the Border Collie dog breed were collected in Hungary to examine genetic diversity within the breed and its different lines. The database was based on available herd books dating from the development of the breed (in the late 1800s) to the present day. The constructed pedigree file consisted of 13,339 individuals, of which 1566 dogs (born between 2010 and 2016) composed the alive reference population which was active from breeding perspective. The breed is subdivided by phenotype, showing a thicker coat, harmonic movement, a wide skull, and heavier bones for the show type, and a thinner or sometimes short coat and smaller body for the working line, while the mixed line is quite heterogeneous (a combination of the above). Thus, the reference population was dissected according to the existing lines. The number of founders was 894, but eight individuals were responsible for contributing 50% of the genetic variability. The reference population had a pedigree completeness of 99.6% up to 15 generations and an inbreeding coefficient of 9.86%. Due to the changing breed standards and the requirements of the potential buyers, the effective population size substantially decreased between 2010 and 2016. Generation intervals varied between 4.09 and 4.71 years, where the sire paths were longer due to the later initial age of breeding in males compared to females. Genetic differences among the existing lines calculated by fixation indices are not significant; nonetheless ancestral inbreeding coefficients are able to show contrasts.

Download Full-text

Analysis of Genetic Diversity in the Czech Spotted Dog

Animals ◽

10.3390/ani10081416 ◽

2020 ◽

Vol 10 (8) ◽

pp. 1416

Author(s):

Karolína Machová ◽

Anita Kranjčevičová ◽

Luboš Vostrý ◽

Emil Krupa

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Effective Population Size ◽

Reference Population ◽

Pedigree Analysis ◽

Inbreeding Coefficient ◽

Random Genetic Drift ◽

Effective Population ◽

Founding Population ◽

The Mean

Loss off genetic diversity negatively affects most of the modern dog breeds. However, no breed created strictly for laboratory purposes has been analyzed so far. In this paper, we sought to explore by pedigree analysis exactly such a breed—the Czech Spotted Dog (CSD). The pedigree contained a total of 2010 individuals registered since the second half of the 20th century. Parameters such as the mean average relatedness, coefficient of inbreeding, effective population size, effective number of founders, ancestors and founder genomes and loss of genetic diversity—which was calculated based on the reference population and pedigree completeness—were used to assess genetic variability. Compared to the founding population, the reference population lost 38.2% of its genetic diversity, of which 26% is due to random genetic drift and 12.2% is due to the uneven contribution of the founders. The reference population is highly inbred and related. The average inbreeding coefficient is 36.45%, and the mean average relatedness is 74.83%. The effective population size calculated based on the increase of inbreeding coefficient is 10.28. Thus, the Czech Spotted Dog suffered significant losses of genetic diversity that threaten its future existence.

Download Full-text

Genetic base and inbreeding of Canadienne, Brown Swiss, Holstein and Jersey cattle in Canada

Animal Genetic Resources Information ◽

10.1017/s1014233900001590 ◽

2003 ◽

Vol 33 ◽

pp. 11-19

Author(s):

C. Hansen ◽

J.N.B. Shrestha ◽

R.J. Parker ◽

G.H. Crow ◽

J.N. Derr

Keyword(s):

Population Size ◽

Effective Population Size ◽

Effective Population ◽

Brown Swiss ◽

Jersey Cattle ◽

Inbreeding Coefficients ◽

Genetic Base ◽

Current Production ◽

Holstein Bulls ◽

Cattle Breeders

SummaryThe narrowing of the genetic base is of major concern to many cattle breeders and this is a consequence of a small effective population size and an increase in the inbreeding coefficient in cattle populations. Studies of pedigrees of cattle populations found in Canada showed that the effective population size and rate of inbreeding over a 12-year period (1983–94) were 123 and 0.412 percent for Canadienne, 975 and 0.054 percent for Brown Swiss, and 2 183 and 0.024 percent for Jersey cattle populations. Over the same period, the year to year trends in inbreeding coefficients based on co-ancestry was 0.11 percent for Canadienne and 0.07 percent for Brown Swiss cattle populations, and 0.37 percent for Holstein bulls used by the artificial insemination industry. Inbreeding was not found to be a major problem in any of the populations examined. However, only 10 bulls of their respective breed sired 61 percent of the Canadienne, 21 percent of the Brown Swiss, and 29 percent of the Jersey cattle populations, and 41 percent of the Holstein bulls in the bull studs. More and more breeders are demanding proven sires to increase milk production from fewer cows resulting in the narrowing of the genetic base of the national cattle populations. Newer technology that provides precise genetic modification could further contribute to the narrowing of the genetic base compromising the ability to sustain current production and respond to changing markets in the long-term.

Download Full-text