Assessment of the genetic variability using pedigree analysis of the Sahiwal breed in Kenya

2016 ◽  
Vol 59 ◽  
pp. 7-14 ◽  
Author(s):  
S. Mwangi ◽  
T.K. Muasya ◽  
E.D. Ilatsia ◽  
A.K. Kahi
Keyword(s):  
Genetic Variability ◽  
Genetic Drift ◽  
Reference Population ◽  
Pedigree Analysis ◽  
Breeding Strategy ◽  
Progeny Testing ◽  
Founding Population ◽  
Effective Selection ◽  
Inbreeding Level ◽  
Year 2000

Summary Pedigree analysis using genealogical information of 18 315 animals born between 1949 and 2008 was done to quantify genetic variability of the Sahiwal population in Kenya. Generation intervals for sire pathways were longer than dam pathways and increased over year periods, from about 4–16 years. The later was due to use of old bulls for breeding in the last 2 year groups and cessation of progeny testing in the year 2000. Average inbreeding level in last year period studied was 1.2 percent. Genetic variability of the population as assessed based on gene origin statistics decreased over the years. The ratio of effective number of founders to founders of 0.06 showed unequal contribution of founders to the reference population. However, since the founding population, ancestors contributed equally as shown by the ratio of f e/f a of 0.94, which could also be due to lack of effective selection in this population. The ratio of f g/f a of 0.63 indicated genetic loss of genetic variability occurred through genetic drift in the Kenyan Sahiwal population. The small number of ancestors (16) that accounted for 50 percent of the total variation in the reference population suggested overuse of a small number of some animals as parents over generations. The smaller ratio of f g/f e compared with f a/f e also confirms loss of genetic variability in the population by genetic drift than bottlenecks. Therefore the breeding strategy for the Sahiwal population in Kenya should incorporate tools that balance rate of genetic gain and the future rate of inbreeding.

scholarly journals Pedigree Analysis of Mangalica Pig Breeds

2016 ◽  
Vol 16 (3) ◽  
pp. 701-709 ◽  
Author(s):  
János Posta ◽  
Péter Szabó ◽  
István Komlósi
Keyword(s):  
Genetic Structure ◽  
Genetic Variability ◽  
Gene Pool ◽  
Reference Population ◽  
Pedigree Analysis ◽  
Small Populations ◽  
Gene Conservation ◽  
Generation Interval ◽  
Pig Breeds ◽  
Gene Origin

AbstractAn effective gene conservation programme requires the knowledge of genetic variability of the population. The genetic structure of Mangalica pig breeds (Blonde, Red and Swallow-bellied) was studied from pedigree records. Herdbook data available up to 2011 of registered Mangalica pig breeds (Blonde, Red and Swallow-bellied) were analysed. The number of complete generations was 6 for Blonde and 5 for Red and Swallow-bellied Mangalica whereas the average complete generation equivalent was between 3.51 and 6.01. The average level of inbreeding of the reference population was low (4.07–5.87%). The investigated breeds could be considered as small populations based on the probability of gene origin. The most important ancestor contributed between 9 and 16% of the gene pool of the reference populations. The longest generation interval was found for the sire-to-son pathways whereas the shortest for dam-to-daughter pathways for each breed.

scholarly journals Genetic Variability of Cold-Blooded Horses Participating in Genetic Resources Conservation Programs, Using Pedigree Analysis

2019 ◽  
Vol 19 (1) ◽  
pp. 49-60 ◽  
Author(s):  
Grażyna Polak
Keyword(s):  
Genetic Variability ◽  
Genetic Resources ◽  
Reference Population ◽  
Pedigree Analysis ◽  
Pedigree Information ◽  
Effective Population ◽  
Conservation Programs ◽  
Data Set ◽  
Genetic Resources Conservation ◽  
Resources Conservation

AbstractTwo types of Polish local cold-blooded horses – Sztumski and Sokólski, covered by genetic resources conservation programs, were analyzed for founder’s contribution, genetic structure and inbreeding. In both populations, created in the early twentieth century, were used the same stallions, mainly Ardennes, Belgians and Bretons. The aim of the study was to analyze the genetic variability of Sztumski and Sokólski cold-blooded horses, using pedigree information. The reference population contained 2359 horses: 1129 Sztumski and 1230 Sokólski included in conservation programs in 2014. The data set consisted of a total of 12,821 ancestor pedigrees. The results showed that in the analyzed population the number of founders was 1139 for Sztumski and 1118 for Sokólski horses; effective population size and effective number of founders were 688.8; 156.9 and 704.5; 111.4, respectively. The mean coefficient of inbreeding was 1.54 for Sztumski and 1.56 for Sokólski horses. In the gene pool the most important contribution was of Ardennes horses (43.67% in Sztumski and 46.82% in Sokólski horses), followed by Belgian horses (18.32% and 9.3%, respectively). The most important ancestors in both populations were Ardennes sires Roll-tan 699 and Gustaw 2807, and German cold-blooded sires Elbgang 1504 and Bär.

Genetic variability of a Criollo cattle population under conservation

2005 ◽  
Vol 143 (2-3) ◽  
pp. 209-216 ◽  
Author(s):  
L. M. MELUCCI ◽  
C. DÍAZ ◽  
C. A. MEZZADRA
Keyword(s):  
Genetic Variability ◽  
Population Size ◽  
Genetic Drift ◽  
Germplasm Conservation ◽  
Reference Population ◽  
Effective Number ◽  
Effective Population ◽  
The Impact

The active germplasm Bank of the Integrated Unit (Facultad de Ciencias Agrarias, Unversidad Nacional de Mar del Plata and the Experimental Station of INTA) at Balcarce, keeps both in vivo (live herd) and in vitro Criollo Cattle (samples of semen and embryos cryogenically), with the aim of preserving genetic variability for potential future use. Parameters based on probable origin of genes, on population size and on the estimation of components of (co)variances for birth and weaning weights were estimated to evaluate the genetic variability of the material contained in the Bank. The information available came from 667 individuals, of which 84 had unknown parents, and 142 half-founders (only one parent known), having a mean number of births per year of 24 calves from four different sires. AI was performed during the mating season almost every year. The evolution of effective number of founders (fe), effective number of ancestors (fa), effective number of founder genomes (Ng) and the ratio fe/fa over different periods from the creation of the Bank, were analysed. Annual increase of inbreeding coefficient (F) was 0·2% and the effective population size (Ne) was estimated as 23, 14 and 25 individuals for the periods defined by years 1978–82, 1983–87 and 1993–97, respectively. The ratio fe/fa was higher in the years where the ratio number of sires/number of dams was lower, indicating that the impact of the effective number of sires is more important than the effective number of females in generating genetic bottlenecks. When the reference population was taken for the period 1989–97, 16·45 out of the 85·63 founders of the population made contributions not explained by other ancestors, but if possible losses of genomes due to genetic drift are considered, the number of genomes still present was reduced to 9·09 indicating a possible narrow genetic bottleneck in the last period. The Ng/fe ratio was 0·11, 0·10 and 0·11 for the reference populations defined by years 1989–92, 1993–97 and 1989–97, respectively. The main objective in germplasm conservation programmes should be the maintenance of genetic variability. Thus, matings in the population under conservation should be designed in order to mate those animals that maximize the effective number of genome founders (Ng) to avoid losses due to genetic drift.

scholarly journals Analysis of Genetic Diversity in the Czech Spotted Dog

Animals ◽  
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.

scholarly journals Pedigree analysis in White Shorthaired goat: First results

2013 ◽  
Vol 56 (1) ◽  
pp. 547-554
Author(s):  
M. Oravcová
Keyword(s):  
Genetic Variability ◽  
Information Needs ◽  
Reference Population ◽  
Pedigree Analysis ◽  
Pedigree Information ◽  
Effective Population ◽  
Mean Values ◽  
First Results ◽  
Marginal Contributions ◽  
The Individual

Abstract. Pedigree records of 1 682 animals of the White Shorthaired goat in Slovakia were investigated. The reference population was defined as the animals born from 2008 to 2011 with at least one ancestor known in the second ancestral generation (670 animals kept in eight flocks). The numbers of founders (286), ancestors (256), effective founders (73), effective ancestors (45) and founder genome equivalents (32) were assessed. Fifteen ancestors were needed to explain 50 % of genetic variability. Marginal contributions of the ten most influential ancestors varied between 5.45 % and 2.47 % and accounted for 39.8 % of genetic variability. The mean values of inbreeding and co-ancestry were 0.69 % and 1.55 %, respectively. The effective population size was assessed to consist of 182 and 142 individuals, depending whether it was calculated from the individual increase in inbreeding or the individual increase in co-ancestry. The number of maximum generations traced, fully traced generations and equivalent complete generations traced were 5.62, 1.97 and 3.04, respectively. The first, second and third ancestral generation were 100 %, 83 % and 71 % complete, respectively. The completeness decreased to as low as 35 % and 11 % in the fourth and fifth generation. To be able to keep genetic links across generations in touch, the amount of pedigree information needs to be increased. This is a serious requirement for appropriate monitoring and management of genetic relations within the population.

scholarly journals Genetic variability in the brazilian criollo horse breed

2003 ◽  
Vol 33 (1) ◽  
pp. 137-142 ◽  
Author(s):  
Myriam Elizabeth Vinocur ◽  
Karin Erica Brass ◽  
Mara Iolanda Batistella Rubin ◽  
Carlos Antonio Mondino Silva
Keyword(s):  
Genetic Variability ◽  
Rio Grande ◽  
Blood Groups ◽  
Rio Grande Do Sul ◽  
Average Heterozygosity ◽  
Horse Breed ◽  
Allelic Frequencies ◽  
Blood Types ◽  
Inbreeding Level

Allelic frequencies of 7 blood groups and 8 protein systems were determined in 6 herds of Criollo horse breed raised in Rio Grande do Sul, Brazil. Analysis of these frequencies showed a significant isolation component (Fst = 0.0866; p<0.01) and construction of dendogram using Nei´s D confirmed this difference among the 6 herds. The highest values measuring genetic variability on 15 blood types were average heterozygosity: 0.4631; total number of alleles: 87 and probability of exclusion: 98%. When all herds were considered together, the inbreeding level (Fis) was zero. These results indicate that the Criollo horses have a large genetic variability.

scholarly journals Level of Inbreeding in Norik of Muran Horse: Pedigree vs. Genomic Data

2019 ◽  
Vol 67 (6) ◽  
pp. 1457-1463 ◽  
Author(s):  
Radovan Kasarda ◽  
Nina Moravčíková ◽  
Ondrej Kadlečík ◽  
Anna Trakovická ◽  
Marko Halo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Quality Control ◽  
Genomic Analysis ◽  
Genomic Data ◽  
Reference Population ◽  
Pedigree Analysis ◽  
Snp Markers ◽  
Runs Of Homozygosity ◽  
Current Generation ◽  
Genomic Inbreeding

The objective of this study was to analyse the level of pedigree and genomic inbreeding in a herd of the Norik of Muran horses. The pedigree file included 1374 animals (603 stallions and 771 mares), while the reference population consisted of animals that were genotyped by using 70k SNP platform (n = 25). The trend of pedigree inbreeding was expressed as the probability that an animal has two identical alleles by descent according to classical formulas. The trend of genomic inbreeding was derived from the distribution of runs of homozygosity (ROHs) with various length in the genome based on the assumption that these regions reflect the autozygosity originated from past generations of ancestors. A maximum of 19 generations was found in pedigree file. As expected, the highest level of pedigree completeness was found in first five generations. Subsequent quality control of genomic data resulted in totally 54432 SNP markers covering 2.242 Mb of the autosomal genome. The pedigree analysis showed that in current generation can be expected the pedigree inbreeding at level 0.23% (ΔFPEDi = 0.19 ± 1.17%). Comparable results was obtained also by the genomic analysis, when the inbreeding in current generation reached level 0.11%. Thus, in term of genetic diversity both analyses reflected sufficient level of variability across analysed population of Norik of Muran horses.

scholarly journals Assessing losses of genetic variability in the endangered Mallorquí horse

2010 ◽  
Vol 55 (No. 10) ◽  
pp. 456-462 ◽  
Author(s):  
I. Álvarez ◽  
L.J. Royo ◽  
L. Pérez-Pardal ◽  
I. Fernández ◽  
L. Payeras ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Gene Diversity ◽  
Receptor Gene ◽  
Reference Population ◽  
Coat Colour ◽  
Conservation Strategies ◽  
Effective Number ◽  
Total Contribution ◽  
Melanocortin 1 Receptor ◽  
Future Viability

Information contained in the studbook of the endangered Mallorqu&iacute; horse was analysed to assess the genetic variability of the breed. Also, the effect of selection for coat colour variation was assessed using a set of 15 microsatellites genotyped on 68 Mallorqu&iacute; reproductive individuals previously diagnosed for the presence of the chestnut allele on the melanocortin-1 receptor gene. Mean inbreeding for the whole pedigree (310 individuals) was 2.5% while that for the individuals born during the last three years of recording (reference population) was 4.7%. Only 70% of all the founders have genetic representation in the reference population. A comparison of the parameters such as effective number of founders, effective number of ancestors and founder genome equivalents documented that the losses of founder genes occurred very soon after the implementation of conservation strategies. The parameter F<sub>IS</sub> computed from genealogical information was positive (0.029) for the whole population and negative (&ndash;0.024) for the reference population, thus illustrating the effort of the Mallorqu&iacute; horse breeders to avoid matings between relatives in later generations. A total of 14 individuals were heterozygotes for the chestnut allele (allele frequency of 10.6%). The rejection for reproduction of the chestnut heterozygote individuals would not affect the overall gene diversity of the population. However, the total allelic richness would decrease both at the within-subpopulation (1.2%) and total contribution level (0.4%). The chestnut heterozygote individuals are a within-breed reservoir of rare alleles that should be preserved to avoid risks for the future viability of the breed.

scholarly journals Pedigree and Molecular Analyses in the Assessment of Genetic Variability of the Polish Greyhound

Animals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 353
Author(s):  
Małgorzata Goleman ◽  
Ireneusz Balicki ◽  
Anna Radko ◽  
Iwona Rozempolska-Rucińska ◽  
Grzegorz Zięba
Keyword(s):  
Genetic Variability ◽  
Litter Size ◽  
Gene Diversity ◽  
Population Based ◽  
Pedigree Analysis ◽  
Molecular Testing ◽  
Pedigree Data ◽  
Kinship Matrix ◽  
Average Litter Size ◽  
The Mean

The aim of the study was to assess the genetic variability of the Polish Greyhound population based on pedigree analysis and molecular DNA testing and to determine the degree of relatedness among individuals in the population. Pedigree data of 912 Polish Greyhounds recorded in pedigree books since they were opened for this breed were analyzed. For molecular testing, DNA was obtained from cheek swabs taken from 235 dogs of the tested breed. A panel of 21 markers (Short Tandem Repeat—STR) was used. The mean inbreeding determined for the Polish Greyhound population based on pedigree analyses was low and amounted to 11.8%, but as many as 872 individuals of the 912 dogs in the studied population were inbred. A total of 83 founders (at least one unknown parent) were identified, among which 27 founders had both unknown parents. Full-sibling groups consisted of 130 individuals, with a minimum and maximum litter size of 2 and 16, respectively. The average litter size was 5.969. Gene diversity calculated based on the mean kinship matrix was 0.862 and the population mean kinship was 0.138. The founder genome equivalent based on the mean kinship matrix was 3.61; the founder genome surviving level was 12.34; the mean Ne was estimated at 21.76; and the Ne/N ratio was 0.135. The FIS inbreeding coefficient for 21 STR was negative, and the mean FIS value for all loci had a low negative value (−0.018). These values suggest a low level of inbreeding in the examined breed as well as the avoidance of mating related animals.

Sign in / Sign up

Export Citation Format

Share Document