Pedigree analysis of the Turkish Arab horse population: structure, inbreeding and genetic variability

The objective of this study was to use pedigree analysis to evaluate the population structure, genetic variability and inbreeding in Iranian buffaloes. The analysis was based on the pedigree information of 42 285 buffaloes born from 549 sires and 6376 dams within 1697 herds. Pedigree information used in this study was collected during 1976 to 2012 by the Animal Breeding Centre of Iran. The CFC program was applied to calculate pedigree statistics and genetic structure analysis of the Iranian buffaloes. Also, the INBUPGF90 program was used for calculating regular inbreeding coefficients for individuals in the pedigree. The analysis of pedigree indicated that inbreeding coefficient ranged from 0% to 31% with an average of 3.42% and the trend of inbreeding was significantly positive over the years (P < 0.0001). Average coancestry was increased in recent years and overall generation interval was 6.62 years in Iranian buffaloes. Founder genome equivalent, founder equivalent, effective number of founders and effective number of non-founders were increased from 1976 to 2002, but their values decreased from 2002 onwards. A designed mating system to avoid inbreeding may be applied to this population of buffalo to maintain genetic diversity.

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Genetic variability and population structure based on pedigree information for Muzaffarnagari sheep in India

Small Ruminant Research ◽

10.1016/j.smallrumres.2020.106182 ◽

2020 ◽

Vol 191 ◽

pp. 106182

Author(s):

Ajoy Mandal ◽

Hasan Baneh ◽

B.V. Subramanyam ◽

D.R. Notter

Keyword(s):

Population Structure ◽

Genetic Variability ◽

Pedigree Information

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Genetic variability and population structure in a collection of inbred lines derived from a core germplasm of castor

Journal of Plant Biochemistry and Biotechnology ◽

10.1007/s13562-016-0356-8 ◽

2016 ◽

Vol 26 (1) ◽

pp. 27-34 ◽

Cited By ~ 6

Author(s):

S. Senthilvel ◽

Mobeen Shaik ◽

K. Anjani ◽

Ranjan K. Shaw ◽

Poornima Kumari ◽

...

Keyword(s):

Population Structure ◽

Genetic Variability ◽

Inbred Lines ◽

Core Germplasm

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

Animal Genetic Resources/Ressources génétiques animales/Recursos genéticos animales ◽

10.1017/s2078633616000199 ◽

2016 ◽

Vol 59 ◽

pp. 7-14 ◽

Cited By ~ 2

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.

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Population structure of Czech cold-blooded breeds of horses

Archives Animal Breeding ◽

10.5194/aab-54-1-2011 ◽

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

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Genome-wide genetic diversity, population structure and admixture analysis in Eritrean Indigenous Cattle

South African Journal of Animal Science ◽

10.4314/sajas.v49i6.12 ◽

2020 ◽

Vol 49 (6) ◽

pp. 1083-1092

Author(s):

S Goitom ◽

M.G. Gicheha ◽

F.K. Njonge ◽

N Kiplangat

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variability ◽

Population Differentiation ◽

Principal Component ◽

Vital Role ◽

Group Method ◽

Indigenous Cattle ◽

Ecological Zones ◽

Genome Wide

Indigenous cattle play a vital role in subsistence and livelihood of pastoral producers in Eritrea. In order to optimally utilize and conserve these valuable indigenous cattle genetic resources, the need to carry out an inventory of their genetic diversity was recognized. This study assessed the genetic variability, population structure and admixture of the indigenous cattle populations (ICPs) of Eritrea using a genotype by sequencing (GBS) approach. The authors genotyped 188 animals, which were sampled from 27 cattle populations in three diverse agro-ecological zones (western lowlands, highlands and eastern lowlands). The genome-wide analysis results from this study revealed genetic diversity, population structure and admixture among the ICPs. Averages of the minor allele frequency (AF), observed heterozygosity (HO), expected heterozygosity (HE), and inbreeding coefficient (FIS) were 0.157, 0.255, 0.218, and -0.089, respectively. Nei’s genetic distance (Ds) between populations ranged from 0.24 to 0.27. Mean population differentiation (FST) ranged from 0.01 to 0.30. Analysis of molecular variance revealed high genetic variation between the populations. Principal component analysis and the distance-based unweighted pair group method and arithmetic mean analyses revealed weak substructure among the populations, separating them into three genetic clusters. However, multi-locus clustering had the lowest cross-validation error when two genetically distinct groups were modelled. This information about genetic diversity and population structure of Eritrean ICPs provided a basis for establishing their conservation and genetic improvement programmes. Keywords: genetic variability, molecular characterization, population differentiation

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