scholarly journals History of registered Gyr breed in Brazilian Northeast: population structure and genetic improvement of growth traits

2010 ◽  
Vol 40 (6) ◽  
pp. 1385-1391 ◽  
Author(s):  
Carlos Henrique Mendes Malhado ◽  
Paulo Luiz Souza Carneiro ◽  
Ana Claudia Mendes Malhado ◽  
Jorge André Matias Martins ◽  
Raimundo Martins Filho ◽  
...  
Keyword(s):  
Population Structure ◽  
Population Size ◽  
Effective Population Size ◽  
Growth Traits ◽  
Cattle Breed ◽  
Population Expansion ◽  
Phenotypic Change ◽  
Northeast Brazil ◽  
Pedigree Data ◽  
Effective Population

This paper provides an evaluation of the population structure, phenotype and genetic trends of registered Gyr herd cattle in northeast Brazil. The study provides important baseline information for the management, conservation and potential population expansion of this economically and culturally important cattle breed. Pedigree data were analyzed for individuals born between 1964 and 2006. Body weight values were adjusted to 205 and 365 days of age for animals born between 1978 and 2006. Phenotypic change of zebu Gyr in northeast Brazil is solely due to environmental improvement. However, there is potential for artificial selection for weight gain in young cattle. Effective population size decreased during the 1990s and the average inbreeding coefficient increased during the studied period. An increase of the effective population size of Gyr in northeast Brazil is strongly recommended, along with an increase in the management of the mating process to prevent inbreeding and to maintain the genetic variability of the breed.

scholarly journals DNA Sequence Variation and the Recombinational Landscape in Drosophila pseudoobscura: A Study of the Second Chromosome

Genetics ◽  
1999 ◽  
Vol 153 (2) ◽  
pp. 859-869 ◽  
Author(s):  
Martha T Hamblin ◽  
Charles F Aquadro
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Dna Sequence ◽  
Sequence Variation ◽  
Population Expansion ◽  
Drosophila Pseudoobscura ◽  
Effective Population ◽  
Standing Variation ◽  
Dna Sequence Polymorphism ◽  
Slightly Deleterious Mutations

Abstract The relationship between rates of recombination and DNA sequence polymorphism was analyzed for the second chromosome of Drosophila pseudoobscura. We constructed integrated genetic and physical maps of this chromosome using molecular markers at 10 loci spanning most of its physical length. The total length of the map was 128.2 cM, almost twice that of the homologous chromosome arm (3R) in D. melanogaster. There appears to be very little centromeric suppression of recombination, and rates of recombination are quite uniform across most of the chromosome. Levels of sequence variation (θW, based on the number of segregating sites) at seven loci (tropomyosin 1, Rhodopsin 3, Rhodopsin 1, bicoid, Xanthine dehydrogenase, Myosin light chain 1, and ribosomal protein 49) varied from 0.0036 to 0.0167. Generally consistent with earlier studies, the average estimate of θW at total sites is 1.5-fold higher than that in D. melanogaster, while average θW at silent sites is almost 3-fold higher. These estimates of variation were analyzed in the context of a background selection model under the same parameters of mutation rate and selection as have been proposed for D. melanogaster. It is likely that a significant fraction of the higher level of sequence variation in D. pseudoobscura can be explained by differences in regional rates of recombination rather than a larger species-level effective population size. However, the distribution of variation among synonymous, nonsynonymous, and noncoding sites appears to be quite different between the species, making direct comparisons of neutral variation, and hence inferences about effective population size, difficult. Tajima’s D statistics for 6 out of the 7 loci surveyed are negative, suggesting that D. pseudoobscura may have experienced a rapid population expansion in the recent past or, alternatively, that slightly deleterious mutations constitute an important component of standing variation in this species.

scholarly journals Legacy of draught cattle breeds of South India: Insights into population structure, genetic admixture and maternal origin

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0246497
Author(s):  
Vandana Manomohan ◽  
Ramasamy Saravanan ◽  
Rudolf Pichler ◽  
Nagarajan Murali ◽  
Karuppusamy Sivakumar ◽  
...  
Keyword(s):  
Population Structure ◽  
Population Size ◽  
Effective Population Size ◽  
South India ◽  
Genetic Admixture ◽  
Zebu Cattle ◽  
Effective Population ◽  
Cattle Breeds ◽  
South Indian ◽  
Indian Cattle

The present study is the first comprehensive report on diversity, population structure, genetic admixture and mitochondrial DNA variation in South Indian draught type zebu cattle. The diversity of South Indian cattle was moderately high. A significantly strong negative correlation coefficient of -0.674 (P<0.05) was observed between the effective population size of different breeds and their estimated FIS. The genetic structure analysis revealed the distinctness of Kangayam, Vechur and Punganur cattle from the rest of the zebu breeds. The results showed the influence of Hallikar breed in the development of most Mysore type cattle breeds of South India with the exception of Kangayam. Bayesian clustering analysis was performed to assess the taurine admixture in South Indian zebu cattle using purebred Jersey and Holstein-Friesian as reference genotypes. Relatively high levels of taurine admixture (>6.25%) was observed in Punganur, Vechur, Umblachery and Pulikulam cattle breeds. Two major maternal haplogroups, I1 and I2, typical of zebu cattle were observed, with the former being predominant than the later. The pairwise differences among the I2 haplotypes of South Indian cattle were relatively higher than West Indian (Indus valley site) zebu cattle. The results indicated the need for additional sampling and comprehensive analysis of mtDNA control region variations to unravel the probable location of origin and domestication of I2 zebu lineage. The present study also revealed major concerns on South Indian zebu cattle (i) risk of endangerment due to small effective population size and high rate of inbreeding (ii) lack of sufficient purebred zebu bulls for breeding and (iii) increasing level of taurine admixture in zebu cattle. Availability of purebred semen for artificial insemination, incorporation of genomic/molecular information to identify purebred animals and increased awareness among farmers will help to maintain breed purity, conserve and improve these important draught cattle germplasms of South India.

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 Genetic diversity, population structure, and effective population size in two yellow bat species in south Texas

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10348
Author(s):  
Austin S. Chipps ◽  
Amanda M. Hale ◽  
Sara P. Weaver ◽  
Dean A. Williams
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
North America ◽  
Wind Energy ◽  
Population Size ◽  
Effective Population Size ◽  
Microsatellite Loci ◽  
South Texas ◽  
Population Substructure ◽  
Effective Population

There are increasing concerns regarding bat mortality at wind energy facilities, especially as installed capacity continues to grow. In North America, wind energy development has recently expanded into the Lower Rio Grande Valley in south Texas where bat species had not previously been exposed to wind turbines. Our study sought to characterize genetic diversity, population structure, and effective population size in Dasypterus ega and D. intermedius, two tree-roosting yellow bats native to this region and for which little is known about their population biology and seasonal movements. There was no evidence of population substructure in either species. Genetic diversity at mitochondrial and microsatellite loci was lower in these yellow bat taxa than in previously studied migratory tree bat species in North America, which may be due to the non-migratory nature of these species at our study site, the fact that our study site is located at a geographic range end for both taxa, and possibly weak ascertainment bias at microsatellite loci. Historical effective population size (NEF) was large for both species, while current estimates of Ne had upper 95% confidence limits that encompassed infinity. We found evidence of strong mitochondrial differentiation between the two putative subspecies of D. intermedius (D. i. floridanus and D. i. intermedius) which are sympatric in this region of Texas, yet little differentiation using microsatellite loci. We suggest this pattern is due to secondary contact and hybridization and possibly incomplete lineage sorting at microsatellite loci. We also found evidence of some hybridization between D. ega and D. intermedius in this region of Texas. We recommend that our data serve as a starting point for the long-term genetic monitoring of these species in order to better understand the impacts of wind-related mortality on these populations over time.

scholarly journals Genomic Tools for the Conservation and Genetic Improvement of a Highly Fragmented Breed—The Ramo Grande Cattle from the Azores

Animals ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 1089
Author(s):  
Andreia J. Amaral ◽  
Ana L. Pavão ◽  
Luis T. Gama
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Genome Wide Association Study ◽  
Cattle Breed ◽  
Production Traits ◽  
Effective Population ◽  
Age At First Calving ◽  
Large Effective Population Size ◽  
Genomic Inbreeding ◽  
Genomic Regions

Ramo Grande is a local cattle breed raised in the archipelago of Azores, with a small and dispersed census, where inbreeding control is of utmost importance. A single nucleotide polymorphism (SNP) Beadchip array was used to assess inbreeding, by analysis of genomic regions harboring contiguous homozygous genotypes named runs of homozygosity (ROH), and to estimate past effective population size by analysis of linkage disequilibrium (LD). Genetic markers associated with production traits were also investigated, exploiting the unique genetic and adaptation features of this breed. A total of 639 ROH with length >4 Mb were identified, with mean length of 14.96 Mb. The mean genomic inbreeding was 0.09, and long segments of ROH were common, indicating recent inbred matings. The LD pattern indicates a large effective population size, suggesting the inflow of exotic germplasm in the past. The genome-wide association study identified novel markers significantly affecting longevity, age at first calving and direct genetic effects on calf weight. These results provide the first evidence of the association of longevity with genes related with DNA recognition and repair, and the association of age at first calving with aquaporin proteins, which are known to have a crucial role in reproduction.

Phenotypic characterization, population structure, breeding management and recommend breeding strategy for Fogera cattle (Bos indicus) in Northwestern Amhara, Ethiopia

2016 ◽  
Vol 58 ◽  
pp. 13-29 ◽  
Author(s):  
Endalkachew Girma ◽  
Kefyalew Alemayehu ◽  
Solomon Abegaze ◽  
Damitie Kebede
Keyword(s):  
Population Structure ◽  
Population Size ◽  
Effective Population Size ◽  
Breeding Strategy ◽  
Phenotypic Characterization ◽  
Cattle Population ◽  
Effective Population ◽  
Indigenous Cattle ◽  
Horn Length ◽  
Coat Pattern

SummaryThe study was carried out in selected districts in the Northwestern Amhara, from October 2012 to May 2013. The objective of the study were to undertake on-farm and on-station phenotypic characterization of Fogera Cattle in comparison with two different local cattle population, to characterize the population structure and to identifying trait preferences, breeding management and to recommend breeding strategy for Fogera cattle. Both purposive and random samplings were employed. Data were gathered through semi-structured questionnaire, focus group discussions, field observations, census data, direct count and body measurements. About 126 smallholder farmers were interviewed. About 21 quantitative and 17 qualitative phenotypic data types were also generated from 332 cattle. The Effective population size (Ne) and rate of inbreeding (ΔF) were calculated from the counted population structure data. Both GLM procedures of SAS and descriptive statistics of SPSS software's were employed for data analyses. The results indicated that Fogera cattle were kept mostly for milk (97.62 percent). The main threats identified for the survival of Fogera cattle were scarcity of feed resources and interbreeding with other indigenous cattle, which are less demanding in terms of feed. Fogera cattle population has specific morphological appearance. Generally about 65.2 percent of male pure-Fogera cattle population are having large hump and large dewlap (93.5 percent) with cervico-thoracic (82.6 percent) hump position and long tail (97.8 percent), respectively. The coat pattern of male pure-Fogera cattle is dominated by the spotted coat pattern (82.6 percent) with 43.5 percent white black and 39.1 percent black white coat colour. Female Fogera cattle have medium (94.4 percent) hump size at cervico-thoracic positions (73.2 percent), large dewlap (62.7 percent) and long tail which is well below the hock (91.5 percent). The coat pattern of female pure-Fogera cattle is dominated by white spotted (80.3 percent) with 43.0 percent white black and 33.1 percent black white coat colour Most of the quantitative traits were highly significantly (P≤ 0.001) affected by breed type. Except horn length and horn space all of quantitative traits for both sexes of pure-Fogera cattle from on-station were significantly (P≤ 0.05) larger than those of the on-farm. The average linear body measurement taken on a total of 46 male pure-Fogera cattle populations were 42.68 ± 0.56 cm (mouth circumference), 16.35 ± 0.72 cm (horn length), 37.04 ± 1.16 cm (dewlap width) and 129.17 ± 1.33 cm (height at wither). The average linear body measurements for female pure-Fogera cattle were 38.23 ± 0.18 cm (mouth circumference), 13.81 ± 0.37 cm (horn length), 27.20 ± 0.42 cm (dewlap width) and 123.68 ± 0.52 cm (height at wither). The population structure were dominated by Pure-Fogera constituting 37.02 percent, Interbred with Fogera (33.71 percent) and non-Fogera (29.23 percent). The effective population size of pure-Fogera cattle was 4295, with 9016 total population. The average inbreeding level for the population was 0.012 percent. Inbreeding is at a low level and the effective population size is large. The calculated parameters indicate satisfactory genetic diversity in Fogera cattle. Milk yield, colour, power, body size and growth rate of Fogera were the most dominant traits perceived to be good by the respondents. The special qualification of this breed is to live at high amount of flooding areas with adapting other very challenging environment. Pure breeding of pure-Fogera, interbred with Fogera and non-Fogera type of breeds was used for breeding practice with natural mating. The Andassa Research Center established in 1964 as Fogera cattle population improving centre, but according to different source, population viability and population structure indicated that the population are not viable and highly admixture with other indigenous cattle breeds. According to this in order to improve the population status of Fogera cattle we recommended control with open-nucleus breeding strategy. So in order to minimize the risk status of this breed and conserve for the future generation any responsible agent should be given priority.

Examination of the relationship between inbreeding and population size

1985 ◽  
Vol 17 (1) ◽  
pp. 97-106 ◽  
Author(s):  
John H. Relethford
Keyword(s):  
Population Structure ◽  
Linear Regression ◽  
Population Size ◽  
Effective Population Size ◽  
Linear Regression Model ◽  
Historical Change ◽  
Human Populations ◽  
Effective Population ◽  
The Common ◽  
The Relationship

SummaryA method is presented for examining the relationship between effective population size and accumulated random inbreeding in human populations. For a set of populations, the inverse of inbreeding is regressed on effective population size using a linear regression model. This procedure allows testing of several hypotheses regarding the common and unique influences on population structure. Deviations from the expected curve suggest demographic or historical change. This method is applied to surname data from nine Irish isolates. The results show that the method is very useful in assessing differential influences on population structure.

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.

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

2010 ◽  
Vol 90 (3) ◽  
pp. 331-340 ◽  
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

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