scholarly journals Genetic Structure Analysis of the Pura Raza Español Horse Population through Partial Inbreeding Coefficient Estimation

Animals ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1360
Author(s):  
Davinia I. Perdomo-González ◽  
María J. Sánchez-Guerrero ◽  
Antonio Molina ◽  
Mercedes Valera

The aim of this work was to analyze genetic parameters such as the inbreeding coefficient (F), relatedness coefficient (AR) and partial inbreeding coefficient (Fij) of the whole PRE population, and the ancestors which account for 50% of the total genetic variability of the current population, from genealogical information. The average F of the whole PRE population (328,706 animals) has decreased from 8.45% to 7.51% in the least 20 years. The Fij was estimated for the whole PRE population, resulting in a database of 58,772,533 records containing one record for each Fij that each animal receives from a certain common ancestor (CA). A total of 10,244 CAs contributed to the Fij with an average of 5370 descendants, with each descendant having an average of 170 CAs. Over the generations, the number of CAs has increased, while the proportion of Fij by each one has decreased. In addition, the contributions of the more influential ancestors have changed. The increased census, the limited use of artificial insemination and our increased knowledge about inbreeding depression and the animals’ breeding values allow breeders to select horses more for their functionality and conformation than for their pedigree reputation, which is the cause of all these changes.

2017 ◽  
Vol 57 (3) ◽  
pp. 422
Author(s):  
Derly Rodríguez Sarmiento ◽  
Emanuela Tullo ◽  
Rita Rizzi

Genetic variability and structure of the population were studied in 7949 registered Normande cattle in Colombia. The pedigree was deep with 18 traced generations, but there were some incomplete genealogical information for the cattle born in the more distant past. The average number of complete and equivalent complete generations was 2.42 and 5.21, respectively. The average pedigree completeness index for five generations was 0.62, which increased over time, and a significant difference between sexes was found (males: 0.82 ± 0.11; females: 0.62 ± 0.38). The average generation interval was 7.57 years. The number of founders, effective founders, ancestors, and founder genomes were 575, 115, 47, and 22.22, respectively, which suggests that an unequal use of founders and a random loss of alleles from founders occurred over time. The level of inbreeding was 0.019 and increased to 0.023, when the inbreeding coefficient was calculated by assigning inbreeding of contemporaries to founders. These levels of inbreeding lead to an effective population size of 138.5 and 117.9 and to a 0.36% and 0.42% rate of inbreeding, respectively. Out of 267 herds with more than five registered breeding animals, only one nucleus herd was present, whereas 117 and 119 were classified as multiplier and commercial herds, respectively. About 92% of calves were sired by French bulls; but the use of Colombian bulls for breeding is increasing. The Colombian Normande breed is at an acceptable level of genetic variability, although some losses of founder alleles have occurred. As the level of inbreeding has been increasing, inbreeding and mating strategies should be monitored in order to maintain the genetic diversity of the breed.


Author(s):  
Ljiljana Vapa ◽  
Mihajla Djan ◽  
Dragana Obreht ◽  
Biljana Tosovic-Maric ◽  
Milan Vapa ◽  
...  

One of the possible reasons for pheasant population number decline in past several years might be loss of adaptability in populations originated from breeding stations caused by inbreeding depression. Due to fact that adaptability is a consequence of genetic structure of the populations, the aim of this paper was the analysis of genetic variability in pheasant population from breeding station Ristovaca using molecular markers. Allozyme variability of 20 putative gene loci was detected by polyacrylamide gel electrophoresis. Polymorphism was revealed in 5 loci: Est-1, Pgd, Sod, Gpi-2 and Odh. The values of genetic variability measures - heterozigosity polymorphism, fixation indices and H/P ratio indicate low level of genetic variability and possible presence of inbreeding depression within pheasant population.


2022 ◽  
Vol 52 (5) ◽  
Author(s):  
Joel Domínguez-Viveros ◽  
Antonio Reyes-Cerón ◽  
Juan Fernando Saiz-Pineda ◽  
Cesar Villegas-Gutiérrez ◽  
Guadalupe Nelson Aguilar-Palma ◽  
...  

ABSTRACT: This study analyzed the Sardo Negro breed pedigree (41,521 animals registered from 1958 to 2019) to determine its structure, evolution, and genetic variability (GV). The population genetic parameters evaluated were effective number of founders (fe) and ancestors (fa), pedigree integrity, additive genetic relationship (AGR); number of complete generations (NCG), maximum generations traced (NMGT), and equivalent complete generations (NECG); effective population size (Ne), inbreeding coefficient (F), and generation interval (GI). The average GI was 7.45 years. A total of 7,804 founders and 4,856 ancestors were identified for a fe of 185 and a fa of 97. The average and maximum values of NCG, NECG, and NMGT were 1.6 and 5.0, 2.5 and 6.5, 4.3 and 12, with Ne estimates of 15.9, 25.9, and 69.0, respectively. The increase in F, linked to Ne, ranged from 0.72% to 3.1% per generation. The average values for F and AGR were 3.6% and 1.0%, respectively. The proportion of inbred individuals was 32.0%, with F values ranging from 0.01 to 62.2% and an average of 11.3%. The rate of inbred population was 1.3% per year. The annual rate of AGR was 0.04%. For the continuity and projection of the breed, the evolution of F as a function of Ne and the possible implications of the selection schemes must be considered. The genetic variability sustained over time results from the Ne.


2010 ◽  
Vol 39 (12) ◽  
pp. 2640-2645 ◽  
Author(s):  
João Cruz Reis Filho ◽  
Paulo Sávio Lopes ◽  
Rui da Silva Verneque ◽  
Robledo de Almeida Torres ◽  
Roberto Luiz Teodoro ◽  
...  

The objective of the present study was to evaluate the genetic structure of Gyr cattle selected for milk production. Files of pedigree and production were composed of 27,610 animals. The ENDOG program was used for the calculation of individual inbreeding coefficient (F) and coefficient of average relatedness (AR), effective number of animals(Ne), effective number of founders (f e) and ancestors (f a), and generation interval (GI). Individual inbreeding coefficients and average relatedness in the population were 2.82% and 2.10%, respectively. It was observed a reduction in the effective number of animals, especially after publication of the results of the first progeny test. The estimated effective number of founders was 146 and 75 for the ancestrals. Out of those, only 28 ancestors accounted for the origin of 50% of the population genes. The average generation interval was 8.41 years and it was longer for males than for females. For maintaining genetic variability in future generations, it should be invested mating strategies that reduce inbreeding and which do not use massively only some high breeding value sires.


2011 ◽  
Vol 102 (3) ◽  
pp. 333-343 ◽  
Author(s):  
K.C. Albernaz ◽  
K.L. Silva-Brandão ◽  
P. Fresia ◽  
F.L. Cônsoli ◽  
C. Omoto

AbstractIntra- and inter-population genetic variability and the demographic history of Heliothis virescens (F.) populations were evaluated by using mtDNA markers (coxI, coxII and nad6) with samples from the major cotton- and soybean-producing regions in Brazil in the growing seasons 2007/08, 2008/09 and 2009/10. AMOVA indicated low and non-significant genetic structure, regardless of geographical scale, growing season or crop, with most of genetic variation occurring within populations. Clustering analyzes also indicated low genetic differentiation. The haplotype network obtained with combined datasets resulted in 35 haplotypes, with 28 exclusive occurrences, four of them sampled only from soybean fields. The minimum spanning network showed star-shaped structures typical of populations that underwent a recent demographic expansion. The recent expansion was supported by other demographic analyzes, such as the Bayesian skyline plot, the unimodal distribution of paired differences among mitochondrial sequences, and negative and significant values of neutrality tests for the Tajima's D and Fu's FS parameters. In addition, high values of haplotype diversity (Ĥ) and low values of nucleotide diversity (π), combined with a high number of low frequency haplotypes and values of θπ<θW, suggested a recent demographic expansion of H. virescens populations in Brazil. This demographic event could be responsible for the low genetic structure currently found; however, haplotypes present uniquely at the same geographic regions and from one specific host plant suggest an initial differentiation among H. virescens populations within Brazil.


2021 ◽  
Author(s):  
Julissa Rojas-Sandoval ◽  
Pedro Acevedo-Rodríguez

Abstract Genetics: The chromosome number reported for C. dactylon varies from 2n = 18 to 2n = 36 with diploid and polyploid populations (Cook et al., 2005). Ramakrishan and Singh (1966) and Sarandon (1991) have found differences in total biomass and biomass partition according to the origin of the population. Sarandon (1991) points out that characters are highly heritable, which means that high genetic variability for biomass production and variable architecture allows an ample base for selection, which in most cases is induced by herbicides, mechanical control or forage production. Reproductive Biology: C. dactylon is wind-pollinated and generally self-incompatible, suffering from inbreeding depression when genotypes are self-pollinated. Quantitative traits such as seed yield and forage yield can be dramatically negatively affected by inbreeding depression (Cook et al., 2005). In diploid populations, caryopses are formed after zygote formation. In polyploids, which are sterile, caryopses may be apomictic. Physiology: This C4 plant (Kissmann, 1991) has high rates of accumulation under adequate irradiance, water and nutrient supply and may consume 75 kg of N, 20 kg of P and more than 1,500,000 litres of water for 5000 kg/ha of biomass dry matter (Fernandez, 1991). In the south of Santa Fe province, Argentina, a maximum biomass of 8000 kg/ha may be generated under a summer crop of maize or sunflower with >75% located in the first 10 cm of the soil profile (Lombardo, 1973), whereas in Balcarce (Argentina) about 5000 kg/ha is commonly found in maize or sunflower stubble. Phenology: A photoperiod of 13 hours induces flowering. Low night temperatures coupled with high diurnal temperatures induces blooming (Nir and Koller, 1976). A reduction in irradiance drastically decreases inflorescence production (Moreira, 1975). In North America, annual plants reproduce during spring and perennial plants reproduce all year long (USDA-NRCS, 2014). Longevity: C. dactylon grows as both an annual and perennial grass. The annual growth-form becomes dormant and turns brown when nighttime temperatures fall below freezing or average daytime temperatures are below 10°C (Cook et al., 2005). Activity Patterns: Seeds may be the route of invasion in weed-free fields through the faeces of cows (Rodriguez, personal communication). Rhizome biomass exhibits an annual cyclic pattern and, as with any perennial weed, low temperatures reduce biomass and viability is lost as a consequence of the consumption of materials due to respiration and maintenance. The digestibility of stocked material is severely decreased, implying a loss in forage quality (Vaz Martins, 1989). This is a character that has largely improved in cultivated varieties. Each node has a physiological self-governing structure in relation to the apex, but is highly dependent on substances from other plant parts. The mother plant determines the runner growth pattern on the soil surface according to the sugar-gibberellin balance (Montaldi 1970). Node disconnection may be caused by natural decay and cultivation and produces damage in the breakdown zone and changes in hormone and nutrient relationships. It is widely demonstrated that rhizome or runner fragmentation induces the activation of buds. The proportion of activated buds increases as the number of buds per segment decreases (Moreira, 1980; Kigel and Koller, 1985; Fernandez and Bedmar, 1992). The cultivation method is mainly responsible for vegetative propagation fragmentation. The higher the cultivation intensity, the smaller the segments produced (Kigel and Koller, 1985). Population Size and Structure This weed produces an enormous number of small seeds (0.25-0.30 mg), the viability and dormancy of which are highly variable according to genotype and the conditions when formed. The seed is important because it confers high genetic variability on the population. Perez et al. (1995) recorded a very low germination rate. Uygur et al. (1985) obtained up to 15% germination at constant temperatures of 35-40°C, and 50% at temperatures alternating between 20 and 30°C. Moreira (1975) obtained up to 80% germination with the help of nitrate, chilling and alternating temperatures, and Elias (1986) recorded up to 96% germination from heavier samples of seed. Seeds remain viable in the soil for at least 2 years (Caixinhas et al., 1988). As a rule, cultivars have relatively high viability. Osmo-conditioning of Bermuda grass seeds with PEG followed by immediate sowing improved seed germination and seedling growth under saline conditions (Al-Humaid 2002). The probability of emergence and successful establishment of C. dactylon decreases with the depth of the fragment, but increases with the weight of the node and internode (Perez et al., 1998). Growth from plants originated from a runner may exhibit a different biomass partition than that from plants originated from a rhizome (Fernandez, 1986). From sprouting onwards, weed growth is controlled mainly by temperature (optimum 25-30°C) and radiation, but also by humidity and soil fertility. The efficiency of carbohydrate reserve usage during sprout growth is highly dependent on temperature and the type of vegetative structure; it is maximum at 20°C and is higher for rhizomes than for stolons (Satorre et al., 1996). Runners and rhizome growth begins 30 days after growth but only if soil temperature is >15°C. Rates of 15 g/g/day have been recorded in Argentina (Lescano de Ríos, 1982).


2013 ◽  
Vol 43 (6) ◽  
pp. 978-984 ◽  
Author(s):  
Vanice Dias Oliveira ◽  
Allivia Rouse Carregosa Rabbani ◽  
Ana Veruska Cruz da Silva ◽  
Ana da Silva Lédo

This research had as objective to characterize genetically individuals of physic nut cultivated in experimental areas in Sergipe, Brazil by means of RAPD molecular markers. Leaves of 40 individuals were collected and DNA was isolated using CTAB 2% method. Were used 30 primers RAPD for DNA amplification, and this data was used to estimate the genetic similarity among the pairs of individuals, using Jaccard coefficient, and group them out for the UPGMA method. Also, the genetic structure and diversity of the populations were assessed using AMOVA. Of the 100 fragments generated, 29 of were polymorphic. A similarity average of 0.54 among the individuals was found and the amplitude similarities varied from 0.18 to 1.00. One of them (U5) was unit clusters and formed by the most divergent individuals. AMOVA indicated that there is more variation within (63%) the population. In conclusion, it was possible verify genetic variability in physic nut using RAPD markers at these experimental areas.


2017 ◽  
Vol 53 ◽  
pp. 248-253
Author(s):  
E. S. Cheburanova ◽  
O. A. Epishko ◽  
T. I. Kuzmina

Objective: identification of carrier animals of the hereditary anomaly SCID and HYPP of the population of horses bred on breeding horse farms of the Republic of Belarus. Methods: genetic, biological. DNA diagnosis of genotypes in the gene severe combined immunodeficiency (SCID) and hyperkaliemic periodic paralysis (HYPP) was performed using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) in the research laboratory «DNA Technology» of educational establishment «Grodno State Agrarian University». We tested 50 horses of different breeds, kept on different breeding horse farms of Belarus. DNA was isolated from buccal epithelium by perchlorate method with double purification (according to the method of Zinovieva). A study of the genetic structure of the horse population for hereditary anomalies of severe combined immunodeficiency and hyperkalemic periodic paralysis was performed using modern equipment. Amplification was carried out using the C1000 Touch thermal cycler (BioRad, USA). The visualization of the gel was carried out using the gel-documenting system Gel Doc XR + (Bio- Rad, USA). Main results. The use of modern methods for the genetic diagnosis of hereditary diseases of agricultural animals not only at birth to exclude from the process of reproduction of animal carriers of hereditary anomalies, but also reduces funding for their maintenance and cultivation. In the studies we used the PCR method based on the use of specific oligonucleotides with which the amplification of the necessary fragment of the 163 gene occurs in healthy individuals and 158 in the mutation carriers, which makes it possible to identify the hereditary SCID disease. We tested 50 animals of the upper and Arabian breeds, as well as horses with an admixture of Arabian blood, among which no carriers of the hereditary anomaly were found. In studies, the PCR-RFLP analysis method was used, based on the use of distinctive primers due to which the necessary fragment of the gene is amplified, which makes it possible to identify the hereditary HYPP disease. Amplified fragments were subjected to the action of restriction enzymes, with the help of which it is possible to determine the genotype of the animal under study. We tested 50 animals of the upper and Arabian breeds, as well as horses with an admixture of Arabian blood, among which no carriers of the hereditary anomaly were found. Conclusions. Severe combined immunodeficiency (SCID) is an autosomal recessive disease that occurs in humans, mice, horses and dogs. Carriers of this hereditary disease are born without visible anomalies, but after 2 weeks they become ill from any infection and die, since they can not develop an antigen-specific immune response. Hyperkaliemic periodic paralysis (HYPP) is an autosomal dominant disease that occurs in horses at the age of 2, when the animal begins, is strengthened to exercise. Symptoms of this disease are weakness of the muscles, periodic spasms, paralysis, which can lead to death. Presumably, there were no carriers of severe combined immunodeficiency in the Republic of Belarus, since breeding farms for breeding horses did not use biological material of Arabian and local breeds of horses for insemination. With subsequent importation of Arabian horses, as well as breeds that have an admixture of Arab blood, it is necessary to conduct DNA testing for the presence of severe combined immunodeficiency (SCID). According to the results of the conducted studies to identify the hereditary disease of hyperkalemic periodic paralysis (HYPP) in the horse population, no carriers were found, as well as sick animals. Presumably, there were no carriers of this disease on the territory of the republic, as evidenced by parallel studies conducted in other European countries, where no carrier or sick animal was found. This suggests that the disease was localized during the time, and also did not leave the territory of the American continent.


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