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Geographical locations of the 12 Chinese indigenous goat populations sampled. The two-letter or three-code letter besides the black point in the figure corresponds to the populations sampled as follows: East Tibetan goat, ET; Neimonggol goat, NM; Liaoning goat, LN; Taihang goat, TA; Wu goat, WU; Nanjiang Brown goat, NJB; Chuandong White goat, CDW; Black goat, BL; Matou goat, MT; South-east Tibetan goat, SET; North Tibetan goat, NT; Small-xiang goat, SX.
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Twelve Chinese indigenous goat populations were genotyped for twenty-six microsatellite markers recommended by the EU Sheep and Goat Biodiversity Project. A total of 452 goats were tested. Seventeen of the 26 microsatellite markers used in this analysis had four or more alleles. The mean expected heterozygosity and the mean observed heterozygosity...
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... Tanto En total se detectaron 203 alelos distribuidos en los 28 loci analizados, obteniéndose un promedio de 7.250 ± 3.318 alelos por locus. La diversidad alélica observada fue similar a la reportada en poblaciones caprinas de España (Martínez, 2011) y superior al reportado en poblaciones nativas de China (Li, 2002). El número efectivo de alelos fue menor (4.008 ± 1.775) lo que indica una distribución no equitativa en la frecuencia de los alelos, además de que un marcador no presentó variación polimórfica. ...
ESTÁN INCLUIDOS LOS TRABAJOS DE 18 UNIVERSIDADES MEXICANAS EN RECURSOS ZOOGENÉTICOS DE ESPECIES DOMÉSTICAS Y SILVESTRES
... Tanto En total se detectaron 203 alelos distribuidos en los 28 loci analizados, obteniéndose un promedio de 7.250 ± 3.318 alelos por locus. La diversidad alélica observada fue similar a la reportada en poblaciones caprinas de España (Martínez, 2011) y superior al reportado en poblaciones nativas de China (Li, 2002). El número efectivo de alelos fue menor (4.008 ± 1.775) lo que indica una distribución no equitativa en la frecuencia de los alelos, además de que un marcador no presentó variación polimórfica. ...
... Tanto En total se detectaron 203 alelos distribuidos en los 28 loci analizados, obteniéndose un promedio de 7.250 ± 3.318 alelos por locus. La diversidad alélica observada fue similar a la reportada en poblaciones caprinas de España (Martínez, 2011) y superior al reportado en poblaciones nativas de China (Li, 2002). El número efectivo de alelos fue menor (4.008 ± 1.775) lo que indica una distribución no equitativa en la frecuencia de los alelos, además de que un marcador no presentó variación polimórfica. ...
... With Ethiopia's growing human population, urbanization, economic development, and domestic and export markets, there is a huge opportunity to increase sheep production using diverse indigenous sheep [2]. The first step in conserving and exploiting these diverse sheep populations is obtaining a thorough understanding of the genetic diversity that exists [4,5]. The ability to select superior animals for breeding is enabled by the presence of genetic diversity. ...
The objective of this work was to study genetic diversity by comparing whole genome sequence data of Rutana, Gumuz and Washera sheep found in Amhara and Benishanguel gumuz regional states of Ethiopia. We employed variant calling format tools version 0.1.15 to calculate some genetic diversity indices such as observed heterozygosity, expected heterozygosity, inbreeding coefficient, and nucleotide diversity. The results revealed that, observed heterozygosity ranged from 0.33 in Gumuz to 0.34 in Rutana and Washera sheep. Expected heterozygosity ranged from 0.37 in Rutana to 0.38 in Gumuz and Washera sheep. Expected heterozygosity was found to be higher than observed heterozygosity. Higher inbreeding coefficient (0.12) was recorded for Gumuz sheep compared to 0.09 of Rutana and Washera sheep. Mean nucleotide diversity values were 0.0029, 0.0030 and 0.0028 for Gumuz, Rutana and Washera sheep, respectively. Higher values of nucleotide diversity were recorded. Population structure analysis using principal component analysis revealed no clear separation between Gumuz, Rutana and Washera sheep populations with possibility of gene flow attributed to geographical location proximity. The smaller population size, closed breeding system, genetic drift and uncontrolled (non-random) mating might lead to higher rate of inbreeding in Gumuz, Rutana and Washera sheep, requiring timely intervention. This intervention helps to prevent inbreeding depression and extinction of these valuable breeds of sheep, which helps in sustaining the livelihood of sheep keepers in lowlands and highlands. Nevertheless, the whole-genome analysis revealed high within-breed variation. Uncovered areas of studies like mapping quantitative trait loci, identifying genes underpinning productivity traits such as carcass quantity and meat quality could be carried out on diversified sheep resources identified by the current study. Identifying the genomic regions and biological pathways that contribute to explaining variability in these traits is of great importance for selection purposes. Designing conservation-based within-breed sheep selective breeding programs are recommended considering economically important traits into account.
... All measures of genetic diversity revealed that there was substantial genetic variation within and across the three breeds studied. The substantial genetic variation has also (Barker et al., 2001;Kim et al., 2002;Li et al., 2002;Behl et al., 2003;Chenyambuga et al., 2004;Jandurova et al., 2004;Kumar et al., 2005;Iamartino et al., 2005;Takahashi et al., 2008). Although varying among populations, observed mean heterozygosity was lower than the expected mean heterozygosity for all the populations. ...
... This level of differentiation among the populations is within the range of F st values reported in the literature. A value of 0.146 was found in indigenous goats of sub-Saharan Africa (Chenyambuga et al., 2004); 0.105 in 12 Chinese indigenous goat populations (Li et al., 2002); 0.17 in Swiss goat breeds (Saitbekova et al., 1999); 0.073 in Italian goat populations (Iamartino et al., 2005); 0.202 in goats from Korea and China (Kim et al., 2002); and 0.227 in Asian goats (Barker et al., 2001). The overall F is value (0.26) was higher and significantly different from zero indicating departure from random mating and suggested that some of the studied loci were homozygous in the populations. ...
Gene flow, genetic structure and differentiation of Kutchi, Mehsana and Sirohi breeds of goat from North-Western India were evaluated based on 25 microsatellite markers so as to support breed conservation and improvement decisions. The microsatellite genotyping was carried out using an automated DNA sequencer. The gene diversity across the studied loci for the Kutchi breed varied from 0.57 (ILST 065) to 0.93 (OarFCB 304, OMHC 1, ILSTS 058) with an overall mean of 0.79±0.02. The corresponding values for Mehsana and Sirohi breeds were 0.16 (ILST 008) to 0.93 (OMHC 1, ILSTS 058) with an average of 0.76±0.04, and 0.50 (ILSTS 029) to 0.94 (ILSTS 058) with an average of 0.78±0.02, respectively. The Mehsana breed had lowest gene diversity among the 3 breeds studied. All the populations showed an overall significant heterozygote deficit (Fis). The Fis values were 0.26, 0.14 and 0.36 for Kutchi, Mehsana and Sirohi goat breeds, respectively. Kutchi and Mehsana were more differentiated (16%) followed by Mehsana and Sirohi (13%).The measures of standard genetic distance between pairs of breeds indicated that the lowest genetic distance was between Kutchi and Sirohi breeds (0.73) and the largest genetic distance was between Mehsana and Kutchi (1.0) followed by Sirohi and Mehsana (0.75) breeds. Mehsana and Kutchi are distinct breeds and this was revealed by the estimated genetic distance between them. All measures of genetic variation revealed substantial genetic variation in each of the populations studied, thereby showing good scope for their further improvement. (Key Words : Microsatellite Loci, Genetic Variation, Genetic Distance and Breed Assignment, Goat)
... Table 4 shows that the alleles were detected at the carbonic anhydrase locus in both populations sampled. Carbonic anhydrase polymorphism was highly informative (Shannon Information Index <0.60: Li et al. 2002;Yang et al.1999). The observed number of alleles across both populations are more than the effective number of alleles expected; the effective number of alleles was 1.99 (Ibadan) and 1.57 (Ijebu-Ode) with an overall mean of 0.94. ...
Carbonic anhydrase polymorphism in West African Dwarf (WAD) goat populations, from Oyo and Ogun States was investigated using the cellulose acetate electrophoresis system. Blood samples of 5 mL were collected from 60 WAD goats (30 from Ibadan (Oyo State) and 30 from Ijebu-Ode (Ogun State)), via the jugular veins and placed into heparinised bottles. The results of the electrophoresis analyses were subjected to statistical analysis using Tools For Population Genetic Analysis (TFPGA) software. The results revealed that two alleles, CAF and CAS govern the three genotypes (CAFF, CAFS and CASS) with CASS being prevalent. Allele frequencies ranged from 0.24 for CAF in Ijebu-Ode to 0.76 in CAS also from Ijebu-Ode while the genotype frequencies ranged from 0.09 in CAFF from Ijebu-Ode to 0.61 in CASS also from the Ijebu-Ode population. Deviation from the Hardy-Weinberg equilibrium was significant (P E(0.47) was higher than the observed heterozygosity HO(0.25) Wright analysis showed that the populations sampled were from inbred populations with a positive FIT and FIS value (0.47, and 0.06 respectively) implying deficiency in heterozygote and the FST value of 0.45 indicating greater genetic differentiations among the populations giving opportunity for improvement.
... Likewise, Spencer and Woolnough (2010) reported 5 to 23 alleles per locus in Australian dromedary Camels. It was previously reported that the microsatellite loci should have more than four alleles per locus to minimize standard error (SE) of distance estimates (Li et al., 2002). In general, the average of alleles in a particular population is mainly depend on size of the sample (n) and the availability of unique alleles of very low frequencies. ...
In this study, twenty microsatellite markers were applied to study the genetic polymorphism in Maghateer Camels in the Kingdom of Saudi Arabia. About 50 unrelated Maghateer camels were selected and hair roots were subjected for the extraction of total genomic DNA. The selected microsatellite forward-, and revised-primers amplified 19 SSR markers from the Camels. In the experimental condition, CMS25 and VOLP67 markers did not yield any genomic amplification from the DNA of Camels. A total of nineteen microsatellite loci have been determined as polymorphic nature. In this experiment 155 alleles were obtained by the loci of 19 microsatellites, range of 4 to 16 alleles per locus and the mean of 8.158 alleles per locus. The observed heterozygosity (Ho) range varied from 0.280 to 1.000 and the mean value was determined as 0.717. The mean expected heterozygosity (He) was found to be 0.667 and the range varied between 0.282 and 0.871. In Maghateer population, the effective number (mean) was found to be 3.599. A total of 12 loci were determined in this study. In the selected Camel population no bottleneck in nearest past or no potent heterozygote excess was obtained based on standardized differences, sign and tests such as Wilcoxon tests and L shaped distribution of mode-shift test. The present findings showed the utility of these 19 microsatellite loci for analyzing genetic polymorphism in Camelus dromedarius (dromedary camel). Keywords: Dromedary, Maghateer, Microsetellite, Heterzygosity
... AMOVA was conducted to elucidate the partitioning of the level of genetic variability of Omani goats; 90% of the total genetic diversity occurred within the Omani breeds, whereas only 10% occurred from differences between breeds. The AMOVA results for the Omani breeds were very similar to those obtained for Chinese goat populations (Li et al., 2002). In contrast, the values were much higher than those obtained for Nigerian goat populations, in which the between-breed diversity only accounted for 4% of the genetic diversity and the withinbreed diversity for 96% (Ojo et al., 2015). ...
The genetic diversity of most global goat populations has been assessed in recent decades using nuclear markers but remains unstudied in the south Arabian Peninsula, particularly in the Sultanate of Oman, despite the importance of these animals for the local economy and food supply. Therefore, the present study provides a
comparative analysis of the genetic diversity of five native Omani goat populations and evaluates possible admixture rates with the four most frequently imported goat populations from geographically proximal countries. A data set based on 11 highly informative microsatellite locus genotypes from nine populations was used to estimate population genetic parameters. The summary statistics for the parameters depicted relatively highly diverse populations (Ho=0.667, He=0.663) with relatively low and mostly non-significant levels of inbreeding (FIS). Furthermore, population substructure estimators (AMOVA) and population differentiation coefficient (FST) indicated weak genetic differentiation among populations (P < 0.001). A finer analysis of the population substructure and differentiation using STRUCTURE, discriminant analyses of principal components (DAPCs) and a neighbor-joining (NJ) tree supported a scenario in which a high level of gene flow between populations from close geographical locations is the main evolutionary driving force. Thus, any future conservation strategies and breeding programs should attempt to preserve unique alleles that might be favorable for the limited feed available in desert ecosystems as well as economic traits.
... Specifically, it was demonstrated that training population size, number of markers and heritability increased PA in both simulation and empirical populations (Combs & Bernardo, 2013;Liu et al., 2018;Marulanda, Melchinger, & Wurschum, 2015). Breed-specific alleles were also found to play an important role in the development of population structure in animal (Li et al., 2002). Therefore, the ratio of breedspecific alleles and common alleles could be a crucial factor when GP was conducted across distinct populations. ...
Genomic prediction (GP), which could predict the breeding value of crop plants genotyped with molecular markers, has been carried out in multiple species. Prediction accuracy (PA) of GP depends on various factors, including genetic relatedness and genetic basis. In this study, we examined the rationale for the low PA of GP when the training and validation populations were distinct using 170 temperate inbred lines and 210 tropical and subtropical inbred lines, respectively. All inbred lines were evaluated for 17 traits and genotyped with 550K high‐density markers. The results show that: (a) the influences of heritability and marker number on PA reflected variations in phenotypic variance captured by the genetic information; (b) the low PA of GP when the training and validation populations represent structured subpopulation is related to the ratio of subpopulation‐common alleles (RSCA) and the genetic relatedness between the two subpopulations; (c) RSCA and PA increased with the increase of genetic relatedness, suggesting that these three factors were related. Our findings would provide references when performing GP, and guidance when designing breeding populations.
... Foram coletadas amostras de bulbos capilares de cada animal, colocados em envelopes e acondicionados em freezer até o momento da extração do DNA. Foram analisados 27 marcadores microssatélites TGLA122 (George set al., 1992); BM1329, BM6506, BM6526, BM8125 (Bishop et al., 1994); CSSM66, ETH225 (Barendese et al., 1994); CSRM60, SPS115 (Mooreet et al., 1993), MM12 (Mommens et al., 1994); ILSTS011, MAF209, MAF65, SRCRSP8 (Luikart et al., 1999); HSC, McM527, INRA6 (Isag, 2002); BM1818, INRA023 (Li et al., 2002); CSRD247 (FAO, 2004); OarFCB11, OarFCB48, OarFCB304 (Yang et al. 1999); ETH10 (Solinas-Toldo et al., 1993); INRA63, INRA5 (Vaiman et al., 1994), HAUT27 (Thieven et al., 1997), para a realização das análises. Amplificados pelo método da PCR, segundo protocolo da Martínez et al. (2004). ...
... As médias das frequências alélicas encontradas nos caprinos locais foram inferiores as reportadas por Li et al. (2002), estudando raças de cabras nativas chinesas (6,90). Para Buchanan et al. (1994) as diferenças que ocorrem nas frequências alélicas entre populações indicam se os marcadores podem ser utilizados para identificar ou alocar indivíduos dentro de raças ou a região de origem. ...
Acasalamentos duvidosos são uma das causas dos erros nos programas de conservação e de melhoramento genético de raças. Os testes de paternidades são ferramentas que podem contribuir para minimizar esses erros pois tem sido usados para identificar paternidade duvidosa. O presente trabalho teve como objetivo definir um painel para teste de paternidade em caprinos para auxiliar programas de conservação e melhoramento de raças. Foram genotipados 381 animais de 10 populações caprinas sendo seis ecotipos locais brasileiros e quatro raças exóticas utilizadas atualmente no Brasil (Alpina, Anglo-Nubiana, Boer e Saanen). Realizou-se nove sistemas multiplex, totalizando 27 microssatélites. Foram estimados o PIC, as probabilidades de exclusão dos marcadores e o equilíbrio de Hardy-Weinberg (EHW) nas populações, seguida de determinação da probabilidade de identidade (PI). Para o sistema de 27 microssatélites a probabilidade de exclusão combinada (PE) foi de 0,999 e 0,999 (PE1 e PE2) e, 21 microssatélites apresentaram PIC 0,60, onde quatro apresentaramse monomórficos em algumas populações. Para compor o novo painel foram escolhidos 9 marcadores dos quais oito comuns aos dois grupos estudados (caprinos locais e exóticos), sendo o BM1818 mais informativo nas populações locais e, o marcador BM6506 nas populações exóticas. A probabilidade de exclusão combinada com o grupo dos microssatélites foi de 0,994 e 0,999 (PE1 e PE2). Baseado no cálculo das probabilidades de identidade dentro das populações foi possível discriminar um indivíduo entre um milhão (106). Os resultados indicaram a possibilidade de empregar poucos microssatélites na investigação de paternidade em caprinos, com alto grau de confiabilidade, minimizando assim custos para o criador.
