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Nali and Chokla thin tailed, brown-faced reputed carpet wool sheep breeds from Northwestern arid and semi-arid region of India were characterized for population structure and genetic variability using 25 Food and Agriculture Organization (FAO) proposed ovine specific microsatellite markers. The results revealed high level of genetic variability in...
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... of Bikaneri group are important thin tailed, brown-faced carpet wool sheep mainly confined to Northwestern arid and semi-arid agro climatic zone of the country. Nali, a light brown-faced sheep also known as Hisar type, is native of Ganganagar, Churu and Jhunjhunu districts of Rajasthan and southern parts of Hisar and Rohtak districts of Haryana (Fig. 1), and is a good carpet wool type with the densest and heaviest fleeces among the sheep of Rajasthan. Need is being felt to conserve this breed in lights of its involvement in largescale cross-breeding programmes. Chokla also known as Shekhawati/Chapper is found around Sikar and bordering areas of Bikaner, Jaipur and Nagaur districts of ...
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... and is a good carpet wool type with the densest and heaviest fleeces among the sheep of Rajasthan. Need is being felt to conserve this breed in lights of its involvement in largescale cross-breeding programmes. Chokla also known as Shekhawati/Chapper is found around Sikar and bordering areas of Bikaner, Jaipur and Nagaur districts of Rajasthan (Fig. 1). As an admixture it is also seen in Jhunjhunu and Churu districts. Sheep farmers generally name this breed as "Ratomunda", means the sheep with dark brown/tan face. Chokla grows the finest wool of all the Rajasthani breeds and is, therefore, also known as Rajasthan Merino. Natural reasons and indiscriminate cross-breeding with exotic ...
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... Twelve SSR markers were selected from the literature based on the following criteria: (i) homogeneous repartition on the chromosomes; (ii) optimal amplification and resolution; (iii) ability to detect high rates of polymorphism for both goats and sheep; (iv) adequacy of observed fragment sizes with those reported in selected studies (Sodhi et al., 2006;Traoré et al., 2009;Pramod et al., 2009;Missohou et al., 2011;Awobajo et al., 2015;Sharma et al., 2016;Ocampo et al., 2016;Dossybayev et al., 2019); (v) absence of outlier loci effects (Negrini et al., 2012); and (vi) suitability to be used in a multiplexed PCR reaction, according to the step-by-step protocol of Henegariu et al. (1997) and the FAO guidelines (FAO, 2011). The 12 SSR loci were distributed in two multiplex sets of 6 SSR markers ( Table 2). ...
In this technical note, we report the development of a reliable standardized protocol based on the multiplex SSR-PCR approach for genotyping the two small ruminant species, goats and sheep. The method is based on PCR conditions optimization allowing 12 informative microsatellites (SSR) markers to be co-amplified in two multiplex sets of 6 SSR markers, followed by a co-migration into one run onto a genetic analyzer. The performance of the assay was tested on a total of 207 goats and 197 sheep, originating from different breeds and localities sampled mainly in Benin, but also to lesser extent in Belgium. The optimized assay showed that the 12 selected markers were suited to amplify all the loci distributed between the two species with valuable genetic information, specific-species allelic patterns and similar polymorphism information content. The validated loci were polymorphic with high allele numbers for the two species, ranging from 6 to 21 for goats and 7 to 15 for sheep, with average 10.58 alleles per locus for goats and 11.33 for sheep, respectively. The Polymorphic Information Content (PIC) of selected markers averaged a value of 0.712 for goats and 0.751 for sheep. The differentiation of SSR alleles at an intraspecific resolution level allowed different heterotic groups to be detected, such as geographical or breeding groups. The newly developed genotyping kit could be successfully applied in diverse genetic variability studies and relatedness analyses, as well as for population structure assessment, parentage determination and traceability concerns, within and among sheep and goat species.
... Moreover, it can negatively affect animal health. Higher heterozygote deficiency is generally observed in Indian sheep breeds 15,22,36 . Results for Poonchi (− 0.007) and Bonpala (− 0.021) can be interpreted as possible signs of outbreeding, most likely due to a recent admixture of two (or more) populations. ...
Sheep farming has been fundamental to many civilizations in the world and is practiced in India since antiquity. Several thousand years of adaptation to local environmental conditions and selective breeding have evolved 44 sheep breeds in India. They are paramount in terms of economic, scientific, and cultural heritage. Genetic characterization information is imperative for sustainable utilization and conservation of ovine heritage. In this study, the genetic diversity, differentiation, and structure of 11 indigenous sheep breeds from three different agro-ecological zones of India were explored with genomic microsatellite loci and mitochondrial DNA (D loop). The estimated diversity parameters indicated that populations retained high levels of genetic diversity (Na = 8.27 ± 0.17; Ho = 0.65 ± 0.01), which provides an optimistic viewpoint for their survival. However, significant inbreeding was also observed in the nine populations. Moderate genetic differentiation existed among the groups (FST = 0.129 ± 0.012), and most likely clusters existing in the dataset are seven. Phylogenetic clustering was in line with the geographical locations of sheep populations. Mitochondrial sequences revealed high haplotype diversity with the existence of maternal haplogroups A, B, and C, and signals of population expansion. Decreased genetic diversity and unique maternal lineage (C) in endangered Tibetan and Bonpala sheep breed, warrant their immediate scientific management. Overall, the quantitative data reported here on the extant variability, and genetic relationships among the Indian sheep breeds, provide critically important inputs that will be valuable for the decision-making process on their management, both for the conservation of endangered breeds, and formulation of breeding programs to check genetic erosion.
... The PIC values ranged from 0.19 (ILSTS011) to 0.79 (TGLA13) with a mean value of 0.53 across all 12 loci studied(Table 4.20). Reasonably high PIC values (PIC > 0.5) observed for most of the markers are indicative of the usefulness of microsatellites for biodiversity evaluation in these breeds[266],[251]. The mean PIC value obtained in the present study reflected the high level of polymorphisms of the used set of microsatellites and further substantiated the suitability of these markers in genetic studies of Iranian and Iraqi sheep breeds. ...
Sheep is one of the most important domestic animal population in Iran and Iraq, where meat and wool production are the essential breeding objectives for Iranian and Iraqi sheep. Therefore, evaluation of genetic diversity of sheep breeds is necessary for implementing the utmost suitable breed-area conservation programs. Conservation and breeding programmers of sheep species depend upon the determination of genetic diversity. Today, in sheep species, microsatellite loci are commonly used to evaluate population structure and genetic diversity in both breeds and varieties. In the present study, within and between breed genetic diversity in seven Iranian and Iraqi sheep breeds (Ghezel, Makui, Baluchi, Kurdi, Awassi, Naaimi and Arabi; in total represented by 140 individuals) more studied using 12 microsatellite markers selected from the list suggested by the International Society for Animal Genetics (ISAG). The genomic DNA extraction from blood was done according to the Samadi Shams conventional protocol. Touch-down PCR specific program designed to simultaneously amplify the locus and minimize nonspecific and sttuter bands. The amplified products were separated using 2% metaphor agarose gel electrophoresis at 65 v for 2 or 3 hours, depending on the expected allele sizes. For statistical analysis, individual genotypes are measured at each location or allele size using UVdoc software, then in preparation of input files for each specific package, CONVERT version 1.31, and CREAT version 1.1 packages were employed. The molecular measurement indexes such as genotype and allele frequencies, the observed number of alleles (Na), effective number of alleles (Ne), observed (Ho), expected (He) heterozygosity’s, Shannon index (I), Polymorphism Information Content (PIC), Inbreeding coefficient (FIS), F-statistics (FIS, FIT and FST), genetic distance, allele admixture and population structure, clustering, analysis of molecular variance (AMOVA), and bottleneck index were calculated. The used different software and the computational package included, POPGENE version 1.32, Arlequin version 3.5.2.2, GenAlEx version 6.5, STRUCTURE version 2.3.4, and BOTTLENECK version 1.2.02.
In Iranian sheep breeds, the average observed number of alleles and the number of effective alleles for the Ghezel, Makui, Kurdi, and Baluchi breeds were (4.16, 4, 3.66 and 3.58) and (2.49, 2.46, 2.45 and 2.47), respectively. The mean Shannon index was 0.982, 0.939, 0.965, and 0.959 values for Ghezel, Makui, Kurdi, and Baluchi breed, respectively. The PIC values were ranged from 0.09 (ILSTS011) to 0.75 (TGLA13). The average inbreeding coefficient (FIS) from 0.144 (Kurdi) to 0.306 (Makui). Furthermore, the lowest genetic distance was seen between Makui and Baluchi breeds (0.120), but the
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highest was between Ghezel and Kurdi breeds (0.884). The results of this research showed the normal ‘L’-shaped distribution of the mode-shift analysis test and the lack of bottleneck in the studied populations. Generally, key findings emerge that Iranian sheep breeds carry reasonable within and between genetic diversity.
Results of Iraqi sheep breeds demonstrated that OarFCB226 and TGLA13 have the highest and lowest polymorphism across populations respectively, additionally Awassi and Arabi exhibited the highest and lowest diversity during study respectively. Also, the highest and lowest genetic distance were belonging Arabi- Naaimi and Naaimi- Awassi, respectively. Furthermore, the L-shape curve pattern illustrated all investigated populations suffering from size reduction and bottleneck. We can conclude that these results could be helped to establish the open-close nucleus.
In the comparison of Iranian and Iraqi sheep breeds, our results demonstrated that mean number of alleles (Na) per loci 4.66, and some results are lower than those recommended by the FAO (Na ≤ 4), while the mean effective number of alleles (Ne) 2.49. The Averaging Shannon information index (I) 1.121. Also, the inbreeding coefficient (FIS) showed that most of the microsatellite markers were significant (P ≤ 0.05). The breeds genetically separated into two clusters, one including Ghezel, Makui, Kurdi, and Baluchi Iran sheep breeds, and the second cluster includes Awassi, Naaimi, and Arabi Iraq sheep breeds. There was no serious genetic reduction in the effective size of this breed, as indicated L-shaped in studied populations. The present study was able to demonstrate a reasonable genetic variation and polymorphism across microsatellite loci studied breeds.
... Mean PIC were 0.683, 0.699, 0.697 and 0.657 for BR, QFG, QFT and DM, respectively. Reasonably high PIC values (PIC > 0.5) observed for most of the markers are indicative of the usefulness of microsatellites for biodiversity evaluation in these breeds (Sodhi et al. 2006 ;Amareswari et al. 2017). Most of the microsatellites employed showed positive F (IS) values (Table 4). ...
... The low coefficient (0.081) for BR may be explained by the absence of any directional selection for this breed. Similar results were reported by Sodhi et al. (2006) and Arora and Bhatia (2004) for Indian sheep. ...
... The present values of genetic differentiation are lower than those reported for Swiss goat breeds (Saitbekova et al. 1999) and similar to those reported for Asian goat populations (Barker et al. 2001) and Indian cattle breeds (Mukesh et al. 2004). However, F(ST) values obtained in this study are higher than those found for Nakali and Chokla sheep (Sodhi et al. 2006). ...
Genetic diversity of native ovine Barbarine (BR=80) and Queue Fine de l’Ouest (QF=150) breeds as well as the exotic D’man (DM=70) breed were investigated using a panel of ten microsatellite markers. The markers used were all polymorphic and exhibited high levels of polymorphism. The total number of observed alleles across all breeds was 83. The allelic frequency distribution was heterogeneous and tests of genotype frequencies for deviation from HWE revealed significant
departure from HWE of all populations for the TGLA48 and MCM527 loci. The mean expected and observed heterozygosity for the BR, QF and DM populations varied from 0.69 to 0.74 and 0.58 to 0.67, respectively. The average Polymorphism information content (PIC) was 0.683, 0.699, 0.697 and 0.657 for BR, QFG, QFT and DM, respectively. The mean F (ST) was 0.149 and indicated that most (85.1%) of total genetic variation raised from differences among individuals and only
14.9% came from differences among breeds. Per pair estimator of F(ST) indicated a low to moderate differentiation between BR and QF but a relatively high (F(ST) > 0.15) differentiation between Tunisian native (BR and QF) and DM breeds. Genetic distance and factorial analyses showed that genetic distances observed between BR-DM and between QFDM were larger than those found between BR-QF breeds.
... All experimental procedures in this study were approved (Approval No. 16 Available at www.veterinaryworld.org/Vol.11/June-2018/7.pdf Animals A total of 125 blood samples were collected from five different sheep breeds (25 samples each) including Awassi, Romanov, Charollais, Assaf, and Suffolk. ...
... In this study, Awassi breed showed the highest average PIC value (0.59) while Romanov had the lowest PIC value (0.48). These results are lower than that reported in Kilakarsal sheep breed [14], but similar to those reported in Chokla thin-tailed sheep [16]. Mutation and selection jointly influence the level of polymorphism at microsatellite loci. ...
Aim: This study was conducted to study the genetic and population structure of local (Awassi) and exotic (Romanov, Charollais, Assaf, Awassi, and Suffolk) sheep breeds in Jordan using eight microsatellite markers.
Materials and Methods: A total of 125 sheep were used (25 from each breed) in the study. The number of alleles (A), the mean values of observed (Ho) and expected (He) heterozygosity, polymorphism information content (PIC), fixation index as a measure of heterozygote deficiency or excess, and Hardy-Weinberg equilibrium (HWE) were analyzed using PopGen and CERVUS softwares. Nei's standard genetic distances among breeds and dendrogram of unweighted pair group method with arithmetic mean (UPGMA) were calculated and constructed using PopGen software.
Results: A total of 40 alleles were detected with an average number of alleles of 5. The mean Ho value was higher than the mean He value for all breeds. Awassi breed showed the highest average PIC value while Romanov had the lowest. There was a significant (p
... In India, almost all the descript breeds of different livestock have been characterized by using microsatellite markers. The studies done by (Sodhi et al., 2005 andMukesh et al., 2004 andSharma et al., 2006;Bhatia, 2009a and2009b) have indicated the presence of adequate genetic diversity in the studied Indian native breeds. ...
... The recent awareness campaigns for the conservation of genetic resources were encouraged to carry out studies of genetic diversity in different breeds and species of livestock. 28 Several studies have successfully used microsatellite molecular markers to estimate the genetic diversity within and among different breeds and species of livestock 2,4,29,30 . Microsatellite markers are neutral co-dominant markers, abundant in the genome, easy to access and highly reproducible 6 . ...
In Saudi Arabia, the sheep production systems are mainly managed under farmer production systems, so their genetic management has led to increased homozygosity and hence productivity loss. The aim of this study was to genetically characterize 47 individuals of Awassi (Naeimi) sheep breed using a panel of eighteen microsatellite markers. Blood samples were used to extract genomic DNA followed by polymerase chain reaction (PCR). Results showed that 159 alleles were generated by the 18 microsatellites loci with an average of 8.833 alleles per locus. The DYMS1 SSR marker showed the highest number of alleles per locus (14) while OarAE129 showed the lowest (3). The expected heterozygosity (He) ranged from 0.541 to 0.860 with an average of 0.755 whereas the average observed heterozygosity (Ho) was 0.800 with a range of 0.319 to 1.000. The mean effective allele number was 4.643 which ranged from 2.177 to 7.219. Seven out of the 18 loci encountered significant departure from Hardy Weinberg Equilibrium (p < 0.05). The mean of Shannon index was 1.691 which ranged from 0.896 to 2.223. The results indicated the utility of using microsatellite loci in studying the genetic diversity in sheep populations of Saudi Arabia.
... The Na in our study was less than previously reported for African, Indian, and Swiss sheep breeds (18,19,39,40,41,42) using the same microsatellite markers. This may suggest loss of genetic diversity in the populations under study. ...
Pakistan is rich in sheep genetic resources. Balkhi, Hashtnagri, and Michni are neighboring sheep populations found in Khyber Pakhtunkhwa province of Pakistan. In this study, we analyzed the genetic structures and bottleneck incidents within these sheep populations using 31 microsatellite DNA markers. Total numbers of 116, 100, and 95 alleles, with average numbers of 3.20, 3.26, and 3.74 alleles per locus were observed, respectively, in Balkhi, Hashtnagri, and Michni population. Mean observed heterozygosity was 0.402 in Balkhi, 0.416 in Hashtnagri, and 0.522 in Michni population. All the three sheep populations showed significantly high inbreeding. Michni population was found to be in mutation drift equilibrium, showing the absence of genetic bottleneck. The data of Balkhi and Hashtnagri indicated the presence of genetic bottleneck in these populations. These results suggest a moderate level of genetic diversity within Michni population that may be useful for breed improvement programs. Hashtnagri and Balkhi populations having low within breed genetic variability may contain some valuable characteristics that need to be conserved.
... The effective number of alleles (Ne) ranged from 2.757 (OarHH35) to 10.0 (OarFCB48) with a mean value of 5.5. According to data shown in the present study allelic diversity found in greater extent in comparison to earlier reported study by (Sodhi et al., 2005;Mukesh et al., 2006;Sodhi et al., 2003;Sodhi et al., 2004;Sharma et al., 2016). Thus, it can be concluded that sufficient genetic variability exists in Marwadi sheep despite its declining population. ...
... Polymorphic information content (PIC) value ranged between 0.589 (HH35) and 0.856 (OarVH72, RM4) with a mean value of 0.763. The mean PIC value (0.763) in the present study is higher than earlier reported in Chokla, 0.605 (Sodhi et al., 2005;Mukesh et al., 2006), Magra, 0.648 (Arora and Bhatia, 2006), Tibetan 0.632 (Sharma et al., 2016), Nali, 0.613 (Sodhi et al., 2005;Mukesh et al., 2006) sheep breed. Accordingly, all the m arkers considered for this study are highly informative (PIC>0.5) to characterize Marwadi sheep breed population and showed abundant genetic diversity in this population. ...
... Polymorphic information content (PIC) value ranged between 0.589 (HH35) and 0.856 (OarVH72, RM4) with a mean value of 0.763. The mean PIC value (0.763) in the present study is higher than earlier reported in Chokla, 0.605 (Sodhi et al., 2005;Mukesh et al., 2006), Magra, 0.648 (Arora and Bhatia, 2006), Tibetan 0.632 (Sharma et al., 2016), Nali, 0.613 (Sodhi et al., 2005;Mukesh et al., 2006) sheep breed. Accordingly, all the m arkers considered for this study are highly informative (PIC>0.5) to characterize Marwadi sheep breed population and showed abundant genetic diversity in this population. ...
The Genetic variability of Marwadi sheep was studied using 18 microsatellite markers, proposed by The Food and Agriculture
Organization and the International Society for Animal Genetics (FAOISAG). A total of 158 alleles ranging between 4 to 15 were found
across 18 microsatellite loci. The most polymorphic marker was OarFCB48 with a total of 15 alleles and least polymorphic loci was
TGLA377 with 4 alleles were detected. The high genetic variation (MNA=8.7) was observed in Marwadi sheep compare to other
reported breed in Rajasthan. All studied loci contained high PIC value (>0.5) in the present study, where mean PIC value (0.751) is
higher than earlier reported study on sheep in India, which indicates highly informativeness of markers to characterize Marwadi sheep
breed population and showed abundant genetic diversity in this population. Further, the expected gene diversity (Hexp) ranged from
0.637 (OarHH35) to 0.900 (OarFCB48) with an overall mean of 0.797 and observed heterozygosity (Hobs) across 18 loci ranged
between 0.300 (TGLA137) and 0.900 (OarVH72, BM757) with a mean of 0.602 were estimated. The present study has shown a high
level of genetic variability in Marwadi sheep, suggesting good breeding practices were carried out in the farms and other places
where samples were collected. Similarly, all the loci were detected highly polymorphic with 100% value of polymorphism observed in
Marwadi sheep breed. The high polymorphic information content (PIC) value indicating informativeness of markers to characterize
Marwadi sheep population. Hence, these markers could be used in various applications like conservation programmes, biodiversity
studies and disease diagnosis.
... It can be said that there is loss of heterozygosity in four microsatellite loci studied considering F IS value is also known as the inbreeding coefficient. It is noteworthy that obtained general mean of F ST value is higher than earlier studies (Cemal et al. 2013;Ben Sassi-Zaidy et al. 2014;Ocampo et al. 2016) and lower than others (Sodhi et al. 2006;Yilmaz et al. 2014). The differences between the previous literature and the present study were mainly due to non-comparative aspects such as studied microsatellite and breed differences. ...
Exposition of variations between breeds is very important for genetic diversity. Determination of this variation is needed to reveal population structure and relationship between populations and planning national breeding and conservation programmes. This study was carried out in 296 animals from 12 different local sheep breeds (Barbarine, Ouled Djellal, Ifilene, Srandi, Darâa, Rembi, Berbere, Taâdmit, Hamra, Sidaou, Tazegzawt and D’men) reared in different regions of Algeria. Fifteen microsatellite markers were used to determine between breed genetic diversity. The population of 12 sheep breeds studied from Algeria exhibited a high number of alleles (24.67) and polymorphic information content (0.90). Observed heterozygosity values were lower than expected for all molecular markers except INRA0123 locus. Obtained GST value from the present study indicated that 1.9% of total genetic variation resulted from the differences between the breeds. The present study supplied important information to understand between breed genetic differences. Moreover, it has provided the opportunity to discuss with previously reported results. In light of these findings, it can be said that studied microsatellite markers can be successfully used to determine genetic diversity and population structure in Algerian sheep breeds.
