Negative Inbreeding Coefficient Research Articles

Genetic diversity and population structure of four Anatolian sheep revealed by genome-wide ddRADseq data

This is the first wide-scale study to reveal next-generation sequencing-based and comprehensive study to reveal genetic diversity, population structure, and phylogenetic relationships of some of Türkiye's indigenous fat-tailed sheep breeds. A total of 80 animals belonging to Akkaraman (AKR), Güney Karaman (GKR), Morkaraman (MKR), and Karakaş (KRK) sheep breeds were genotyped with genome-wide of 296.097 single nucleotide polymorphisms (SNPs) data recovered from double digest restriction site-associated DNA sequencing (ddRADseq) libraries processed by Illumina HiSeq X Ten instrument. Minor allele frequency (MAF) ranged from 0.311 (MKR) to 0.316 (AKR and GKR). Observed heterozygosity (HO) values were higher than expected values (HE) across all populations with a mean of 0.307. Negative inbreeding coefficient (FIS) values were observed in four sheep populations varying between −0.034 (AKR) to −0.060 (MKR). Cross-entropy criterion-based ADMIXTURE analysis demonstrated that four Anatolian sheep breeds were represented by two ancestral populations in which GKR and AKR were distinct, while KRK and MKR were mixed populations. Genetic distance-based tree, discriminant analysis of principal components (DAPC), and ADMIXTURE analyses confirmed that GKR, which is believed to be derived from the AKR breed, has become genetically different from other sheep populations. Moreover, no migration from and into the GKR breed was detected, while a migration edge was drawn from the KRK and MKR clade into the AKR breed by the TreeMix algorithm. This study confirmed that high-density SNP data obtained from advanced next-generation sequencing (NGS) platforms are efficient in genetically distinguishing animal breeds, even varieties. It is recommended that further NGS-based studies could be carried out to better characterize different indigenous livestock populations raised in Türkiye.

Polymorphism of the glutathioneperoxidase-1 gene (GPX-1 g. 189 T/C) and biochemical parameters of the blood serum of Holstein cattle

The study examined the polymorphism of the glutathione peroxidase-1 gene (GPX-1, g. 189 T/C) effect on the GPx enzyme activity and biochemical parameters in the blood serum of Holstein cows of indigenous and foreign selection. The work was carried out in the Lenin Breeding Farm Integrated Agricultural Production Center (IAPC) and the Mukhametshin Z.Z. Peasant Farm Enterprise (PFE) of the Republic of Tatarstan. DNA genotyping by the locus of the Bos taurus GPX-1-Bsc4 I gene was performed by PCR-RFLP. As a result of genetic typing of cattle, 2 alleles (C and T) and 3 genotypes (CC, TC and TT) were identified. The classification carried out by PIC values in two populations of Holstein cattle showed that there is a moderate polymorphism of the GPX-1 gene. A negative inbreeding coefficient (F) indicates excessive outbreeding in both populations. In both populations, the numerical advantage of heterozygous genotype TC cows is 60.1 and 56.7 % of the total livestock. Indigenous breeding cows, compared with imported cattle had higher: GPx activity, AST, ALT, cholesterol level, total protein and albumin fraction. Analysis of the association between the GPX-1 gene polymorphism and the GPx enzyme level indicates that the activity of this enzyme varies depending on the genotype, and there is also a variation in the biochemical parameters of the Holstein cattle blood serum.

Molecular Characterization and Phylogenetics in the Rhizophora Species Complex at Pichavaram, Tamil Nadu: A Potential Resource for Phyto-Pharmacology

Mangroves are spatially limited bioresources known for their potential pharmacological uses. The genus Rhizophora is a conspicuous one reported to have enormous biopotentials in treating inflammation, diabetes, and rheumatism. However, mangroves are recently experiencing severe threats due to the over-exploitation of valuable tannin resources, climate change, and other anthropogenic pressures. R × annamalayana, a natural hybrid in Pichavaram, is rare in its distribution and a source of bioactive compounds with anticancer properties. The pure nature of the hybrid makes it more vulnerable to extinction. Therefore, domestication, conservation, and sustainable use of valuable resources are needed on a date. Poor genetic structure in mangroves is reported to be one of the reasons for extinction. Hence, understanding the population genetic structure of the genus is of paramount importance. Therefore, the present study aimed to understand the population genetic structure of the Rhizophora species complex in Pichavaram with the following objectives, to carry out the molecular characterization of the putative hybrid and to examine the phylogenetic relationship to its parental species using microsatellite markers. The study identified that putative hybrid R. × annamalayana (mean HE = 0.592) has more significant variability than the putative parents R. apiculata (mean HE 0.611) and R. mucronata (mean HE = 0.667). The negative inbreeding coefficient value or Wright’s Index in R. × annamalayana (- 0.190) suggests ample variation among the putative hybrids. The putative hybrid is genetically more proximal to R. apiculata than R. mucronate. Phylogenetic studies indicate that ten samples out of fifteen were clustered with R. mucronata, and the rest five grouped with R. apiculata indicating the varying paternal and maternal combinations.

Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers

This study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic information which would help in the selection of parental lines for a breeding program. The study found that the average polymorphism information content value of 0.288 which indicates a moderate genetic diversity for this L. acutangula germplasm. STRUCTURE analysis (ΔK at K = 6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. When plotted, the STRUCTURE bars to the area of collection, we observed an admixed genotype from surrounding accessions and a geneflow confirmed by the value of FST = 0.137. AMOVA based on STRUCTURE clustering showed a low 12.83% variation between subpopulations that correspond well with the negative inbreeding coefficient value (FIS = − 0.092) and low total fixation index (FIT = 0.057). There were distinguishing fruit shapes and length characteristics in specific accessions for each subpopulation. The genetic diversity and different fruit shapes in the L. acutangula germplasm could benefit the ridge gourd breeding programs to meet the demands and needs of consumers, farmers, and vegetable exporters such as increasing the yield of fruit by the fruit width but not by the fruit length to solve the problem of fruit breakage during exportation.

Recovery process of genetic diversity through seed and pollen immigration at the northernmost leading‐edge population of Fagus crenata

AbstractThe range expansion of a plant species begins with colonization of ecological empty patches from posterior source populations. This process involves stochastic loss of genetic diversity. However, the founder population could restore genetic diversity by gene flow from posterior populations via seeds and pollen and its recovery affects evolutionary potential for species expansion. To clarify the recovery process of genetic diversity during species range expansion, gene flow via seeds and pollen was investigated at the expansion front of Fagus crenata. Based on eight nuclear microsatellite genotypes of a total of 150 individuals and 225 seeds at the northernmost leading‐edge population, genetic diversity, fine‐scale spatial genetic structure (FSGS), and genetic differentiation from other five northern populations were investigated. Moreover, both seed and pollen immigration and their effects on genetic diversity at different successional stages were analyzed. The leading‐edge population showed lower genetic diversity and substantial genetic differentiation, reflecting its strong genetic drift. Non‐significant FSGS and a negative inbreeding coefficient for mature trees may indicate that the earliest generation consisted of founders from foreign seed sources. The significant proportion of seed and pollen immigration increased the number of different alleles for later successional stages. The effective number of pollen parents from foreign sources (20.8) was markedly higher than that from the local source (2.1). These results indicated that pollen immigration incorporated new and rare alleles and increased the genetic diversity of the population. However, the proportion of foreign gene flow decreased during succession, probably due to the increased reproductive success of local individuals as they reached maturity and grew in size.

Assessment of genetic diversity using microsatellite markers to compare donkeys (Equus asinus) with horses (Equus caballus).

ObjectiveThe study aimed to evaluate the diversity of donkey populations by comparing with the diversity of Thoroughbred and Jeju Halla horses; identified breeding backgrounds can contribute to management and conservation of donkeys in South Korea.MethodsA total of 100 horse (50 Thoroughbreds and 50 Jeju Halla horses) and 79 donkeys samples were genotyped with 15 microsatellite markers (AHT4, AHT5, ASB2, ASB17, ASB23, CA425, HMS1, HMS2, HMS3, HMS6, HMS7, HTG4, HTG10, LEX3, and VHL20), to identify genetic diversity and relationships among horses and donkeys.ResultsThe observed number of alleles per locus ranged from 1 (ASB17, HMS1) to 14 (AHT5), with a mean value of 4.87, 8.00, and 5.87 in Thoroughbreds, Jeju Halla horses, and donkeys, respectively. Of the 15 markers, AHT4, AHT5, ASB23, CA425, HMS2, HMS3, HTG4, HTG10, and LEX3 loci had relatively high polymorphism information content (PIC) values (PIC>0.5) in these three populations. Mean levels of genetic variation were HE = 0.6721 and HO = 0.6600 in Thoroughbreds, HE = 0.7898 and HO = 0.7100 in Jeju Halla horses, and HE = 0.5635 and HO = 0.4861 in donkeys. Of the 15 loci in donkeys, three loci had negative inbreeding coefficients (FIS), with a moderate mean FIS (0.138). The FIS estimate for the HTG4 marker was highest (0.531) and HMS6 marker was lowest (−0.001). The total probability of exclusion value of 15 microsatellite loci was 0.9996 in donkeys.ConclusionGenetic cluster analysis showed that the genetic relationship among 79 donkeys was generally consistent with pedigree records. Among the three breeds, donkeys and Thoroughbred horses formed clearly different groups, but the group of Jeju Halla horses overlapped with that of Thoroughbred horses, suggesting that the loci would be suitable for donkey parentage testing. Therefore, the results of this study are a valid tool for genetic study and conservation of donkeys.

SNP-based analysis reveals unexpected features of genetic diversity, parental contributions and pollen contamination in a white spruce breeding program

Accurate monitoring of genetic diversity levels of seedlots and mating patterns of parents from seed orchards are crucial to ensure that tree breeding programs are long-lasting and will deliver anticipated genetic gains. We used SNP genotyping to characterize founder trees, five bulk seed orchard seedlots, and trees from progeny trials to assess pollen contamination and the impact of severe roguing on genetic diversity and parental contributions in a first-generation open-pollinated white spruce clonal seed orchard. After severe roguing (eliminating 65% of the seed orchard trees), we found a slight reduction in the Shannon Index and a slightly negative inbreeding coefficient, but a sharp decrease in effective population size (eightfold) concomitant with sharp increase in coancestry (eightfold). Pedigree reconstruction showed unequal parental contributions across years with pollen contamination levels between 12 and 51% (average 27%) among seedlots, and 7–68% (average 30%) among individual genotypes within a seedlot. These contamination levels were not correlated with estimates obtained using pollen flight traps. Levels of pollen contamination also showed a Pearson’s correlation of 0.92 with wind direction, likely from a pollen source 1 km away from the orchard under study. The achievement of 5% genetic gain in height at rotation through eliminating two-thirds of the orchard thus generated a loss in genetic diversity as determined by the reduction in effective population size. The use of genomic profiles revealed the considerable impact of roguing on genetic diversity, and pedigree reconstruction of full-sib families showed the unanticipated impact of pollen contamination from a previously unconsidered source.

Pheno-genetic studies of apple varieties in northern Pakistan: A hidden pool of diversity

Apple (Malus × domestica) is a main fruit crop of cold temperate regions and traded globally. Despite being a comparatively well documented plant cultigen, available germplasm in many remote regions is still unexplored and threatened. Increasing market demands for modern cultivars and farmers’ preference for high yields may lead to the gradual loss of indigenous varieties. Gilgit-Baltistan in northern Pakistan – a mountainous and remote apple growing region – was selected to study local cultigen diversity by assessing varietal richness and diversity, arboriculture activities as well as phenotypic and genotypic characters of available germplasm. In total, 106 individual apple trees were sampled, and 35 tree owners from seven villages of the two valleys Ishkoman and Baltistan were interviewed. Dendrometric parameters, fruit traits (qualitative and quantitative), and varietal diversity in each village were measured. Genetic variation was estimated using eleven SSR markers and synonyms and homonyms were identified based on cluster analysis.Sixty-one multi-locus genotypes (MLG; mean genotype diversity: 58 %) and 18 putative clones (comprising 2 to 9 ramets) were identified. Varietal diversity was highest in Baltistan where even a wild apple relative (Malus baccata) was discovered. Mean genetic diversity was moderate (He = 0.677), while negative inbreeding coefficients indicated excess of heterozygotes in three genetic clusters. A moderate correlation (r = 0.627, p = 0.001) between phenotypic and genetic dendrograms suggested genetically linked fruit traits, which merits further exploration.Considering the high genetic and phenotypic variability, Gilgit-Baltistan appears a promising source of apple germplasm for future breeding programs. The promotion of local varieties may allow farmers to diversify their produce and derived sources of income as well as to maintain a historically important bio-cultural heritage of Gilgit-Baltistan. To this end, comprehensive conservation strategies combined with further participatory research will be needed.

Population genetic structure and diversity of the East Balkan Swine (Sus scrofa) in Bulgaria, revealed by mitochondrial DNA and microsatellite analyses.

The East Balkan Swine (EBS) is the only indigenous pig breed in Bulgaria. We analyzed the mitochondrial DNA (mtDNA) control region and 21 microsatellite loci for 198 individuals from 11 farms in Bulgaria. Obtained 11 mtDNA haplotypes including three novel ones were grouped to two major clades, European clade E1 (146/198 individuals, 73.7%) and Asian clade A (52/198, 26.3%). The mixture of the two clades may have resulted from historical crossbreeding between the European and Asian pig breeds. Clade A was frequent in southeastern Bulgaria (Burgas Province), but less frequent or absent in northeastern Bulgaria (Varna and Shumen Provinces). The distribution of Europe- and Asia-specific haplotypes relative to EBS farm locations could be attributed to regional differences of breeding systems (e.g., crossbreeding with imported commercial pigs). A microsatellite analysis showed high heterozygosities for all the EBS farms, and negative inbreeding coefficients presumably due to crossing with commercial pigs or wild boars and/or efforts to reduce inbreeding by farmers. Bayesian clustering analyses showed that all farm populations are genetically well distinguishable from one another. Although diversity has been maintained by the efforts of farmers and a breeding association, the effective population size remains small, and conservation efforts should be continued.

Analysis of genetic diversity and population structure in endangered Populus wulianensis based on 18 newly developed EST-SSR markers

Populus wulianensis is an endangered tree species endemic to Shandong Province, China. Genetic diversity assessments represent the basis and a prerequisite for protecting endangered species. In our study, a total of 116 individuals of P. wulianensis from 4 extant populations (3 wild populations and 1 artificial population that covered the entire geographic distribution of the species) were analyzed using 18 expressed sequence tag-simple sequence repeat (EST-SSR) markers to assess their genetic diversity and population structure. The 18 EST-SSR markers had high levels of polymorphisms (PIC = 0.698), and 202 alleles were amplified. The present study revealed high genetic diversity at the population level (Na = 4.847, NR = 3.000, HS = 0.624, HE = 0.611, I = 1.114, and PPL = 98.6%) and the species level (HT = 0.741). Private alleles were detected in all four populations (including the artificial population JYS). Negative inbreeding coefficients (FIS<0) indicated that the populations of P. wulianensis produced too many heterozygotes due to outbreeding and that there might be a risk of outbreeding depression. The AMOVA results showed that 19.05% and 80.95% of the total variation occurred among and within populations, respectively. Obvious genetic differentiation between populations (FST = 0.191) and a high level of gene flow (Nm = 2.566) were detected, indicating that gene flow is not the main cause of genetic differentiation among populations. The results of UPGMA cluster analysis, PCoA and structure analysis (ΔK = 4) showed that the 4 populations were clustered into four groups and suggested that the natural population ZHS gave rise to the artificial population JYS. The genetic bottleneck analysis results suggested that three populations (ZHS, JXS and JYS) recently experienced bottleneck events. These genetic results are of great significance for scientifically formulating conservation strategies for endangered P. wulianensis.

Genetic diversity and population structure inChrysolepis chrysophylla(golden chinquapin; Fagaceae): SSRs vs SNPs

Simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) genotypes on the same plant samples of Chrysolepis chrysophylla (Douglas ex Hook.) Hjelmq. (Fagaceae; golden chinquapin) from 22 sites were used to determine genetic diversity and population structure. One site of C. sempervirens (Kellogg) Hjelmq. allowed interspecific vs. intraspecific comparisons. SSRs and SNPs yielded many similar results. Among-site variation contributed 13% to 17% of the genetic variation and Fstestimates of 0.14 to 0.17 were in the range expected among Fagaceae species rather than among populations within a species. The northern sites tended to group separately on the first two axes of multivariate scatterplots from southern sites. Sites in two geographically isolated areas were divergent: (i) the Hood Canal, Washington population was relatively more genetically distant from other golden chinquapin sites than was our C. sempervirens site; (ii) three coastal southern California sites were moderately diverged. The Hood Canal site had a negative inbreeding coefficient, fewer alleles, lower heterozygosity, and differed from the Skamania County, Washington site as well as all other sites. Hood Canal trees are distinguished by disjunct geography and by these molecular results. This suggests that the golden chinquapin near Hood Canal be treated as a management unit, and potential conservation actions are discussed.

Genetic characterization of selected Nile tilapia in Santa Catarina

Different Nile tilapia stocks belonging to the fish breeding program of the Epagri (Empresa de Pesquisa Agropecuaria e Extensao Rural de Santa Catarina) were characterized by microsatellite markers. A total of nine stocks (S1 to S9) were evaluated, and for each stock the caudal fin of 30 individuals were sampled. A total of 75 alleles were found at the 11 microsatellite loci used (UNH104, UNH108, UNH160, UNH208, UNH222, UNH848, UNH879, UNH898, UNH952, UNH998). Among the loci used, only UHN160 showed significance for null alleles in stocks S1, S2, S3 and S5. The average number of alleles per loci was 6.8, while the average number of alleles per tilapia stock was 4.4. Five unique alleles were identified between the stock S1 and S5. The observed heterozygosity values (Ho) exceeded the expected heterozygosity (He), resulting in a negative inbreeding coefficient (FIS = -0.092). FST for the total population was 0.109, demonstrating moderate genetic differentiation between the stocks. According to the Euclidean distance, three groups were formed as follows: I - S6, S7 and S9; II - S2, S3 and S4; and III - S1, S5 and S8. However, the existence of two groups can be observed from the PCoA representation: I - S6, S7, S8 and S9; and II - S1, S2, S3, S4 and S5. The formation of these two genetic groups is consistent with the genealogy of stocks. The formation of group III (S1, S5 and S8) in the dendrogram can be explained by the higher average observed heterozygosity values of these stocks. Bayesian analysis revealed the formation of 16 groups with an FST value of 0.2107. This result reinforces the existence of variability existing in the Epagri breeding program, from which it is possible to form heterotic groups to enable the direction of potential crosses to obtain genetic gain. The study enabled genotypic characterization of the tilapia brood stock used in the Epagri breeding program, determining the genetic distance between the stocks, which will enable more accurate selection of individuals for mating for the next generation. It was possible to verify that there is high heterozygosity within the stocks, and moderate genetic differentiation between the stocks. Furthermore, all evaluated markers were polymorphic for this brood stock and will be used to characterize the next generations.

Genetic diversity in natural populations of noble crayfish (Astacus astacus L.) in north-western Poland on the basis of combined SSR and AFLP data.

BackgroundConservation of noble crayfish (Astacus astacus) populations is becoming particularly important since the number of individuals is rapidly declining across the distribution range of the species in Europe. Five crayfish populations in northwestern Poland have been constantly monitored for two decades. However, the genetic structure of these populations has not been analysed, although this information is important to devise effective conservation strategies.MethodsNoble crayfish were collected in the autumn of 2014 by scuba diving in Lakes Graniczne, Babinki, Biwakowe, Sęki and Kwisno, all of which are situated in the Bytów Lakeland of northwestern Poland. Genetic diversity of the five populations was assessed based on allele variability in nine SSR regions and six AFLP primer combinations.ResultsMicrosatellite results analysed with AMOVA showed that the diversity between populations corresponds to 18% of total variability, which was confirmed by similar results obtained using AFLP. Additionally, significant genetic diversity was revealed by high average FST values. All of the studied crayfish populations significantly deviated from the expected Hardy–Weinberg genetic equilibrium and were characterised by negative values of inbreeding coefficient (FIS).DiscussionThe invariably negative inbreeding coefficients (FIS) suggest a low number of mating individuals, a possible consequence of the phenomenon known as genetic bottleneck. However, additional comprehensive analyses are needed to assess the genetic structure, origin and vulnerability of the remaining populations of noble crayfish in the Bytów Lakeland of northwestern Poland, which have high conservation value and are particularly important as a live genetic bank for breeding and restitution purposes.

Diversity, genetic structure, and population genomics of the tropical tree Centrolobium tomentosum in remnant and restored Atlantic forests

The rapid pace of deforestation and fragmentation that took place in the Brazilian Atlantic Forest and other global hotspots for biodiversity conservation has motivated ecosystem restoration efforts. The genetic viability of restored tree populations and their potential to conserve genetic diversity remains, however, unclear. Here, we assessed the genetic viability and potential to conserve the genetic diversity of restored populations of Centrolobium tomentosum, a native legume tree, in the Brazilian Atlantic Forest, based on a genotyping by sequencing (GBS). We have successfully generated a total of 2877 single nucleotide polymorphism (SNP) markers across the whole C. tomentosum genome. Surprisingly, restoration sites presented overall higher levels of genetic diversity compared to natural remnant areas and negative inbreeding coefficient (FIS), mainly in juveniles’ trees from newer restored areas, indicating an excess of heterozygotes probably due to the founding event. The most likely number of genetic clusters found was two (K = 2), suggesting that diverse seed sources were used to produce seedlings for restoration. Clear signs of gene flow from restored to natural remnants areas had also been detected when diversity values of adults and juveniles were contrasted. Even though we did not find any clear relation of the genetic diversity and landscape composition, the low percentage of forest and high levels of fragmentation are likely reducing patch connectivity in some areas. LOSITAN detected 88 SNP outliers under positive selection, but analysis with Bayescan failed to support this evidence. In conclusion, our post hoc evaluation of restored tree populations indicated that the old restored area is stable and new areas have great potential to contribute to conserving genetic diversity and increasing the chances of the natural populations to persist over time.

Genetic outcomes of translocation of bighorn sheep in Arizona

ABSTRACTTranslocation is an important management tool that has been used for &gt;50 years in Arizona, USA, to increase bighorn sheep (Ovis canadensis) population densities and to restore herds to suitable habitat throughout their historical range. Yet, translocation can also alter the underlying genetic diversity and spatial structure of managed wildlife species in beneficial or detrimental ways. To evaluate the long‐term effect of translocation actions on bighorn sheep, we characterized statewide genetic structure and diversity using microsatellite and mitochondrial DNA data in 16 indigenous and translocated (supplemented or reintroduced) Arizona populations sampled between 2005 and 2012. Populations that were recipients of translocated animals showed no reduction in genetic diversity with allelic richness and heterozygosity estimates equivalent to, and in some cases greater than, indigenous source populations. The indigenous population occupying the Silver Bell Mountains population displayed the lowest indices of genetic diversity but shared mitochondrial DNA haplotypes with the Mohawk Mountains, Sierra Pinta, and Cabeza Prieta populations, indicating past connectivity and potential opportunities for genetic management if warranted. Bayesian clustering on genetic similarity and genetic divergence estimates corroborated previous work differentiating Rocky Mountain bighorn sheep (O. c. canadensis) and 2 desert lineages corresponding with Nelson's (O. c. nelsoni) and Mexican desert bighorn sheep (O. c. mexicana). In northern Arizona, assignment tests confirmed the presence of 2 indigenous metapopulations of Nelson's desert bighorn sheep in the Black Mountains and Grand Canyon and indicated that gene flow from the Grand Canyon population has likely played a role in maintaining genetic diversity and mitigating founder effects among multiple translocated populations in the area. In southern Arizona, we detected genetic structure consistent with 2 metapopulations of Mexican desert bighorn sheep representing a departure from current management practices that consider this lineage to be a single genetic unit. Several lines of genetic evidence presented in this study suggest that the Bill Williams River area is the contemporary contact zone for the 2 desert lineages; however, the degree to which translocation has enhanced introgression is unknown. Despite relative isolation from other herds, the translocated Rocky Mountain bighorn sheep population in eastern Arizona had high levels of allelic richness and heterozygosity and a negative inbreeding coefficient, conceivably as a result of multiple translocation events from sources in Colorado and New Mexico, USA. Although translocation management has successfully contributed to the reestablishment of bighorn sheep populations in Arizona without diminishing genetic diversity, future translocation should proceed with caution to preserve the genetic integrity and potential local adaptation within the Nelson's and Mexican desert bighorn sheep metapopulations identified in this study. © 2019 The Wildlife Society.

Genetic diversity of Saudi native chicken breeds segregating for naked neck and frizzle genes using microsatellite markers.

ObjectiveRecently, there has been an increasing interest in conservation of native genetic resources of chicken on a worldwide basis. Most of the native chicken breeds are threatened by extinction or crossing with ecotypes.MethodsSix Saudi native chicken breeds including black naked neck, brown frizzled, black, black barred, brown and gray were used in the current study. The aim of the current study was to evaluate genetic diversity, relationship and population structure of Saudi native chicken breeds based on 20 microsatellite markers.ResultsA total of 172 alleles were detected in Saudi native chicken breeds across all 20 microsatellite loci. The mean number of alleles per breed ranged from 4.35 in gray breed to 5.45 in normally feathered black with an average of 8.6 alleles. All breeds were characterized by a high degree of genetic diversity, with the lowest heterozygosity found in the brown breed (72%) and the greatest in the frizzled and black barred populations (78%). Higher estimate of expected heterozygosity (0.68) was found in both black breeds (normal and naked neck) compared to the other chicken populations. All studied breeds showed no inbreeding within breed (negative inbreeding coefficient [FIS]). The phylogenetic relationships of chickens were examined using neighbor-joining trees constructed at the level of breeds and individual samples. The neighbor-joining tree constructed at breed level revealed three main clusters, with naked neck and gray breeds in one cluster, and brown and frizzled in the second cluster leaving black barred in a separate one.ConclusionIt could be concluded that the genetic information derived from the current study can be used as a guide for genetic improvement and conservation in further breeding programs. Our findings indicate that the Saudi native chicken populations have a rich genetic diversity and show a high polymorphism.

Single nucleotide polymorphism of the growth hormone (GH) encoding gene in inbred and outbred domestic rabbits

Taking into consideration that the growth hormone (GH) gene in rabbits is a candidate for meat production, understanding the genetic diversity and variation in this locus is of particular relevance. The present study comprised 86 rabbits (Oryctolagus cuniculus) divided into 3 groups: New Zealand White (NZW) outbred rabbits; first-generation inbred rabbits (F&lt;sub&gt;1&lt;/sub&gt;) and second-generation inbred rabbits (F&lt;sub&gt;2&lt;/sub&gt;). They were analysed by polymerase chain reaction-based restriction fragment length polymorphism method. A 231 bp fragment of the polymorphic site of the GH gene was digested with Bsh1236 restriction enzyme. Single nucleotide polymorphisms for the studied GH locus corresponding to 3 genotypes were detected in the studied rabbit populations: CC, CT and TT. In the synthetic inbred F&lt;sub&gt;1&lt;/sub&gt; and F&lt;sub&gt;2&lt;/sub&gt; populations, the frequency of the heterozygous genotype CT was 0.696 and 0.609, respectively, while for the homozygous CC genotype the frequency was lower (0.043 and 0.000), and respective values for the homozygous TT genotype were 0.261 and 0.391. This presumed a preponderance of the T allele (0.609 and 0.696) over the C allele (0.391 and 0.304) in these groups. In outbred rabbits, the allele frequencies were 0.613 (allele C) and 0.387 (allele Т); consequently, the frequency of the homozygous CC genotype was higher than that of the homozygous TT genotype (0.300 vs. 0.075). Observed heterozygosity for the GH gene was higher than expected, and the result was therefore a negative inbreeding coefficient (Fis=–0.317 for outbred NZW rabbits; –0.460 for inbred F&lt;sub&gt;1&lt;/sub&gt; and –0.438 for inbred F&lt;sub&gt;2&lt;/sub&gt;), indicating a sufficient number of heterozygous forms in all studied groups of rabbits. The application of narrow inbreeding by breeding full sibs in the synthetic population did not cause a rapid increase in homozygosity.

Genetic Diversity in Cultured and Wild Population of Clarias gariepinus (Burchell, 1822) in Nigeria Using Random Amplified Polymorphic DNA (RAPD) and Microsatellite DNA

The population structure and genetic diversities of Clarias gariepinus from the cultured population at Chi Farm (Ajanla) and wild population at Asejire Reservoir (Asejire) were analysed using Random Amplified Polymorphic DNA (RAPD) and Microsatellite DNA markers. Using a CTAB protocol, genomic DNA was extracted from the caudal fins of 20 samples of live specimen collected from each population. Seven RAPD primers and seven pairs of microsatellite DNA primers were used to amplify different loci on the extracted genomic DNA by Polymerase Chain Reaction and the resultant DNA fragments were analysed on agarose gel. The RAPD primers amplified a total of 474 loci with 697 bands in all samples for the seven primers studied. The cultured population from Chi farm showed a total of 366 bands, while the wild population from Asejire Reservoir displayed 331 bands. The cultured population showed a negative inbreeding coefficient (F) of -0.173 ± 0.209, which statistically suggests excess heterozygosity, while a positive but low inbreeding coefficient of 0.042 ± 0.243 was estimated for the wild population. The Analysis of Molecular Variance (AMOVA) for both genetic markers indicated significant difference (p=0.01) between the two populations. The result of the study suggests a loss or on-going loss of genetic variability, which needs conservation intervention in the two populations studied.

Molecular genetic studies on Nellore and Deccani sheep using microsatellite markers

The study was undertaken to understand the genetic architecture of Deccani and Nellore sheep breeds and to assess the genetic distance between the breeds. Allele diversity, genetic variability and population structure in the two breeds were estimated using 30 microsatellite markers. A total of 100 sheep, 50 each from Deccani and Nellore breeds were genotyped. The total number of alleles observed was 254 and 260 in Deccani and Nellore, respectively. The mean expected heterozygosity among the breeds ranged from 0.79 (Deccani) to 0.80 (Nellore) whereas the mean observed heterozygosity levels ranged from 0.77 in Deccani to 0.78 in Nellore sheep. The overall mean inbreeding coefficient was 0.029 in Deccani and 0.031 in Nellore sheep and of the 30 loci studied, 14 loci in Deccani and 16 loci in Nellore sheep showed negative inbreeding coefficient indicating the presence of outbreeding. However, eight loci (BM1314, BM6506, BM8125, ILSTS28, MAF70, MCM140, OarCB226 and OarFCB128) showed positive, mild to moderate inbreeding ranging from 0.007 to 0.25 in Deccani and 0.066 to 0.37 in Nellore sheep studied. The FIS values ranged from -0.372 to 0.74, FST values ranged from 0.001 to 0.172 and FIT values ranged from -0.370 to 0.728 between the Deccani and Nellore sheep breeds studied. The PIC values ranged from 0.498 to 0.886 with a mean of 0.773 in Deccani and from 0.574 to 0.894 with a mean of 0.777 in Nellore breed. The information generated from the present study will be valuable for setting conservation priority of these two breeds.

Diversity of Algerian oases date palm (Phoenix dactylifera L., Arecaceae): Heterozygote excess and cryptic structure suggest farmer management had a major impact on diversity.

Date palm (Phoenix dactyliferaL.) is the mainstay of oasis agriculture in the Saharan region. It is cultivated in a large part of the Mediterranean coastal area of the Sahara and in most isolated oases in the Algerian desert. We sampled 10 oases in Algeria to understand the structure of date palm diversity from the coastal area to a very isolated desert location. We used 18 microsatellite markers and a chloroplast minisatellite to characterize 414 individual palm trees corresponding to 114 named varieties. We found a significant negative inbreeding coefficient, suggesting active farmer selection for heterozygous individuals. Three distinct genetic clusters were identified, a ubiquitous set of varieties found across the different oases, and two clusters, one of which was specific to the northern area, and the other to the drier southern area of the Algerian Sahara. The ubiquitous cluster presented very striking chloroplast diversity, signing the frequency of haplotypes found in Saudi Arabia, the most eastern part of the date palm range. Exchanges of Middle Eastern and Algerian date palms are known to have occurred and could have led to the introduction of this particular chlorotype. However, Algerian nuclear diversity was not of eastern origin. Our study strongly suggests that the peculiar chloroplastic diversity of date palm is maintained by farmers and could originate from date palms introduced from the Middle East a long time ago, which since then, hasbeen strongly introgressed. This study illustrates the complex structure of date palm diversity in Algerian oases and the role of farmers in shaping such cryptic diversity.