Simultaneous determination of subspecies and geographic origins of 110 rice cultivars by microsatellite markers

Rice varieties of different subspecies types (indica rice and japonica rice) across various geographical origins (Hunan, Jiangsu, and Northeast China) were monitored using microsatellite markers (simple sequence repeats, SSR). 110 representative rice cultivars were collected from the main crop areas. Multiple methods including clustering analysis (neighbor-joining (NJ) method, unweighted pair-group method with arithmetic mean (UPGMA) method), principal component analysis (PCA) and model-based grouping were applied. The study revealed that 25 pairs of SSR markers exhibited a broad range of polymorphism information content (PIC) values, ranging from 0.240 to 0.830. Furthermore, our study successfully achieved a higher overall mean correct rate of 99.09% in determining the geographical origin of rice. Simultaneously, it accurately classified indica rice and japonica rice. These findings are significant as they provide an SSR fingerprint of 110 high-quality rice cultivars, serving as a valuable scientific resource for the detection of rice adulteration and traceability of its origin.

Genetic resources of common ash (Fraxinus excelsior L.) in Poland

BACKGROUND

Knowledge of genetic structure and the factors that shape it has an impact on forest management practices. European ash (Fraxinus excelsior L.) has declined dramatically throughout its range as a result of a disease caused by the fungus Hymenoscyphus fraxineus. Despite the need for conservation and restoration of the species, genetic data required to guide these efforts at the country level are scarce. Thereofore, we studied the chloroplast and nuclear genetic diversity of 26 natural common ash populations (1269 trees) in Poland.

RESULTS

Chloroplast polymorphisms grouped the populations into two geographically structured phylogenetic lineages ascribed to different glacial refugia (the Balkans and the Eastern Alps). However, the populations demonstrated high genetic diversity (mean AR = 12.35; mean Ho = 0.769; mean He = 0.542) but low differentiation based on nuclear microsatellites (FST = 0.045). Significant spatial genetic structure, consistent with models of isolation by distance, was detected in 14 out of 23 populations. Estimated effective population size was moderate-to-high, with a harmonic mean of 57.5 individuals per population.

CONCLUSIONS

Genetic diversity was not homogeneously distributed among populations within phylogenetic gene pools, indicating that ash populations are not equal as potential sources of reproductive material. Genetic differences among populations could be related to their histories, including founder effects or gene flow between evolutionary lineages (admixture). Our results suggest that ash stands across Poland could be treated as two main management units (seed zones). Therefore, despite the homogenizing effect of pollen gene flow known for this species, the genetic structure should be taken into account in the management of the genetic resources of the common ash. Although ash dieback poses an additional challenge for the management of genetic resources, efforts should be directed towards protecting populations with high genetic diversity within defined phylogenetic units, as they may be an important source of adaptive variation for future stands.

Development of a novel molecular tool to study molecular ecology of Ornithomya (Hippoboscidae) avian louse flies

Louse flies (Diptera: Hippoboscidae) are obligatory hematophagous ectoparasites of birds and mammals. These widely distributed parasitic flies may have a significant impact on wild and farm animals by feeding on their blood and transmitting bloodborne pathogens. However, despite their ecological importance, louse flies are clearly underrepresented in host-parasite research and implementation of genetic approaches in this group is generally hampered by lacking molecular tools. In addition, louse flies that parasitize long-distance migrants can travel long distances with their avian hosts, facilitating the large-scale spread of pathogens across landscapes and geographic regions. Given the wide diversity of louse flies that parasitize a variety of avian hosts, their direct negative impact on host survival, and their high potential to transmit bloodborne pathogens even along avian migration routes, it is surprising that our knowledge of louse fly ecology is rather modest and incomplete. Here, we aimed to develop a novel molecular tool for polyxenous avian louse flies from the genus Ornithomya, which are among the most common and widely distributed representatives of Hippoboscidae family, to improve research of their genetic population structure and molecular ecology. Using the Illumina Mi-seq sequencing, we conducted a genome-wide scan in Ornithomya avicularia to identify putative microsatellite markers. A panel of 26 markers was selected to develop amplification protocols and assess polymorphism in the Central European population of O. avicularia, as well as to test for cross-amplification in a congeneric species (O. chloropus). A genome-scan in O. avicularia identified over 12 thousand putative microsatellite markers. Among 26 markers selected for a population-wide screening; one did not amplify successfully and three were monomorphic. 22 markers were polymorphic with at least two alleles detected. Two markers showed presence of null alleles. A cross-amplification of microsatellite markers in O. chloropus revealed allelic polymorphism at 14 loci, with the mean allelic richness of 3.78 alleles per locus (range: 2-8). Our genome-wide scan in O. avicularia provides a novel and powerful tool for molecular research in Ornithomya louse flies. Our panel of polymorphic microsatellite loci should allow genotyping of louse flies from geographically distinct populations and from a wide spectrum of avian hosts, enhancing population genetic and phylogeographic research in Ornithomya.

Detection of genetic divergence among putative ethyl methane sulfonate mutants of super basmati using microsatellite markers

BACKGROUND

Seeds of super basmati were mutagenized with different ethyl methane sulphonate (EMS) doses for creating genetic variability.

METHODS AND RESULTS

A total of 48 randomly selected putative EMS mutants of super basmati were analyzed to dissect the genetic diversity by using 25 SSR primers located on twelve chromosomes of rice. SSRs analysis revealed that wide-range of genetic diversity is present among mutants of super basmati. A sum of 91 alleles were identified, out of these, 82 alleles were polymorphic and the rest of nine alleles were monomorphic in nature. The range of allele number was 2-10 with mean of 3.64 alleles/locus. The value of polymorphic information content was range between 0.039 (RM5) and 0.878 (RM44) with mean of 0.439 for each locus. A number of polymorphic markers showed unique bands of various sizes ranges from 75 to 1000 bp, during genetic dissection of mutant population. Dendrogram divided whole mutant population into four major groups. Phylogenic analyses revealed that 40-96%genetic similarity is present among individuals of mutant population.

CONCLUSION

It is concluded that EMS induced genetic variability and SSRs markers (RM44, RM154, RM1, RM252, RM334, RM487, RM110 and RM257) could be handy for the selection of rice mutants as parents for functional genomic and molecular breeding program.

Robust preimplantation genetic testing of the common F8 Inv22 pathogenic variant of severe hemophilia A using a highly polymorphic multi-marker panel encompassing the paracentric inversion

BACKGROUND

Hemophilia A (HEMA) is an X-linked bleeding disorder caused by reduced/absent coagulation factor VIII expression, as a result of pathogenic variants in the F8 gene. Preimplantation prevention of HEMA should ideally include direct pathogenic F8 variant detection, complemented by linkage analysis of flanking markers to identify the high-risk F8 allele. Linkage analysis is particularly indispensable when the pathogenic variant cannot be detected directly or identified. This study evaluated the suitability of a panel of F8 intragenic and extragenic short tandem repeat markers for standalone linkage-based preimplantation genetic testing for monogenic disorder (PGT-M) of the Inv22 pathogenic variant, an almost 600 kb paracentric inversion responsible for almost half of all severe HEMA globally, for which direct detection is challenging.

METHODS

Thirteen markers spanning 1 Mb and encompassing both F8 and the Inv22 inversion interval were genotyped in 153 unrelated females of Viet Kinh ethnicity.

RESULTS

All individuals were heterozygous for ≥ 1 marker, ~ 90% were heterozygous for ≥ 1 of the five F8 intragenic markers, and almost 98% were heterozygous for ≥ 1 upstream (telomeric) and ≥ 1 downstream (centromeric) markers. A prospective PGT-M couple at risk of transmitting F8 Inv22 were fully informative at four marker loci (2 intra-inversion, 1 centromeric, 1 telomeric) and partially informative at another five (2 intra-inversion, 3 centromeric), allowing robust phasing of low- and high-risk haplotypes. In vitro fertilization produced three embryos, all of which clearly inherited the low-risk maternal allele, enabling reliable unaffected diagnoses. A single embryo transfer produced a clinical pregnancy, which was confirmed as unaffected by amniocentesis and long-range PCR, and a healthy baby girl was delivered at term.

CONCLUSION

Robust and reliable PGT-M of HEMA, including the common F8 Inv22 pathogenic variant, can be achieved with sufficient informative intragenic and flanking markers.

Population structure and genetic diversity of Tamarix chinensis as revealed with microsatellite markers in two estuarine flats

Background

Tamarix chinensis Lour. is a 3-6-meter-tall small tree with high salt- and alkali- tolerance and aggressive invasiveness, mainly distributed in the eastern part of China in warm-temperate and subtropical climate zones, yet there is little information available regarding genetic diversity and population structure.

Methods

A total of 204 individuals of nine T. chinensis populations were investigated for genetic diversity and population structure using a set of 12 highly polymorphic microsatellite markers.

Results

The total number of alleles detected was 162, the average number of effective allele was 4.607, the average polymorphism information content (PIC) value of the 12 loci was 0.685, and the mean observed heterozygosity (Ho) and the mean expected heterozygosity (He) was 0.653 and 0.711, respectively. Analysis of molecular variance (AMOVA) showed a 5.32% genetic variation among T. chinensis populations. Despite a low population differentiation, Bayesian clustering analysis, discriminant analysis of principal components (DAPC) and the unweighted pair group method with arithmetic mean (UPGMA) clearly identified three genetic clusters correlated to the populations' geographic origin: the northern populations including those from Yellow River Delta, the Fangshan (FS) population from Beijing, the Changyi (CY) population from Bohai Bay, the Huanjiabu (HHJ) population from Hangzhou Bay, and the remaining two populations from Hangzhou Bay. There was a significant relationship between the genetic distance and geographical distance of the paired populations. Gene flow (Nm) was 4.254 estimated from FST.

Conclusion

T. chinensis possessed high genetic diversity comparable to tree species, and although the population differentiation is shallow, our results classified the sampled populations according to sampling localities, suggesting the different origins of the study populations.

Assessment of variations in productive performance of two different plumage color varieties of Japanese quail and their reciprocal crosses

This study aimed to detect the phenotypic differences between the brown (BB) and white (WW) feathered quails and their reciprocal crosses (BW and WB) over two successive generations. The WW and cross quails, especially the BW, had the heaviest body weights, throughout the studied period, with significant variations between the two studied generations (P<0.05). Moreover, the WW and BW possessed the largest egg production during the F1, while in the F2, the BB had superiority among the studied quails with a prominent superiority of the F2 over the F1 (P<0.05). However, the F1 had higher egg weights than F2 with superiority of WW quails compared to the others (P<0.05). Also, the WW quails had the lowest lipid contents of the eggs. These phenotypic variations among the studied quails might be preliminarily explained by the results of the analyzed microsatellite markers despite the few markers used. The high variability among the BW and WB quails might be due to the larger number of alleles (N_A and N_e) and the lower values of F_IS with low heterozygosity levels (H_O and H_e). Moreover, the BW and BB were the closest, while WB and WW were the farthest because of the high and low genetic identities and the high and low genetic distance between them, respectively. So the obtained results might introduce an initial scientific basis for evaluating and employing the genetic properties of BB, WW, BW, and WB quails in further genetic improvement program, and more microsatellite markers are recommended.

Development of novel microsatellite markers for population differentiation and detection of natural selection in wild populations of butter catfish, Ompok bimaculatus (Bloch, 1794)

BACKGROUND

Butter catfish (Ompok bimaculatus) is a preferred species in South East Asia, with huge aquaculture potential. However, there is limited information about genetic stock composition due to insufficient markers. The goal of this study was to develop de novo microsatellite markers.

METHODS AND RESULTS

For sequencing, genomic SMRT bell libraries (1.5 Kbp size) were prepared for O. bimaculatus. A total of 114 SSR containing sequences were used for primer designing. Polymorphic loci were validated by genotyping 83 individuals from four distant riverine populations, viz., Brahmaputra, Bichiya, Gomti and Kaveri. A total of 30 microsatellite loci were polymorphic, of which five were found to be associated with functional genes and eight (four positive and four negative) loci were found to be under selection pressure. A total of 115 alleles were detected in all loci and PIC ranged from 0.539 to 0.927 and pair-wise F_ST values from 0.1267 to 0.26002 (p < 0.001), with an overall F_ST value of 0.17047, indicating the presence of population sub-structure. Cross-species transferability of 29 loci (96.67%) was successful in congener species, Ompok pabda.

CONCLUSION

The novel SSR markers developed in this study would facilitate stock characterization of natural populations, to be used in future selection breeding programs and planning conservation strategies in these species. Identified non-neutral markers will give insights into the effect of local adaptation on genetic differentiation in the natural population of this species.

Genome-wide characterization leading to simple sequence repeat (SSR) markers development in Shorea robusta

Tropical rainforests in Southeast Asia are enriched by multifarious biota dominated by Dipterocarpaceae. In this family, Shorea robusta is an ecologically sensitive and economically important timber species whose genomic diversity and phylogeny remain understudied due to lack of datasets on genetic resources. Smattering availability of molecular markers impedes population genetic studies indicating a necessity to develop genomic databases and species-specific markers in S. robusta. Accordingly, the present study focused on fostering de novo low-depth genome sequencing, identification of reliable microsatellites markers, and their validation in various populations of S. robusta in Uttarakhand Himalayas. With 69.88 million raw reads assembled into 1,97,489 contigs (read mapped to 93.2%) and a genome size of 357.11 Mb (29 × coverage), Illumina paired-end sequencing technology arranged a library of sequence data of ~ 10 gigabases (Gb). From 57,702 microsatellite repeats, a total of 35,049 simple sequence repeat (SSR) primer pairs were developed. Afterward, among randomly selected 60 primer pairs, 50 showed successful amplification and 24 were found as polymorphic. Out of which, nine polymorphic loci were further used for genetic analysis in 16 genotypes each from three different geographical locations of Uttarakhand (India). Prominently, the average number of alleles per locus (Na), observed heterozygosity (Ho), expected heterozygosity (He), and the polymorphism information content (PIC) were recorded as 2.44, 0.324, 0.277 and 0.252, respectively. The accessibility of sequence information and novel SSR markers potentially enriches the current knowledge of the genomic background for S. robusta and to be utilized in various genetic studies in species under tribe Shoreae.

Genetic diversity and population structure of sorghum [Sorghum bicolor (L.) Moench] genotypes in Ethiopia as revealed by microsatellite markers

In the tropical and semi-arid regions of Africa, sorghum [Sorghum bicolor (L.) Moench] is mainly grown as a major food security crop. Understanding the extent and pattern of genetic variability is a prerequisite criterion for sorghum improvement and conservation. The genetic diversity and population structure of 100 genotypes of sorghum were profiled using 15 microsatellite loci. A total of 108 alleles, with an overall mean of 7.2 alleles per locus, were produced by all of the microsatellite loci used due to their high polymorphism. Polymorphic information content values ranging from 0.68 to 0.89 indicated that all of the loci are effective genetic tools for analysing the genetic structure of sorghum. Different diversity metrics were used to evaluate genetic diversity among populations, and Nei's gene diversity index ranged from 0.74 to 0.81 with an overall mean of 0.78. Poor genetic differentiation (FST: 0.02; p < 0.0001) was found, where 98% of entire variability was accounted by the within populations genetic variability, leaving only 2.32% among populations. The highest genetic differentiation and Nis's genetic distance were observed between the sorghum populations of the Southern Nation and Nationalities Peoples and Dire Dawa regions. Due to increased gene flow (Nm = 10.53), the clustering, principal coordinate analysis and STRUCTURE analysis failed to categorize the populations into genetically different groups corresponding to their geographic sampling areas. In general, it was found that the microsatellite loci were highly informative and therefore valuable genetic tools to unfold the genetic diversity and population structure of Ethiopian sorghum genotypes. Among the five populations studied, sorghum populations from Amhara and Oromia had the highest genetic variation, indicating that the regions could be perhaps hotspots for useful alleles for the development of better-performing genotypes, and also for designing appropriate germplasm management strategies.

Predominant Clonal Reproduction with Infrequent Genetic Recombination of Phaeoacremonium minimum in Western Cape Vineyards

Phaeoacremonium minimum is an important esca and Petri disease pathogen that causes dieback of grapevines in South Africa. Little is known regarding the reproductive strategy of the pathogen. Sexual reproduction could lead to a better adaptation of the pathogen to disease management strategies by combining alleles through recombination. The study aimed to investigate the genetic diversity and recombination potential of eight populations in the Western Cape, from six commercial vineyards and two nursery rootstock mother blocks. This was achieved by developing and applying nine polymorphic microsatellites and mating-type-specific markers. Thirty-seven genotypes were identified from 295 isolates. Populations were characterised by the same dominant genotype (MLG20 occurring 65.43%), low genotypic diversity (H) and high numbers of clones (81.36% of dataset). However, genotypes from the same sampling sites were not closely related based on a minimum spanning network and had high molecular variation within populations (94%), suggesting that multiple introductions of different genotypes occurred over time. Significant linkage disequilibrium among loci (r̅d) further indicated a dominant asexual cycle, even though perithecia have been observed in these four populations. The two rootstock mother blocks had unique genotypes and genotypes shared with the vineyard populations. Propagation material obtained from infected rootstock mother blocks could lead to the spread of more genotypes to newly established vineyards. Based on our results, it is important to determine the health status of rootstock mother blocks. Management strategies must focus on reducing aerial inoculum to prevent repeated infections and further spread of P. minimum genotypes.

Construction and characterization of microsatellite markers for the Neptune whelk, Neptunea cumingii

BACKGROUND

The Neptune whelk, Neptunea cumingii, is an economic gastropod endemic to the East Asia Warm Temperate Biotic Subregion. The study of the development in microsatellite markers maybe beneficial for assessing the genetic diversity and conservation of resources on this dwindling species.

METHODS AND RESULTS

The microsatellite markers were constructed and characterized through Illumina high-throughput sequencing and capillary electrophoresis techniques. Eleven polymorphic microsatellite loci were screened and validated. The observed heterozygosity and expected heterozygosity of each locus showed a range from 0.0600 to 0.6508 and from 0.7380 to 0.9375, respectively. The average Shannon's information index and polymorphism information content were 2.0828 and 0.8325, respectively. Deviation from all loci was generated from Hardy-Weinberg equilibrium.

CONCLUSIONS

The 11 microsatellite markers developed in this study show polymorphic status. These markers are expected to be highly informative for further analysis of genetic diversity in N. cumingii.

Assessment of genetic diversity and relationship of the two Sanga type cattle of Botswana based on microsatellite markers

The study was performed to evaluate genetic variation on two Sanga type cattle found in Botswana: Tswana and Tuli using twelve microsatellite markers. All amplified loci were polymorphic with 75 and 77 alleles genotyped in the Tswana and Tuli populations, respectively. The total number of alleles per locus ranged from 2 (BM1818) to 10 (TGLA227) with total mean of 6.25 for Tswana and 6.43 for Tuli population. Almost all the markers showed high polymorphic information content (PIC) apart from BM1818 (0.375) and INRA23 (0.393) which were moderately informative in Tswana population. Most of the markers were in Hardy-Weinberg equilibrium except for CSSRM60 and CSSM66 loci in Tswana population and ETH10, ETH225 and CSSM66 loci in Tuli population. A total of 103 unique alleles were genotyped across the two breeds with 49-shared, and 26 and 28 were unique to Tswana and Tuli populations, respectively. The expected heterozygosity (He) values were higher than the observed heterozygosity (Ho) in both populations: Tswana (He = 0.7895 ± 0.033 vs Ho = 0.631 ± 0.091) and Tuli (He = 0.8123 ± 0.033 vs Ho = 0.556 ± 0.021). The inbreeding coefficient was 0.200 ± 0.002 and 0.332 ± 0.001 in Tswana and Tuli populations, respectively. Analysis of molecular variance revealed 6.8% of the total genetic variation corresponding to differences between the two breeds and 93.2% within populations. The genetic identity between the two breeds was 56% and there were similar levels of multilocus heterozygosity and allelic diversity in the two breeds. The use of Tswana and Tuli breeds in a crossbreeding programme is likely to result in minimal heterosis and therefore not recommended.

Genome survey of Misgurnus anguillicaudatus to identify genomic information, simple sequence repeat (SSR) markers, and mitochondrial genome

BACKGROUND

The dojo loach Misgurnus anguillicaudatus is an important economic species in Asia because of its nutritional value and broad environmental adaptability. Despite its economic importance, genomic data for M. anguillicaudatus is currently unavailable.

METHODS AND RESULTS

In the present study, we conducted a genome survey of M. anguillicaudatus using next-generation sequencing technology. Its genome size was estimated to be 1105.97 Mb by using K-mer analysis, and its heterozygosity ratio, repeat sequence content, GC content were 1.45%, 58.98%, and 38.03%, respectively. A total of 376,357 microsatellite motifs were identified, and mononucleotides, with a frequency of 42.57%, were the most frequently repeated motifs, followed by 40.83% dinucleotide, 7.49% trinucleotide, 8.09% tetranucleotide, and 0.91% pentanucleotide motifs. The AC/GT, AAT/ATT, and ACAG/CTGT repeats were the most abundant motifs among dinucleotide, trinucleotide, and tetranucleotide motifs, respectively. Besides, the complete mitochondrial genome was sequenced. Based on the Maximum Likelihood and Bayesian inference analyses, M. anguillicaudatus yingde in this study was the "introgressed" mitochondrial type. Seventy microsatellite loci were randomly selected from detected SSR loci to test polymorphic, of which, 20 microsatellite loci were assessed in 30 individuals from a wild population. The number of alleles (Na), observed heterozygosity (Ho), and expected heterozygosity (He) per locus ranged from 7 to 19, 0.400 to 0.933, and 0.752 to 0.938, respectively. All 20 loci were highly informative (PIC > 0.700). Eight loci deviated from Hardy-Weinberg equilibrium after Bonferroni correction (P < 0.05).

CONCLUSIONS

This is the first report of genome survey sequencing in M. anguillicaudatus, genome information, mitochondrial genome, and microsatellite markers will be valuable for further studies on population genetic analysis, natural resource conservation, and molecular marker-assisted selective breeding.

Genetic diversity of indigenous guinea fowl (Numida meleagris) using microsatellite markers in northern Togo

Indigenous guinea fowl is an important animal resource for improving rural household income. In order to provide molecular data for a sustainable management of this poultry resource, an assessment of the genetic diversity and phylogenic relationships was undertaken on seven guinea fowl phenotypes from two agroecological zones (Dry Savannah and Atakora) of Togo. Genotyping was carried out using 18 microsatellite markers on 94 individuals from Dry Savannah (59) and Atakora (35) zones. The results obtained showed a high genetic diversity, with six as an average alleles per locus and an observed heterozygosity of 0.512. However, the F_IS values varied from 0.047 (Lavender) to 0.257 (Albino), reflecting a deficit of heterozygotes, which suggests low to moderate inbreeding levels. The genetic distances between phenotypes are low, ranging from 0.0068 (Bonaparte-Pearl grey) to 0.1559 (Lavender-Albino), unlike the strong genetic identities that reflect a strong genetic similarity between the seven phenotypes of indigenous guinea fowl studied. These results indicate the existence of a single indigenous guinea fowl population, derived from three probable parental populations, with a high within population genetic diversity (phenotypic or agroecological zone). These results could be of use to conservation and improvement programs aiming at the maintenance and sustainable exploitation of this important socio-cultural and economic resource in Togo.

(Boraginaceae)

BACKGROUD

Tournefortia argentea L. f. is a hexaploid shrub or tree species with ecological and evolutionary significances, which forms the fringe of vegetation closest to the sea on tropical coral islands. Previous studies have never addressed on genetic information, and thus genomic resources remain scarce.

METHODS AND RESULTS

We used nine individuals from different islands to identify polymorphic microsatellites of T. argentea by Illumina high-throughput sequencing. Thirty-five polymorphic microsatellite markers were developed. Characteristics of each locus were tested using 48 individuals collected from three populations of T. argentea. A total of 320 alleles were found across the 35 microsatellite loci. The number of alleles per locus ranged from 5 to 15, with an average of 9.1. Observed and expected heterozygosities in each locus per population varied from 0.000 to 1.000 and from 0.000 to 0.893, respectively.

CONCLUSIONS

In this study, we report the development of 35 polymorphic microsatellite markers based on Illumina high-throughput sequencing. These markers will facilitate the investigations of genetic diversity, population structures and evolutionary history of T. argentea.

Morphometric and microsatellite-based comparative genetic diversity analysis in Bubalus bubalis from North India

To understand the similarities and dissimilarities of a breed structure among different buffalo breeds of North India, it is essential to capture their morphometric variation, genetic diversity, and effective population size. In the present study, diversity among three important breeds, namely, Murrah, Nili-Ravi and Gojri were studied using a parallel approach of morphometric characterization and molecular diversity. Morphology was characterized using 13 biometric traits, and molecular diversity through a panel of 22 microsatellite DNA markers recommended by FAO, Advisory Group on Animal Genetic Diversity, for diversity studies in buffaloes. Canonical discriminate analysis of biometric traits revealed different clusters suggesting distinct genetic entities among the three studied populations. Analysis of molecular variance revealed 81.8% of genetic variance was found within breeds, while 18.2% of the genetic variation was found between breeds. Effective population sizes estimated based on linkage disequilibrium were 142, 75 and 556 in Gojri, Nili-Ravi and Murrah populations, respectively, indicated the presence of sufficient genetic variation and absence of intense selection among three breeds. The Bayesian approach of STRUCTURE analysis (at K = 3) assigned all populations into three clusters with a degree of genetic admixture in the Murrah and Nili-Ravi buffalo populations. Admixture analysis reveals introgression among Murrah and Nili-Ravi breeds while identified the Gojri as unique buffalo germplasm, indicating that there might be a common origin of Murrah and Nili-Ravi buffaloes. The study provides important insights on buffalo breeds of North India that could be utilized in designing an effective breeding strategy, with an appropriate choice of breeds for upgrading local non-descript buffaloes along with conservation of unique germplasm.

Characterization of novel genotyping-by-sequencing (GBS)-based simple sequence repeats (SSRs) and their application for population genomics of Capoeta aculeata (Valenciennes, 1844)

BACKGROUND

The species Capoeta aculeata (Valenciennes, 1844) is one of the most important freshwater species endemic to Iran. However, the investigation of the population genetic structure of this species is limited by the low number of molecular markers currently described.

METHODS AND RESULTS

In this study, we implemented next generation sequencing technology to identify polymorphic microsatellite markers and investigate the population genetic structure of C. aculeata sampled from three geographical sites in Iran. We characterized and developed 36 novel polymorphic microsatellite markers and these loci were examined in 120 individuals from three populations occurring in the Zagros basin. The average number of alleles per locus varied from 1.7 to 16 (average = 7.89). The results showed that, the polymorphism information content (PIC) of these simple sequence repeat (SSR) loci varied from 0.254 to 0.888. The observed heterozygosity (H_O) per locus ranged from 0.170 to 0.881, while the expected heterozygosity (H_E) per locus was from 0.170 to 0.881. Among these SSR loci, 20 loci deviated significantly from the Hardy-Weinberg equilibrium after Bonferroni correction (p < 0.05).

CONCLUSIONS

These microsatellite markers could provide a valuable tool for future population and conservation genetics studies of C. aculeate and other closely related species.

Genetic diversity and phylogenetic relationships within local pigs in southern Benin

The current context of climate change requires the conservation of local zoogenetic resources already very well adapted to the traditional breeding system, rough feeding, and heat and cold stress. This study assessed genetic diversity in local pigs in southern Benin, as a prerequisite for their sustainable use and sustainable management in Benin. A total of 69 individuals including 54 local pigs, 7 Large-White, and 8 hybrids (local pigs × Bush-pig) were genotyped by using 17 microsatellite markers. On the average, 8.94 alleles were detected per locus. Average expected and observed heterozygosities were respectively 0.51 and 0.46. Polymorphic information content was 0.61, and genetic diversity was 0.53. A phylogenetic tree gathered local pigs into three genetic clusters. Genetic structural analyses revealed introgression of Large-White's genes into the local pig's genome. Three groups were identified: hybrids (subpopulation 1), a mixture of Large-White and local pigs (subpopulation 2), and only local pigs (subpopulation 3). Symmetrical allelic distances were higher between subpopulations 1 and 2 (0.787) and then 1 and 3 (0.713). The same trend was detected for genetic distances between pairs of subpopulations. Genetic differentiation between subpopulations 2 and 3 was very weak as a consequence of high gene flow (10.82). Molecular variance analysis showed that 77% of genetic diversity within populations was related to variability between the individuals. These results showed that local pigs in southern Benin are threatened by genetic erosion and suggest prompt actions to implement sustainable conservation strategies.

Production of Doubled Haploid Embryos from Cork Oak Anther Cultures by Antimitotic Agents and Temperature Stress

Cork oak (Quercus suber L.) is a forest tree species of the family Fagaceae. It is characterized by long life cycles which hamper doubled haploid plant production to obtain homozygotes and pure lines. The time-consuming method of repeated backcrossings by conventional breeding techniques to produce pure lines is impractical in woody species. Nevertheless, biotechnology has offered new tools to make it possible. A doubled haploid plant or embryo is one that is developed by the doubling of a haploid set of chromosomes. A protocol to produce doubled haploids of cork oak has been developed through microspore embryogenesis. By a heat stress treatment, the microspores inside the anther leave the gametophytic pathway and react shifting their development to the sporophytic pathway by means of which haploid embryos are obtained. Chromosome duplication of haploids from cork oak anther cultures occurs either spontaneously or may be induced by the application of antimitotic agents (e.g., colchicine, oryzalin, amiprophos-methyl). Furthermore, a genetic test is designed through microsatellite markers to elucidate whether the diploid embryos obtained are originally haploids which spontaneously duplicated their genome, or alternatively those embryos are generated from the diploid tissue of the anther wall. Here we describe a detailed protocol to produce doubled haploid individuals from cork oak anther cultures by using temperature stress and antimitotic agents.

Genetic evidence substantiates transmission of Trichinella spiralis from one swine farm to another

BACKGROUND

Trichinella spiralis ranks seventh in the risk posed by foodborne parasites. It causes most human cases of trichinellosis and is the most frequent cause of Trichinella outbreaks on pig farms and in wild boar, worldwide. Veterinary inspectors seek the source of outbreaks in hopes of limiting the spread. Established molecular tools are inadequate for distinguishing among potential T. spiralis infection sources because genetic variability in these zoonotic pathogens is limited in Europe. Microsatellite markers proved successful in tracing an outbreak of T. britovi, a related parasite harboring much more genetic variation. Here, we successfully employed microsatellite markers to determine the genetic structure of T. spiralis isolates from two pig outbreaks, discovering notable uniformity among parasites within each farm and discovering an epidemiological link between these two outbreaks.

METHODS

The individual larvae from five isolates of T. spiralis from two pig farms and from ten wild boars were genotyped using nine microsatellite markers to examine their genetic structure.

RESULTS

Notably uniform parasite populations constituted each farm outbreak, and the parasites from the first and second outbreaks resembled each other to a notable degree, indicating an epidemiological link between them. Wild boar harbored more genetically variable larval cohorts, distinguishing them from parasites isolated from domestic pigs.

CONCLUSIONS

Microsatellite markers succeeded in distinguishing isolates of the highly homogeneous T. spiralis, aiding efforts to track transmission. Each outbreak was composed of a homogenous group of parasites, suggesting a point source of contamination.

Genome skimming-based simple sequence repeat (SSR) marker discovery and characterization in Grevillea robusta

Proteaceae, a largely southern hemisphere family consisting of 80 genera distributed in Australia and southern Africa as its centres of greatest diversity, also extends well in northern and southern America. Under this family, Grevillea robusta is a fast-growing species got popularity in farm and avenue plantations. Despite the ecological and economic importance, the species has not yet been investigated for its genetic improvement and genome-based studies. Only a few molecular markers are available for the species or its close relatives, which hinders  genomic and population genetics studies. Genetic markers have been intensively applied for the main strategies in breeding programs, especially for the economically important traits. Hence, it is of utmost priority to develop genomic database resources and species-specific markers for studying quantitative genetics in G. robusta. Given this, the present study aimed to develop de novo genome sequencing, robust microsatellites markers, sequence annotation and their validation in different stands of G. robusta in northern India. Library preparation and sequencing were carried out using Illumina paired-end sequencing technology. Approximately, ten gigabases (Gb) sequence data with 70.87 million raw reads assembled into 425,923 contigs (read mapped to 76.48%) comprising 455 Mb genome size (23 × coverage) generated through genome skimming approach. In total, 9421 simple sequence repeat (SSR) primer pairs were successfully designed from 13,335 microsatellite repeats. Afterward, a subset of 161 primer pairs was randomly selected, synthesized and validated. All the tested primers showed successful amplification but only 13 showed polymorphisms. The polymorphic SSRs were further used to estimate the measures of genetic diversity in 12 genotypes each from the states of Punjab, Haryana, Himachal Pradesh and Uttarakhand. Importantly, the average number of alleles (Na), observed heterozygosity (Ho), expected heterozygosity (He), and the polymorphism information content (PIC) were recorded as 2.69, 0.356, 0.557 and 0.388, respectively. The availability of sequence information and newly developed SSR markers could potentially be used in various genetic analyses and improvements through molecular breeding strategies for G. robusta.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01035-w.

Genetic diversity and genetic relatedness in Plasmodium falciparum parasite population in individuals with uncomplicated malaria based on microsatellite typing in Eastern and Western regions of Uganda, 2019-2020

BACKGROUND

Genetic diversity and parasite relatedness are essential parameters for assessing impact of interventions and understanding transmission dynamics of malaria parasites, however data on its status in Plasmodium falciparum populations in Uganda is limited. Microsatellite markers and DNA sequencing were used to determine diversity and molecular characterization of P. falciparum parasite populations in Uganda.

METHODS

A total of 147 P. falciparum genomic DNA samples collected from cross-sectional surveys in symptomatic individuals of 2-10 years were characterized by genotyping of seven highly polymorphic neutral microsatellite markers (n = 85) and genetic sequencing of the Histidine Rich Protein 2 (pfhrp2) gene (n = 62). ArcGIS was used to map the geographical distribution of isolates while statistical testing was done using Student's t-test or Wilcoxon's rank-sum test and Fisher's exact test as appropriate at P ≤ 0.05.

RESULTS

Overall, 75.5% (95% CI 61.1-85.8) and 24.5% (95% CI14.2-38.9) of parasites examined were of multiclonal (mixed genotype) and single clone infections, respectively. Multiclonal infections occurred more frequently in the Eastern region 73.7% (95% CI 48.8-89.1), P < 0.05. Overall, multiplicity of infection (MOI) was 1.9 (95% CI 1.7-2.1), P = 0.01 that was similar between age groups (1.8 vs 1.9), P = 0.60 and regions (1.9 vs 1.8), P = 0.43 for the < 5 and ≥ 5 years and Eastern and Western regions, respectively. Genomic sequencing of the pfhrp2 exon2 revealed a high level of genetic diversity reflected in 96.8% (60/62) unique sequence types. Repeat type AHHAAAHHATD and HRP2 sequence Type C were more frequent in RDT-/PCR + samples (1.9% vs 1.5%) and (13% vs 8%), P < 0.05 respectively. Genetic relatedness analysis revealed small clusters of gene deleted parasites in Uganda, but no clustering with Eritrean parasites.

CONCLUSION

High level of genetic diversity of P. falciparum parasites reflected in the frequency of multiclonal infections, multiplicity of infection and variability of the pfhrp2 gene observed in this study is consistent with the high malaria transmission intensity in these settings. Parasite genetic analysis suggested spontaneous emergence and clonal expansion of pfhrp2 deleted parasites that require close monitoring to inform national malaria diagnosis and case management policies.

Warming and elevated CO2 induces changes in the reproductive dynamics of a tropical plant species

Tropical plant species are vulnerable to climate change and global warming. Since flowering is a critical factor for plant reproduction and seed-set, warming and elevated atmospheric carbon dioxide concentrations (eCO₂) are crucial climate change factors that can affect plant reproductive dynamics and flowering related events in the tropics. Using a combined free-air CO₂ enrichment and a free-air temperature-controlled enhancement system, we investigate how warming (+2 °C above ambient, eT) and elevated [CO₂] (~600 ppm, eCO₂) affect the phenological pattern, plant-insect interactions, and outcrossing rates in the tropical legume forage species Stylosanthes capitata Vogel (Fabaceae). In comparison to the control, a significantly greater number of flowers (NF) per plot (+62%) were observed in eT. Furthermore, in warmed plots flowers began opening approximately 1 h earlier (~09:05), with a canopy temperature of ~23 °C, than the control (~09:59) and eCO₂ (~09:55) treatments. Flower closure occurred about 3 h later in eT (~11:57) and control (~13:13), with a canopy temperature of ~27 °C. These changes in flower phenology increased the availability of floral resources and attractiveness for pollinators such as Apis mellifera L. and visitors such as Paratrigona lineata L., with significant interactions between eT treatments and insect visitation per hour/day, especially between 09:00-10:40. In comparison to the control, the additive effects of combined eCO₂ + eT enhanced the NF by 137%, while the number of A. mellifera floral visits per plot/week increased by 83% during the period of greatest flower production. Although we found no significant effect of treatments on mating system parameters, the overall mean multilocus outcrossing rate (tm = 0.53 ± 0.03) did confirm that S. capitata has a mixed mating system. The effects of elevated [CO₂] and warming on plant-pollinator relationships observed here may have important implications for seed production of tropical forage species in future climate scenarios.

Depicting the mating system and patterns of contemporary pollen flow in trees of the genus Anadenanthera (Fabaceae)

Anadenanthera (Fabaceae) is endemic to the Neotropics and consists of two tree species: A. colubrina (Vell.) Brenan and A. peregrina (L.) Speg. This study examined the mating system and contemporary gene flow of A. colubrina (Acol) and A. peregrina (Aper) in a highly fragmented area of the Atlantic Forest to provide valuable information that informs conservation strategies. Reproductive adults from forest remnants [n _{A. colubrina} = 30 (2.7 ha), n _{A. peregrina} = 55 (4.0 ha)] and progeny-arrays (n _{A. colubrina} = 322, n _{A. peregrina} = 300) were genotyped for seven nuclear microsatellite markers. Mating system analyses revealed that A. colubrina is a mixed mating species (t_m = 0.619) while A. peregrina is a predominantly outcrossing species (t_m = 0.905). For both Anadenanthera species, high indices of biparental inbreeding were observed (Acol = 0.159, Aper = 0.216), resulting in low effective pollination neighborhood sizes. Categorical paternity analysis revealed different scales of pollen dispersal distance: the majority of crossings occurring locally (i.e., between nearby trees within the same population), with moderate pollen dispersal coming from outside the forest fragments boundaries (Acol _mp = 30%, Aper _mp = 35%). Nevertheless, pollen immigration from trees outside the populations for both species suggests that the populations are not reproductively isolated. This study highlights the importance of evaluating both mating system and contemporary gene flow for a better understanding of the biology of Anadenanthera species. This information should be considered to ensure the effective conservation and management practices of these plant species.

Detection and application of novel SSR markers from transcriptome data for Astronium fraxinifolium Schott, a threatened Brazilian tree species

Astronium fraxinifolium is an endangered tree species from Brazil. Due to its significance in environmental reforestation, as well as the continued exploitation of its wood, it is necessary to develop management programs that support the conservation of the species. Simple sequence repeats (SSR) or microsatellite markers are widely used in population genetic studies across a range of diverse organisms. In this study, we present the first SSR markers developed for A. fraxinifolium as well as their frequency and distribution based on transcriptome data. From transcriptome data, we identified more than 100 thousand sequences presenting microsatellites, with a predominant distribution of trinucleotide repeats. From the initial screening, we selected 20 microsatellite loci which were validated and evaluated for genetic indices in two natural populations. All loci were polymorphic, ranging from four to 11 alleles per locus. The observed and expected heterozygosities ranged from 0 to 1.0 and from 0.533 to 1.0, respectively, while the genetic differentiation (G_ST = 0.363) was greater within than between populations. The developed SSR loci from RNA-Seq data provides a foundation for future studies on genetic diversity and population structure, mating system, and gene flow for A. fraxinifolium populations and related species, aiming at conservation and management.

Population Structure of Phytophthora infestans from a Single Location in Poland Over a Long Period of Time in Context of Weather Conditions

Phytophthora infestans (Mont.) de Bary is a destructive potato pathogen. Changing weather conditions are among the factors that influence the pathogen population structure. In this study, 237 P. infestans isolates were collected from a single unprotected experimental field in an area with high late-blight pressure located in Boguchwała in the southeastern part of Poland during 15 growing seasons (2000-2014). The isolates were assessed for mating type, mitochondrial haplotype, resistance to metalaxyl, virulence, and polymorphism of 14 single-sequence repeat markers (SSRs). The results revealed 89 unique genotypes among the 237 P. infestans isolates. Eighty-seven isolates belonged to genotype 34_A1, which was detected in all the years of research except 2012. Isolates of P. infestans from individual years were very similar to each other, as shown by Nei's genetic identity based on 14 SSR markers. The obtained results on isolate characteristics were analyzed in terms of meteorological data (air temperature and precipitation) and indicated that frost, long winters, and hot, dry summers did not directly affect the P. infestans population structure. We described the variability in metalaxyl resistance and virulence among isolates of the P. infestans genotype 34_A1.

Genome-wide association study (GWAS) of major QTLs for bunch and oil yield related traits in Elaeis guineensis L

Oil palm (Elaeis guineensis Jacq.) is a long breeding cycle perennial crop with a genome size of 1.8 Gb. This is the first report of GWAS on large number of 310 African germplasm using 400 SSR markers till date. Highly significant correlation was found between leaf area (LA) and rachis length (RL) (0.75) followed by bunch weight (BW) and bunch index (BI) (0.65), whereas negative correlation was observed between bunch number (BN) and average bunch weight (ABW). First two principal component analysis (PCA) together explained maximum amount of variation (84.5 %). The PCA1 revealed that group 2 (Guinea Bissau and Cameroon) and group 4 (Zambia and Cameroon) genotypes are best suitable for BN, BI and BW traits. GWAS of six bunch yield and seven bunch oil yield traits with SSRs resulted in the identification 43 significant quantitative trait loci (QTLs) by mixed linear model (MLM) approach. Seven SSR loci were found to be linked to oil to dry mesocarp (ODM) on chromosomes 1,4,7,10,12 and 15. The SSR locus mEgCIR1753 for ODM was significantly linked at a p of ≤0.05 which explained 34.6 % of phenotypic variance. The important parameters like ODM, OWM and OB were located on 4, 10, 11 and 15 chromosomes. The leaf area and ODM were associated with candidate genes representing of low-temperature-induced 65 kDa proteins. The identified markers can be effectively used for marker assisted selection of high yielding oil palm genotypes.

Genetic and physiological variation in two strains of Japanese quail

Background

Detecting the genetic and physiological variations in two Japanese quail strains could be used to suggest a new avian model for future breeding studies. Consequently, two estimations were performed on two Japanese quail strains: gray quail strain (GJQS) and white jumbo quail strain (WJQS). The first estimation was conducted on carcass characteristics, breast muscles, breast concentration of collagen type I, and body measurements. In contrast, blood samples were collected for the second estimation for genomic DNA extraction and genetic analysis.

Results

A total of 62 alleles out of 97 specific alleles (63.92%) were detected overall loci (14 microsatellite loci) for the two strains. A total of 27 specific alleles of WJQS were observed, and 35 were obtained for GJQS. The percentage of similarity was 48.09% ranged from 4.35 with UBC001 to 100% with GUJ0051. WJQS had greater body weights and a higher value of pectoral muscle and supracoracoideus muscle than GJQS. The breast muscles of GJQS exhibited a higher concentration of type I collagen than the WJQS. Furthermore, males showed higher concentrations of collagen type I than females. WJQS showed a higher body length, chest girth, chest length, thigh length, thigh girth, drumstick length, and drumstick girth (cm) than GJQS. WJQS showed more significant differences in carcass traits compared with GJQS.

Conclusion

The physiological differences between WJQS and GJQS were ascertained with microsatellite markers, which indicated high polymorphism between these strains. These observations provided a scientific basis for evaluating and utilizing the genetic resources of WJQS and GJQS in a future genetic improvement program.

Transcriptome analysis of Anastrepha fraterculus sp. 1 males, females, and embryos: insights into development, courtship, and reproduction

BACKGROUND

Anastrepha fraterculus sp. 1 is considered a quarantine pest in several American countries. Since chemical control applied in an integrated pest management program is the only strategy utilized against this pest, the development of pesticide-free methods, such as the Sterile Insect Technique, is being considered. The search for genes involved in sex-determination and differentiation, and in metabolic pathways associated with communication and mating behaviour, contributes with key information to the development of genetic control strategies. The aims of this work were to perform a comprehensive analysis of A. fraterculus sp. 1 transcriptome and to obtain an initial evaluation of genes associated with main metabolic pathways by the expression analysis of specific transcripts identified in embryos and adults.

RESULTS

Sexually mature adults of both sexes and 72 h embryos were considered for transcriptome analysis. The de novo transcriptome assembly was fairly complete (62.9% complete BUSCO orthologs detected) with a total of 86,925 transcripts assembled and 28,756 GO annotated sequences. Paired-comparisons between libraries showed 319 transcripts differently expressed between embryos and females, 1242 between embryos and males, and 464 between sexes. Using this information and genes searches based on published studies from other tephritid species, we evaluated a set of transcripts involved in development, courtship and metabolic pathways. The qPCR analysis evidenced that the early genes serendipity alpha and transformer-2 displayed similar expression levels in the analyzed stages, while heat shock protein 27 is over-expressed in embryos and females in comparison to males. The expression of genes associated with courtship (takeout-like, odorant-binding protein 50a1) differed between males and females, independently of their reproductive status (virgin vs mated individuals). Genes associated with metabolic pathways (maltase 2-like, androgen-induced gene 1) showed differential expression between embryos and adults. Furthermore, 14,262 microsatellite motifs were identified, with 11,208 transcripts containing at least one simple sequence repeat, including 48% of di/trinucleotide motifs.

CONCLUSION

Our results significantly expand the available gene space of A. fraterculus sp. 1, contributing with a fairly complete transcript database of embryos and adults. The expression analysis of the selected candidate genes, along with a set of microsatellite markers, provides a valuable resource for further genetic characterization of A. fraterculus sp. 1 and supports the development of specific genetic control strategies.

Microsatellite Analysis of Genetic Diversity and Population Structure of the Iranian Kurdish Horse

Native breeds are essential for national stocks and genetic reservoir; therefore, the preservation of indigenous breeds is a key policy priority for countries around the world. Many conservationists would assert that genetic diversity is a prerequisite for adaptive evolution, and preserving genetic diversity will need conservation efforts for the long-term survival of domestic species. This study intended to evaluate the genetic diversity of the Iranian Kurdish horse population based on microsatellite indicators, which can partially prevent it from becoming extinct. Fifty-eight tail hair and blood samples were randomly collected from Kurdistan, Kermanshah, Ilam, West Azerbaijan, Isfahan, Kerman, Hamadan, and Tehran. Genomic DNA extraction was performed by a modified salting out method. The polymerase chain reaction amplification conditions were also separately undertaken for each marker. All microsatellite loci revealed polymorphisms in the studied population. Genetic variation was examined using 12 microsatellite loci (HMS7, HMS3, HMS2, HMS6, ASB2, ASB23, VHL20, HTG10, LEX33, ASB17, AHT4, and AHT5). We found that the means of the observed and effective number of alleles were 7.58 and 4.95, with the minimum and maximum values for each of these indices associated with the loci of HMS2 and ASB17, respectively. Moreover, the mean of observed and expected heterozygosity, polymorphism information content, and Shannon's Information Index of the Iranian Kurdish population were 0.77, 0.78, 0.75, and 1.67, respectively, indicating a high degree of genetic diversity in the entire studied population. More specifically, we acquired a range of new alleles in the Iranian Kurdish horse breed that differed in their genetic structure to those of other Iranian breeds in other studies. This study provides an exciting opportunity to improve our knowledge of genetic information which will be beneficial as a base to identify purebred Kurdish horses for a further Iranian Kurdish horse genetic and breeding program.

Microsatellite genotyping reveals extensive genetic diversity in bovine Neospora caninum from the humid Pampa region in Argentina

Neospora caninum is an apicomplexan protozoan and a major cause of abortion in cattle worldwide. In the Argentinian Humid Pampa, bovine neosporosis causes severe economic losses. Despite this, information on the genetic structure of N. caninum in this region is limited. Therefore, this study aimed to genetically characterize N. caninum isolates associated with bovine abortion in the Humid Pampa region. For this purpose, spontaneous bovine fetal tissues submitted for diagnosis to the Veterinary Diagnostic Service at INTA Balcarce during 2008-2019 were assessed by PCR, indirect fluorescent antibody test (IFAT), and histologic analysis. PCR-positive samples were tested by multilocus microsatellite genotyping (MLGs) using 9 microsatellite markers. Thirty-one different genotypes were identified from 32 samples with at least seven markers. Argentinian MLGs were grouped into two clonal clusters when analyzed using eBURST network and principal coordinate analysis. No segregation based on the year of collection, animal biotype, or geographic origin was observed. In addition, the presence of linkage disequilibrium supported the clonal propagation of Argentinian MLGs. One Argentinian subpopulation was associated with isolates from Spain, Uruguay, Brazil, and Mexico, and the other one was linked to isolates from Scotland, Spain, and Germany. These findings reveal the presence of two clonal subpopulations of N. caninum in the Humid Pampa.

Genetic characterization and population structure of different coat colour variants of Badri cattle

The present study aimed to genetically characterize the Badri cattle and its three colour variants and assess their population structure using 24 microsatellite markers. Out of 96 animals analyzed, 32 each were collected from grey (GVBC), brown (BrVBC) and black (BVBC) colour variants of Badri cattle (BC). The genetic diversity parameters including allele frequencies, observed and effective number of alleles, observed and expected heterozygosity, PIC, Shannon's indices and F-statistics were estimated using POPGENE software. Bottleneck analysis was performed using both qualitative and quantitative approaches. A total of 274 alleles (50 private and 224 shared) were scored for BC, GVBC, BrVBC and BVBC with mean number of 11.417, 9.083, 9.125 and 9.083 alleles, respectively. All populations exhibited average heterozygosity estimate > 0.5 indicating existence of substantial genetic variability, concurrent with revelations from Shannon's indices. Observed mean PIC estimates (> 0.74) were indicative of optimum informativeness of used microsatellite markers. The mean inbreeding estimates (F) in GVBC, BrVBC and BVBC were 0.041, - 0.024 and 0.016, respectively. The pair wise genetic (> 0.91) pointed towards similarity between different colour variant populations. STRUCTURE analysis also revealed clear admixture for the three Badri colour variants indicating absence of genetic differentiation. The present study revealed first-hand information that populations of Badri cattle with different phenotypes with respect to coat colour are genetically related and can be considered as a single breed. The comprehensive knowledge generated for Badri cattle will help in designing breeding plan for its genetic improvement and deciding the conservation priorities.

Genome-wide microsatellites and species specific markers in genus Phytophthora revealed through whole genome analysis

Genome wide microsatellite maps shall support Phytophthora systematics through the development of reliable markers, enabling species discrimination and variability analyses. Whole genome sequences of 17 Phytophthora accessions belonging to 14 species were retrieved from GenBank and the genome-wide microsatellites in each species were mined. A total of 51,200 microsatellites, including dinucleotide to decanucleotide motifs, have been identified across all the species and each one was characterized for uniqueness and repeat number. The P. infestans T30-4 genome had the highest (6873) and P. multivora 3378 had the lowest number of microsatellites (1802). Dinucleotide motifs (63.6%) followed by trinucleotide motifs (30.1%) were most abundant in all the genome. From 14 species, 250 microsatellites which are unique for the respective genomes are detailed along with their primer combinations and product sizes. P. sojae had the highest number of unique microsatellite motifs. Genome wide microsatellite maps for all the 14 Phytophthora species including the chromosome, position, motif, repeat number, forward and reverse primer sequences and expected PCR product size, for every microsatellite are presented. Markers based on the unique microsatellites could be used to identify each species, whereas the ones common to all species could be used to identify the genetic variability. Furthermore, to confirm the results, pure cultures of P. capsici, P. nicotianae and P. palmivora were procured from the Phytophthora Repository, DNA was isolated and the unique markers were screened across the species. The characteristic markers developed have confirmed the genome analysis results.

Microsatellite fingerprinting and analysis of intra-population divergence in morphotaxonomic traits in a large Musa (AAB genome) germplasm

Plantain (Musa spp. AAB genome) is a major staple with an incredibly enormous potential for domestic and global trade that can serve as a vital source of income for many developing countries. The fruits are extraordinarily significant, providing an important and cheap source of dietary energy, vitamins, and several essential minerals to millions of consumers within the humid and sub-humid tropics. As molecular characterization is important for sustainable exploitation of crops, the extent of genetic and agro-morphological differentiation in a large Musa population of 109 accessions was evaluated using 10 microsatellite (SSR) markers and 14 morphotaxonomic descriptors, as a basis for selection of high yielding varieties. Measurement of DNA diversity delineated the plantains into 2 major groups and 8 distinct clusters, each with several sub-clusters. There was equally a very wide diversity detected in morphotaxonomic traits including pseudostem girth, number of bunches per plant, number of hands per bunch, number of fruits per bunch, number of fruits per hand, bunch weight, length of plant cycle, and flowering to harvest interval, which varied significantly (p < 0.05) amongst the accessions. Selection based on cluster analysis using standard morphological data also delineated the cultivars into 8 distinct clusters, with one of these containing samples that were most distant to all others and exhibited a 'double bunching' phenotype at fruiting; tacitly implying the presence of significant variability that symbolizes an excellent opportunity to bring about genetic improvement through selection of improved varieties. Principal component analysis based on morphotaxonomic traits revealed 7 attributes which contributed to 79.95% of total variation that was quite similar to the 71.87% detected using microsatellite fingerprinting. Correlation analysis between selected agronomic traits demonstrated that pseudostem girth was positively associated with bunch weight, number of hands per bunch, number of fruits per bunch, number of fruits per hand, and flowering to harvest interval across all accessions. Collectively, the data in this study suggest that plantain accessions with very unique traits expressing paramount horticultural significance are available within the diverse germplasm evaluated and are currently being collected for future breeding purposes to broaden the genetic base of this important crop.

First de novo genome specific development, characterization and validation of simple sequence repeat (SSR) markers in Genus Salvadora

Salvadoraceae constitutes ecologically imperative desert families of 3 genera-Azima, Dobera and Salvadora. Under genus Salvadora of this family, S. oleoides is a keystone species of socio-economic and medicinal value. This species naturally grows in the arid zones but currently experiencing severe fragmentation due to land use change and reduced regeneration, which may have resulted in the depletion of genetic diversity. Hence, it is up-most important to develop genomic resources for studying the population genetics in S. oleoides. This study aims to develop robust microsatellites markers, which were not yet reported in genus Salvodora due to lack of genome sequence information. We developed novel microsatellites markers in S. oleoides using Illumina paired-end sequencing technology. In total, 14,552 simple sequence repeat (SSR) markers were successfully designed from 21,055 microsatellite repeats detected in the 13 Gb raw sequence data. Afterwards, a subset of 101 SSRs were randomly selected and validated, 94 primers were successfully amplified and 34 showed polymorphisms. These SSRs were used to estimate the measures of genetic diversity in three natural populations of state Rajasthan and Gujarat. Importantly, average number of alleles (N_a), observed heterozygosity (H_o), expected heterozygosity (H_e), and polymorphism information content (PIC) were recorded as 2.4, 0.529, 0.357, and 0.326, respectively. Furthermore, 15 primers were evaluated in S. persica for cross-transferability, and all were successfully amplified but only eight showed polymorphisms. This study has been conducted first time for S. oleoides and pioneer among the native species of arid-zone in India.

Novel microsatellite markers for evaluation of genetic diversity in the tetraploid flame azalea, Rhododendron calendulaceum (Ericaceae)

Microsatellite markers have become a popular and useful tool for investigating evolutionary processes at shallow taxonomic scales such as within a species or between extremely closely related species. Rhododendron sect. Pentanthera is a closely related group of deciduous azaleas that demonstrate both naturally occurring and horticulturally derived hybridization. Two species, flame azalea and Cumberland azalea, represent a particularly recalcitrant evolutionary problem, which will benefit from the development of rapidly evolving molecular markers. Microsatellite markers were specifically developed for Rhododendron calendulaceum, the flame azalea, for use in studies of genetic structure and potential hybridization with its close relative Rhododendron cumberlandense, the Cumberland azalea. Forty-eight primer pairs designed from paired-end Illumina MiSeq data were screened for robust amplification. Sixteen of these pairs were PCR-amplified in the presence of fluorescently labeled primers and genotyped in 66 flame azalea individuals from three geographically dispersed populations. Fifteen primer pairs were both reliable and polymorphic and exhibit ample variability for use in downstream population-level investigations. Cross-amplification in all other members of Rhododendron sect. Pentanthera was highly successful, suggesting broad utility across the entire clade. The novel microsatellite markers presented here functioned well within the target species and amplified with high success in the remaining members of the clade. They represent a significant improvement to the genetic toolkit available for Rhododendron sect. Pentanthera, and particularly for the flame/Cumberland azalea evolutionary problem.

SSR loci survey of technical hemp cultivars: The optimization of a cost-effective analyses to study genetic variability

Our study aimed to optimize a selection of a suitable combination of SSRs (Simple Sequence Repeats) for determination of technical Cannabis cultivars and genetic variability level. We used sequences of 23 published SSR families (107 alleles) and amplified them in 28 cultivars. One of the alleles possesses no selective information (SSR family CAN1660) due to its presence in every single tested cultivar. We excluded it, together with another 11 least informative alleles. After data filtration, we used 96 alleles to do recursive sub-sampling of random alleles' sets. We found a minimal set of 8 alleles (in three different combinations) to distinguish 28 analyzed cultivars from each other. Our results contribute to saving resources and to reduce the performance time of the molecular analysis.

Comparative population genetic analyses suggest hybrid origin of R hododendron pubicostatum, an endangered plant species with extremely small populations endemic to Yunnan, China

Gene flow between sympatric congeneric plants is thought to be very common and may pose serious threats to endangered species. In the present study, we evaluate the genetic diversity and divergence of three sympatric Rhododendron species in Jiaozi Mountain using newly developed microsatellites through the Illumina MiSeq sequencing approach. Genetic diversity of all three Rhododendron species studied was moderate in comparison to genetic parameters previously reported from species of this genus. Interestingly, genetic structure analysis of the three species identified a possible hybrid origin of the threatened Rh. pubicostatum. This sympatry should be considered a unimodal hybrid zone, since R h. pubicostatum is predominant here. Unimodal hybrid zones are uncommon in Rhododendron, despite the fact that hybridization frequently occurs in the genus. Issues pertaining to the conservation of R h. pubicostatum resulting from admixture of genetic material from its parental species are discussed.

Genetic structure, gene flow pattern, and association analysis of superior germplasm resources in domesticated upland cotton (Gossypium hirsutum L.)

Gene flow patterns and the genetic structure of domesticated crops like cotton are not well understood. Furthermore, marker-assisted breeding of cotton has lagged far behind that of other major crops because the loci associated with cotton traits such as fiber yield and quality have scarcely been identified. In this study, we used 19 microsatellites to first determine the population genetic structure and patterns of gene flow of superior germplasm resources in upland cotton. We then used association analysis to identify which markers were associated with 15 agronomic traits (including ten yield and five fiber quality traits). The results showed that the upland cotton accessions have low levels of genetic diversity (polymorphism information content = 0.427), although extensive gene flow occurred among different ecological and geographic regions. Bayesian clustering analysis indicated that the cotton resources used in this study did not belong to obvious geographic populations, which may be the consequence of a single source of domestication followed by frequent genetic introgression mediated by human transference. A total of 82 maker-trait associations were examined in association analysis and the related ratios for phenotypic variations ranged from 3.04% to 47.14%. Interestingly, nine SSR markers were detected in more than one environmental condition. In addition, 14 SSR markers were co-associated with two or more different traits. It was noteworthy that NAU4860 and NAU5077 markers detected at least in two environments were simultaneously associated with three fiber quality traits (uniformity index, specific breaking strength and micronaire value). In conclusion, these findings provide new insights into the population structure and genetic exchange pattern of cultivated cotton accessions. The quantitative trait loci of domesticated cotton identified will also be very useful for improvement of yield and fiber quality of cotton in molecular breeding programs.

Genome-wide microsatellite characteristics of five human Plasmodium species, focusing on Plasmodium malariae and P. ovale curtisi

Microsatellites can be utilized to explore genotypes, population structure, and other genomic features of eukaryotes. Systematic characterization of microsatellites has not been a focus for several species of Plasmodium, including P. malariae and P. ovale, as the majority of malaria elimination programs are focused on P. falciparum and to a lesser extent P. vivax. Here, five human malaria species (P. falciparum, P. vivax, P. malariae, P. ovale curtisi, and P. knowlesi) were investigated with the aim of conducting in-depth categorization of microsatellites for P. malariae and P. ovale curtisi. Investigation of reference genomes for microsatellites with unit motifs of 1–10 base pairs indicates high diversity among the five Plasmodium species. Plasmodium malariae, with the largest genome size, displays the second highest microsatellite density (1421 No./Mbp; 5% coverage) next to P. falciparum (3634 No./Mbp; 12% coverage). The lowest microsatellite density was observed in P. vivax (773 No./Mbp; 2% coverage). A, AT, and AAT are the most commonly repeated motifs in the Plasmodium species. For P. malariae and P. ovale curtisi, microsatellite-related sequences are observed in approximately 18–29% of coding sequences (CDS). Lysine, asparagine, and glutamic acids are most frequently coded by microsatellite-related CDS. The majority of these CDS could be related to the gene ontology terms “cell parts,” “binding,” “developmental processes,” and “metabolic processes.” The present study provides a comprehensive overview of microsatellite distribution and can assist in the planning and development of potentially useful genetic tools for further investigation of P. malariae and P. ovale curtisi epidemiology.

Genetic characterization of Neospora caninum from Northern Italian cattle reveals high diversity in European N. caninum populations

Recent studies have revealed extensive genetic variations among Neospora caninum, a cyst-forming protozoan parasite that is one of the main causes of bovine abortion in the cattle industry worldwide. Previous genetic studies based on multilocus microsatellite genotyping (MLGs) of different Ibero-American populations showed a high genetic diversity. These studies provided clear clues of a predominant clonal propagation in cattle and population sub-structuring partially associated with geographical origin. Although, these reports were limited to a reduced number of countries. In this study, the N. caninum isolates from aborted bovine fetuses and stillbirths and a goat abortion from Northern Italy were investigated genetically using 9 microsatellite markers. Complete or nearly complete isolate profiles were obtained from 30 fetuses and stillbirths. An extensive genetic diversity was also found in this Italian N. caninum population. The study of genetic relationships among Italian MLGs using network (eBURST) and principal component analyses based on the allele-sharing coefficient (PCoA) showed different clonal subpopulations disseminated throughout Northern Italy without apparent segregation depending on the geographic origin, cattle breed, or time of collection. The presence of linkage disequilibrium supports a predominant clonal propagation of Italian N. caninum. In addition, most of Italian MLGs segregated from other global populations including Spain, Argentina, Mexico, Brazil, Germany, and Scotland, suggesting the existence of specific N. caninum subpopulations in the Northern Italy and different subpopulations of N. caninum circulating in Europe.

Development and characterization of ten novel microsatellite loci for the emu (Dromaius novaehollandiae) and genetic diversity of Japanese farm populations

The emu (Dromaius novaehollandiae) is a useful poultry animal farmed for fat, meat, and eggs. Genetic structure and relationships among farmed emu populations in Japan are unknown and the number of microsatellite markers for genetic analysis of the emu is insufficient. In this study, we isolated 16 microsatellites from the emu genome and developed ten new microsatellite markers. These microsatellite markers were used to characterize three farm emu populations in Japan. The number of alleles ranged from 3 to 13 and the expected (H_E) and observed heterozygosity (H_O) of these microsatellite loci was 0.187-0.802 and 0.179-0.647, respectively. The polymorphic information content ranged from 0.176 to 0.786. Positive inbreeding coefficient (F_IS) values were detected in all tested populations, and they ranged from 0.027 to 0.540. These results suggest that farm populations of the emu in Japan resulted from inbreeding. The fixation index (F_ST) values ranged from 0.026 to 0.061, and phylogenetic trees and population structure analysis confirmed no definitive genetic differentiation among the three populations. Therefore, these populations are at a relatively low level of genetic differentiation at present. The microsatellite markers developed in our study can be utilized for genetic analysis and preservation of genetic resources in the emu.

Biodiversity of Pyricularia oryzae Cav. in rice-growing regions of the south of Russia using PCR method

The purpose of this research by the way of investigating the molecular genetic structure of a highly variable fungal phytopathogen Pyricularia oryzae Cav., to determine effective genes for the development of a strategy for immunogenetic protection against rice blast in conditions of epiphytotic development of the disease in the south of Russia, which would combine high efficacy with both environmental friendliness and resource and energy saving, to ensure country's food security. The knowledge of local pathotype diversity of Pyricularia oryzae Cav. and the (a)virulence genes in rice-growing regions of Russia may allow the prediction of new races and its interaction in local agro-ecology. The identification of virulence gene may become an indispensable theoretical basis for the development of genetic sources with long-lasting resistance to rice blast. Based on molecular and genetic approaches, the genetic structure and biodiversity of the phytopathogenic fungus Pyricularia oryzae Cav. in the south of Russia were considered. The monitoring was studied and it isolated 57 strains of the pathogen from the damaged herbal material collected from the fields in eight agro-ecological rice-growing regions of the Krasnodar Region (Russian Federation): Krasnoarmeysky, Kalininsky, Krymsky, Abinsky, Temryuksky, Seversky, Slavyansky districts, Krasnodar, Rostov Region (Russian Federation)-Proletarsky district and the Republic of Adygea (Russian Federation). A multiplex PCR technique was applied on the basis of fragment analysis to identify the virulent fungal isolates. 33 fungal genotypes with unique genetic profiles were identified among the studied races of Pyricularia oryzae Cav. Their DNA profiles were created. The studied isolates of the pathogen of rice blast were classified using morphological and microbiology cultural features. Based on the phytopathological test using differentiation rice varieties, the quantitative and qualitative composition of (a)virulence genes in fungal races was established. Effective genes for pathogen resistance, which are recommended for breeding programs for the development of rice varieties resistant to rice blast, were identified in the south of Russia.

Short Tandem Repeats Used in Preimplantation Genetic Testing of Β-Thalassemia: Genetic Polymorphisms For 15 Linked Loci in the Vietnamese Population

BACKGROUND

β-thalassemia is one of the most common monogenic diseases worldwide. Preimplantation genetic testing (PGT) of β-thalassemia is performed to avoid affected pregnancies has become increasingly popular worldwide. In which, the indirect analysis using short tandem repeat (STRs) linking with HBB gene to detect different β-globin (HBB) gene mutation is a simple, accurate, economical and also provides additional control of contamination and allele-drop-out ADO.

AIM

This study established microsatellite markers for PGT of Vietnamese β-thalassemia patient.

METHODS

Fifteen (15) STRs gathered from 5 populations were identified by in silico tools within 1 Mb flanking the HBB gene. The multiplex PCR reaction was optimized and performed on 106 DNA samples from at-risk families.

RESULTS

After estimating, PIC values were ≥ 0.7 for all markers, with expected heterozygosity and observed heterozygosity values ranged from 0.81 to 0.92 and 0.53 to 0.86, respectively. One hundred percent of individuals had at least seven heterozygous markers and were found to be heterozygous for at least two markers on either side of the HBB gene.

CONCLUSION

In general, a pentadecaplex marker (all < 1 Mb from the HBB gene) assay was constituted for β-thalassemia PGT on Vietnamese population.

Strong genetic structure revealed by microsatellite variation in Callicarpa species endemic to the Bonin (Ogasawara) Islands

Adaptive radiation is the diversification of a founding population into multiple taxa that are differentially adapted to diverse ecological niches. The three Callicarpa (Lamiaceae) species endemic to the Bonin Islands are considered to represent an example of adaptive radiation on oceanic islands. All three species are distributed in the Chichijima Island Group and grow in different habitats, while only one species, C. subpubescens, is distributed among other island groups. Particularly, in the Hahajima and Mukojima Island Groups, C. subpubescens grows in various habitats and shows relatively high morphological variation. We investigated genotypes of the three Callicarpa species at 14 microsatellite markers to elucidate genetic differentiation within and between species or island groups and between different habitats or morphologies. We found that genetic differentiation within C. subpubescens in the Hahajima and Mukojima Island Groups was equally as high as that between the three species in the Chichijima Island Group, while differentiation within C. subpubescens in the Chichijima Island Group was much lower. Analyses such as a Bayesian clustering analysis showed that genetically distinct groups were associated with the three species in the Chichijima Island Group, whereas they showed strong genetic structure within C. subpubescens in the Hahajima and Mukojima Island Groups among different habitats and morphologies. These results indicated that ecological diversification occurred in the Hahajima and Mukojima Island Groups. Meanwhile, high genetic differentiation among different island groups was also observed, reflecting isolation by distance. It implies that non-ecological factors such as geographic isolation also played important roles in genetic differentiation in Callicarpa species in the Bonin Islands. These findings suggest that the Callicarpa species in the Bonin Islands are differentiated into multiple genetic groups by both ecological and non-ecological factors.

Genetic variability and effective population size in Hymenaea stigonocarpa (Fabaceae) germplasm collection: tools for breeding programs and genetic conservation

The conservation of plant genetic resources is essential for breeding programs. Regarding the native species of the Brazilian Cerrado biome, many studies have demonstrated their high potential for use in both medicines and foods. Hymenaea stigonocarpa, a tree with wide occurrence in the Cerrado, has economic importance, and due its extractive use, the establishment of a breeding program is relevant for sustainable use and conservation. Thus, the first germplasm collection of the species was installed at the Federal University of Goiás (UFG). To know the magnitude of genetic variability and how it was distributed in the collection, 353 individuals, distributed in 119 families from 24 subpopulations collected in the Cerrado biome, were genotyped using capillary electrophoresis. Nine pairs of microsatellite markers were genotyped. The UFG germplasm collection showed a high level of genetic diversity (mean [Formula: see text] = 0.554) at the evaluated loci. By Analysis of Molecular Variance (AMOVA), a significant genetic structure was detected (θ_P = 0.152, p < 0.01), which was expected since the subpopulations that originated the germplasm collection were collected in geographically distant locations. In addition, the germplasm collection had a population effective size of 54.9 and presented an allelic representation of 79.89% compared to 32 natural subpopulations. These results demonstrate that the germplasm collection preserves a high genetic diversity of H. stigonocarpa with a population effective size considered sufficient for the conduction of a breeding program.

Genetic diversity and relationships among three Southern African Nguni cattle populations

The Nguni cattle breed has distinct populations that are adapted to the different ecological zones of Southern Africa. This study was carried out to assess genetic diversity and establish the relationships among South African (SA), Mozambican (Landim), and Swazi Nguni cattle populations, using 25 microsatellite markers. Genotypic data were generated from deoxyribonucleic acid (DNA) samples of 90 unrelated individuals of the three cattle populations, collected from government conservations and stud herds. DNA profiles of five local beef breeds were used as the reference populations. Most of the 25 microsatellite markers were highly polymorphic across the studied populations, with an overall polymorphic information content (PIC) mean of 0.676. Genetic diversity within populations was high with expected heterozygosity varying from 0.705 ± 0.024 (Landim) to 0.748 ± 0.021 (SA Nguni) and mean number of alleles being highest in the SA Nguni (7.52 ± 0.42). Average observed heterozygosity (0.597 ± 0.046) compared to the expected heterozygosity (0.719 ± 0.022) was lowest for the Swazi Nguni, which also had a high number of Hardy-Weinberg Equilibrium (HWE) deviated loci (13), confirming the relatively high level of inbreeding (0.158 ± 0.058) in that population. Analysis of molecular variance revealed only 9.61% of the total variation between the populations and 90.39% within populations. A short genetic distance (0.299) was observed between Landim and Swazi Nguni, with the SA Nguni (> 0.500) being the most genetically distant population. The distant relationship between SA Nguni and the other two Nguni cattle populations was further confirmed by a principal coordinates analysis. The three Nguni populations clustered independently from each other, despite some evidence of admixture. Therefore, it can be concluded that SA Nguni, Landim, and Swazi Nguni populations in Southern Africa exhibit high levels of genetic diversity and are genetically distant; with the two latter populations being less genetically apart. These results present useful information for the development of strategies for regional management of animal genetic resources, through conservation and sustainable utilisation.

Genetic assessment of three Fagaceae species in forest restoration trials

Restoring isolated patches of forest ecosystems in degraded landscapes could potentially lead to genetic loss and inbreeding. Therefore, this study determined the occurrence of genetic diversity among the tree species Castanopsis tribuloides, C. calathiformis, and Lithocarpus polystachyus all of which were proven previously to be effective native tree species in the restoration of upland evergreen forests in northern Thailand when using the seed sample collection method. We tested our hypothesis as to whether the genetic diversity of a plant population that had been planted from the seeds of 4–6 adult trees would be lower and whether incidences of fixation index (Fis) would be higher among the second generation seedlings of these three Fagaceae species in isolated forest restoration trial plots. Microsatellite primers were selected from the entire genome sequence of C. tribuloides and the genetic sequences of C. tribuloides, L. polystachyus, and C. calathiformis were analyzed. Our results indicated a high degree of genetic diversity (He) in C. tribuloides (0.736) and C. calathiformis (0.481); however, a low level of genetic diversity was observed in L. polystachyus (0.281) within the restored forest. The fixation index for the second generation of L. polystachyus and C. calathiformis in the restored forest showed evidence of inbreeding. These results imply the efficiency of the seed sample collection method and verify that it does not reduce the level of genetic diversity in C. tribuloides and C. calathiformis. However, it may result in incidences of an inbreeding phenomena, suggesting the need to increase the number of adult trees used at the seed collection stage.

Genetic diversity among cultivated and wild Panax ginseng populations revealed by high-resolution microsatellite markers

Background

Ginseng (Panax ginseng Meyer) is one of the world's most valuable medicinal plants with numerous pharmacological effects. Ginseng has been cultivated from wild mountain ginseng collections for a few hundred years. However, the genetic diversity of cultivated and wild ginseng populations is not fully understood.

Methods

We developed 92 polymorphic microsatellite markers based on whole-genome sequence data. We selected five markers that represent clear allele diversity for each of their corresponding loci to elucidate genetic diversity. These markers were applied to 147 individual plants, including cultivars, breeding lines, and wild populations in Korea and neighboring countries.

Results

Most of the 92 markers displayed multiple-band patterns, resulting from genome duplication, which causes confusion in interpretation of their target locus. The five high-resolution markers revealed 3 to 8 alleles from each single locus. The proportion of heterozygosity (H_e) ranged from 0.027 to 0.190, with an average of 0.132, which is notably lower than that of previous studies. Polymorphism information content of the markers ranged from 0.199 to 0.701, with an average of 0.454. There was no statistically significant difference in genetic diversity between cultivated and wild ginseng groups, and they showed intermingled positioning in the phylogenetic relationship.

Conclusion

Ginseng has a relatively high level of genetic diversity, and cultivated and wild groups have similar levels of genetic diversity. Collectively, our data demonstrate that current breeding populations have abundant genetic diversity for breeding of elite ginseng cultivars.