Simple Sequence Repeat Alleles Research Articles

Understanding the Temporal Dynamics of Invasive Late Blight Populations in India for Improved Management Practices.

The microbial oomycete pathogen Phytophthora infestans causes severe epidemics of potato late blight in crops globally. Disease management benefits from an understanding of the diversity of pathogen populations. In this study, we explore the dynamics of P. infestans populations in the late blight-potato agro-ecosystem across the Indian subcontinent. Investigations of the macroecological observations at the field level and microbial ecological principles provided insights into future pathogen behavior. We use a comprehensive simple sequence repeat allele dataset to demonstrate that an invasive clonal lineage called EU_13_A2 has dominated populations over 14 years across India, Bangladesh, and Pakistan. Increasing levels of subclonal variation were tracked over time and space, and, for the first time, populations in Asia were also compared with the source populations from Europe. Within India, a regional pathogen population structure was observed with evidence for local migration, cross-border movement between surrounding countries, and introductions via imports. There was also evidence of genetic drift and between-season transmission of more strongly pathogenic subclones with a complete displacement of some subclonal types. The limited introduction of novel genotypes and the use of resistant potato cultivars could contribute to the dominance of the 13_A2 lineage. The insights will contribute to the management of the pathogen in these key global potato production regions.

High throughput pre-breeding evaluation of Greek oregano (Origanum vulgare L. subsp. hirtum) reveals multi-purpose genotypes for different industrial uses

Origanum vulgare L. subsp. hirtum (commonly known as Greek oregano) is a perennial species of the Lamiaceae family that counts numerous applications in the food and pharmaceutical industry. The exploitation of Greek oregano germplasm lies in its unique diversity in secondary metabolites, which are accumulated in the aerial parts of the plant. For the industrial exploitation of this crop the starting germplasm is of high importance in terms of valorizing well characterized chemotypes with desired and stable agronomic and phytochemical traits. For this reason, a pre-breeding evaluation of twenty-one accessions collected and preserved under the same environmental conditions was performed in order to develop a descriptive database containing: a) morphometric traits, b) the genetic structure, c) the extensive metabolic fingerprint in terms of volatile composition, polyphenolic and triterpenoid content, and d) the ‘bio-activity’ on the embryonic development of Ascaridia galli eggs for highly divergent accessions. This study revealed the existence of essential oil rich chemotypes superior in morphometric characteristics, containing high carvacrol content (> 75%) and traces of thymol (< 5%), according to the requested international standards. Apart from genotypes considered as ‘high yield essential oil-producers’ (> 6%), accessions of highly productivity of ‘green’ raw materials rich in polyphenols and triterpenoids were also identified. According to their rosmarinic acid content, Greek oregano accessions were classified in three groups; 1) those with significantly high concentration (1640–2726 mg 100 g−1 dry weight), 2) those expressing intermediate content (1103–1200 mg 100 g−1 dry weight), and 3) the ones with significantly low content (< 873 mg 100 g−1 dry weight). A total of 118 polymorphic alleles were identified using sequence-related amplified polymorphism (SRAPs) and simple sequence repeat (SSRs) markers, while 2 genetic clusters based on a single data matrix with SRAPs and SSRs alleles, were identified. The presence of private bands in some accessions was also observed, which can be used in future breeding programs for germplasm authentication purposes. As a result this study provides a comprehensive knowledge on metabolic and genetic diversity of Greek oregano accessions native to Greece, as well as powerful tools for the selection of starting genetic materials for subsequent breeding studies to create superior cultivars. The multifaceted approach was developed to exploit the genetic resources of Greek oregano in further breeding programs for subsequent selection of genotypes with desired traits.

Genetic diversity of fig (Ficus carica L.) germplasm from the Mediterranean basin as revealed by SSR markers

Fig (Ficus carica L.) tree is cultivated worldwide and is highly appreciated for its fruit, which is consumed fresh or dried, having high nutritional and pharmaceutical value and for these reasons there is an increasing interest for its cultivation. In the present study, an ex situ collection of 60 fig accessions (41 indigenous Greek and 19 from other Mediterranean countries) was established and its diversity was analyzed using eight simple sequence repeat (SSR) loci. Greek fig genotypes showed relatively low allelic variation (the average number of SSR alleles per locus was 3.75), an excess of heterozygosity (mean He = 0.489 and Ho = 0.557), and extensive outbreeding (mean F index − 0.151). Cluster analysis showed that the established fig population exhibited weak genetic structure, with most of the genetic variation (89%) being present within individual members of the clusters. Both cluster and principal coordinate analysis confirmed that there is little correlation between genetic makeup and geographical origin of the fig accessions. Polymorphism information content with an average of 0.421 was reasonably informative. An identification key scheme for fig cultivars that will be useful in cultivar discrimination and intellectual property protection was developed. This work will contribute to a sustainable fig production regionally and worldwide, through the establishment and conservation of a reference fig collection, providing germplasm for future breeding efforts.

DNA databases of an important tropical timber tree species Shorealeprosula (Dipterocarpaceae) for forensic timber identification

International timber trade communities are increasingly demanding that timber in the wood supply chain be sourced from sustainably harvested forests and certified plantations. This is to combat illegal logging activities to prevent further depletion of our precious forests worldwide. Hence, timber tracking tools are important to support law enforcement officials in ensuring only sustainably harvested timbers are traded in the market. In this study, we developed chloroplast DNA (cpDNA) and simple sequence repeat (SSR) databases as tracking tools for an important tropical timber tree species, Shorealeprosula from Peninsular Malaysia. A total of 1410 individual trees were sampled from 44 natural populations throughout Peninsular Malaysia. Four cpDNA regions were used to generate a cpDNA haplotype database, resulting in a haplotype map comprising 22 unique haplotypes derived from 28 informative intraspecific variable sites. This cpDNA database can be used to trace the origin of an unknown log at the regional level. Ten SSR loci were used to develop the SSR allele frequency database. Bayesian cluster analysis divided the 44 populations into two genetic clusters corresponding to Region A and Region B. Based on conservativeness evaluation of the SSR databases for individual identification, the coancestry coefficients (θ) were adjusted to 0.1900 and 0.1500 for Region A and B, respectively. These databases are useful tools to complement existing timber tracking systems in ensuring only legally sourced timbers are allowed to enter the wood supply chain.

Genetic characterization of cultivated apple (Malus x domestica Borkh.) in Morocco using microsatellite (SSR) markers

Genetic diversity of 27 apple genotypes from four geographical regions of Morocco was analyzed using 26 simple sequence repeat (SSR) primers. In total, 195 polymorphic SSR alleles were detected, with sizes ranging from 78 to 209 bp. The results obtained for the average number of alleles per locus (7.5), effective number of alleles (4.62), Shannon information index (1.66), expected heterozygosity (0.76), observed heterozygosity (0.74) and polymorphism information content (0.76) showed a moderate level of polymorphism, which suggests that Moroccan apple cultivars exhibit significant genetic diversity. Over the 26 SSR loci used, the probability of identity P (ID) was 4.62 10 −29 indicating that most markers were highly discriminating and powerful for cultivars characterization. The principal coordinate analysis and hierarchical classification suggested the presence of four well defined groups, which was confirmed later by model based population structure. Furthermore, strong genetic differentiation between these four groups was also detected (FST = 0.28) . Most of the individuals segregated into the four groups showing a membership coefficient greater than 0.80, which indicates their better genetic integrity. A parentage analysis, however, shows that cultivars from the four regions are minimally hybridized. After comparing SSR profiles and genotypes names, we conclude that the problem of homonyms and/or labeling errors appear in the studied cultivars.Thus, based on genetic profiles, two individuals (Beldi 1/Beldi 2 and Laakri 5/Laakri 6) found to be duplicated. Additionally, some cultivars with the same name are grouped in different clusters suggesting the existence of possible homonymy. Lastly, the present work confirms the usefulness of SSR markers for the elimination of duplications and characterization of diversity and hybrid characters of apple genotypes in Morocco.

One plus one makes seven: Intricate phylogeographic patterns in Odontites vernus (Orobanchaceae: Rhinantheae) in the Iberian Peninsula

The Odontites vernus group is the most widespread of the genus Odontites, occupying the temperate regions of Eurasia and northern Morocco. The group contains three species, all inhabiting the Iberian Peninsula, where O. vernus s.l. (sensu lato) exhibits remarkable morphological variability and includes diploid and tetraploid individuals corresponding to the two subspecies that occur there. We collected 301 individuals from 100 sampling sites covering the entire distribution of O. vernus in the Iberian Peninsula and genotyped them using 12 simple sequence repeat (SSR) markers. Their ploidy level was estimated by flow cytometry, and two cpDNA regions (rps16 intron and trnK-rps16) were sequenced. We found 129 diploids and 172 tetraploids distributed following a mosaic parapatry model, while only two mixed-ploidy populations were discovered. The 20 haplotypes found fit two well-defined haplogroups, to some extent correlated with estimated ploidy levels. The frequencies of the SSR alleles shared by both cytotypes, as well as those of the private alleles corresponding to the tetraploid cytotype, indicate that tetraploids likely originated at least twice through autopolyploidy. Additionally, the results from SSR markers were structured in a higher number of groups than did the cpDNA sequences. Thus, the genetic distance analysis detected four groups, but the Bayesian analysis of population structure identified seven, with only low levels of gene flow detected among groups. The distributions of the seven genetic groups coincide with well-known refugium areas within the Iberian Peninsula during the climatic oscillations of the Quaternary. Thus, the results give additional support to the “refugia within refugia” hypothesis.

Method for identification of 10 SSR markers from monkey genomes and its statistical inference with One & Two-way ANOVA

DNA tracts that include simple sequence repeats (SSRs), sometimes known as genetic "stutters), are composed of a few to many tandem repetitions of a short base-pair motif. These sequences frequently mutate, changing the amount of repetitions. SSRs are frequently found in promoters, untranslated regions, and even coding sequences, therefore these alterations can significantly affect practically every aspect of gene activity. SSR alleles can also contribute to normal diversity in brain and behavioural features. Mutational expansion of certain triplet repeats is the cause of a number of inherited neurodegenerative diseases. Due to its importance in genetic research, in this paper we explored Ten SSR markers TAGA, TCAT, GAAT, AGAT, AGAA, GATA, TATC, CTTT, TCTG and TCTA that are identified from the genomes of Eleven distinct monkeys: A.Nancymaae, C.C.Imitator, C.Atys, M.Leucophaeus, P.Paniscus, R.Bieti, R.Roxellana, S.Boliviensis, T.Syrichta, C.A.Palliatus and M.Nemestrina using pattern matching mechanism. We identified 4bp SSR from eleven monkey dataset's Unchr chromosome mainly in this paper. The proposed approach finds the exact place/location of the SSR's and number of times that it appears in the given genome sequence. The identified patterns are analyzed with One-way and Two-way ANOVA that gives better analysis which is useful for genomic studies. Also, this 4bp Ten SSR markers data is a valuable to illustrate genetic variation of genomic study.•The great specificity of data sets produced from monkey genomes with pattern matching has been demonstrated.•These findings show that SSR identification could be a useful tool for determining genome similarity and comparability.•Researchers can use the raw sequencing data to conduct additional bioinformatics analysis.

Comparison of selection methods for the establishment of a core collection using SSR markers for hazelnut (Corylus avellana L.) accessions from European germplasm repositories

Hazelnut (Corylus avellana L.) is one of the most important tree nut crops in Europe. Germplasm accessions are conserved in ex situ repositories, located in countries where hazelnut production occurs. In this work, we used ten simple sequence repeat (SSR) markers as the basis to establish a core collection representative of the hazelnut genetic diversity conserved in different European collections. A total of 480 accessions were used: 430 from ex situ collections and 50 landraces maintained on-farm. SSR analysis identified 181 genotypes, that represented our whole hazelnut germplasm collection (WHGC). Four approaches (utilizing MSTRAT, Power Core, and Core Hunter’s single- and multi-strategy) based on the maximization (M) strategy were used to determine the best sampling method. Core Hunter’s multi-strategy, optimizing both allele coverage (Cv) and Cavalli-Sforza and Edwards (Dce) distance with equal weight, outperformed the others and was selected as the best approach. The final core collection (Cv-Dce30) comprised 30 entries (16.6% of genotypes). It recovered all SSR alleles and preserved parameter variations when compared to WHGC. Entries represented all six gene pools obtained from the population structure analysis of WHGC, further confirming the representativeness of Cv-Dce30. Our findings contribute towards improving the conservation and management of European hazelnut genetic resources and could be used to optimize future research by identifying a minimum number of accessions on which to focus.

Genetic variation and relationships between Azerbaijani and Turkish olive genetic resources.

Olive (Olea europaea L.) is one of the most economically important crop from east to the west around the world. The aim of this research was to investigate the genetic relationship among 41 olive genotypes, including 11 well-known Turkish cultivars and 30 Azerbaijani olive genotypes using simple sequence repeat (SSR) markers. In this study, 19 SSR markers were amplified 115 polymorphic SSR alleles. The number of polymorphic alleles ranged from 3 to 10 with an average of 6.05. The observed heterozygosity (Ho) varied from 0.05 to 0.93 with an average of 0.63 and expected heterozygosity (He) differed from 0.26 to 0.86 with an average of 0.72. The polymorphism information content (PIC) ranged from 0.23 to 0.85 with a mean of 0.68. A UPGMA cluster analysis grouped olive genotypes into two distinct clusters and both clusters were divided into two subgroups. Similarly, STRUCTURE analysis assigned olive genotypes into two different gene pools (K = 2) and four gene pools were identified representing the two subgroups by STRUCTURE analysis for K = 4. The genetic similarity of olive genotypes ranged from 0.36 to 0.95. These results revealed that there was a high genetic variation among 30 Azerbaijani olive genotypes. 'Ayvalık 1'and 'Ayvalık 2' from Azerbaijani olive genotypes were different from Turkish local olive cultivar, "Ayvalık" indicating homonymy. This research also highlighted that Azerbaijani olive genotypes were totally distinct from Turkish olive cultivars demonstrating that these olive genotypes might have been imported to Azerbaijan from different countries other than Turkey. The outcomes of this study indicated that these diverse olive genotypes could be useful for development of new olive varieties in Azerbaijan and future breeding programs between two countries could be enhanced by means of these results.

Simple Sequence Repeat and S-Locus Genotyping to Assist the Genetic Characterization and Breeding of Polyploid Prunus Species, P. spinosa and P. domestica subsp. insititia

Polyploid Prunus spinosa (2n = 4 ×) and P. domestica subsp. insititia (2n = 6 ×) represent enormous genetic potential in Central Europe, which can be exploited in breeding programs. In Hungary, 16 cultivar candidates and a recognized cultivar ‘Zempléni’ were selected from wild-growing populations including ten P. spinosa, four P. domestica subsp. insititia and three P. spinosa × P. domestica hybrids (2n = 5 ×) were also created. Genotyping in eleven simple sequence repeat (SSR) loci and the multiallelic S-locus was used to characterize genetic variability and achieve a reliable identification of tested accessions. Nine SSR loci proved to be polymorphic and eight of those were highly informative (PIC values ˃ 0.7). A total of 129 SSR alleles were identified, which means 14.3 average allele number per locus and all accessions but two clones could be discriminated based on unique SSR fingerprints. A total of 23 S-RNase alleles were identified and the complete and partial S-genotype was determined for 10 and 7 accessions, respectively. The DNA sequence was determined for a total of 17 fragments representing 11 S-RNase alleles. ‘Zempléni’ was confirmed to be self-compatible carrying at least one non-functional S-RNase allele (SJ). Our results indicate that the S-allele pools of wild-growing P. spinosa and P. domestica subsp. insititia are overlapping in Hungary. Phylogenetic and principal component analyses confirmed the high level of diversity and genetic differentiation present within the analysed accessions and indicated putative ancestor–descendant relationships. Our data confirm that S-locus genotyping is suitable for diversity studies in polyploid Prunus species but non-related accessions sharing common S-alleles may distort phylogenetic inferences.

Morphological, Molecular and Genomic Characterization of Two Inter-Subspecific Hybrids between Olive Cultivars and Olive Subspecies

Two inter-subspecific F1 hybrids have been obtained by crossing olive cultivars (‘Frantoio’ and ‘Coratina’) with pollen donors from olive subspecies (Olea europaea subsp. cuspidata) to enrich the germplasm of cultivated olive in southern China. This study aimed to investigate the characterization of morphological traits and molecular markers in the two hybrids and their parents of crosses. The morphological study showed a significant difference between genotypes according to the main discriminative parameters on qualitative and quantitative traits of leaf, fruit, and endocarp. A set of six co-dominant polymorphic simple sequence repeats (SSRs) were used for molecular identification, and SSR analysis confirmed that two progenies were the offspring of their cited parents based on the presence of parental specific SSR alleles. Three single-copy nuclear loci (SCNL) primer pairs were used for amplification of single-copy genes in the two progenies and their parents and after then PCR products were sequenced. Sequence alignment analysis on the effective data showed a total of 15 different base sites between two progenies, which were confirmed as true inter-specific hybrids between olive cultivars and subsp. cuspidata.

Genetic structure, clonality and diversity in commercial pomegranate (Punica granatum L.) cultivars

The pomegranate fruit is one of the most important horticultural products due to the presence of polyphenols, anti-oxidant and anti-fungal compounds. In the present study, we report the genetic fingerprinting, as well as genetic diversity in some Iranian commercial pomegranate cultivars by using simple sequence repeats (SSRs). In total 188 pomegranate trees of 47 presumed genotypes were used in genetic analyses. Based on multivariate and Bayesian statistical analyses, different genetic groups as well as clonal genotypes were identified. AMOVA, G’Nei as well as Jost D revealed significant genetic differentiation of the studied genotypes. LFMM analysis identified two potentially adaptive SSR alleles which differentiated pomegranate genotypes based on environmental conditions. Mantel test did not show correlation between genetic distance and geographical distances of the studied genotypes. Some of the hybrid plants obtained had new alleles which were not present in parental genotypes. These findings may be utilized in future selection and breeding pomegranate in the country.

English

Cape gooseberry (Physalis peruviana L.) is a neglected high potential crop, knowledge of the genetic diversity of the genotypes domesticated in Kenya is limited. To understand the genetic diversity and structure within and between Cape gooseberry germplasm, 70 accessions from six selected counties were analyzed using 15 pairs of highly polymorphic SSR primers. In this study, a total of 61 polymorphic SSR alleles were identified with mean polymorphic information content (PIC) of 0.43. Analysis of Molecular Variance (AMOVA) revealed that 92.8% of the total genetic variation was within accessions whereas variation among accessions accounted for 7.2% of the total genetic variation. Genetic diversity parameters among the 70 accessions revealed that Cape gooseberry was more diverse than previously recorded. Based on the SSR data, the 70 accessions were classified into five main phylogenetic groups, which corresponded to the county of origin through factorial analysis, principal component analysis (PCA), and phylogenetic analysis. Seven core SSR primer pairs, namely SSR1, SSR2, SSR10, SSR11, SSR123, SSR138, and SSR146 were found to have a wide applicability in genotype identification of cape gooseberry, and thus they are recommended for use in genetic characterization of germplasm collected from other counties not covered by the present study. This study demonstrated the existence of considerable genetic diversity in Cape gooseberry accessions growing in selected counties in Kenya and can therefore be used as a basis for future breeding programs in the development of hybrids with desirable traits. This wider genetic diversity is vital for posterity as it will help cope with unpredictable climatic changes and human needs. &nbsp; Key words: Simple sequence repeats (SSRs), genetic diversity, germplasm, Physalis peruviana L., polymorphic information content (PIC).

Genetic diversity and population structure of bread wheat varieties grown in Bulgaria based on microsatellite and phenotypic analyses

Determining the genetic diversity and population structure of the modern hexaploid wheat varieties currently grown in Bulgaria is fundamental for selection of genotypes with desirable traits resilient under climatic fluctuations and development of successful crop improvement programmes. In this study, simple sequence repeat (SSR) markers were used to characterize a population of 117 modern wheat varieties (Triticum aestivum L.) from Bulgaria and several Western, Central and Eastern European countries. The genetic diversity was higher in the Western and Central European varieties than in the Bulgarian and the remaining Eastern European ones. Model-based population structure analysis defined 2 sub-populations (K = 2) dividing the Central and Western European varieties from the Bulgarian ones. Subsequent genetic structure analysis at K = 3 revealed an additional separation of the Bulgarian varieties in two distinct sub-populations. The phenotypic diversity among the varieties was evaluated in the fields of Dobrudzha Agricultural Institute, G. Toshevo in North-Eastern Bulgaria for three consecutive years. The distribution of the varieties in the biplot analysis in terms of grain yield and its components revealed differences in their adaptation to the agro-climatic conditions of North Bulgaria according to their geographical origin. These results and the prevalence of specific SSR alleles in the sub-populations suggest distinct adaptive mechanisms to specific agro-ecological regions. The data will be of interest for both breeders and farmers and could serve as a basis for wheat improvement programmes and further association mapping for important agronomic traits expressed under different environmental conditions. Supplemental data for this article is available online at https://doi.org/10.1080/13102818.2021.1996274 .

SSRgenotyper: A simple sequence repeat genotyping application for whole-genome resequencing and reduced representational sequencing projects.

PREMISEMany programs can identify simple sequence repeat (SSR) motifs in genomic data. SSRgenotyper extends SSR identification to en masse genotyping from resequencing data for diversity panels and linkage mapping populations.METHODS AND RESULTSSSRgenotyper will find and genotype SSRs from SAM files and an SSR reference FASTA. Several outputs are possible, including a simple table with the SSR marker name, position, and SSR alleles, defined by the repeat number of the repeat motif. Specific output files include a GENEPOP‐formatted file for downstream genetic diversity analyses and a traditional A, H, B mapping file output that is phased to the parents of the population for biparental linkage map construction. Linkage maps produced using SSRgenotyper genotypes were highly collinear with physical maps and correctly inferred known phylogenies.CONCLUSIONSSSRgenotyper provides an easy‐to‐use, accurate, and scalable SSR genotyping platform for whole‐genome resequencing data. SSRgenotyper is freely available at https://github.com/dlewis27/SSRgenotyper.

Production of doubled-haploid(DH) selfed-progenies in ‘Banpeiyu’ pummelo [Citrus maxima (Burm.) Merr.] and its genetic analysis with simple sequence repeat markers

The genetic analysis of five haploid plants (BX1-BX5) of ‘Banpeiyu’ pummelo (BP), [Citrus maxima (Burm.) Merr.] using 32 simple sequence repeat (SSR) markers carried out for the purpose of confirming their gynogenetic origin and genetic differences. As the results, all the haploid plants possessed only either one of the BP alleles, confirming that they are gynogenetic origin. We also confirmed that BX1 and its doubled haploid (BX1-DH) have exactly the same SSR alleles. Interestingly, all the five haploids had common alleles on the linkage group (LG) 6 in the case of three markers. Then, we performed self-pollination of DH plants and reciprocal crosses between DH and BP, which has strong self-incompatibility. The seeds obtained by these crosses germinated in vitro or ex vitro normally and developed into diploid seedlings, except for one tetraploid seedling. Genetic analysis of these seedlings with 32 SSR markers revealed that segregation ratios of the 32 loci in the 30 BP inbred, 30 BP x DH and 30 DH x BP progenies mostly fitted to the expected ratios. However, significantly distorted segregation ratios were found in one, five and three SSR markers for BP inbred, BP x DH and DH x BP progenies, respectively. All of the 30 DH inbred progenies showed exactly the same SSR alleles as the original DH. This is the first example in which self and back cross progenies of DH in fruit crops were genetically analyzed using SSR markers.

Genetic diversity of Juglans sigillata Dode germplasm in Yunnan Province, China, as revealed by SSRs

AbstractIron walnut, Juglans sigillata Dode, restricted to southwestern China, has its centre of distribution in Yunnan Province which has a varied climate, geography and rich plant diversity. Yunnan contains abundant J. sigillata germplasm. In this study, a provincial-scale set of walnut germplasm resources (14 populations comprising 1122 individuals) was evaluated for genetic diversity based on 20 simple sequence repeat (SSR) loci. The number of SSR alleles per locus ranged from 7 to 27, with an average of 17.55. Mean allelic richness and mean private allelic richness ranged from 3.40 to 4.62 and 0.11 to 0.36, with average of 3.93 and 0.30, respectively. Expected heterozygosity (He) varied from 0.26 to 0.78, with an average of 0.57. Polymorphism information content ranged from 0.22 to 0.79, with an average of 0.57. Genetic differentiation (FST) was 0.05, indicating that only 5% of total genetic variability was inter-populational, a finding supported by an analysis of molecular variance and STRUCTURE analysis. Relatively high gene flow (Nm = 6.70) was observed between populations. A unweighted pair-group method with arithmetic analysis classified the 14 populations into two major groups. Mantel testing uncovered a significant correlation between geographic distance and genetic distance (r = 0.33, P = 0.04). Overall, the research revealed a moderately high level of genetic diversity in the germplasm and low genetic differentiation among populations, which showed great potential for further development and exploitation of this resource.

Founder events influence structures of Aspergillus flavus populations.

SummaryIn warm regions, agricultural fields are occupied by complex Aspergillus flavus communities composed of isolates in many vegetative compatibility groups (VCGs) with varying abilities to produce highly toxic, carcinogenic aflatoxins. Aflatoxin contamination is reduced with biocontrol products that enable atoxigenic isolates from atoxigenic VCGs to dominate the population. Shifts in VCG frequencies similar to those caused by the introduction of biocontrol isolates were detected in Sonora, Mexico, where biocontrol is not currently practiced. The shifts were attributed to founder events. Although VCGs reproduce clonally, significant diversity exists within VCGs. Simple sequence repeat (SSR) fingerprinting revealed that increased frequencies of VCG YV150 involved a single haplotype. This is consistent with a founder event. Additionally, great diversity was detected among 82 YV150 isolates collected over 20 years across Mexico and the United States. Thirty‐six YV150 haplotypes were separated into two populations by Structure and SplitsTree analyses. Sixty‐five percent of isolates had MAT1‐1 and belonged to one population. The remaining had MAT1‐2 and belonged to the second population. SSR alleles varied within populations, but recombination between populations was not detected despite co‐occurrence at some locations. Results suggest that YV150 isolates with opposite mating‐type have either strongly restrained or lost sexual reproduction among themselves.

Assessment of genetic integrity of Siberian wild rye (Elymus sibiricus L.) germplasm conserved ex situ and under accelerated aging using microsatellite markers

Genetic changes in Siberian wild rye (Elymus sibiricus L.) germplasm conserved ex situ and with accelerated aging were studied using microsatellite markers. Five accessions, divided and deposited in the National Medium-term Genebank of Forage Germplasm of China (NMGFC) and the National Genebank of China (NGC) since 1998, were sampled. Four recently-regenerated accessions were selected to assess genetic changes under accelerated aging conditions using a thermostat-controlled cabinet at 45 °C for 7–13 days to obtain seeds with germination rates (Gr) of approximately 80%, 50%, and < 30%. Twenty-four simple sequence repeat (SSR) markers were used to screen 70 seeds of each sample and 137 SSR alleles in a naturally-aged germplasm set and 113 SSR alleles in an accelerated aging germplasm set were scored. Loss of alleles was observed with respect to the primer pair and sample in the NMGFC compared to that in the NGC, but no significant differences were found for each accession in seeds stored in NMGFC compared to that in seeds stored in NGC. Among-sample differences were the largest contributors to total SSR variation, at 70.6% and 76.2% for naturally-aged and accelerated-aging samples, respectively. Gr did not separate samples in either germplasm set based on genetic association analysis. Prominent changes in genetic diversity were found both in naturally-aged and accelerated-aging samples, with significant decreases in Shannon’s information index and Nei’s genetic diversity for cases with Gr ≤ 30% for both germplasm sets. These results should be valuable to improve the safe conservation of forage, especially for Elymus (family Gramineae).

Genetic Diversity Analysis of 41 Chili Pepper Genotypes [Capsicum annuum L.] Based on SSR Markers

&lt;p&gt;Chili (Capsicum annuum L.) is an important horticultural crop which possesses high genetic diversity. Their genetic diversity needs to be assessed through molecular marker-based analysis to facilitate chili breeding scheme. The objective of the study was to analyze the genetic diversity of 41 chili genotypes using Simple Sequence Repeat (SSR) markers. Eleven SSR markers were used to amplify all genotypes through PCR technique, visualized on Polyacrylamide Gel Electrophoresis (PAGE). The data were analyzed using NTSYSpc version 2.1 and PowerMarker version 3.25 softwares. Results showed that the average of&lt;br /&gt;SSR alleles was 7.9 with a range of 4-11 alleles per marker. All SSR markers showed PIC value &amp;gt;0.5, indicating their suitable use for chili genetic studies. Cluster analysis of 41 genotypes generated three main groups according to coefficient similarity of 77.4%. The genetic clusters appeared as reflection of the genetic background of each genotype. In addition, the SSR markers used can identify potential parent as indicated by the genetic distance between genotypes. The highest genetic diversity (0.698) was demonstrated by combinations of Yuni × Ayesha, Yuni × Ayesha 2, and Yuni × Namira. The estimated genetic diversity produced by SSR markers in this study should be useful as guidance for chili breeders to select suitable parents for new cultivar development for high productivity and resistance to diseases.&lt;/p&gt;