SSR Diversity Research Articles

SSR diversity and hybridization of wild apples (Malus spp.) growing in the Guadarrama and Ayllón mountain ranges (Central Spain)

Aim of study: The crab apple tree (Malus sylvestris (L.) Mill.) is a wild crop relative of the apple tree (M. domestica Borkh.). Hybridization and genetic exchange between these species has been studied in some European regions, but there is no record in Spain. This work aimed to characterise a set of 330 feral and crab apples.
 Area of study: Guadarrama and Ayllón mountain ranges (Central Spain).
 Material and methods: We used 12 microsatellites to detect intermediate profiles. To do so, diversity, multivariate and population structure Bayesian analyses were performed on the sample, adding a total of 28 crab apples, feral and widespread apples varieties as references.
 Main results: We found a large molecular diversity in this Malus germplasm, scoring a mean of 28.58 alleles per locus (A); an observed heterozygosity (Ho) of 0.80 and a very low value of inbreeding coefficient (Fis =0.06). On the other hand, we found from our Bayesian population analysis three populations (one per species and a third one very admixed) apparently not spatially correlated and a substantial level of intermediate genetic profiles, as around 47% of the feral trees and 35% of crab apples may be hybrids.
 Research highlights: Connectivity in the crab apple genetic pool is still functional and interspecific gene flow may be relevant. Nevertheless, further conservation measures and research must be carried to understand the population dynamics between both species.

Genetic diversity and differentiation in south-western Australian bloodwoods (

An understanding of how variation is shared within and among closely related species is important for understanding evolutionary processes and managing biological diversity. We studied genetic structure in the three species occurring in south-western Australia that form the small and distinct monophyletic section Calophyllae of the genus Corymbia. We compared diversity in nuclear microsatellites and chloroplast DNA sequences in two species with patchy distributions, namely, Corymbia haematoxylon (Maiden) K.D. Hill & L.A.S. Johnson and Corymbia ficifolia (F. Muell.) K.D. Hill & L.A.S. Johnson, with that in the widespread congener, C. calophylla (Lindl.) K.D. Hill & L.A.S. Johnson. Consistent with predictions for the influence of range and abundance on genetic structure in the Australian flora, population differentiation was higher in the two restricted patchy species than in the widespread, semicontinuous C. calophylla. Genetic diversity in C. haematoxylon was similar to that in C. calophylla, but diversity was lower in the highly localised C. ficifolia, likely owing to genetic bottlenecks. All three species were distinguished by nuclear SSR variation, but C. haematoxylon and C. ficifolia each shared chloroplast haplotypes with C. calophylla from incomplete lineage sorting of ancestral variation and introgression. Limited evidence of recent hybridisation in two populations of C. haematoxylon was also present.

Variation for Grain Morphology, Molecular Diversity and Aroma Analysis in Specialty Rice of Assam

The nature and magnitude of genetic diversity of aromatic rice accessions collected from different agro climatic zones of Assam were evaluated in the present study . Grain morphology and molecular diversity was investigated for a collection of fourteen genotypes. In molecular genetic analysis 32 random SSR markers and 1 gene- based marker (Aroma-1) were included, out of which 16 informative SSR were employed for genetic analysis on the basis of their amplification. Molecular taxonomy and genetic divergence analysis revealed considerable variation among the tested aromatic lines. Of the 18 SSR variation in 14 genotypes, the value of PIC ranged from 0.1326 (RM337) to 0.5408 (RM496). The phylogenetic relations indicate presence of diverse genetic origin of the aromatic rice collection. Aroma analysis with gene based marker (Aroma- 1) amplified a unique band in Bokul Joha which is different from rest of the genotypes indicating probable presence of alternative allelic constitution of BADH2 gene for aroma.

Virulence and SSR Diversity of Brown Planthopper (Nilaparvata lugens) Adapted on Differential Rice Host Varieties

Brown planthopper biotype 1, 2, 3 and a representative field population are required for resistance screening of promising rice lines in Indonesia, but the current biotype stocks has shown deviation in virulence patterns. The objectives of this study were to develop a set of brown planthopper populations with differential virulence and to investigate their genetic variability using SSR marker. Females originated from two field populations were selected on variety Mudgo (carries Bph1 gene) or ASD7 (bph2 gene) using honeydew excretion as the virulence parameter. Selection cycles resulted in population T, M, A, and R, which was raised and adapted on variety TN1 (carries no Bph gene), Mudgo, ASD7, and Rathu Heenathi (Bph3, Bph17), respectively. Population R was the most virulent as expected and can be used to represent a field population, but the remaining populations still showed high virulence level. AMOVA and PCoA results based on analysis with 38 SSR primer pairs revealed partial genetic separation among populations, with population R was the most genetically distant from the remaining populations. The desired virulence character of the remaining populations is expected could be achieved after further selection and prolonged adaptation on their respective hosts.

PARENTAL SELECTIONS IN SORGHUM (SORGHUM BICOLOR L.) ON THE BASIS OF HETEROSIS AND COMBINING ABILITY IN ASSOCIATION WITH SSR DIVERSITY IN SUB-TROPICAL PLAINS OF UTTARAKHAND, INDIA

Selection of genetically diverse and complementary parents for important key traits is most difficult task in any hybrid breeding programme. The objective of this study was to estimate heterosis and relative combining abilities with associated SSR diversity for identification of unique sorghum genotypes. A total of forty crosses and thirteen parental lines including five cytoplasmic male sterile (CMS) lines and eight pollinator lines with two standard check varieties were phenotyped using six agro-morphological traits and genetic diversity was estimated by using five polymorphic SSR markers. Sorghum genotypes were crossed with CMS lines using a line × tester mating design and 40 hybrids, 13 parents and two check varieties were field-evaluated using alpha lattice design with three replications. General combining ability (GCA), specific combining ability (SCA) and heterosis for grain yield and other associated attributes were determined. SSR diversity estimates were ranged from 0.54 to 0.90. Among CMS lines, 11A2 and MR750A2 and among pollinators, UPC2 and M35-1 were reported as best general combiners. A2 cytoplasm was found to be more efficient to produce more heterotic combination with experimental lines. Cross, 11A2 x UPC2 gave best results of heterosis for most of the characters. MR750 A2 x UPC2, 11A2 x UPC2, ICSA467 x UPC2, ICSA467 x CS3541, ICSA 467 x RS29, ICSA 467 x M35-1 and 11A2 x M35-1 revealed significant and positive values of heterosis, SCA and GCA. However, no direct correlation was detected with heterosis and molecular diversity for most of the characters. These results may be used for the exploitation of hybrid vigor in sorghum breeding programmes

Pathotype and SSR variation in Phytophthora sojae from the Argentinean Pampas

AbstractGenetic variation in Phytophthora sojae was compared between northern (NPS) and southern (SPS) Pampeana sub‐regions, in the core soya bean region of Argentina. Ninety‐three isolates from plants and soil were evaluated in the present study. The pathotype for each isolate was determined using the hypocotyl technique on a set of eight differentials. For neutral genetic diversity evaluation, eight SSRs markers were utilized. Thirty pathotypes were determined, including 19 in SPS and 23 in NPS. The number of isolates for each locality and region was unevenly distributed. Pathotype variation was high for P. sojae samples compared among fields and within isolates from single fields. SSR variation studies resulted in an elevated haplotype composition, partitioned at all, but the regional levels. P. sojae populations from Argentina have evolved towards a complex epidemiological scenario, with no evidence of geographic correlation at the pathotypic nor the neutral genetic level. It is likely that future works aiming at elucidating the evolution of pathogenesis in this species will need to include non‐neutral markers, specifically associated to avr loci. The results of the present work are considered a useful contribution to the adequate and sustainable management of this pathogen in the main soya bean area of Argentina.

<b>Linkage disequilibrium and population structure in <i>Fragaria chiloensis</i> revealed by SSR markers transferred from commercial strawberry

The Chilean strawberry [ Fragaria chiloensis (L.) Mill.] is the maternal progenitor of the commercial strawberry ( Fragaria ´ ananassa Duch.), which is characterized by fruits with high organoleptic quality and is well-suited to areas where drought and salinity represent a constraint on crop growth and productivity. We examined the patterns of linkage disequilibrium, genetic diversity and population structure among 54 accessions of F. chiloensis to understand the genetic basis of this species. We used a core microsatellite marker set (n = 95) from a consensus linkage map of strawberry. A transferability rate of 82.1% (78/95) was found, and 38 markers were selected for this study. The SSR primers produced a total of 259 alleles, which varied between 112 and 342 bp. Lower genetic diversity at the species level (H E = 0.17, Shannon’s index = 0.28) was found compared to previous studies of this species. No climatic region pattern for SSR diversity was observed. Structure analysis suggests that the accessions are grouped into three significantly differentiated clusters. Pairwise estimates of φ ST indicated a low degree of differentiation between the three genetic groups (φ ST = 0.023 to 0.06). These groups are in concordance with potential glacial refugia in the region, with many accessions being an admixture of them.

Evaluation of maize genotypes for fodder quality traits and SSR diversity

Maize is an important fodder resource for ruminants. The yield and quality of fodder is governed by genetic variability and interaction of genotypes with environment. Therefore, it is prerequisite to evaluate the available variability for fodder traits in maize. For this, 75 genotypes were evaluated in three replications for 2 years. Data were recorded on eight morphological traits including green fodder yield and dried fodder samples were evaluated for eight fodder quality traits. Wide range of estimates for fodder quality and productivity characters except DFF and LSR reflects the existence of significant variations among genotypes. ANOVA revealed significant variety × year interaction for seven traits. Plant height, stem girth, leaf-length and -width demonstrated positive correlation with green fodder yield per plant. Inverse association was observed between crude protein and cell wall component (NDF, hemicellulose). First three principle components explained 44.28% of the total variation. Two-way clustering grouped the genotypes and traits into five and three major clusters, respectively. During SSR analysis, a total of 133 alleles from 21 primers were generated with mean PIC value was 0.58. The genetic distance between genotypes was ranging between 0.16 and 0.75 with an average of 0.49. All genotypes were clustered in three main groups and clustering was consistent with genotype origin. A weak correlation was identified between morphological and molecular distance. Eventually results suggested that both morphotypes and molecular markers should exploit simultaneously to reveal the true genetic diversity to get maximum heterosis through hybridization.

Genetic Characterization of Genetic Resources of <i>Aegilops tauschii</i>, Wheat D Genome Donor, Newly Collected in North Caucasia

For the purpose of broadening the available genetic resources to improve wheat breeding and to elucidate wheat evolution, 16 accessions of Aegilops tauschii newly collected in North Caucasia named NCT accessions were characterized genetically based on morphology, chloroplast SSR variation and AFLP. Ae. tauschii is one of the most important wild wheat genetic resources because it is the progenitor of the D genome of hexaploid wheat. Since Caucasia is considered to be a center of diversity of both cultivated and wild wheat, a lot of studies have been conducted to evaluate the diversity of Caucasian genetic resources including Ae. tauschii. Such kind of analyses, however, focused on Transcaucasia but little attention has been paid to North Caucasia because of the lack of available genetic resources. Based on the molecular analyses in this study, the 16 NCT accessions were generally divided into two groups although morphologically those are classified into the same subspecies. The grouping also represented geographical distribution, that is, the northern part group and Derbent group. This division is consistent with the two major genepools in Ae. tauschii reported in previous studies. The northern part and Derbent groups correspond to Eurasian wide genepool (called Tauschii genepool) and Caucasia and Caspian coast limited genepool (Strangulata genepool), respectively. Regarding to chloroplast, all the 16 accessions were genotyped as HG7, the most major haplogroup of the species. Although all the 16 NCT accessions were categorized into ssp. tauschii morphologically, accessions of Derbent group showed a tendency to have larger spikelets. Among them, especially NCT3 had the quite large size of spikelets and grains that are at almost the largest level in ssp. tauschii. The results of this study filled the missing information of Ae. tauschii and will be helpful for future utilization.

Dissecting maize diversity in lowland South America: genetic structure and geographic distribution models.

BackgroundMaize landraces from South America have traditionally been assigned to two main categories: Andean and Tropical Lowland germplasm. However, the genetic structure and affiliations of the lowland gene pools have been difficult to assess due to limited sampling and the lack of comparative analysis. Here, we examined SSR and Adh2 sequence variation in a diverse sample of maize landraces from lowland middle South America, and performed a comprehensive integrative analysis of population structure and diversity including already published data of archaeological and extant specimens from the Americas. Geographic distribution models were used to explore the relationship between environmental factors and the observed genetic structure.ResultsBayesian and multivariate analyses of population structure showed the existence of two previously overlooked lowland gene pools associated with Guaraní indigenous communities of middle South America. The singularity of this germplasm was also evidenced by the frequency distribution of microsatellite repeat motifs of the Adh2 locus and the distinct spatial pattern inferred from geographic distribution models.ConclusionOur results challenge the prevailing view that lowland middle South America is just a contact zone between Andean and Tropical Lowland germplasm and highlight the occurrence of a unique, locally adapted gene pool. This information is relevant for the conservation and utilization of maize genetic resources, as well as for a better understanding of environment-genotype associations.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0874-5) contains supplementary material, which is available to authorized users.

Complete plastid genome sequence of Primula sinensis (Primulaceae): structure comparison, sequence variation and evidence for accD transfer to nucleus.

Species-rich genus Primula L. is a typical plant group with which to understand genetic variance between species in different levels of relationships. Chloroplast genome sequences are used to be the information resource for quantifying this difference and reconstructing evolutionary history. In this study, we reported the complete chloroplast genome sequence of Primula sinensis and compared it with other related species. This genome of chloroplast showed a typical circular quadripartite structure with 150,859 bp in sequence length consisting of 37.2% GC base. Two inverted repeated regions (25,535 bp) were separated by a large single-copy region (82,064 bp) and a small single-copy region (17,725 bp). The genome consists of 112 genes, including 78 protein-coding genes, 30 tRNA genes and four rRNA genes. Among them, seven coding genes, seven tRNA genes and four rRNA genes have two copies due to their locations in the IR regions. The accD and infA genes lacking intact open reading frames (ORF) were identified as pseudogenes. SSR and sequence variation analyses were also performed on the plastome of Primula sinensis, comparing with another available plastome of P. poissonii. The four most variable regions, rpl36–rps8, rps16–trnQ, trnH–psbA and ndhC–trnV, were identified. Phylogenetic relationship estimates using three sub-datasets extracted from a matrix of 57 protein-coding gene sequences showed the identical result that was consistent with previous studies. A transcript found from P. sinensis transcriptome showed a high similarity to plastid accD functional region and was identified as a putative plastid transit peptide at the N-terminal region. The result strongly suggested that plastid accD has been functionally transferred to the nucleus in P. sinensis.

Phenotypic and genotypic intra-diversity among Anatolian durum wheat “Kunduru” landraces

Kunduru is an important Anatolian landrace having peculiar traits that are appreciated by farmers and breeders. 33 accessions known as Kunduru collected by ICARDA from six geographical provinces of Turkey, were used to study the phenotypic and genotypic intra-diversity. Kunduru landraces exhibited high intra-diversity for most of the studied morphological traits. GPC (12.10–14.90%), vitreousness (75–100%), TKW (31.80–56.70 g), YP (4.70–8.00 ppm), b*-value (14.30–19.50), ash content (1.60–2.0%) and gluten strength (14–60 ml) showed marked variations. Gliadin and glutenin banding patterns showed high polymorphism. 65 alleles were detected with 14 SSR markers, giving a mean of 6.77 alleles per locus. The average PIC value was 0.44 and ranged from 0.11 to 0.70. The average genetic distance between pairs of landraces was 0.47 and ranged between 0.11 and 0.72. This study showed that Kunduru landraces maintains high allelic variation. PCoA indicated that eco-geographical variables have a significant effect on SSR diversity as well as morphological traits. Many of the landraces studied are in danger of disappearing from the local farmers' fields; this study demonstrates the importance of maintaining and conserving this precious genetic resources.

SSR and RAPD-Based Genetic Diversity in Cotton Germplasms

SSR and RAPD-Based Genetic Diversity in Cotton Germplasms

Molecular diversity analysis in Wheat genotypes using SSR markers

Molecular diversity of the seven wheat ( Triticum aestivum L.) genotypes was evaluated using 50 SSR primers. Genetic distances were calculated using unweighted pair group of arithmetic mean (UPGMA) procedure. A high degree of genetic polymorphism was observed among the wheat varieties with average genetic polymorphism 70%. SSR diversity data was generated using above primers and a total of 114 alleles were detected with an average of 2.71 alleles per locus. The number of alleles per locus ranged from 2 to 6 and the percent of polymorphism ranged from 20% for the Xwmc254 to 100% for the Xbarc26. The average genetic diversity based on SSR markers was 0.465 with a range of 0.037- 0.892. Our results suggested that the classification based on genotypic markers of these wheat genotypes would be useful for wheat breeders to plan crosses for positive traits. The results obtained suggested that the wheat microsatellite markers could be used to distinguish wheat genotypes and to estimate genetic diversity. The present study also indicates that microsatellite markers permit the fast and high throughout fingerprinting of accessions from a varieties collection in order to assess genetic diversity.

Diversity Level, Spearman’s Ranking and Core Collections from 98 Rice Germplasm through Quantitative, Qualitative and Molecular Characterizations

Ninety-eight genotypes (40 genotypes of Balam, 27 of Jesso-Balam, 21 of Kartiksail and 10 of Dhaliboro groups, respectively) of similar or duplicate named rice accessions along with HYV’s were studied for quantitative, qualitative and molecular characters at Bangladesh Rice Research Institute during 2009-12. For estimating diversity level, the genotypes were divided into five populations. The PIC ranged from 0.50 (Dhaliboro) to 0.74 (Balam) with 0.69 for HYVs, indicating the existence of more diversity and broader genetic base in Balam land race cultivars. Similarly, genetic diversity with an average of 0.83 ranged from 0.55 (Dhaliboro) to 0.77 (Balam) and 0.73 for HYV’s. The Shannon’s information index ranged from 1.00 (Dhaliboro) to 1.73 (Balam) and it was 1.48 for HYV’s. The number of different allele ranged from 3.56 (Dhaliboro) to 7.80 (Balam), while the number of effective allele from 2.63 (Dhaliboro) to 5.11 (Balam) and it was 5.18 and 4.14 for HYV population, respectively. Analysis of molecular variance showed that the maximum percentage of variation was present among individuals within populations (85%), followed by among populations (15%). The spearman’s rank correlation coefficient was found highly significant (rs=0.51; t=2.98) between ranking of inter-genotype (D=√D2) and Nei’s genetic distances, indicating strong association between them. The correlation tests revealed that SSR diversity analysis is the most powerful method for grouping. But, combination of quantitative and molecular methods may be the best. Finally, 21 core collections were selected from Balam group. The selected core accessions need to conserve as active collection in Genebank, utilize as parents in hybridization programs and develop QTL map for unlocking valuable genes.

Patterns of SSR variation in bread wheat (Triticum aestivum L.) seeds under ex situ genebank storage and accelerated ageing

Maintaining seed viability and germplasm integrity is a challenging task in conservation of plant genetic resources, as seeds under storage will lose viability and genetic changes will occur. Attempt was made to analyze the patterns of genetic changes in wheat germplasm under ex situ genebank storage and accelerated ageing treatments. A set of 16 naturally aged wheat accessions under ex situ genebank storage since 1994 were sampled. Four recently regenerated wheat accessions were selected, four random seed samples were chosen from each accession, and three of them were exposed to three different accelerated ageing treatments. These 32 seed samples in two germplasm sets displayed a range of germination rates from 4 to 98 %. Thirty-seven microsatellite markers representing 21 wheat chromosomes were applied to screen 12 seeds of each sample and 449 SSR alleles were scored. Large SSR variation was found in each germplasm set. There was 73.1 % of the total SSR variation present among the naturally aged samples and 78.2 % present among the accelerated ageing samples. Several analyses for genetic association consistently revealed no clear genetic separations among samples of high or low germination rates in both germplasm sets. Samples under different accelerated ageing treatments did not show much genetic differentiations from the original sample of each accession. Mantel tests revealed non-significant associations between SSR variability and sample germination rates for both germplasm sets. These findings are useful for understanding seed deterioration under different ageing conditions and suggest that genome-wide SSR variability may not provide sensitive markers for the monitoring of wheat seed viability.

Decadal changes in radiative fluxes at land and ocean surfaces and their relevance for global warming

Anthropogenic interference with climate occurs primarily through modification of radiative fluxes in the climate system. Increasing releases of greenhouse gases into the atmosphere lead to an enhancement of thermal radiation from the atmosphere to the surface by presently about 2 W m−2 per decade, thereby causing global warming. Yet not only thermal radiation undergoes substantial decadal changes at the Earth surface, but also incident solar radiation (SSR), often in line with changes in aerosol emissions. Land‐based observations suggest widespread declines in SSR from 1950s to 1980s (‘global dimming’), a partial recovery (‘brightening’) since mid‐1980s, and indication for an ‘early’ brightening in 1930s and 1940s. No similar extended observational records are available over oceans. However, modeling studies, conceptual frameworks and available satellite‐derived records point to the existence of decadal SSR variations also over oceans. SSR changes overall match with decadal variations in observed warming rates, suggesting that SSR variations may effectively modulate greenhouse gas‐induced warming. Specifically, on the Northern Hemisphere, the lack of warming from 1950s to 1980s and its subsequent acceleration in the 1990s fits to the trend reversal from dimming to brightening and associated changes in air pollution levels. From the 1950s to 1980s no warming was also observed over Northern Hemispheric Oceans, in line with conceptual ideas that subtle aerosol changes in pristine ocean areas, effectively amplified by aerosol–cloud interactions, can substantially alter SSR, thereby modulating Sea Surface Temperatures. On the Southern Hemisphere, the absence of significant aerosol levels fits to the observed stable (greenhouse gas‐induced) warming rates since the 1950s. WIREs Clim Change 2016, 7:91–107. doi: 10.1002/wcc.372This article is categorized under: Paleoclimates and Current Trends > Modern Climate Change

Comparison of Agricultural Traits and SSR Diversity of Common Bean (Phaseouls vulgaris L. ) from Korea, China and El Salvador

Yu-Mi Choi1*, Sugyeong Lee1, Do yoon Hyun1, Munsup Yoon2, Sejong Oh1, Myung-Chul Lee1, Jeongro Lee1,Hocheol Ko1, and Onsook Huh1. Korean J. Breed. Sci. 2015;47:245-54. https://doi.org/10.9787/KJBS.2015.47.3.245

The Conservation Value of Peripheral Populations and a Relationship Between Quantitative Trait and Molecular Variation

The adaptive potential of populations and therefore their ability to cope with rapid environmental changes is a question of paramount fundamental and applied importance. However, what is still not clear is the effect of population position within the species range (i.e. core vs. edge) on population adaptive potential, and whether the adaptive potential can be predicted from extent of neutral molecular variation. In this study, we compared the extent and structure of neutral (SSR) and presumably adaptive quantitative trait genetic variation in populations of Triticum dicoccoides sampled at the species range core and two opposite edges, and related this information to multigenerational performance of plants experimentally introduced beyond the range edge. The plants from the species arid edge performed worse than plants from the more mesic core in extreme desert conditions. The core and edge populations did not differ in extent of SSR variation. In contrast to the neutral genetic variation, there was lower quantitative trait variation in the two edge as compared with the core population for many traits, and no trait in any edge population had higher variation than the core population or either of its habitats. Reduced variation in selectively important traits indicates a lower adaptive potential of the two edge as compared with the core population. Our results imply (1) that extent of variation in quantitative traits can predict plant performance in novel environments while extent of variation in molecular markers can not; and (2) caution in usage of peripheral populations in such conservation actions as relocation and creation of new populations. We also warn against usage of neutral molecular variation as a surrogate for selectively important quantitative variation in conservation decisions.

De Novo Assembly of Bitter Gourd Transcriptomes: Gene Expression and Sequence Variations in Gynoecious and Monoecious Lines.

Bitter gourd (Momordica charantia L.) is a nutritious vegetable crop of Asian origin, used as a medicinal herb in Indian and Chinese traditional medicine. Molecular breeding in bitter gourd is in its infancy, due to limited molecular resources, particularly on functional markers for traits such as gynoecy. We performed de novo transcriptome sequencing of bitter gourd using Illumina next-generation sequencer, from root, flower buds, stem and leaf samples of gynoecious line (Gy323) and a monoecious line (DRAR1). A total of 65,540 transcripts for Gy323 and 61,490 for DRAR1 were obtained. Comparisons revealed SNP and SSR variations between these lines and, identification of gene classes. Based on available transcripts we identified 80 WRKY transcription factors, several reported in responses to biotic and abiotic stresses; 56 ARF genes which play a pivotal role in auxin-regulated gene expression and development. The data presented will be useful in both functions studies and breeding programs in bitter gourd.