Simple Sequence Repeat Molecular Markers Research Articles

Genetic diversity and relatedness analysis of nine wild species of tree peony based on simple sequence repeats markers

Tree peony has nine wild species, but the evolutionary relationship of them is still unclear. Here, a total of 274 specimens from 22 natural populations of nine wild species were collected, and their genetic diversity and similarity was analyzed based on Simple Sequence Repeats (SSR) molecular markers. A total of 106 alleles were generated based on 20 primers and with an average of 5.3 alleles per primer. Shannon's information index (I) ranged from 0.6333 to 1.7842, and the average of Nei's genetic diversity coefficient (H) was 0.5771. Polymorphism Information Content (PIC) value varied from 0.29 to 0.77, ten of these primers had high polymorphism (PIC ≥ 0.50). All the above genetic parameters of primers reflect more rich genetic diversity information compared with other researches using SSR molecular markers to study the genetic diversity of tree peony wild species. At the population level, the lowest and highest degree of genetic diversity occurred in Paeonia ludlowii-P1 and P. delavayi-P3 population, respectively. Whereas at species level, the genetic diversity of 9 wild peony species was as follows: P. lutea > P. delavayi > P. rockii > P. qiui > P. ostii > P. decomposita > P. potaninii > P. spontanea > P. ludlowii. Furthermore, cluster analysis at species level divided the nine wild tree peony species into two branches. In branch I, the closest phylogenetic relationship was found between P. ostii and P. rockii, followed by P. spontanea, P. qiui, and P. decomposita. In branch II, the closest relationship occurred between P. lutea and P. delavayi, followed by P. potaninii and P. ludlowii. Clustering results supported the division of tree peonies into two subsects (Delavayanae and Vaginatae), it also supported P. potaninii and P. ludlowii as independent species. The results provided novel insight into the genetic diversity and phylogenetic relationship of nine wild tree peony species. It will help formulate comprehensive protection measures of wild germplasm resources and select proper parents for distant hybridization in the future.

Association analysis between Lipoxygenase activity and SSR markers in wheat grains

Lipoxygenase (LOX) activity is closely related to wheat processing and storage quality. In the present research, ten wheat cultivars were used to compare the effects of genotype, location, year, and their interactions on the LOX activity. Furthermore, 123 wheat cultivars were evaluated for LOX activity with 192 simple sequence repeat (SSR) markers and to identify elite alleles related to LOX activity. The results indicated that LOX activity was highly affected by genotype (variety) than that by the location. A total of 22 SSR molecular marker loci with a significant or very significant correlation with LOX activity were identified on performing association analysis. In 3 years, only one molecular marker locus associated with LOX activity was detected (WMC488); in 2 years, seven molecular marker loci were detected, while in only 1 year, the other 14 molecular marker loci were detected. A total of 7 and 6 marker loci significantly related to LOX activity accounting for 31.2% and 27.2%, respectively, were located in homologous groups 4 and 5, and group 7. This research provided the theoretical basis and the markers for molecular-assisted wheat breeding that facilitate the breeding process in the processing and storage quality of grains.

High-frequency in vitro propagation and assessment of genetic uniformity and micro-morphological characterization of Origanum majorana L. –A highly traded aromatic herb

Origanum majorana (L.) (family Lamiaceae) is a multipurpose medicinal plant with high demand across the pharmaceutical, cosmetic, food, beverage, and perfume industries that has raised concern for its mass propagation through in vitro culture techniques. The present report describes an effective in vitro propagation system for an aromatic medicinal plant Origanum majorana L. The Murashige and Skoog's (MS) medium supplemented with 1.0 mg L-1 6-benzylaminopurine (BAP) initiated a maximum of 4.4 ± 0.22 micro-shoots from the nodal segment explants. The regenerated shoots were further proliferated (98.0 ± 0.22 shoots per explant/culture vessel) on MS medium augmented with 0.5 mg L-1 BAP and 0.25 mg L-1 α-naphthalene acetic acid (NAA). Individual shootlets were rooted on a half-strength MS medium with 1.0 mg L-1 indole-3 butyric acid (IBA) (4.8 ± 0.20 roots/shoots). The rooted plantlets were transplanted into eco-friendly paper cups containing soilrite®: manure; sand (2:1:1) and maintained in the greenhouse for hardening. Inter simple sequence repeats (ISSR) molecular markers were utilized to investigate the somaclonal variations between in vitro developed plants and the mother plant of O. majorana. The band patterns of regenerated plantlets have shown genetic uniformity with the donor plant. The foliar micro-morphological features under in vitro and ex vitro conditions were compared with the mother plant and elucidated morphologically stable plantlets development through gradual acclimatization. This is the foremost report on ISSR molecular marker-based genetic fidelity studies and foliar micro-morphological evaluation of micropropagated plants of O. majorana.

English

Identification of zygotic and nucellar seedlings of Harumanis mango by morphological approach is impossible or hard to be performed. Therefore, this research were to identify zygotic or nucellar seedlings from Harumanis mango polyembryonic seeds through simple sequence repeat (SSR) molecular markers in relation with germination sequence and vigour of seedlings for source of true-to-type cutting material. The results showed that there were 3 seedlings per seed on average. The result from the molecular analysis of 136 seedlings (45 seeds) showed four zygotic seedlings in seeds 1, 15, 29 and 43 representing 8.9% of seeds evaluated. Most of the zygotic seedlings were found towards the end of germination sequence except for seed number 15 and the rest were considered as nucellar seedlings. Based on the fitted logistic regression, the predicted sequence to obtain 90% nucellar seedlings is 5.47. This means that, the germination sequence of less than 6 has 90% chance of getting nucellar seedlings compared to zygotic seedlings. Morphological characters such as number of leaves, stem diameter and leaf area could also be used as references with germination sequence. The results showed that there were significant (p<0.01) relationships between germination sequence and all the growth variables. All growth variables were negatively correlated with germination sequence. This suggested that in order to have 90% chances of getting nucellar seedling (germination sequence below 6), the seedling needs to exhibit several morphology characters; big stem girth, tall plant, high leaf number and large leaf area. Therefore, choosing vigour seedling will increase chances of getting nucellar seedlings, which can be used as cutting source for true-to-type planting material or for breeding purposes.   Key words: Harumanis, molecular, morphology, nucellar, SSR markers, zygotic.

Detection of grain yield QTLs in the durum population Lahn/Cham1 tested in contrasting environments.

Durum wheat (Triticum turgidum L. var durum) is tetraploid wheat (AABB); it is the main source of semolina and other pasta products. Grain yield in wheat is quantitatively inherited and influenced by the environment. The genetic map construction constitutes the essential step in identifying quantitative trait loci (QTLs) linked to complex traits, such as grain yield. The study aimed to construct a genetic linkage map of two parents that are widely grown durum cultivars (Lahn and Cham1) in the Mediterranean basin, which is characterized by varying climate changes. The genetic linkage map of Lahn/Cham1 population consisted of 112 recombinant inbred lines (RILs) and was used to determine QTLs linked to the grain yield in 11 contrasting environments (favorable, cold, dry, and hot). Simple sequence repeat (SSR) molecular markers were used to construct an anchor map, which was later enriched with single nucleotide polymorphisms (SNPs). The map was constructed with 247 SSRs and enriched with 1425 SNPs. The map covered 6122.22 cM. One hundred and twenty-six QTLs were detected on different chromosomes. Chromosomes 2A and 4B harbored the most significant grain yield QTLs. Furthermore, by comparison with several wheat mapping populations, all the A and B chromosomes of Lahn/Cham1 QTLs contributed to grain yield. The results showed that the detected QTLs can be used as a potential candidate for marker-assisted selection in durum breeding programs.

Regeneration and Genetic Fidelity Analysis of <i>Chlorophytum borivilianum</i> Using Flower Stalk as Explant Source

Chlorophytum borivilianum is a critically endangered plant well known for its medicinal properties for diabetes mellitus, diarrhea, arthritis, sterility, and erectile dysfunction, etc. Due to low viability and long dormancy of seeds, in vitro regeneration is required for large scale cultivation of this plant. In the present study, direct plant regeneration was optimized using flower stalk as explant. Nodal segments of flower stalk were sterilized and kept for direct regeneration on different combinations of BAP and KIN supplemented media. The highest, 15.27 ± 1.14 number of shoots were produced on medium containing BAP (2 mg/L) per nodal segment. The multiple shoot clumps regenerated from flower stalk were separated carefully and kept on rooting media. A maximum of 16.87 ± 1.53 roots per plant was observed in MS media having 0.5 mg/L of NAA. The rooted plantlets were shifted into the pot containing soilrite for hardening and acclimatization. The genetic stability of hardened plants was confirmed by start codon targeted, and inter simple sequence repeats molecular markers. All the 18 randomly selected plantlets showed similar genetic homogeneity to the mother plant. It is the first report on in vitro regeneration along with the genetic fidelity analysis of the regenerated plantlets from flower Stalk of C. borivilianum. As the standardized method of regeneration and mass multiplication is quite efficient and genetically stable, the protocol will be useful for the large-scale production of C. borivilianum to meet the market demand.

Molecular characterization of parents and hybrid progenies of conilon coffee.

The objective of the present work was the molecular characterization of 11 parents and 101 hybrid progenies of conilon coffee, obtained through diallel crosses from the breeding program of the Instituto Capixaba de Pesquisa, Assistência Técnica e Extensão Rural (Incaper, ES, Brazil). The analyses were performed with 18 Simple Sequence Repeat (SSR) molecular markers, obtaining a total of 32 alleles. SSR markers were classified as moderately informative (PIC = 0.37), being efficient in characterizing individuals. High genetic diversity was verified in the 112 genotypes, based on the greater values of observed heterozygosity about to the expected heterozygosity (0.55 and 0.44, respectively), negative values for the fixation index (F) (-0.14), and the formation of distinct groups by UPGMA. These results indicate high genetic variability among the conilon coffee genitors, which remained similar and persisting in the progenies. The average dissimilarity between parents was 0.29 and between progenies 0.34. The progenies 38 and 40 and the parent P11 were considered the most divergent in the study. The genetic variability found can be explored in the genetic breeding of the conilon coffee and guide crossings between diversified and compatible genetic materials, for the composition of novel cultivars for the state of Espírito Santo.

GENETIC DIVERSITY IN AMBURANA (Amburana cearensis) ACCESSIONS: HIERARCHICAL AND OPTIMIZATION METHODS

ABSTRACT The evaluation of accessions in a germplasm bank is essential for determining the potential parents in conservation programs, especially for native trees. This study aimed to determine the genetic diversity among 68 Amburana cearensis genotypes from different locations in the state of Pernambuco, Brazil. Their genetic patterns were evaluated by Inter Simple Sequence Repeat (ISSR) molecular markers and genetic divergence was evaluated through multivariate analyses using different clustering methods. The optimization method used (Tocher) was in agreement with all the hierarchical models used, in which clustering of the genotypes occurred similarly, specifically for the accession BB116, which is an important genetic material to be preserved and studied. Among the various hierarchical methods applied, the Average Linkage method exhibited higher discrimination power, allowing identification of a larger number of divergent groups, thus implying wide genetic diversity among A. cearensis accessions.

Determination of Raspberry Cultivar Authenticity Based on Multiplexed Microsatellite Fingerprinting

ABSTRACT Raspberries (Rubus idaeus L.) are important vegetatively propagated fruit plants. They are used as food, as medicinal plants, and in pharmaceutical and cosmetic industry. For the protection of intellectual property rights, it is very important to have efficient methods that enable fast and accurate identification of cultivars. Raspberry cultivars can be differentiated in two ways: on the phenotypic level with morphological descriptors and on the molecular level with molecular markers. Among the frequently used are SSRs, which are highly informative, easy to score and have a good genome coverage. Considering 19 previously published SSR molecular markers, we selected the most specific loci for each selected genotype and developed specific fingerprint for each of the genotypes included in the study: four red raspberry cultivars (‘Polka,’ ‘Glen Ample,’ ‘Meeker,’ ‘Rose de Côte d’Or’) and two genotypes named Sicoly and Dieffenbach. The aim of our investigation was to demonstrate the differentiation between studied raspberry genotypes by specific amplified fragment patterns, which were unique for each genotype and were based on simple sequence repeats (SSRs). Furthermore, the developed fingerprints were successfully tested on randomly chosen, unknown genotypes.

De novo assembly, annotation, marker discovery, and genetic diversity of the Stipa breviflora Griseb. (Poaceae) response to grazing.

Grassland is one of the most widely-distributed ecosystems on Earth and provides a variety of ecosystem services. Grasslands, however, currently suffer from severe degradation induced by human activities, overgrazing pressure and climate change. In the present study, we explored the transcriptome response of Stipa breviflora, a dominant species in the desert steppe, to grazing through transcriptome sequencing, the development of simple sequence repeat (SSR) markers, and analysis of genetic diversity. De novo assembly produced 111,018 unigenes, of which 88,164 (79.41%) unigenes were annotated. A total of 686 unigenes showed significantly different expression under grazing, including 304 and 382 that were upregulated and downregulated, respectively. These differentially expressed genes (DEGs) were significantly enriched in the "alpha-linolenic acid metabolism" and "plant-pathogen interaction" pathways. Based on transcriptome sequencing data, we developed eight SSR molecular markers and investigated the genetic diversity of S. breviflora in grazed and ungrazed sites. We found that a relatively high level of S. breviflora genetic diversity occurred under grazing. The findings of genes that improve resistance to grazing are helpful for the restoration, conservation, and management of desert steppe.

Large-scale advances in SSR markers with high-throughput sequencing in Euphorbia fischeriana Steud

Euphorbia fischeriana Steud is a very important medicinal herb and has significant medical value for healing cancer, edema and tuberculosis in China. The lack of molecular markers for Euphorbia fischeriana Steud is a dominant barrier to genetic research. For the purpose of developing many simple sequence repeat (SSR) molecular markers, we completed transcriptome analysis with the Illumina HiSeq 2000 platform. Approximately 9.1 million clean reads were acquired and then assembled into approximately 186.3 thousand nonredundant unigenes, 53,146 of which were SSR-containing unigenes. A total of 76,193 SSR loci were identified. Of these SSR loci, 28,491 were detected at the terminal position of ESTs, which made it difficult to design SSR primers for these SSR-containing sequences, and the residual SSRs were thus used to design primer pairs. Analyzing the results of these markers revealed that the mononucleotide motif A/T (44,067, 57.83% of all SSRs) was the most abundant, followed by the dinucleotide type AG/CT (9430, 12.38%). Using 100 randomly selected primer pairs, 77 primers were successfully amplified in Euphorbia fischeriana Steud, and 79 were successfully amplified in three other related species. The markers developed displayed relatively high quality and cross-species transferability. The large number of EST-SSRs exploited successfully in Euphorbia fischeriana Steud for the first time could provide genetic information for research on linkage maps, variety identification, genetic diversity analysis, and molecular marker-assisted breeding. How to cite: Li H, Ma Y, Pei F, et al. Large-scale advances in SSR markers with high-throughput sequencing in Euphorbia fischeriana Steud. Electron J Biotechnol 2021;49. https://doi.org/10.1016/j.ejbt.2020.11.004

The genetic diversity and population structure of two endemic Amazonian quillwort (Isoetes L.) species.

BackgroundTwo endemic lycophyte species Isoetes cangae and Isoetes serracarajensis have been recently described in the State of Pará in the Amazon forest located in northern Brazil. Isoetes L. has survived through three mass extinctions. Plants are considered small-sized, heterosporous, and can display a great diversity of physiological adaptations to different environments. Thus, the current study aimed to estimate the genetic variation of the populations of I. cangae and I. serracarajensis to generate information about their different mechanisms for survival at the same geographical location that could point to different reproductive, adaptative and dispersal strategies and should be considered for effective conservation strategies.MethodsThe genetic diversity and population structure of I. cangae and I. serracarajensis were investigated using Inter Simple Sequence Repeat (ISSR) molecular markers. Total genomic DNA was isolated, and the genetic diversity parameters were calculated.ResultsThe sixteen primers produced 115 reproducible bands, 87% of which were polymorphic. A high level of polymorphic loci (81.74% and 68.48%) and a high Shannon index (Sh = 0.376 and 0.289) were observed for I. cangae and I. serracarajensis, respectively. The coefficient of genetic differentiation between population areas (GST) showed a higher value in I. serracarajensis (0.5440). Gene flow was higher in I. cangae (1.715) and lower in I. serracarajensis populations (0.419). Overall, the results further show that I. serracarajensis and I. cangae are two species with considerable genetic variation and that these differences may reflect their habitats and modes of reproduction. These results should be considered in the development of effective conservation strategies for both species.

Growth rate and genetic structure of Sinapis arvensis susceptible and herbicide resistant populations originating from Greece

Weed resistance to herbicides is a serious agricultural issue that threatens the sustainability of world food production, as its widespread appearance has reduced the diversity of weed control practices and posed economic and environmental risks. Wild mustard (Sinapis arvensis), a very competitive weed in winter cereals, has evolved resistance to ALS-inhibiting herbicides used in Greece. As growth rate and genetic structure of weeds affect their competitive ability against crops, the purpose of this work was to study the effect of geographical origin and resistance profile on growth rate and genetic structure of five S. arvensis populations. In particular, the cross-resistant to tribenuron and imazamox P2, P3 and P4 populations originating from the counties of Larissa, Phthiotida, and Pieria, respectively, the resistant to tribenuron P1 originating from Chalkidiki and the susceptible PS originating from Thessaloniki were evaluated. The growth rate was studied by determining fresh weight, number of leaves, height, and seed weight of plants, whereas the genetic structure by using six inter simple sequence repeat (ISSR) molecular markers. Regarding growth rate, the b slope values of the linear equation fitted on fresh weight regression against sampling time were 10.87, 9.94 and 11.41 for P2, P3 and P4 populations, respectively, which were higher than those of P1 (8.03) and PS (6.79) populations, while the b slopes of leaf number were 3.8 and 4.63 for P3 and P1 populations, which were higher than those of PS (2.1), P2 (2.79) and P4 (2.84). The use of ISSR markers showed also differences between populations in their genetic structure parameters [genetic diversity (h), Shannon index (I), number of alleles (Na), percentage of polymorphic loci for each population (P%), variance among and within populations, and FST value, that is a measure of differentiation among populations due to genetic structure], which attributed to origin and herbicide resistance profile. The ISSR bands indicated that 80% of the molecular variation was within populations and 20% among populations. In addition, the dendrogram produced by the combination of GenALEx and MEGA7 statistical software, along with the corresponding PCoA graphical output indicated similar groups of the individuals belonging in these populations.

Construction of a breeding parent population of Populus tomentosa based on SSR genetic distance analysis

Parent selection is the core of hybrid breeding. The breeding strategy involving the parental identification of superior open-pollinated progeny of Populous tomentosa germplasm resources can significantly improve the efficiency of parental matching. However, due to some factors such as loose powdering time and pollen competitiveness, the offspring derived from open-pollination families which do not undergo completely random mating. Although hybrid combinations based on the male identification method have a high combining ability, this method cannot easily cover the mating combinations of all male and female specimens in the germplasm bank. In addition, the performance of superior plants in open-pollinated families also affects the selection result. If the trait performance value is higher than the population average, then the special combining ability of the reconstructed hybrid combination may be overestimated. Obtaining a solution to the above problems is of great significance for improving the efficiency and accuracy of selecting hybrid parents of P. tomentosa. In this study, 24 pairs of SSR (Simple Sequence Repeats) molecular markers were used to analyze the genetic differentiation of P. tomentosa germplasm resources. The results showed that the genetic variation of the P. tomentosa population was derived from individuals within the provenance, indicating that high genetic diversity is preserved in provenances. The correlation analysis showed that there was a significant positive correlation between the special combining ability of planting height and diameter at breast height (dbh) of the 34 full-sib progeny population and the genetic distance between the parents. Then, the genetic distance between 18 female plants with high fertility and 68 male plants with large pollen quantity was analyzed using this correlation. Fifteen female parents and 12 male parents were screened out, and 52 hybrid combinations with high specific combining ability for growth traits were predicted. Furthermore, for the male parent identification of superior individual plants, we constructed the breeding parent population including 10 female parents and 5 male parents, generating 14 hybrid combinations with potentially high combining ability. The results of the hybridization test showed that the specific combining ability of plant height and dbh was significantly higher than the controlled pollination. Moreover, genetic distance and paternal identification can be used to rapidly and efficiently construct hybrid parent combinations and breeding parent populations.

Genome survey sequencing of Atractylodes lancea and identification of its SSR markers.

Atractylodes lancea (Thunb.) DC. is a traditional Chinese medicine rich in sesquiterpenes that has been widely used in China and Japan for the treatment of viral infections. Despite its important pharmacological value, genomic information regarding A. lancea is currently unavailable. In the present study, the whole genome sequence of A. lancea was obtained using an Illumina sequencing platform. The results revealed an estimated genome size for A. lancea of 4,159.24 Mb, with 2.28% heterozygosity, and a repeat rate of 89.2%, all of which indicate a highly heterozygous genome. Based on the genomic data of A. lancea, 27,582 simple sequence repeat (SSR) markers were identified. The differences in representation among nucleotide repeat types were large, e.g., the mononucleotide repeat type was the most abundant (54.74%) while the pentanucleotide repeats were the least abundant (0.10%), and sequence motifs GA/TC (31.17%) and TTC/GAA (7.23%) were the most abundant among the dinucleotide and trinucleotide repeat motifs, respectively. A total of 93,434 genes matched known genes in common databases including 48,493 genes in the Gene Ontology (GO) database and 34,929 genes in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. This is the first report to sequence and characterize the whole genome of A. lancea and will provide a theoretical basis and reference for further genome-wide deep sequencing and SSR molecular marker development of A. lancea.

Fingerprint identification of white clover cultivars based on SSR molecular markers.

White clover (Trifolium repens L.) is an important perennial legume forage with high productivity and quality. To strengthen the basic research on the genetic characteristics, fingerprint identification and adaptability of white clover germplasm resources, Simple sequence repeat (SSR) molecular markers were applied to 10 white clover cultivars to assess the genetic diversity and related lines of white clover at the molecular level in order to lay a theoretical foundation for the selection of high-quality seeds and cultivars of white clover. A total of 120 different bands were amplified by 29 pairs of SSR primers with good polymorphism, of which 103 (89.5%) were polymorphic. Meanwhile, the PIC of each primer was 0.181-0.588, with an average of 0.329. Analysis of molecular variance revealed that 57% of the genetic variation occurred within cultivars and 43% occurred among cultivars. The results of cluster analysis and the principal coordinate analysis revealed that the parental relationships of the 10 cultivars, with the 'Purple' cultivar very distantly related to the other 9 cultivars and the closest parental relationship between 'Ladino' and 'Sulky'. The fingerprints constructed by three representative primers (gtrs679, gtrs319, and gtrs678) have a strong identification ability. In summary, the SSR markers had good polymorphism and could be used for DNA fingerprint analysis of white clover cultivars.

Seed genetic purity testing of F1 Benincasa hispida var. chieh-qua hybrids using SSR molecular marker analysis

To ensure that farmers can access high-quality seeds, it is essential to find a simple, rapid and accurate method to assess seed purity. In recent years, heterosis in chieh-qua has been widely applied to production. Using the whole genome sequence of chieh-qua, we designed simple sequence repeat (SSR) primers specific for chieh-qua. The parental lines of nine hybrids were screened using 200 SSR primers, seven of which exhibited polymorphisms. The bands were clear, stable and reproducible. We found dominant and co-dominant bands between the parents of the nine hybrids. The seven pairs of SSR primers were successfully used to assess genetic purity of the nine chieh-qua hybrids. The SSR molecular marker purity assessment results were consistent with the results obtained from a field grow-out test (GOT). However, the use of SSR markers provided a more accurate, reliable and faster method for seed purity testing than the GOT. We propose using SSR molecular marker technology to assess the genetic purity of chieh-qua hybrid seeds. With this method, the seed quality can be determined faster, which may help to accelerate the chieh-qua breeding process.

Indigenous Mota-named coarse rice germplasm is distinct from fine-grained rice collected from south-central coastal Bangladesh as compared with the morphological descriptors and molecular markers

While crop enhancement can be performed using the agronomical adaptive traits of local crop varieties, human actions and climatic conditions alter their diversity. An assessment and characterization of 20 germplasm accessions of Mota-named coarse rice diversity alongside eight fine-grained rice from the south-central region of Bangladesh is our primary objective. In this original study, we perform the evaluation of genetic variability of Mota-named coarse rice in comparison with the fine rice from south-central coastal Bangladesh using morphological characteristics and SSR molecular markers. Nineteen morphological descriptors showed distinct variations. Three prominent groups surfaced from simple sequence repeat (SSR). Eighty-seven percent and 13% of genetic variation within and among populations were observed, respectively, using analysis of molecular variance. Five subpopulations emerged from model-based structure study. The studied SSR loci showed 0.642 (for mean polymorphism content value per primer), 0.862 (as highest value), and 0.683 (as average value) for gene diversity of every locus. Geographical information-based molecular analysis revealed high allelic richness (18–21) in the upazilas (counties) of Bauphal, Galachipa, and Dumki, all in the district of Patuakhali, division of Barisal. Morphological–molecular analysis of Mota-named coarse rice germplasm revealed a considerable amount of genetic diversity and a prominent level of population structure. Our results provide information useful for future breeding and conservation programs.

English

The assessment of genetic diversity among improved crop germplasm can facilitate the expansion of the genetic base for crop improvement in breeding program. However, little effort has been made to assess the level of genetic relatedness among released varieties and elite soybean [Glycine max (L.) Merr.] genotypes. The objective of this study was to determine the degree of genetic diversity that exists among released and elite soybean genotypes in Uganda. In this study, 21 polymorphic simple sequence repeat (SSR) molecular markers were used to determine the degree of genetic diversity and varietal identification among 34 soybean genotypes. A total of 59 alleles with an average of 2.85 alleles per locus were detected. The polymorphic information content (PIC) values ranged from 0.208 on BE806308 to 0.741 on Satt411, with an average of 0.5870. The expected heterozygosity varied from 0.208 on BE806308 to 0.725 on Satt411, with an average of 0.548 per marker. The dendrogram constructed based on Jaccard’s genetic similarities among 34 soybean genotypes identified three major clusters, with six of the released varieties belonging to cluster I. The majority of elite genotypes including three recently released cultivars; Maksoy 4N, Maksoy 5N and Maksoy 6N were grouped in cluster II and III. The results showed moderate genetic variation among the soybean genotypes, which could accelerate genetic vulnerability. Therefore, there is need to widen the genetic base of the working germplasm through the use of techniques such as pre-breeding and novel biotechnology techniques such as mutation breeding and CRISPR to create genetic variation necessary to cope with the dynamics of biotic and abiotic stresses that affect soybean production in Uganda.   Key words: Glycine max, genetic relationship, microsatellite or simple sequence repeat (SSR), molecular markers, genetic vulnerability.

SSRMMD: A Rapid and Accurate Algorithm for Mining SSR Feature Loci and Candidate Polymorphic SSRs Based on Assembled Sequences.

Microsatellites or simple sequence repeats (SSRs) are short tandem repeats of DNA widespread in genomes and transcriptomes of diverse organisms and are used in various genetic studies. Few software programs that mine SSRs can be further used to mine polymorphic SSRs, and these programs have poor portability, have slow computational speed, are highly dependent on other programs, and have low marker development rates. In this study, we develop an algorithm named Simple Sequence Repeat Molecular Marker Developer (SSRMMD), which uses improved regular expressions to rapidly and exhaustively mine perfect SSR loci from any size of assembled sequence. To mine polymorphic SSRs, SSRMMD uses a novel three-stage method to assess the conservativeness of SSR flanking sequences and then uses the sliding window method to fragment each assembled sequence to assess its uniqueness. Furthermore, molecular biology assays support the polymorphic SSRs identified by SSRMMD. SSRMMD is implemented using the Perl programming language and can be downloaded from https://github.com/GouXiangJian/SSRMMD.