SSR Primer Pairs Research Articles

Plant parasitic nematodes occurrence and genetic diversity of banana cultivars grown in Tanzania

The genetic diversity of bananas (Musa spp.), one of the most economically important crops in Tanzania, is underestimated with scarce reports available. In addition, cultivation of banana is severely constrained by plant parasitic nematodes (PPN). We assessed genetic diversity and population structure of 159 banana varieties from four agro-ecological zones (Northern, Southern highlands, Lake and Zanzibar islands) of Tanzania using 20 SSR markers analysed with UPGMA method. We also, assessed the PPN occurrence through isolation and counting of PPN from each banana genotype where leaf samples were collected. SSR primer pairs were polymorphic; and generated 63 distinct reproducible bands. The polymorphic information content values of each SSR marker ranged from 0.50 to 0.75 indicating high level of genetic diversity among banana varieties. The 159 banana varieties were grouped into two clusters: A and B, based on UPGMA cluster and population structure analysis. A total of 128 independent and 31 overlapping genotypes were identified. Higher kinship among genotypes was observed in cluster A compared with cluster B. Some of the clusters in A and B genotypes showed high genetic distance. The most prevalent and abundant nematode species was Pratylenchus goodeyi with a mean count of 63%, followed by Radopholus similis (31%) and P. coffeae (6%). The results from this study provides a foundation for understanding genetic variability of bananas existing in Tanzania and PPN occurrence that will be valuable information for breeding disease and pest-resistant bananas with high yield traits.

Genetic Diversity Analysis of Hybrid Rice Parental Lines and Genetic Purity Assessment of Hybrid Seeds of China

Thirty-five pairs of SSR primers were used for genetic diversity analysis and DNA fingerprinting of 31 hybrid rice core parental lines developed in central- and southern-China using one japonica rice line and three inbred rice lines as the check varieties. The average number of alleles (Na) per SSR locus was 4.02, with a range of two to eight, the effective number of alleles (Ne) was 83.16 with a mean of 2.38, ranging from 1.19 to 4.66. The polymorphic information content (PIC) ranged from 0.16 to 0.79, with an average number of 0.52. The results of the cluster analysis indicated that the check varieties viz., one japonica rice and three inbred rice, were clustered into two groups with similarity coefficients of 0.62 and 0.71 respectively indicating their relatedness. Thirty-one hybrid rice parental lines were clustered into 6 groups according to their different types, pedigrees and regions of development with similarity coefficients of approximately 0.76. The highest genetic similarity coefficient (0.94) was observed between Y58S and C815S, and the lowest (0.63) was observed between Quan9311A and Peiai64S. The purity of one hybrid rice cultivar was tested using characteristic marker and the field test, and it was demonstrated that the purities obtained using the two methods were similar. This research will be helpful for rice breeding, new cultivar registration and seed production.

Generation Mean Analysis and Molecular Markers for Salinity Tolerance during Wheat Germination and Seedling Stage

Generation mean analysis for salt tolerance in wheat was studied on P1, P2, F1, F2, BC1 and BC2 populations of three crosses. The cross-1 was between the salt tolerant Sakha-8 and sensitive Sham-8, cross-2 was between two salt tolerant varieties (Sakha-8 x Line-6) while cross-3 was between salt tolerant Line-6 and sensitive Sham-8. The genotypes were evaluated under control (0.0 mM NaCl) and salinity stress (150.0 mM NaCl) at germination and seedling stage for seven traits. The model of additive/dominance is inadequate for explaining the inheritance of all traits in control and salinity treatments in three crosses. The presence of epistasis in addition to the predominance of non-additive gene effects for all traits except SL indicated that the conventional selection procedure may not be effective enough to improve them. Therefore postponement of plant selection in later generations or the crosses between the selected segregants followed by selfing can be suggested to accumulate alleles favorable for the improvement of these traits. The molecular markers analysis revealed that only four SRAP primer combinations, three TRAP primer combinations and three SSR primer pairs generated polymorphic bands form the tested genotypes. The five polymorphic bands SRAP-2570bp, SRAP-3760bp, TRAP-1205bp, TRAP-3450bp and SSR-2215bp appeared only in the tolerant genotypes. These markers may be considered as specific markers for salt tolerance. The identified markers in this study would allow implementation of marker-assisted selection to screen wheat segregating populations for salt tolerance.

Analysis of the genetic structure and morphology of Polygonatum cyrtonema in Anhui Province, eastern China revealed three distinct genetic groups

Polygonatum cyrtonema Hua, a rhizome‐propagating herb endemic to China, is used in many traditional Chinese medicines and foods. The hilly mountains in western and southern Anhui province is one of its main natural distribution and artificial cultivation areas. We assessed the genetic diversity and structure of P. cyrtonema germplasm resources in Anhui by nine pairs of SSR primers and selected morphological characters. The results showed that the 13 sampled populations of P. cyrtonema possessed normal levels of genetic diversity but could be clustered into three distinct genetic groups. The levels of within‐group genetic diversity was similar among the three groups, but their distribution areas and morphological characters were remarkably different. Group I was confined to the Tianmu (including Jiuhua) Mountains, group II was distributed in the Huangshan Mountains, and group III was restricted to the Dabie Mountains. Furthermore, the leaf length:width ratio significantly differed among groups, and the peduncle length of group I was significantly shorter than that of the other two groups. Levels of genetic differentiation among the three groups was close to that between different species within the genus. Thus, the three genetic groups of P. cyrtonema should be considered as independent units for conservation and breeding management in the Anhui region.

Genetic diversity and genetic structure evaluation of cultivated Chinese wolfberry (Lycium barbarum) based on microsatellite population genetics

A total of 178 Chinese wolfberry individuals from 17 populations were detected by 7 pairs of SSR primers to evaluate genetic diversity and structure, using software GenALEx 6.5,NTSYS,STRUCTURE, the effects of cultivation on genetic diversity and structure were clarified aiming to find the strategies for genetic management and sustainable use. The results showed that the genetic diversity of cultivated Chinese wolfberry was low. The average number of alleles N_A, expected heterozygosity H_E, observed heterozygosity H_O, and Shannon's information index H' was 3.9, 0.443 7, 0.556 6, 0.788 1, respectively. STRUCTURE, UPGMA clustering and PCA test indicated that Chinese wolfberry varieties were severely intermixed but no differentiation among varieties. Mantel test showed no significant correlation between genetic distance and geographic distance. AMOVA analysis showed that genetic variation mainly occurred among individuals within the population(84.58%, P<0.001), and there was almost no genetic differentiation between varieties(3.63%, P<0.001) and between populations(11.79%, P<0.001). The cultivation has caused a significant decline in the genetic diversity of Chinese wolfberry, which may cause inbreeding decline. New germplasm resources should be sought from the wild to improve the existing cultivars. On the other hand, there are obvious homogenization and germplasm intermixing between cultivated varieties and populations. Meanwhile, Chinese wolfberry cultivars should be purified and prevented from flowing into the wild population, in case of causing pollution of the wild germplasm.

Development and application of SSR loci in monoploid reference genome of sugarcane cultivar

<p indent="0mm">Sugarcane is one of the most important sugar crops in the world. However, it is difficult to develop SSR on a large scale since the genome of cultivar has not been sequenced, which limits the genetic improvement of sugarcane. In this study, a template of monoploid sugarcane genome was assembled using a set of 4660 BAC library sequences (with a cumulative length of 382 Mb, predicting 25,316 genes) from cultivar ‘R570’. SSR loci were identified by using MISA (Microsatellite identification tool) software. The distribution characteristics of the monoploid genome ‘R570’ was comprehensively analyzed by comparing with the SSR loci of four Gramineae plants (<italic>Sorghum bicolor</italic>,<italic> Zea mays</italic>,<italic> Oyrza sativa</italic>, and <italic>Brachypodium distachyon</italic>). Fifty pairs of primers with TG and AG repeat motifs were designed to verify the amplification efficiency and polymorphism by PCR amplification in four <italic>Saccharum</italic> clones (R570, ROC1, LA purple, and SES208) and twenty four core parents of sugarcane. A total of 27,241 SSR loci were identified, with an average of 6.29 SSR loci per BAC clone and an average density of 71.33 SSR Mb^–1 which was much lower than that of sorghum (350.00 SSR Mb^–1). The mono-nucleotide (11,079) and tri-nucleotide repeat motifs (6447) accounted for 64.33% of the total SSR loci. The number and proportion of tri-nucleotide repeat motifs were the largest in the four Gramineae plants. In addition, A/T (accounting for 84.8%) motif had the highest proportion and C/G (accounting for 15.2%) motif the lowest proportion in the mono-nucleotide repeat motifs and TGT/ACA (accounting for 16.04%) motif had the highest proportion in the trinucleotide repeat motifs. In general, the genomes in Gramineae plants are rich in A/T repeat motifs. In the polymorphism validation of 50 pairs of primers (41 pairs of TG motif and 9 pairs of AG motif), 45 pairs of primers (90%) were found to be able to amplify successfully, of which 35 (70%) were polymorphic in 4 sugarcane clones. Furthermore, 20 pairs of polymorphic SSR primers were used to detect 24 core parents of sugarcane, a total of 95 alleles were amplified with an average of 4.75 alleles per primer, verifying the application feasibility of these primers for the genetic diversity analysis in sugarcane. The development of SSR markers from the monoploid genome of cultivars ‘R570’ not only enriches the number of SSR markers available in sugarcane genetic analysis, but also facilitates the genetic diversity analysis of sugarcane population and the genetic mechanism dissection of important agronomic traits, which provides a foundation for the in-depth research of molecular breeding in sugarcane.

SSR-Based Genetic Identity of Sugarcane Clones and its Potential Application in Breeding and Variety Extension

Sugarcane variety regional test and integrated demonstration play an important role in identifying new varieties of high yield, disease resistance and wide adaptability. In this study, 15 SSR primer pairs were used to assess the genetic diversity among 68 sugarcane clones involved in three cycles of national regional tests and four cycles of integrated demonstrations in China. In total, 141 DNA fragments of 100 to 350 bp in length were identified, of which 139 fragments (98.58%) were polymorphic. Clustering analysis of UPGMA algorithm based on the Nei genetic similarity coefficient divided the 68 sugarcane clones into five groups. Group I only had one clone YT00-318 due to its high heterogeneity. Groups II, III, VI and V contained 4, 6, 5 and 52 sugarcane clones, respectively. A small subgroup A in group V was identified at the genetic similarity coefficient 0.890 that contained ROC22, FN07-3206, FN40, GT09-12 and LC07-150. ROC22 was a check variety with wide adaptability, high cane yield, high sugar and several other excellent characteristics; the other four clones might have a high potential of release by sharing the same excellent traits. Principal component analysis showed that the 68 sugarcane clones within quadrants I, II, III and IV showed a high homogeneity, and no series of clones obviously gathered together. The SSR fingerprint information of the 68 sugarcane clones has been drawn into a SSR fingerprint map for the identification of sugarcane clones in Chinese sugarcane breeding programs.

ДНК-фингерпринтинг сортов клевера лугового (Trifolium pratense L.) на основе SSR-анализа

The results of experimental studies on polymorphism of 10 red clover cultivars of Russian selection are presented. Informative primer pairs that can be used for the identification of markers during intervariety differentiation were determined. Based on SSR fingerprints, molecular genetic formulas of the studied cultivars were compiled. Samples of genomic DNA of each cultivar were obtained from pooled aliquots of the plant tissue, each containing 30 seedlings. Eleven pairs of SSR primers developed for structural analysis of the red clover genome were used in genotyping. Unique amplification fragments were found with SSR locus RCS1307 for Trifon and Topaz cultivars, as well as with SSR locus RCS3095 for Trio and Mars cultivars, which can serve as identification DNA markers The results of this study are of practical importance for the molecular genetic certification of breeding achievements, which is necessary to assess the quality and genetic uniformity of seeds and to control hybridization in the breeding process. forage crops, red clover, DNA fingerprinting, SSR loci, cultivar identification This study was funded from the federal budget within the framework of a state assignment (project no. 0442-2019-0001 АААА-А19-119122590053-0).

Usage of microsatellite markers for characterization of polyploids: a case study in reference to hexaploid bamboo species

Abstract Microsatellite markers are most valuable tools for characterization of plant genetic resources or population genetic analysis. Since they are codominant and allelic markers, utilizing them in polyploid species remained doubtful. In such cases, microsatellite markers are usually analyzed by treating them as dominant marker. In the current study, it has been showed that despite of losing the advantage of co-dominance, microsatellite markers are still powerful tool for genotyping of polyploid species because of availability of large number of reproducible alleles per locus. It has been studied by genotyping of nineteen sub populations of Dendrocalamus hamiltonii (hexaploid bamboo species) with seventeen polymorphic SSR primer pairs. Among these, ten primers gave typical banding pattern of microsatellite marker as expected in diploid species but rest seven gave unusual pattern i.e. more than two bands per locus per genotype. In such case genotyping data are generally analyzed by considering as dominant markers. Given these facts, data were analyzed in both ways as dominant and codominant. All the seventeen primer were first scored as non-allelic data and analyzed; later ten primer pairs giving standard banding pattern were analyzed as allelic data and the results were compared. The UPGMA clustering and genetic structure showed that results obtained with both the data sets were very similar, and therefore the SSR marker could be utilized to characterize polyploid species by considering them as dominant marker. The study is highly useful to widen the scope of SSR markers applications and beneficial to the researchers dealing with polyploid species.

Genome-wide genetic diversity detection and population structure analysis in sweetpotato (Ipomoea batatas) using RAD-seq

Sweetpotato (Ipomoea batatas L.) is one of the most important food and grain-forage crops globally. It has been planted in >100 countries. Due to the complexity of the sweetpotato genome, its research is far behind other major food crops. At present, limited information about the sweetpotato genome is available. Thus, it is central to find an efficient approach for the investigation of sweetpotato genome. In this study, RAD-seq (Restriction site-associated DNA sequencing) was used to evaluate sweetpotato genetic structure diversity and to develop relevant SSR markers. The study yielded >128 Gb reliable sequence data from 81 sweetpotato accessions. By analyzing polymorphic tags from each accession, a total of 55,622 restriction-site associated DNA sequencing tags (RAD-seq) were found, containing 907,010 SNP. Genetic analysis divided 81 accessions into five major clusters based on their SNP genotype, which matches the results of genetic analysis and the genetic family tree. In addition, 18,320 SSRs loci were detected and 9336 SSR primer pairs were developed. Eighty-three primer pairs were amplified in different sweetpotato genotypes, 76 of which successfully amplified polymorphism bands. These results provide significant information about sweetpotato genome, which can be used to identify novel gene and to further develop the gene chip. And more significant, clustering results based on the SNP genotype provide an essential reference for breeders to match parent plants in breeding program. Additionally, SSR markers developed in this study will supply a wealth of markers for marker-assisted selection in sweetpotato breeding.

The different origins of artificially-induced unreduced female gametes and their effect on transmitted parental heterozygosity in Populus

The induction of unreduced gametes via chromosome doubling is an effective way to produce triploids. During this process, the transmitted parental heterozygosity varies by different origins of unreduced gametes. In this study, a total of 110 allotriploid individuals from two cross combinations who shared only one male parent were obtained by chromosome doubling of megaspore via high temperature treatment in Populus tomentosa. Twenty-six SSR loci, at which the allelic configurations of the female parents ‘MC1’ and ‘MC2’ were heterozygous and different from male parent ‘YX1’, were screened. Among them, five pairs of pericentromeric SSR primers were selected to identify the origins of unreduced female gametes. Our results showed that 30 individuals from 110 allotriploids derived from the first division restitution (FDR), and 80 allotriploids from the second division restitution (SDR) in these two cross combinations. The transmitted parental heterozygosity of unreduced female gametes via FDR were 0.824 and 0.769 in two cross combinations, respectively, which was significantly higher than that of SDR (0.395 and 0.396, respectively). The FDR type unreduced gametes with higher heterozygosity transmitted from parents may be more desirable in triploid breeding. However, no significant difference in transmitted parental heterozygosity was found between the two FDR groups and two SDR groups. Correct elucidation of the origins of unreduced gametes may be conducive to their effective utilization for further sexual hybridization in triploid poplar breeding.

Classification and phylogenetic relationship of 10 fig varieties by RAPD and SSR molecular markers

In this experiment, 24 fig varieties were analyzed by RAPD and SSR. Results showed that 80 loci were amplified by 9 RAPD primers, including 70 polymorphic loci. The polymorphic percentage was 87.50%. A total of 34 allelic variations were detected in 10 pairs of SSR primers, 29 of which were polymorphic bands, and the percentage of polymorphic sites was 85.29%. Correlation analysis of the two markers of genetic identity showed significant correlation, indicating that the two markers were highly consistent in the analysis of fig genetic diversity. Cluster analysis revealed that the RAPD markers showed that the 24 fig varieties had a genetic similarity coefficient of 0.7 and could be divided into four groups. SSR markers showed that the 24 fig varieties can be divided into four groups at the genetic similarity coefficient of 0.66. The results show that the two molecular markers are suitable for the genetic diversity analysis of fig, and they are more reliable when combined than when used alone.

Genetic Diversity of Egyptian Date Palms (Phoenix dactylifera L.) Using Morphological and Molecular Markers

Morphological and molecular analyses were conducted to evaluate the genetic diversity among eleven Egyptian date palms (Phoenix dactylifera L.). Ten SSR primer pairs revealed a high percentage of polymorphism (97.4%) among 38 total number of alleles, while 11 SCoT primers produced 48.5% from 171 amplified fragments. SCoTs recorded effective multiplex ratio (EMR) and PIC values of 7.5 and 0.14, respectively, opposing to 3.7 and 0.26 for SSRs, respectively. A similar marker index has thus resulted in both markers. Nei’s gene diversity (h) was generally low for both marker systems indicating homogeneous nature and narrow genetic background for the studied Egyptian date palms, which was also emphasized through their high genetic similarity estimates. The results of UPGMA cluster analysis and PCoA grouped the eleven date palms according to their geographical location and sex. In addition to classical morphological characters, the current study confirmed the importance of using SCoTs as functionally gene-based multi-loci markers besides nuclear SSR loci to assess the genetic variations and cultivar identification among Egyptian date palm genotypes

Genetic variability evaluation and cultivar identification of tetraploid annual ryegrass using SSR markers.

Annual ryegrass (Lolium multiflorum) is a widely used cool-season turf and forage grass with high productivity and ornamental characteristics. However, the abundant intra-cultivar genetic variability usually hampers the application of conventional techniques for cultivar identification. The objectives of this study were to: (1) describe an efficient strategy for identification of six tetraploid annual ryegrass cultivars and (2) investigate the genetic diversity based on SSR markers. A total of 242 reliable bands were obtained from 29 SSR primer pairs with an average of 8.3 bands for each primer pair and the average value of polymorphic information content (PIC) was 0.304. The result of analysis of molecular variance (AMOVA) revealed that 81.99% of the genetic variation occurred in within-cultivars and 18.01% among-cultivars. The principal coordinate analysis (PCoA) showed that the first two principal axes explain 8.57% (PC1) and 6.05% (PC2) of total variation, respectively. By using multi-bulk strategy based on different filtering thresholds, the results suggested that bands frequency of 40% could be used as a reliable standard for cultivar identification in annual ryegrass. Under this threshold, 12 SSR primer pairs (00-04A, 02-06G, 02-08C, 03-05A, 04-05B, 10-09E, 12-01A, 13-02H, 13-12D, 14-06F, 15-01C and 17-10D) were detected for direct identification of six tetraploid annual ryegrass cultivars, which could be incorporated into conservation schemes to protect the intellectual property of breeders, ensure purity for consumers, as well as guarantee effective use of cultivars in future.

Genetic Diversity Among Old Local Grape Cultivars in South of Syria

This investigation was carried out in Sweida governorate of Syria from 2014 to 2015. The purpose of this investigation was to estimate the genetic diversity among 17 old local grape cultivars using morphological traits and SSR molecular markers. Principal Component Analysis (PCA) of morphological traits revealed that four main components were accountable for 50.34 % of variance, with Eigen values of 16.77%, 13.31%, 10.59% and 9.67%, respectively. While distribution of cultivars was found significantly dependent of first and second components, which separated Aswad Sharar and Derbly cultivars rather than other studied cultivars. Hierarchical cluster of morphological traits showed high diversity among studied cultivars. On the other hand, molecular characterization was conducted using eight informative SSR primer pairs, polymorphism was detected by seven SSR's primers. As a result, 18 polymorphic alleles were revealed with a polymorphism percentage of 100%, which reflected the genetic variation among studied cultivars. Genetic similarity was achieved, where 0.875 was the highest between Zeiny and Khedry cultivars, while the other two cultivars Ebeidy and AhmarMokamaa showed the lowest genetic similarity as 0.077. Cluster analysis of SSR markers grouped the studied cultivars into three clusters as per Jaccard coefficient. The first cluster grouped Ebeidy, Aswad Helwany and Derbly cultivars together, the second cluster contained two cultivars Beiady and Alb Atair, while the third cluster contained the remaining cultivars. Consequently, the results showed high diversity among studied cultivars, and some morphological traits were useful for cultivar discrimination.

Identification and validation of microsatellite markers in strawberry tree(Arbutusunedo L.)

Strawberry tree (Arbutus unedo L.), an evergreen shrub/small tree of the family Ericaceae, is a main constituent of the Mediterranean basin flora; although it is also found in southwestern France, Macaronesia, and Ireland. The small fruits are edible but mostly used for preparation of preserves and jams, and for liquors such as the Portuguese traditional "aguardente de medronho". Traditionally cultivated by small farmers, often in consociation with Quercus sp., strawberry tree is presently emerging as a new important fruit crop cultivated in large orchards by modern export-oriented enterprises. This change of paradigm requires a growing role of plant breeding, upstream of the production process. Genomic tools for this species are mostly limited to the chloroplast genome sequence and to genomic data described in this work. In order to identify strawberry tree microsatellite (SSR) loci we performed partial genome next-generation sequencing using the Ion Torrent technology. The sequenced ~24.6M nucleotides resulted in the identification of 1185 microsatellite markers mostly constituted by dinucleotide motifs. The relative amount of microsatellite dinucleotide motifs (AG/ CT - 71.7%, AC/GT - 20.5%, AT/AT - 2.9%, and CG/CG - 0.3%) is similar to the one observed in other Ericaceae species. Among a tested sample of 40 SSR primer pairs, 20 amplified well-defined PCR products, 12 (30%) were validated as polymorphic. Used in our collaborative project for molecular identification of selected and improved clones, the identified SSR loci constitute a strong tool for a large panoply of applied and fundamental studies of this emerging fruit crop.

Analysis of Genetic Diversity of 45 Guava Germplasm Evaluated Using SSR Markers

ABSTRACT The genetic relationships of 45 individuals of Psidium guajava from six cultivars were analyzed by screening SSR primers with high polymorphism and good repeatability, which provided a scientific basis for the collection, protection, and utilization of guava germplasm resources in China. In this study, we analyzed genetic diversity and cluster of 45 guava materials using 15 pairs of polymorphic SSR primers. The number of polymorphic bands was 65 with the polymorphism ratio of 97.01%, and the molecular weight of the band ranges from 102 bp to 500 bp. Only two polymorphic bands were detected by primer mPgCIR23, which was the least. In contrast, primer mPgCIR08 detected seven bands with the highest number of polymorphic bands. The average polymorphism information content of the markers was 0.60, Nei’s genetic diversity was 0.29, and Shannon’s index was 0.44. Additionally, the variation range of genetic similarity coefficient was 0.37–0.99. The clustering pattern generated from the UPGMA method distinctly grouped the cultivated varieties and the seedling strain into four groups when the genetic similarity coefficient is 0.68. All the seedling strains (except S9) were successfully clustered into three subgroups, which confirmed that they were progenies from three different guava varieties, respectively.

Development and Identification of Expressed Sequence Tag-based SSR Markers Associated with the Heterostyly Trait in Primula forbesii

Heterostylous Primula forbesii is an important ornamental flower in China because of its long-lasting flowers and winter bloom. This study aimed to develop markers of expressed sequence tag–simple sequence repeats (EST-SSRs) that are associated with heterostyly and that can be used for molecular-assisted selective breeding in P. forbesii. We investigated 114,474 unigenes and identified 25,095 SSRs in P. forbesii. Dinucleotide repeats (46.14%), mononucleotide repeats (44.65%), and trinucleotide repeats (8.27%) were the most abundant SSRs. Among the 25,095 SSRs, 10,645 SSR primer pairs were successfully designed, of which 130 primer pairs were randomly selected for further amplification validation using eight accessions of P. forbesii; 98 pairs produced clear and stable polymerase chain reaction (PCR) products, and 28 pairs showed polymorphism. Bulked segregant analysis (BSA) was conducted for the F1 population with respect to thrum style and pin style by scanning 28 polymorphic SSR primer combinations. One SSR marker, c64326, linked to the heterostyly trait at a genetic distance of ≈3.70 cM was identified. The marker c64326 was further validated in two populations with an accuracy of 97.92% and 90.63%. The novel and linked EST-SSR markers can be valuable resources for genetic diversity analysis, mapping, and marker-assisted breeding in P. forbesii.

DNA fingerprint and diversity in aromatic rice by Gn1 gene linked SSR markers

Number of grains per panicle is a limiting factor for the yield of aromatic rice. Toovercome this limitation, itmight behelpful to screenaromatic rice using markers linked to grain number.In this study, an elementary DNA fingerprinting database of the nine aromatic rice cultivars was built using four SSR primer pairs linked to Gn1 gene responsible for grain number in rice. For genotyping of aromatic rice cultivars, DNA was extracted from leaf samples using IRRI standard protocol. Allele scoring was done by using a computer based program Alpha Ease FC 4.0 and data were analyzed by Power Marker version 3.25 software. Nei’s genetic distance value and similarity werecomputed. From the analysis, it was found that a total of 21 alleles were detected with an average number of 5.25 alleles per locus having PIC values ranging from 0.3402 (RM5493) to 0.7883 (RM3452) and the average value 0.6629. The highest gene diversity (0.8148) was observed in loci RM3452,and the lowest gene diversity (0.3404) was observed in loci RM5493.From the study, it can be stated that all of the aromatic rice germplasm have bands of the gene that influence the grain but they showed genetic variability.Information obtained from genotyping of varieties helped to analyze the genetic diversity within and among closely related crop varieties which has the potential for crop improvement and to meet the diverse goals like producing cultivars with increased yield of aromatic rice.&#x0D; Progressive Agriculture 29 (4): 336-344, 2018

Genetic diversity in nine chickpea (Cicer arietinum L.) varieties based on different molecular markers

Nine varieties (BARI Chola-1 to BC-9) of chickpea (Cicer arietinum L.) were studied with respect to isozymes, SDS-PAGE, amplified DNA produced by RAPD- and SSR-markers. The varieties could be characterized by SDS-PAGE bands on the basis of their location, size and intensity. Three isozyme systems, namely acid phosphatase, esterase and peroxidase were investigated of which esterase was found to be suitable for produced distinct polymorphic bands with 57.14% diversity. Ten RAPD primers were producing 74 bands with 93.24% polymorphisms which indicated highly diverse nature. In addition to polymorphism, 12 variety-specific RAPD fragments were identified. Ten SSR primer pairs were producing 20 distinct bands of which 11 were considered as polymorphic (55%). On the basis of RAPD and SSR analysis, BC-1 and BC- 6 were placed in cluster-1 and the remaining varieties were placed in cluster-2. On the other hand, the combined data of three isozymes systems and SDS-PAGE made BC-8 and BC-9 were different and thus placed in cluster-2 while the other seven varieties were placed in cluster-1.