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Micronutrient deficiency is a widespread food-related health problem around the world. The present study was conducted to evaluate a set of 63 advanced breeding lines of bread wheat (Triticum aestivum L.) for grain iron (GFe) and grain zinc (GZn) concentrations, and to characterise the germplasm set via simple sequence repeat (SSR) markers (both genic and random). Substantial variation was found for both micronutrients. GFe concentration ranged from 28.9 to 67.4 mg kg–1 and GZn from 26.3 to 56.6 mg kg–1. Molecular characterisation with six genic and 20 random SSR markers detected 168 alleles with an average of 3.170 alleles per locus. Analysis of genotypic data based on division into two subpopulations revealed 165 alleles with an average of 3.113 alleles per locus in the low GFe–GZn subpopulation, whereas in the high GFe–GZn subpopulation, 149 alleles with an average of 2.811 alleles per locus were detected. Genic SSRs detected a higher average number of alleles (3.273 alleles per locus) than random SSRs (3.143 alleles per locus). Hierarchical clustering using genic markers alone clustered the whole germplasm set into two distinct groups: one possessing low GFe–GZn genotypes, the other with high GFe–GZn genotypes. Study of marker–trait associations (MTAs) identified seven new MTAs (six for GZn and one for GFe) and validated one MTA for GZn concentration. The promising genotypes and MTAs identified during the study will prove useful in wheat bio-fortification programs in the future.

Cowpea is a leguminous crop that has received widespread attention due to its high nutritional value. However, it is prone to losing some of its nutritional content due to the long cooking process. In this study, fourteen cowpea genotypes were evaluated for their chemical properties before and after cooking, along with the effect of different cooking treatments on the cooking time, considered as the main indicator of the cooking quality. Moreover, the correlation between molecular markers (simple sequence repeat (SSR) and intersimple sequence repeat (ISSR)) and the cooking time of cowpea genotypes was determined. The obtained results showed significant differences between all the investigated genotypes before and after the cooking procedure, reflecting significant genotypic and heritability estimates. Kareem 7 and Greenish Black Balady genotypes showed the shortest cooking time. Microwave's treatment manifested the shortest cooking time compared with the other treatments, which appeared as a new approach to improve the cooking quality of cowpea seeds. Spearman's rank correlation showed that the calculated values were smaller than the tabulated value at 0.05, reflecting the existence of a rank correlation between SSR/ISSR‐PCR banding products and the cooking time of cowpea genotypes. Such a study appeared to be a new approach, particularly in Egypt for the proper selection of the optimal cowpea seed on the basis of its cooking quality., Such a study appeared to be a new approach, particularly in Egypt for the proper selection of the optimal cowpea seed on the basis of its cooking quality.

As a medicinal and edible plant, the plum (Prunus mume Sieb. et Zucc.) plays an important role in the treatment of diseases and human health. However, the genetic diversity and genetic composition of medicinal plum species cultivated in China remain incompletely clear, hampering the accurate identification. Here, the genetic diversity and population structure of 40 medicinal plum varieties in China were analyzed using polymorphic simple sequence repeat (SSR) molecular markers, and the lineages compared. SSR allelic analysis was followed by a STRUCTRE analysis. The mean observed heterozygosity (HO) and polymorphism information content were 0.74 and 0.69, respectively. The cumulative probability of identity was very low with a value of 7.17 × 10−19. STRUCTURE analysis provided evidence for three genetic groups. Further, a genetic fingerprint consisting of four pairs of SSR primers has been successfully developed to accurately distinguish 40 varieties of medicinal plum. This study provides reference data which can be used to assist the breeding, quality evaluation, and development of medicinal plum varieties.

Over 450 potato varieties and landraces are preserved as in vitro cultures by the Plant Biotechnology department of Estonian Crop Research Institute. This collection contains germplasm from various countries as well as old Estonian landraces. These potato accessions are periodically grown in the field for verification; however, this is not always sufficient to validate varieties and, in many cases, the true origin or identity of old landraces is not known. A reliable and cost-effective method for fingerprinting Estonian potato germplasm needed to be implemented. Simple sequence repeat (SSR) markers are known as robust and efficient markers for the identification of tetraploid potato. Here, fingerprinting results are presented for 103 genotypes from the Estonian potato collection using 8 SSR markers. It was shown that as few as three markers were sufficient to yield unique fingerprints for the given set of samples. SSR markers were used to estimate the allele copy number with varying success. Additionally, the reproducibility of four of these markers was assessed in two different laboratories, and repeatable results were observed. It was verified that the putative landrace ‘Kuldkera’ has the same genetic fingerprint as the variety ‘Ando’, whilst an expected clone of ‘Early Rose’ is a completely different genotype. Implementation of genetic fingerprinting and these results is of high importance for further potato genebank management and Estonian breeding programme.

Two cultivars of local rice, namely Mentik Wangi and Mentik Susu, have been grown around west to south flank of Merapi volcano. They are highly valued for their good taste and cooking characteristics. An attempt to introduce drought-tolerant rice varieties has been conducted by crossing them with two sources, namely Kasalath and Bluebonnet. Molecular-assisted selection using a set of SSR markers was applied to check the F1 and F2 generation trueness and segregation. This research was conducted in the facilities of Department of Agronomy, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta. The research was a field experiment arranged in a completely randomized design, consisting of Mentik Wangi, Mentik Susu, Bluebonnet, and Kasalath, as well as their crossings’ F1 and F2 plants as treatments. The SSR markers used are RM72, RM228, RM518, and RM20(A). Polymorphism test of the parents showed that polymorphism exists between local and donor parents, thus these markers were considered eligible for the F1 and F2 tests. The heterozygous individuals of F1 were 75% for Bluebonnet × Mentik Wangi, 44.4% for Bluebonnet × Mentik Susu, and 46.7% for Mentik Wangi × Bluebonnet; all were consistent in every primer used. We could not confirm that the F2 populations showed segregation pattern that followed Mendelian segregation in some crosses due to too small size of the sample. Heterozygous individuals in F2 showed the differences pattern for each marker, indicating that the location of the SSR markers were far from each other in the genome.

Eastern filbert blight (EFB), caused by Anisogramma anomala, is a fungal disease threatening the european hazelnut (Corylus avellana) industry in the Willamette Valley of Oregon. The pathogen is endemic to the eastern United States where it causes little damage to the wild Corylus americana but causes severe cankers on most cultivars of the commercially important european hazelnut. The host genetic resistance in ‘Gasaway’ is conferred by a dominant allele at a single locus on linkage group 6 (LG6), and resistance from several other sources has been mapped to the same region. Some fungal isolates can overcome ‘Gasaway’ resistance, prompting a search for other sources of resistance. Resistance from other sources has been mapped to LG2 and LG7, for which additional simple sequence repeat (SSR) markers would facilitate marker-assisted selection (MAS). In this study, an in silico approach was used to develop new polymorphic SSR markers in the EFB resistance regions on LG2 and LG7. Starting with a search of 17 contigs of the ‘Jefferson’ genome sequence, 45 new polymorphic SSR markers were developed, characterized, and placed on the linkage map. The new SSR markers had an average of 10.18 alleles per locus, and average values for expected heterozygosity, observed heterozygosity, polymorphism information content, and frequency of null alleles of 0.72, 0.65, 0.68, and 0.068, respectively. Of the 42 new polymorphic SSRs segregating in the mapping population, 24 were on LG2, 12 were on LG7, and six were placed on other LGs. The new and previously developed SSR markers were used to study six new sources of EFB resistance, four from Russia and two from Crimea. Six resistant selections were crossed with susceptible selections, resulting in 7 progenies. Phenotyping for disease response revealed that segregation in progenies of the two Moscow selections (#2 and #27), one Russian selection (OSU 1187.101), and one Crimean selection (H3R12P62) fit the 1:1 segregation ratio expected for control of resistance by a dominant allele at a single locus; but in progenies of the other Russian selection (OSU 1166.123) and the other Crimean selection (H3R07P11), there was an excess of resistant seedlings. Correlation of disease scores and alleles at SSR loci indicated that resistance from three Russian selections (Moscow selections #2 and #27 and OSU 1166.123) and the Crimean selection H3R12P62 was on LG7, while resistance from Russian selection OSU 1187.101 was on LG2. Resistance from Crimean selection H3R07P11 was not correlated with markers on LG6, or LG2, or LG7. These sources and new SSR markers will be useful in MAS and the pyramiding of resistance genes in the breeding of new EFB-resistant cultivars.

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

Registration of crop varieties under Indian PPV & FR Act requires establishment of their Distinctiveness, Uniformity and Stability (DUS). At present, DUS of crop varieties are being established using morphological traits. DNA marker assay-based DUS testing would complement that based on morphological traits. Four markers, from a total of 220 tested SSR markers were polymorphic among two advanced breeding lines and two elite germplasm accessions (used as candidate varieties), and two released varieties (used as reference varieties) of dolichos bean. The four polymorphic simple sequence repeat (SSR) markers were used to establish distinctness of candidate varieties from reference varieties based on alleles unique to candidate varieties. Uniformity of candidate varieties were established using two criteria, (1) per cent homozygous plants (> 95%) and (2) SSR-homozygous loci ratio (HLR) (> 95%).The candidates which were found uniform at tested SSR loci were deemed stable. The candidate varieties were distinct from reference varieties at two of the four tested polymorphic SSR markers, as evident by the presence of alleles unique to candidate varieties. One hundred per cent homozygous plants and SSR-HLR within all the candidate varieties at all the four tested SSR marker loci suggested uniformity and deemed-stability of candidate varieties. The study demonstrated the utility of SSR markers to establish DUS of ABL/elite germplasm accessions in dolichos bean.

Genetic purity is conventionally performed through grow-out-test (GOT) with morphological characters. Simple sequence repeat (SSR) markers are independent of G X E interaction. Herewith, 16 high yielding varieties of rice were analysed using 55 SSR markers for DNA fingerprinting and identification of genetic impurities: 14 were found to be polymorphic and amplified 48 alleles with an average of 3.43 alleles per each primer pair. The number of alleles amplified ranged from 2 to 6 and the size of the PCR products amplified from these 14 primer pairs ranged from 80 to 450 bp with polymorphic information content (PIC) from 0.14 (RM 346) to 0.99 (RM 5900). PICs at 0.5 or higher are highly informative SSR markers for genetic studies and the study reported (7/14) markers to be highly informative based on PIC values. Besides, the values of effective multiplex ratio, marker index and resolving power for the selected polymorphic primer pairs disclosed that the SSR markers used in the study are highly informative and could be potentially used for distinctness, uniformity and stability (DUS) testing, genetic purity analysis and DNA fingerprinting of rice varieties. Economic analysis of grow-out-test and SSR marker based genetic purity showed that the GOT process incurs Rs. 5.8 (INR) per seed (USD 0.07), while DNA-based marker analysis incurs Rs. 53.75 (INR) or $ 0.71 (USD).

Einkorn (Triticum monococcum L. ssp. monococcum) is an ancient diploid wheat species with many useful traits and used as a wheat gene discovery model. In this research, a total of 41 diploid and tetraploid wheat accessions were tested using simple sequence repeat (SSR) markers. A total of 33 genotypes of T. monococcum along with four genotypes each of tetraploid wheat (T. dicoccon and T. durum) were used as plant material. The analysis utilized 10 polymorphic markers, including a total number of 41 alleles with an average frequency of 4.1 alleles per locus during exploration of the level of genetic variations. Various diversity analyses, which are the effective number of alleles (Ne), gene diversity (h), Polymorphic Information Content (PIC), and Shannon's information index (I), were performed for 10 'A' genome wheat SSR markers. The results showed a narrow variation in einkorn genotypes, supported by Analysis of Molecular Variance (AMOVA), with 66% maximum variation in all genotypes. The structure analysis divided the whole germplasm into two populations. A dendrogram was constructed to determine the genetic similarities using the unpaired group method with arithmetic averages (UPGMA), which separated tetraploid wheat from other genotypes/accessions. Principal Coordinate Analysis (PCoA) co-supported the clustering of UPGMA and structure by differentiating the diploid and tetraploid wheat. These findings will help understand the genetic relationships among these wheat accessions and their use in breeding programs in the future works.

In this study, the molecular profiles of five soybean cultivars (Burangrang, Gema, Grobogan, Panderman, and Sinabung) exhibiting salinity resistance were elucidated. The DNA profiles of the five cultivars were found to differ based on simple sequence repeat (SSR), insertion-deletion polymorphism (InDel)-QS080465, and sequence characterized amplified region (SCAR)-QS08064 markers. Three distinct SSR profiles¾Satt-243, Satt-294, and Satt-308¾and the SCAR-QS08064 marker were only observed in the Grobogan cultivar, whereas the InDel-QS080465 marker was only successfully amplified from the Burangrang, Gema, and Grobogan cultivars. The results indicate that the Grobogan cultivar is the most tolerant soybean cultivar, followed by the Burangrang and Gema cultivars. Results were consistent with those from genetic similarity analysis, which showed that Grobogan is genetically more similar to Burangrang and Gema compared to Sinabung and Panderman. In conclusion, the five soybean cultivars have different molecular profiles that are related to their resistance to salinity. SSR markers, InDel QS080465-152, and SCAR QS08064-383 are molecular markers specific to salinity-resistant cultivars.

Soybean [Glycine max (L.) Merr.] responded differently to storage stress factors. This research work aimed at assessing genetic potentials of fifteen soybean varieties to storage stress via accelerated aging technique and grouping them based on their levels of tolerance to storage stress using simple sequence repeat (SSR). Tolerance of the seed of 15 soybean varieties to storage stress was assessed by subjecting them to accelerated aging for 0, 6, 12, and 24 hours at 42 °C temperature and 100 % relative humidity (RH), after which their quality was assessed to determine their tolerance to storage stress. Same varieties were also stored for 6 months under ambient environment at 65 ± 5 % R.H and 25 ± 2 °C and they were genotyped with 19 simple sequence repeat (SSR) markers. The varieties were grouped on the basis of their levels of tolerance to storage stress. The principal components analysis (PCA) showed that germination rate index (GRI) and germination index (GI) were the major indices responsible for the significant variation in the seedling vigor characters. TGX1835-10E and TGX1448-2E were identified as varieties with good storage ability and therefore recommended for storage improvement in soybean breeding programs. Six SSR markers (Satt 565, Satt 175, Satt 281, Satt 600, Satt 160 and Satt 281) were identified as candidate markers for detection of alleles for tolerance to storage stress.

Erianthus arundinaceus possesses high biomass, vigor, ratoonability and resistance to biotic and abiotic stresses and is considered to be an ideal species for improving sugarcane. In this study, a genome survey sequence was performed in E. arundinaceus, and SSR markers were developed based on a genome survey sequence. A total of 167.36 Gb raw data were obtained and were assembled into 3161 Mb genome sequences, including 15,238,738 scaffolds. The genome size was estimated to be approximately 3.23 Gp based on kmer analysis. In total, 36,616 SSR motifs were identified and characterized, including 60.69% dinucleotide, 34.27% trinucleotide, 3.34% tetranucleotide, 0.98% pentanucleotide and 0.71% hexanucleotide repeats. AG/CT repeat motifs were the most abundant, and GC/CG repeat motifs were somewhat rare, accounting for 54.16% and 2.69% of dinucleotide repeat motifs, respectively. A total of 365 SSR loci were obtained by 20 SSR primer pairs amplified in 20 clones of E. arundinaceus and its related species, and 188 SSR loci were specific to E. arundinaceus. Genetic similarity coefficient analysis by UPMGA methods clustered 20 clones of E. arundinaceus and its related species into two groups. Five clones of E. arundinaceus clustered separately with the remaining clones. These results may establish a foundation for further research investigating the E. arundinaceus genome and identifying genuine hybrids between sugarcane and E. arundinaceus.

Simple Sequence Repeat (SSR) or microsatellite markers have become extremely useful tools in genetic identification and variability studies. To date around one hundred of these markers have been developed in the olive tree (Olea europaea L. subsp. europaea) and the majority of them are di- or tri-nucleotide. The analysis of the numerous articles recently published on plant microsatellite markers, shows however a higher relevance of markers with long core repeat motifs than those with di- or tri-nucleotide repeat motifs. This work presents a new set of highly informative and polymorphic tetra- and hexa-nucleotide SSR markers. The newly designed SSR markers have been employed to genotype the 36 olive cultivars of the core collection from Worldwide Olive Germplasm Bank of Cordoba, Spain (WOGBC). This article describes the allelic profiles of the 36 olive cultivars for a set of ten SSR markers and also a protocol for a multiplex polymerase chain reaction (PCR). The designed multiplex PCR can lead to an optimal amplification of up to five different SSR markers in the same reaction tube. Finally, the use of only four of the set of ten SSR markers employed, allows the differentiation of any cultivar of the WOGBC core collection from the remaining 35 cultivars.

In this study, a total of 20 simple sequence repeat (SSR) markers were used to study the genetic diversity and population structure among 60 accessions of eggplant. Out of 20 SSR markers, 15 were f...

SSR marker is one of the genetic marker s widely applied in plant breeding programs. The application of molecular markers in plant breeding is meant to accelerate the selection of cross - progeny . The research aim ed to identify the SSR primers polymorphism between the parent and control that linked to Al tolerance and verify the cross-progeny of five crosses. The result gained from 37 SSR primers used in this study showed that only nine primers are polymorphic. These nine polymorphic primers are RM257, RM214, RM247, RM205, RM490, RM262, RM569, RM271, and R M19 . The application of polymorphic markers on five cross -progeny which have shown the same band pattern as the parents and tolerant control on the use of 9 SSR primers recorded as follows: RM257 2 lines, RM214 5 lines, RM247 5 lines, RM205 lines, RM490 13 lines, RM262 5 lines, RM569 7 lines, RM271 4 lines, and RM19 6 lines. The selected SSR primers linked to Al tolerance in this research can be used as a reference for molecular breeding strategies to develop new Al tolerance rice varieties in dryland conditions.

Development of wheat (Triticum aestivum L.) varieties with increased yield potentials that are adapted to drought and heat stresses requires genetically differentiated and complementary parents. Th...

Rubus ellipticus Smith. commonly known as ‘Yellow Himalayan raspberry’ is an important member of Rosaceae family with high medicinal importance having antioxidant and antibacterial properties. This study was done with the objective of characterizing 21 R. ellipticus collections from different regions of India, based on morphological descriptors and expressed sequence tags-simple sequence repeat (EST-SSR) markers. Broad phenotypic variability among the R. ellipticus collections was detected by using morphological descriptors. The Euclidian distance matrix discriminated two groups, based on morphological characters. A set of 68 EST-SSR markers were developed based on 7777 unigenes generated by us from ‘Kumarhatti-1’ collection of R. ellipticus using assembled pair—end sequences from Illumina NextSeq 500. The ESTs containing simple sequence repeat motifs were extracted using Microsatellite identification tool and primers were designed. Out of 68 EST-SSRs polymorphism was detected using 61 (89.7%) primer pairs, indicating high genetic variability in the R. ellipticus collections. Effective multiplex ratio, marker index and polymorphism information content were 0.43, 0.24 and 0.50, respectively. The unweighted pair group method with arithmetic mean coincided with the bootstrap analysis and two groups were formed, separating the collections Uttrakhand from the other. Morphological descriptors along with EST-SSR markers proved efficient in detecting the levels of genetic variability among the collections maintained in the field. These results can be used as an additional source of exploitation in R. ellipticus breeding programs.

Camellia oleifera Abel. is a cultivable plant with important economic value. It is very helpful for the scientific utilization, cultivation and preservation of germplasm resources through evaluating the genetic diversity. In this study, we estimated the genetic distances of 135 accessions of C. oleifera using ISSR and SCoT markers, respectively. The genetic dissimilarity coefficients of ISSR markers ranged from 0.56 to 1.00. And the accessions were divided into five groups. While the genetic dissimilarity coefficients of SCoT markers ranged from 0.62 to 1.00, the accessions were divided into four groups. The results demonstrated that C. oleifera germplasms perform a little genetic variation. This is the first report to evaluate the genetic diversity of different C. oleifera germplasms using the ISSR and SCoT molecular markers, and the results provide the useful foundation for plant breeding of C. oleifera.

Seashore paspalum (Paspalum vaginatum) is an important warm-season turfgrass distributed in tropical and coastal areas. It has excellent resistance to abiotic stresses, such as salinity, drought, and low temperature. However, the research on genetic diversity of local P. vaginatum collections from China is limited. In this study, the genetic diversity among 58 P. vaginatum accessions from four different provinces in China and four cultivars were assessed using simple sequence repeat (SSR) markers. The results indicated that a total of 45 alleles were detected by 19 polymorphic markers, with a range of 2 to 4 and an average of 2.4 alleles per marker. The genetic similarity coefficients between each pair of the 58 P. vaginatum accessions and four cultivars ranged from 0.51 to 1.00, with an average of 0.77. The range of variation of Shannon diversity index of each SSR marker was 0.047 to 1.075, with an average of 0.486. The polymorphic information content of each SSR marker varies from 0.016 to 0.577, with an average of 0.249. The results of cluster analysis and principal component analysis (PCA) showed that 58 P. vaginatum accessions and four cultivars were divided into four groups. These results provide the theoretical basis for the genetic diversity assessments and molecular marker–assisted breeding of P. vaginatum species.

Birds and mammals are important seed dispersers of fleshy-fruited plants. Although their behaviors are different, they frequently consume the same species. Thus to understand the dispersal of fleshy-fruited plants, the contribution of birds and mammals to seed dispersal has to be evaluated. Besides, within birds or mammals, some species may functionally different from others. In this study, we examined seed dispersal of the fleshy-fruited tree Swida controversa focusing on the difference between two frugivore groups (birds and mammals), and differences between species within groups. Collected seeds and S. controversa trees were identified using simple sequence repeat (SSR) genotyping, thus enabling to determine the distance between mother tree and dispersed seeds. The avian species were identified by DNA barcoding of feces, whereas the mammalian species were identified by the shape and smell of feces. Most seeds that fell near or under the maternal trees were dispersed by birds, resulting in short seed dispersal distances (average, 13 m). DNA barcoding detected five taxa of avian dispersers. No differences were detected in seed dispersal distance by different avian taxa (i.e., the distance between dispersed seeds and their maternal trees within the research plot); however the rate of seed immigration from outside the research plot by some avian taxa varied significantly. The seed dispersal distance by mammals was significantly further (127 m; min > 50 m) than that by birds. Additionally, immigrated seeds accounted for approximately two-thirds of mammal-dispersed seeds, indicating that these seeds were from outside the research plot, and that mammals significantly contributed to the long-distance seed dispersal of S. controversa. No differences in seed dispersal distance were detected between different mammalian taxa. Overall, this study revealed that birds and mammals show clearly different seed dispersal patterns, and thus, they play different roles in the regeneration of S. controversa.

Background Previously, 3% of the human genome has been annotated as simple sequence repeats (SSRs), similar to the proportion annotated as protein coding. The origin of much of the genome is not well annotated, however, and some of the unidentified regions are likely to be ancient SSR-derived regions not identified by current methods. The identification of these regions is complicated because SSRs appear to evolve through complex cycles of expansion and contraction, often interrupted by mutations that alter both the repeated motif and mutation rate. We applied an empirical, kmer-based, approach to identify genome regions that are likely derived from SSRs. Results The sequences flanking annotated SSRs are enriched for similar sequences and for SSRs with similar motifs, suggesting that the evolutionary remains of SSR activity abound in regions near obvious SSRs. Using our previously described P-clouds approach, we identified ‘SSR-clouds’, groups of similar kmers (or ‘oligos’) that are enriched near a training set of unbroken SSR loci, and then used the SSR-clouds to detect likely SSR-derived regions throughout the genome. Conclusions Our analysis indicates that the amount of likely SSR-derived sequence in the human genome is 6.77%, over twice as much as previous estimates, including millions of newly identified ancient SSR-derived loci. SSR-clouds identified poly-A sequences adjacent to transposable element termini in over 74% of the oldest class of Alu (roughly, AluJ), validating the sensitivity of the approach. Poly-A’s annotated by SSR-clouds also had a length distribution that was more consistent with their poly-A origins, with mean about 35 bp even in older Alus. This work demonstrates that the high sensitivity provided by SSR-Clouds improves the detection of SSR-derived regions and will enable deeper analysis of how decaying repeats contribute to genome structure.

Camellia oleifera Abel. (C. oleifera) is a cultivable plant with important economic value. It is very helpful for the scientific utilization, cultivation and preservation of germplasm resources through evaluating the genetic diversity. In this study, we estimated the genetic relationship of 150 accessions of C. oleifera using morphological and economic traits, as well as SSR molecular marker. Through the variation and cluster analysis of 17 morphological and economic traits, the germplasm was divided into a candidate core breeding group with higher economic traits and a core breeding group with higher morphological traits. The genetic similarity coefficients of SSR markers ranged from 0.05 to 0.91, and the germplasm materials were divided into five groups. The results demonstrated that C. oleifera germplasms perform a rich genetic variation. This is the first report to evaluate the genetic diversity of different C. oleifera germplasms using the morphological and economic traits, together with SSR molecular marker, and the results allow us to find evidence for the origin of varieties, establish core breeding populations and its fingerprint.

In this present study, eight genotypes of Brassica juncea comprising four tolerant (IC-399802, IC-491089, IC-312545, IC-312553) and four susceptible (IC-385686, IC-264131, IC-426392, Laxmi) genotypes for aphid tolerance were used to generate Sequence Characterized Amplified Region (SCAR) markers through dominant PCR based markers (51 RAPD and 12 ISSR markers). 13 RAPD (Random Amplified Polymorphic DNA) and 8 ISSR (Inter Simple Sequence Repeat) markers were found to be polymorphic but only 3 primers OPE16 (RAPD), UBC 839 (ISSR) and UBC 864 (ISSR) were obtained which could distinguish tolerant genotypes from susceptible ones. OPE16 (RAPD) obtained unique band of size approx. 600 bp in susceptible genotypes while it was absent in the tolerant genotypes. Similarly, UBC 839 (ISSR) yielded ~800 bp unique band in bulk tolerant while UBC 864 (ISSR) yielded three bands of ~1200 bp, ~1000 bp, and ~500 bp in tolerant genotypes which was absent in the susceptible genotypes. These unique bands were excised to generate five sets of SCAR markers. Among the five sets of SCAR marker, only BJSCAR F1 and BJSCAR R1 set yielded the promising result in all for 4 susceptible genotypes as well as bulk susceptible and was absent in all the tolerant genotypes and Brassica fruticulosa (highly tolerant to aphid, used as a control). So, this SCAR marker developed could be successfully used in screening of B.juncea genotypes in future breeding programs.

Inter simple sequence repeat (ISSR) marker system was used to evaluate the genetic diversity of local and introduced grasspea (Lathyrus sativus L.) genotypes. A total of 144 bands were amplified using 10 ISSR markers, of which 122 were polymorphic among the accessions. The percentage of DNA polymorphism varied from 66.6% to 96%, with a mean of 86%. UBC 857, UBC 810 and UBC 835 with high effective multiplex ratio (EMR), marker index (MI) and resolving power (RP) values were estimated as the most informative primers for distinguishing L. sativus genotypes. High genetic diversity was detected in the grass pea germplasm. The genetic diversity index (GDI) ranged between 0.42 and 0.92, with an average value of 0.75 for the whole collection. The cluster analysis with 5000 bootstrapping value divided grasspea accessions into four major clusters. Most accessions were placed into the same cluster close to each other with regard to their botanical varieties. Principal coordinate analysis (PCoA) agreed with the cluster analysis and clearly discriminated the accessions into two genetically distinct groups. The first three coordinate axes accounted for 84.3% of the total variation. The result of the cluster and PCoA analyzes underline the importance of consideration of botanical variety traits in grasspea breeding programs. It can be concluded that the present germplasm constitutes an important pool of diversity for further genetic analysis, linkage mapping and breeding activities.

Background: Mungbean is an important pulse crop and it is mainly cultivated in Asia for human consumption. Its small genome and diploid nature make it a well-suited model organism among legume crops. Thus, cost-effective, reliable and highly polymorphic molecular markers distributing the whole genome are needed for diversity, mapping and functional genomics studies in this model species. Methods: The whole-genome sequence of mungbean was obtained and used as a source of identification of simple sequence repeats (SSR). The sequence reads were aligned and SSRs detection was performed using the Phobos plugin tandem repeat finder in the Geneious software program. A total of 12 mungbean genotypes were selected to validate the newly developed SSR markers. Result: In the present study, a total of 12, 49,774 and 11, 86, 386 perfect and imperfect SSR repeats were identified from the mungbean genome. The tri-repeats were the most abundant (26.10%), followed by hexa (20.82%), penta (20.45%), tetra (17.65%) and di-repeats (14.95%). We designed 1330 SSR primers based on the genomic sequence of flanking perfect SSRs (Di and tri-repeats). Among them, 50 SSR primers uniformly distributed across the 11 mungbean chromosomes were selected and used to validate 12 mungbean genotypes. The newly developed genomic SSR markers generated in the present study are a valuable genomic resource for the mungbean breeding programs.

Leaf blight is an important disease of teak which reduces photosynthetic rate and ultimate timber yield in infected trees. Symptomatic leaf samples were randomly collected from three forest reserve...

For the purpose of protecting the rights of Lentinula edodes breeders, we developed a new simple sequence repeat (SSR) marker set consisting only of genetically independent tetranucleotide or longer core motifs. Using available genome sequences for five L. edodes strains, we designed primers for 13 SSR markers that amplified polymorphic sequences in 20 L. edodes cultivars. We evaluated the independence of every possible marker pair based on genotype data. Consequently, eight genetically independent markers were selected. The polymorphic information content values of the markers ranged from 0.269 to 0.764, with an average of 0.409. The markers could distinguish among 20 L. edodes cultivars and produced highly repeatable and reproducible results. The markers developed in this study will enable the precise identification of L. edodes cultivars, and may be useful for protecting breeders’ rights.

We designed 170 new simple sequence repeat (SSR) markers based on the whole-genome sequence data of button mushroom (Agaricus bisporus), and selected 121 polymorphic markers. A total of 121 polymorphic markers, the average major allele frequency (MAF) and the average number of alleles (NA) were 0.50 and 5.47, respectively. The average number of genotypes (NG), observed heterozygosity (HO), expected heterozygosity (HE), and polymorphic information content (PIC) were 6.177, 0.227, 0.619, and 0.569, respectively. Pearson’s correlation coefficient showed that MAF was negatively correlated with NG (−0.683), NA (−0.600), HO (−0.584), and PIC (−0.941). NG, NA, HO, and PIC were positively correlated with other polymorphic parameters except for MAF. UPGMA clustering showed that 26 A. bisporus accessions were classified into 3 groups, and each accession was differentiated. The 121 SSR markers should facilitate the use of molecular markers in button mushroom breeding and genetic studies.

Simple sequence repeats (SSRs) are widely used in cultivar identification, genetic relationship analysis, and quantitative trait locus mapping. Currently, the selection of hybrid progeny plants in molecular marker-assisted breeding mostly relies on SSR markers because of their ease of operation. In Pyrus, a large number of SSR markers have been developed previously. The method to identify polymorphic SSRs quickly is still lacking in cultivated as well as wild pear species. We present a large number of polymorphic SSRs identified using a quick in silico approach applied across 30 cultivated and wild accessions from Pyrus species. A total of 49,147 SSR loci were identified in Pyrus, and their genotypes were evaluated by whole-genome resequencing data of 30 Pyrus accessions. The results show that most SSR loci were dinucleotide repeat motifs located in intergenic regions. The genotypes of all SSR loci were revealed in all accessions. A total of 23,209 loci were detected, with more than one genotype in all Pyrus accessions. We selected 702 highly polymorphic SSR loci to characterize the pear accessions with an average polymorphism information content value of 0.67, suggesting that these SSR loci were highly polymorphic. The genetic relationship of Pyrus species in the neighbor-joining (NJ) tree and population structure showed a clear division between the oriental and occidental accessions. The population structure split all oriental pears into two groups: cultivars and wild accessions. These new findings of the polymorphic SSR loci in this study are valuable for selecting appropriate markers in molecular marker-assisted breeding in Pyrus.

Wild yams (Dioscorea spp.) are important tuber crops used both as vegetable and medicine by the tribal people of Koraput, India. There is deficiency of documented information on genetic structure and diversity of wild yams and its genetic assessment is necessary for crop improvement program. The present study assessed the level of genetic diversity of eight wild and one cultivated yam species of Koraput by using different morphological and molecular markers. Significant variation in different yield and morphological traits was observed among the studied yam species. The major morphological traits such as branch number, stem thickness, tuber depth, tuber length, number of tubers per plant and yield showed high genetic heritability accompanied with high genetic advance and major determinants of phenotypic diversity. Molecular profiling was carried out by taking five simple sequence repeat markers. A total of 10 polymorphic bands with an average of two were detected at the loci of the five markers across the nine yam species. Genetic similarity analysis revealed that some wild yam species such as D. oppositifolia, D. hamiltonii and D. pubera showed higher genetic similarity with cultivated (D. alata) species. The knowledge of the extent of genetic variations of wild yam species is important for planning of the genetic conservation and the utilization of this resource especially for genetic improvement. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12298-019-00691-3) contains supplementary material, which is available to authorized users.

Sugarcane brown rust induced by Puccinia melanocephala is an important global disease. Exploring novel resistance genes and breeding varieties with durable resistance is the most economical and effective way of controlling brown rust. The establishment of complete and high-density molecular genetics maps is a key prerequisite for the discovery and location of sugarcane brown rust resistance genes. To obtain more polymorphic simple sequence repeat (SSR) markers for the construction of genetic linkage maps, six highly resistant varieties and six highly susceptible varieties were used as parents to screen the primers with clear bands, obvious polymorphism, and good repeatability. The highest numbers of polymorphic primers were obtained from the parental group of Liucheng 03-1137 × Dezhe 93-88 (52.38%). Ten pairs of primers including mSSCIR34 exhibited high polymorphism in the parental group of Liucheng 03-1137 × Dezhe 93-88. Here, we recommend ten SSR pairs of polymorphic primers including mSSCIR34 to use in the mapping populations of Liucheng 03-1137 × Dezhe 93-88. The polymorphic primers could facilitate the construction of genetic maps and lay an appropriate foundation for the localization of brown rust resistance genes and development of molecular genetics linkage markers.

Phenolic acids are one of the main active components in Salvia miltiorrhiza root, which have been proved to have extensive pharmacological activities. In this study, quantitative trait loci (QTL) for phenolic acids contents were identified by a new genetic map constructed based on genomic simple sequence repeat (SSR) markers. The results demonstrated that the map comprised eight linkage groups which were in accord with the haploid chromosome number of S. miltiorrhiza (2n = 2x = 16). The map spanned 397.5 cM with average inter-marker distance as 3.6 cM. A total of six QTL were identified through interval mapping, including three salvianolic acid B (SAB) content-related QTL on linkage group (LG) 7, two lithospermic acid (LA) content markers on LG2 and LG4, as well as one rosmarinic acid (RA) content-linked QTL on LG7. These QTL could be used in marker-assisted breeding for the phenolic acids contents of S. miltiorrhiza.

Apple trees are perennial plant and have a characteristic of requiring long period from seed germination to flowering and fruiting. Most Korean apple cultivars are derived from closely related varieties genetically; consequently, they are distributed into grafted seedlings at juvenile stage. Therefore, it is difficult for them to distinguish by morphological traits due to the high similarities without fruit characteristics. We have integrated the high-resolution melting (HRM) analysis with simple sequence repeat (SSR) marker genotyping to identify thirteen apple cultivars originated from South Korea. The patterns of temperature-shifted melting curves were investigated from HRM analysis. The SSR loci used in this study generated a unique melting curve profile for each cultivar allowing their comparison and classification. The combination of the allelic patterns obtained with the just three SSR markers was able to identify thirteen apple cultivars. These results suggest that SSR markers used in combination with HRM analysis can be a fast and accurate method for high-throughput cultivar identification and biodiversity assessment.

SUMMARY Despite extensive studies on cultivated rice, the population structure and genetic diversity of the indica photoperiod- and thermo-sensitive genic male sterility (P/TGMS) lines in China remains unclear. Using 48 simple sequence repeat (SSR) markers, we genotyped a panel of 208 indica P/TGMS lines and confirmed three subgroups, named indica-I, indica-II and indica-III, in indica P/TGMS lines. Further diversity analysis indicated indica-II had the highest genetic diversity. The genetic differentiation between indica-II and indica-III was demonstrated as the largest among the three subgroups. Moreover, indica/japonica component identification was detected that five P/TGMS lines possess indica components less than 0.900. These results improve our knowledge on the genetic background for P/TGMS lines in China and will be beneficial for hybrid rice breeding programs.

Genebanks offer vast amounts of traditional germplasm with potential sources of novel genes against biotic and abiotic stresses. In order to utilize the germplasm in rice breeding programmes, there should be a fast screening approach such as the use of molecular markers. Thus, the current study aimed to evaluate the use of tsv1 resistance-linked simple sequence repeat markers (SSR) for the preliminary screening of Philippine traditional rice germplasm against rice tungro spherical virus (RTSV). The tsv1 resistance-linked SSR markers consisted of two to four repeat motifs with 5–24 base repeats. Expected sizes ranged from 123 to 465 base pairs (bp) with polymorphism information content ranging from 0.23 to 0.73. Genetic analysis showed six major clusters at 50%: Clusters A, B and C had individual accessions, Cluster D had three accessions, Cluster E had 55 and Cluster F had 42 accessions. The study showed the germplasm with alleles linked to tsv1 but should be validated in the future with induced screening. In general, the material consisted of selected germplasm showing the presence of alleles linked to the tsv1 gene. These rice accessions could be a source of resistance to RTSV following further validation. Furthermore, molecular markers provide a useful tool to accelerate the screening of genetic resources for biotic and abiotic stress tolerance.

Pleurotus ostreatus is one of the most important edible mushrooms. Many cultivars have been bred to meet consumer needs. The identification of cultivars based on the morphological characteristics is restricted because fruiting bodies are frequently capricious due to environmental conditions; accordingly, sequence-based methods are required. A total of 546 simple sequence repeat primers derived from the P. ostreatus genome were screened, and one primer, JHH_SSR-184, was found to show polymorphisms on the major cultivars in Korea. The sequences of the polymorphic loci showed variable-number tandem repeat loci-like features enabling cultivar specificity. Thus, these loci might be applicable to discriminate P. ostreatus cultivars.

Triploid breeding is an effective way to obtain seedless hybrids. In addition to artificial breeding, some triploid cultivars occur naturally in the genus Citrus. ‘Yellow Bell’, a new lemon cultivar recently patented in Japan was selected from the small seed of an open-pollinated ‘Villafranca’ fruit. Therefore, it has an unknown pollen parent. To characterize the pollen parent of ‘Yellow Bell’, possible parental cultivars were genotyped using simple sequence repeat markers, and then the parental relationships were estimated by establishing the inheritance of tri-allelic marker genotypes. As a result, the pollen-donating parent of ‘Yellow Bell’ was determined to be ‘Summer Fresh’, which was growing 40 m from the maternal tree in the same orchard. The parentage of ‘Tahiti lime’, a lime cultivar having a long cultivation history, was evaluated in a similar manner and it was confirmed that ‘Mexican lime’ and a true lemon cultivar were the parents.

WOS: 000487041800001, In this study, the genetic relationships of 29 grape genotypes were defined with six SSR (simple sequence repeat) markers, and 65 polymorphic bands were identified, with matrix correlation (r) of 0.79. The expected heterozygosity (He) ranged from 0.783 (VrZAG62) to 0.869 (VVMD7) and the observed heterozygosity (Ho) from 0.483 (VrZAG62) to 0.897 (VVS2). According to the results, the smaller main cluster included only one ancient cultivar, 'Buca Razakisi'. Foca Karasi', an ancient cultivar in the large main group, was separated from other grapes varieties. The first sub-cluster (S1) formed by mainly introduced cultivars included three cultivars, 'Cabernet Sauvignon', 'Cabarnet Franc' and 'Merlot'. The second sub-cluster (S2) was the largest group, and included 19 cultivars, 'Semillion', 'Alicante Boushet', 'Delbele', 'cesme Pembesi', 'Grenache', 'okuzgozu', 'Petit Syrah', 'Papaz Karasi', 'Colombard', 'Harsleleh', 'Moiseylative', 'Sika', 'Muskule', 'Ohannes', 'Cinsaut', 'Kirmizi Sam', 'Kozak Gemresi', 'Siyah Gemre' and 'Yuvarlak Razaki'. The third sub-cluster (S3) included four cultivars, 'Cardinal', 'Italia', 'Hafizali' and 'Malbee'. 'Hafizali is an ancient cultivar and is included in this group. The fourth sub-cluster included only one ancient cultivar, 'Pek uzumu'. Based on the rates of similarities of the cultivars included in this study, the highest rate was recorded for 'okuzgozu-Petit Syrah' (93%) in the second sub-cluster. The results reported here are important as the first steps towards better characterization of these grape genotypes and will aid future germplasm management and breeding efforts., Ege University Scientific Research FundEge University [BAP 2009-ZRF-004], This work was financially supported by Ege University Scientific Research Fund (project number: BAP 2009-ZRF-004)

Background Andrographis alata (Vahl) Nees is a medicinal plant which was reported to have the highest concentration of neoandrographolide that has several therapeutic values. Natural populations of Andrographis alata are dwindling due to destruction of natural habitat and over exploitation. Therefore, in vitro propagation of Andrographis alata was undertaken, and successful method is presented here. Results Micropropagation of Andrographis alata was realized on MS nutrient medium augmented with BAP (10 μM), and multiple shoots were regenerated from nodal explants. Induction of roots was attained from shoots on ¼ concentration of MS nutrient medium supplemented with IBA (1 μM). Randomly amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) analysis showed that there is genetic fidelity in the regenerated plants. Reverse phase high performance liquid chromatographic analysis of regenerated plants showed the presence of neoandrographolide, equivalent to that of mother plants. Conclusions Successful in vitro regeneration of Andrographis alata is presented here, and it is quite useful for its mass multiplication. The micropropagated plants are useful for restoration of plants in nature and for utilization by the pharmaceutical industry for extraction of neoandrographolide.

Background: Joha Rice are aromatic rice landraces, having small to medium grain size, indigenous to Assam, India. Due to the introduction of high yielding hybrid varieties, many endemic rice landraces including Joha Rice, are in a verge of extinction, as these can only be conserved and maintained by repetitive cultivation. As there is a conflict of local names for these landraces, many landraces with similar morphological characters have been reported from various parts. Simple sequence repeat (SSR) markers with longer perfect repeats have earlier proved successful and essential in studying the genetic diversity among rice cultivars. The present study is aimed to evaluate the genetic relationship among fifteen (15) aromatic Joha rice landraces endemic to Upper Brahmaputra Valley, Assam.Methods: In the present investigation, different landraces of Joha rice were surveyed during 2016-2019. 15 landraces were selected, based on their morphological characters and local data. The collected germplasm of Joha rice was grown in the experimental plots and DNA from young, healthy leaves were isolated which were further used for determination of genetic diversity using SSR markers. Thirty-eight SSR markers were used to evaluate the genetic relationship among the fifteen aromatic rice landraces.Result: A total of 110 polymorphic alleles were detected by 34 markers across all the landraces, with an average of 3.25 per locus. The Polymorphic Information Content (PIC) ranged from 0.24 to 0.83, with an average of 0.5 for each marker. The marker RM154, RM454 and RM489 produced maximum six alleles showing PIC value of 0.82, 0.82 and 0.83, indicating a high polymorphism. UPGMA cluster analysis using Jaccard’s similarity index produced a dendrogram clustering the rice landraces in three major groups and five subgroups. Group II, which consisted of five sub-groups and 12 landraces, showed diverse genotypes. These landraces showed significant genetic similarities.

Tea cultivars have been bred by individual selection of landraces and by crossbreeding, but the validation of the parentage is limited. In this study, we performed parentage analysis of 79 tea cultivars in Japan based on SSR markers to confirm or identify the parent-offspring relationships among them. The effectiveness of nine SSR markers for parentage analysis was validated by comparing them to the existing cleaved amplified polymorphic sequence markers. The former markers were detectable more alleles than the latter. Simulation of parentage analysis of the tea cultivars predicted biparental origins for 12 cultivars (‘Houshun’, ‘Mie ryokuhou no. 1’, ‘Surugawase’, ‘Tenmyo’, ‘Yamanoibuki’, ‘Harumidori’, ‘Koushun’, ‘Minekaori’, ‘Okumusashi’, ‘Saemidori’, ‘Sofu’, and ‘Toyoka’), in the first five of which candidate parents of yet-to-be-defined pedigree were newly identified. Comparisons of a total of 41 SSR genotypes confirmed the newly-identified parentages of ‘Asahi’ for ‘Tenmyo’, ‘Rokurou’ for ‘Houshun’, ‘Surugawase’, and ‘Yamanoibuki’, and ‘Yamatomidori’ for ‘Mie ryokuhou no. 1’. The maternity of seven cultivars out of the 12 was also confirmed with chloroplast DNA sequences. Uniparental origins were confirmed for 25 cultivars. This parentage analysis has improved our knowledge of tea pedigrees and will aid in the development of new cultivars.

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

Mimosa caesalpiniifolia Benth. (Fabaceae) is a native tree of the dry tropical forests of northeastern Brazil and can be exploited for logging and reforestation purposes. This study evaluated the physiological quality of seeds and the genetic diversity of a cultivated population of M. caesalpiniifolia, against the background of potential commercial seed production. Nine trees were used in the study. The quality of their seeds was evaluated by germination and vigour tests, and their genetic diversity was accessed using Inter Simple Sequence Repeat (ISSR). The studied tree group presents a moderate genetic diversity and produces seeds with high physiological quality, but with subtle vigour differences, which can be detected by electrical conductivity and potassium leaching tests. Our results suggest that these trees are potentially suitable for commercial seed production. RESUMO Mimosa caesalpiniifolia Benth. (Fabaceae) é uma árvore nativa das florestas tropicais secas do Nordeste do Brasil e pode ser explorada para fins madeireiros e reflorestamento. Este estudo avaliou a qualidade fisiológica de sementes e a diversidade genética de uma população cultivada de M. caesalpiniifolia, tendo como base de sustentação o potencial para produção comercial de sementes. Nove árvores matrizes foram usadas no estudo. A qualidade de suas sementes foi avaliada por testes de germinação e vigor, e sua diversidade genética foi acessada usando o Inter Simple Sequence Repeat (ISSR). O grupo de árvores estudado apresenta uma diversidade genética moderada e produz sementes com alta qualidade fisiológica, mas com sutis diferenças de vigor, que podem ser detectadas por testes de condutividade elétrica e lixiviação de potássio. Esses resultados sugerem que essas árvores são potencialmente adequadas para a produção comercial de sementes.

Background: Tree tomato (Cyphomandra betacea (Cav.) Sendtn.) is a neglected, fast-growing, promising small fruit crop which provides a rich source of nutrition for human consumption. However, the transcriptome atlas of this important species is still lacking.Results: In this study, RNA samples from a broad diversity of tissues (roots, leaves, stems, flowers and fruits) of tree tomato were sequenced using Pacific Biosciences’ long-read single-molecule real-time sequencing technology. A total of 308699 full-length non-chimeric sequences with a mean length of 1005 bp and an N50 length of 1974 bp were obtained from our multi-tissue normalized cDNA libraries. A total of 140327, 104294, 135138, 78300, 53520, 152310 and 53520 transcripts were functionally annotated using Nr, Swiss-Prot, KEGG, KOG, GO, Nt and Pfam databases, respectively. Gene structural characteristics of the full-length transcriptome of tree tomato was subsequently investigated, including the predication of coding sequence and the identification of transcription factor families, long non-coding RNA and simple sequence repeat (SSR) marker. Thirty primers were randomly selected to evaluate the application of SSR markers, 23 of which obtained successfully amplification.Conclusions: This is the first confident characterization of FL transcriptome profiling of tree tomato. The large-scale and high-quality transcriptome atlas and SSR molecular markers provided in the present study will facilitate further genetic studies of this important species.

Background Gleditsia sinensis Lam. (Leguminosae), a dioecious perennial arbor, demonstrates important medicinal properties and economic value. These properties can be harnessed depending on the sex of the plant. However, the sex of the plants is difficult to identify accurately through morphological methods before the flowering. Results We used bulked segregant analysis to screen sex-specific simple sequence repeat (SSR) markers in G. sinensis. Five male and five female plants were pooled to form the male and female bulks, respectively, and subjected to whole-genome sequencing. After high-throughput sequencing, 5,350,359 sequences were obtained, in which 2,065,210 SSRs were searched. Among them, the number of duplicated SSRs was the highest. The male plants could reach 857,874, which accounted for 60.86% of the total number of male plants. The female plants could reach 1,447,603, which accounted for 56.25% of the total model of the female plants. Among all the nucleotide repeat types, the A/T-rich motif was the most abundant. A total of 309,516 female strain-specific SSRs were selected by clustering. After designing the primers, the male and female gene pools were amplified, and five pairs of primers (i.e., 27, 34, 36, 39, and 41) were found to amplify the differential bands in the male and female gene pools. Using the five pairs of primers, we performed PCR verification on 10 individuals of known sex, which constructed the gene pool. The female plants amplified a single fragment of lengths (i.e., 186, 305, 266, 203, and 260 bp) and no male plant strip, thereby completing the identification of the male and female sexes of the G. sinensis. Conclusions This study provides accurate sex identification strategies between female and male plants, thus improving the utilization rate of G. sinensis resources.

In the present investigation, phenotypic evaluation of blast disease reaction was conducted at Ponnampet and Mandya districts of Karnataka, India, which indicated that the rice varieties such as IR64, Jaya, KMP153, IR30864, Mandya Sona-1, Mandya Sona-2, KCP-1, Dodda Byra, and Malgudi Sanna were susceptible to both leaf and neck blasts. Further, the rice varieties that were resistant to leaf blast such as KMP200, DHMAS70Q164-1b, Karibatta, Coimbatore Sanna and others showed susceptible reaction to neck blast only. In contrast, the varieties such as JyothixBR2655, Punkutt Kodi, Sirsi, 222 and Gangadale which were resistant to neck blast were found to be susceptible to leaf blast also. Only one variety, BR2655 showed resistance to both leaf and neck blast diseases. The genotypic studies using simple sequence repeat markers showed that the analysis of the distribution of resistance genes and genotyping of the selected rice varieties, and traditional rice varieties from different ecological regions with allele specific markers helped to identify 20 major blast resistance genes. The individual gene frequencies of the 20 major rice blast resistance genes varied from 10.34 to 100%. Less and more frequency of resistance gene distribution occurred in Pi9 and Pizt gene, respectively. The result of this study would help to create strategies for improving rice blast resistance through genetic studies and plant-pathogen interaction.

Salinity stress is one of the most severe constraints limiting rice production worldwide. Thus, the development of salt-tolerant rice promises to deal with increasing food demand due to climate change effects. This study investigated the salinity tolerance of mutant rice by evaluating phenotype and genotype, using forty-two simple sequence repeat (SSR) markers linked to the salinity tolerance Saltol quantitative trait locus (QTL) in ten cultivars and mutant lines. Results of phenotypic screening showed that the mutant line SKLo/BC15TB and cultivar BC15TB performed salt tolerance, while the mutant line Bao Thai/DT 84 and cultivar DT84DB were sensitive to salt stress. The markers RM 493, RM 562, RM 10748, RM 518, RM 237, and RM 20224 were the most polymorphic in salinity tolerance. Among them, RM 237, RM 10748, and RM 224 showed the highest polymorphism information (PIC = 0.58). This study reveals that the three markers are profitable for classification of salinity tolerance in both cultivar and mutant rice. The mutant line SKLo/BC15TB and cultivar BC15TB were found to be promising candidates for diversity analysis of salt-tolerant rice. Findings of this study are useful for developing new salinity-tolerant rice cultivars towards climate change.

A total of 170 bambara groundnut (Vigna subterranea) accessions were evaluated using both simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers generated using genotyping-by-sequencing (GbS), of which 56 accessions were collected from West and East Java. Principal coordinate analysis (PCoA), population structure, and cluster analysis suggest that the East Java accessions could be a result of the introduction of selected West Java accessions. In addition, the current Indonesian accessions were likely introduced from Southern Africa, which would have produced a very marked founding effect such that these accessions present only a fraction of the genetic variability that exists within this species.

Distinctness, uniformity and stability (DUS) testing of cultivars through morphological descriptors is an important and compulsory part of soybean breeding. Molecular markers are usually more effective and accurate in describing the genetic features for the identification and purity assessment of cultivars. In the present study, we assessed the distinctness and uniformity of five soybean cultivars using both single nucleotide polymorphism (SNP) markers developed by specific-locus amplified fragment sequencing (SLAF-seq) technology, and simple sequence repeat (SSR) markers. The phylogenetic tree and principal component analysis (PCA) from both the SLAF-seq and SSR methods showed a clear distinction among cultivars Zhonghuang 18, Zhonghuang 68 and Zhonghuang 35, while no clear distinction was observed between cultivars Zhonghuang 13 and Hedou 13. Using the SLAF-seq method, we determined the proportion of homozygous loci for the five soybean cultivars. The heterozygosity of each individual plant was estimated for the assessment of cultivar purity and the purity levels of the five soybean cultivars ranged from 91.89% to 93.96%. To further validate the applicability of the SLAF-seq approach for distinctness testing, we used the SNP information of 150 soybean cultivars with different origins. The cultivars were also distinguished clearly. Taken together, SLAF-seq can be used as an accurate and reliable method in the assessment of the distinctness and uniformity of soybean cultivars.