SRAP Markers Research Articles

Gamma ray induced significant phenotypic and metabolomic sugarcane variants derived through in vitro mutagenesis

Sugarcane is an economically important polyploid crop whose genetic complexity and limited fertility poses a challenge for crop improvement programs. Gamma radiation-induced mutagenesis is an alternate approach for generating a diverse array of agronomically useful mutants, accelerating varietal development in long duration crop like sugarcane. To develop agronomically useful mutants of a commercial sugarcane genotype Co 99004, gamma ray inducedin vitro mutagenesis was studied. The phenotypic variants of Co 99004 in V1 generation could be categorized into five distinct phenotypically scorable classes, including three chlorophyll mutants (albina, chlorina and chlorina pigmented) and two green mutants like wild type control. SRAP marker analyses indicated distinct genomic variation among the phenotypic mutants and control plants, with the polymorphic information content (PIC) ranging from 0-0.472. Further, the phylogenetic dendrogram derived from the SRAP marker data grouped the mutants into four distinct clusters clearly differentiating the phenotypic classification. Sequencing of selected SRAP amplicons indicated deletion/insertion of gene specific fragments.Interestingly, the loss of chlorophyll in albina and chlorina mutantsshowed gamma irradiation-induced deletions in the gene encoding FAR1-RELATED SEQUENCE 5-like protein, which is involved in chlorophyll biosynthesis. GC-MS based metabolome profiling showed alteration in tetrapyrrole biosynthesis, MEP(Methylerythritol Phosphate), and fatty acid biosynthesis pathways, indicating a significant metabolic variation in the chlorophyll mutants.Further characterization of the genetically distinct, non-lethal green wild type mutants can lead to the identification of agronomically useful mutants. Further, the loss of function chlorophyll mutants can serve as a good source for comparative genomics studies aimed at gene-trait association.

Jackfruit Genotypes in Southern Nayarit: A Comparative Study of Morphological, Physiological, Physicochemical, Phytochemical, and Molecular Assessments

Jackfruit, primarily cultivated in Nayarit, Mexico, has four notable genotypes: “Agüitada”, “Rumina”, “Licenciada”, and “Karlita”, which require thorough characterization. This study aimed to provide a comprehensive characterization of these genotypes through an integration of morphological, physiological, physicochemical, phytochemical, and DNA fingerprinting analyses. Measurements were taken from physiological maturity to senescence. SSR and SRAP markers were employed for DNA fingerprinting, and a complete randomized design followed by multivariate analysis was used to observe variable relationships. The results revealed that “Rumina” had the largest leaf size, while “Karlita” had the largest fruit size and the highest respiration rate (117.27 mL of CO2·kg−1·h−1). “Licenciada” showed the highest ethylene production (265.45 µL·kg−1·h−1). “Agüitada” and “Licenciada” were associated with orange bulbs, whereas “Rumina” and “Karlita” were associated with yellow ones. Additionally, “Agüitada” demonstrated higher levels of soluble phenols and carotenoids, indicating greater antioxidant capacity. The Jaccard index suggested moderate genetic diversity among the genotypes, and the dendrogram revealed two genetic clusters. “Licenciada” emerged as a promising genotype, combining high genetic diversity with desirable physicochemical traits. This study highlights the need to broaden future genetic analyses to include a wider range of jackfruit genotypes from various regions, offering a more comprehensive understanding of genetic diversity.

Assessing the genetic diversity of Centella asiatica (L.) Urb. and seasonal influence on chemotypes and morphotypes in Thailand

Both genetic variation and harvesting season impact the amounts of bioactive compounds in Centella asiatica. This study investigated the seasonal influence on chemotypes and morphotypes and evaluated the genetic diversity of C. asiatica plants collected throughout Thailand. A total of 25 C. asiatica accessions was planted in the same area in Nakhon Sawan province and harvested during winter, summer, and rainy seasons. Results exhibited that variations in triterpenoid content were observed in different harvesting seasons, with total content of the four triterpenes highest during the summer season (5.98 %DW). Besides, we noted that the amount of phytochemical constituents (total phenolic, total flavonoid and total triterpenoid contents) and antioxidant were higher in winter and summer. The morphotypes were not influenced by season, while leaf area and leaf width negatively correlated with triterpenoid content. Based on chemotypes and morphtypes, we suggested the two elite accessions including Nakhon Prathom (NPT) and Nong Bua Lamphu (NBP) due to high centelloside content and large leaf. A total of 25 C. asiatica accessions was evaluated for genetic diversity by DNA fingerprints (ISSR, SCoT, and SRAP markers), resulting in a moderate genetic diversity, consisting of geography-related two populations without association with chemotypes and morphotypes. Our findings guide farmers in optimizing harvest times, and controlling centelloside content for future smart farming and insights on genetic diversity aid in future breeding and improvement of C. asiatica for medicinal industries.

Assessment of elite pepper breeding lines using molecular markers

In this study, 38 elite breeding pepper lines were genetically analyzed using SRAP markers and tested for resistance to PVY, TSWV, and PMMoV viruses using molecular markers. In the virus resistance tests, 1 line (37-H–D-6) from the Three-lobs population was found to be resistant to all 3 viruses tested. The 19 SRAP primer combinations used for genetic diversity yielded a total of 85 bands, 57 of which were polymorphic among pepper lines. While 2–8 bands per primer were obtained, the number of polymorphic bands ranged from 1 to 6. The average polymorphism rate of the primers was 66.44%. The PIC values ranged from 0.06 to 0.40 (with a mean of 0.18). In addition, the average gene diversity, effective allele number, and Shannon information index values of the primers were 0.21, 1.34, and 0.31, respectively. STRUCTURE analysis showed that the pepper lines were grouped into 4 clusters. PCoA and Q-matrix plots supported the cluster distribution. Some lines of the Sivri and Three-lobs pepper populations were observed as outliers in the plots. Kapia and Three-lobs were more similar to each other. This study showed that SRAP markers can be successfully used for genetic diversity of pepper breeding lines.

Comparative genetic assessment of somatic embryo– and seed-derived plants of two arabica hybrid coffee cultivars using SRAP and SCoT molecular markers and organellar and nuclear genes sequencing

Comparative genetic assessment of somatic embryo– and seed-derived plants of two arabica hybrid coffee cultivars using SRAP and SCoT molecular markers and organellar and nuclear genes sequencing

Molecular Identification of Morus ssp. in Duhok Using Nuclear ITS Region and Chloroplast Matk Gene

Since Mulberries (Morus)is a tree species with a considerable plant variety. Molecular techniques are methods used to distinguish between species accurately, easily and quickly. This study examines a Molecular method for distinguishing different Morus species in the Duhok - Kurdistan region/ Iraq. The method is based on the use of four techniques: matK gene, the ITS region, PCR-RFLP, and SRAP markers. Twelve Morus species have been selected for this study from different region of Duhok. The ITS region's PCR result was 700 bp, but the matK gene's PCR produce was 900 bp. The same restriction site was found for all utilized cultivars when the 700bp of ITS fragment was used for PCR-RFLP with two restriction enzymes, RsaI GT/AC and HaeIII GG/CC. This study also used six combinations of SRAP markers to aid in grouping and identifying genetic similarities. The results of PCR-RFLP demonstrated an insufficient link between Morus physical appearance and genetic traits, but differences across studied cultivars could be identified using SRAP markers. Furthermore, this study demonstrated the possibility of DNA barcoding Morus cultivars, as well as additional sequence analysis and the identification of probable SNP between cultivars.

Genetic Diversity and Population Structure in Chestnut (Castanea spp.) Varieties Revealed by RAPD and SRAP Markers

Genetic Diversity and Population Structure in Chestnut (Castanea spp.) Varieties Revealed by RAPD and SRAP Markers

Analysis of genetic diversity and population structure in some Egyptian Berseem (Trifolium alexandrinum) accessions based on ISSR, SCoT and SRAP markers

Analysis of genetic diversity and population structure in some Egyptian Berseem (Trifolium alexandrinum) accessions based on ISSR, SCoT and SRAP markers

SRAP markers for characterization of the genetic diversity and differentiation of Pinus nigra populations in protected forested areas in Bulgaria, Greece, and Cyprus

The present study aimed to evaluate the genetic diversity and differentiation of Pinus nigra Arnold, the European black pine, populations located in protected forested areas in three countries from the Balkan and Mediterranean region: Bulgaria, Greece, and Cyprus. Totally, 175 DNA samples from P. nigra plants collected from eight populations in these countries were analyzed using three SRAP primer pairs. The applied SRAP markers demonstrated high-resolution power, resulting in the identification of an average of 215 ± 67 polymorphic loci per SRAP primer pair. The analysis of molecular variance (AMOVA) showed that 82% of the observed variation was due to intra-population variation, while 18% was due to inter-population variation. The overall analysis of the population structure suggested low (Fst ≤ 0.01) intra-country differentiation for the populations from Bulgaria and Cyprus and moderate (0.15 ≤ Fst ≤ 0.17) inter-country differentiation. On the contrary, high differentiation between the populations (0.06 ≤ Fst ≤ 0.20) and complex genetic structure were characteristic of the three populations from Greece, relatively closely located in the area of the Pindos National Park. Analysis of the population structure also revealed that one of the Pindos populations belonged to the cluster of Bulgarian populations (Fst ≤ 0.01), showing moderate (Fst ≤ 0.11) to high (Fst ≤ 0.20) genetic differentiation from the other analyzed Pindos populations. The further use of SRAP markers for mapping the genetic diversity among P. nigra populations and identification of local populations diverted from the overall phylogeography-driven pattern in the studied region are discussed.

Genetic diversity of Thailand reserved mulberry germplasm based on morphological characteristics and newly developed EST-SSR and SRAP markers

Genetic diversity of Thailand reserved mulberry germplasm based on morphological characteristics and newly developed EST-SSR and SRAP markers

Evaluation of the genetic diversity and population structure of reticulated iris accessions in the Iraqi Kurdistan region using SCoT and SRAP markers

Evaluation of the genetic diversity and population structure of reticulated iris accessions in the Iraqi Kurdistan region using SCoT and SRAP markers

Medicinal Value, Genetic Diversity, and Genetic Relationship Analysis of Auricularia cornea (Agaricomycetes) Based on ITS, ISSR, and SRAP Markers.

Wild resources of Auricularia cornea (A. polytricha) are abundant in China, and genetic diversity and genetic relationships analysis of A. cornea can provide basis for germplasm resource utilization and innovation and molecular marker-assisted breeding. In this study, 22 Auricularia strains collected were identified as A. cornea based on ITS sequence analysis, and its genetic diversity was examined by ISSR and SRAP markers. The results showed that a total of 415 bands were amplified by 11 selected ISSR primers, with an average amplification of 37.73 bands per primer, and the mean values of Ne, I, and H were 1.302, 0.368, and 0.219, respectively. A total of 450 bands were amplified by 10 SRAP primers, with an average of 45 bands per primer, and the average of Ne, I, and H were 1.263, 0.302, and 0.183, respectively. The unweighted pair-group method with arithmetic means analysis based on ISSR-SRAP marker data revealed that the genetic similarity coefficient between the tested strains was 0.73-0.97, and the strains could be divided into five groups at 0.742, which had a certain correlation with regional distribution. The results of PCOA and population structure analysis based on ISSR-SRAP data also produced similar results. These results demonstrate the genetic diversity and distinctness among wild A. cornea and provide a theoretical reference for the classification, breeding, germplasm innovation, utilization, and variety protection of A. cornea resources.

Genetic diversity assessment of Fusarium oxysporum f. sp. ciceri causing chickpea wilt as revealed by the URP and SRAP marker

Genetic diversity assessment of Fusarium oxysporum f. sp. ciceri causing chickpea wilt as revealed by the URP and SRAP marker

Evaluation of Some Local and Registered Safflower (Carthamus tinctorius L.) Varieties Based on SRAP Markers

Safflower (Carthamus tinctorius L.), a member of the Asteraceae family, is an important plant grown in the world as a source of vegetable oil. In addition, it is a versatile crop that is also used as biodiesel, animal feed, spice, dye, and medicinal plant. In this study, SRAP markers were used to determine the genetic diversity and relationships between four local and three registered safflower cultivars for use in cross-breeding programs. The twelve primer combinations yielded a total of 101 bands, including 33 polymorphic bands. The level of polymorphism of SRAP markers which were represented by the average number of total bands (NTB) (8.4), the average number of polymorphic bands (NPB) (2.8), polymorphic band ratios (PBR%) (34.5%), resolving power (RP) (1.48), effective multiplex ratio (EMR) (1.17), and marker index (MI) (0.43) was low. Conversely, polymorphism information content (PIC) (0.35), Nei’s gene diversity (h) (0.36) and Shannon's information index (I) (0.55) showed a significant genetic variation in the safflower genotypes studied. The polymorphism information content of the SRAP primer combinations used in the study ranged from 0.24 to 0.46, with an average of 0.35. Genetic similarity was calculated according to Dice similarity and varied from 0.12 to 0.92, with a mean genetic similarity (GS) of 0.58. The cophenetic correlation between the Dice similarity matrix and corresponding dendrogram obtained by SRAP (r = 0.95) revealed very good compliance. The genetically close genotypes were Remzibey05 - TR64702 and TR49119 - TR42630 (GS=0.91). Also, Dinçer5-118 and Yenice5-38 were the most genetically distant varieties (GS=0.12). Dinçer5-118 was very different from other genotypes (GS=0.29).

Assessment of the genetic diversity and population structure of Vaccaria hispanica(Mill.) Rauschert germplasms of Türkiye based on SRAP and SSR markers

Assessment of the genetic diversity and population structure of Vaccaria hispanica(Mill.) Rauschert germplasms of Türkiye based on SRAP and SSR markers

Phenotypic and genotypic variability among exotic arabica coffee genotypes using morphological and molecular markers (SRAP)

Coffea arabica is said to have low genetic variability, however more information is still needed about the extent of diversity present in the arabica coffee gene pool by evaluating existing genetic resources present in India. The study therefore was conducted to assess the phenotypic and genotypic variability in arabica coffee germplasm accessions. Significant variation was observed among coffee accessions for the traits studied indicating the presence of diversity. Out of 20 traits, per cent ‘A’ grade bean contributed maximum to the diversity (63.29 %). The 41 arabica coffee accessions were grouped into six clusters. The maximum intra-cluster and inter cluster distance (D2 = 737.34) was revealed by cluster V (7 genotypes) and cluster II and VI (D2 = 8544.21), respectively. Principle Component Analysis displayed 79.50% of variability. Observations on Coffee Leaf Rust disease incidence showed that mean disease severity infection was ranged from 1.34 to 32.67%. On the other hand, molecular analysis of 10 SRAP primers established high rate of polymorphism with an average PIC value of 0.74. The UPGMA clustering grouped arabica coffee genotypes into two major clusters. The similarity matrix coefficient was ranged from 0 to 94%. SRAP marker demonstrated high polymorphism rate can be utilized for future crop improvement program in coffee. Study established high phenotypic but low genetic diversity among the arabica coffee accessions based on morphological and molecular markers, respectively and identified high yielding, coffee leaf rust disease resistant accessions which showed possibility of developing improved varieties through breeding.

Mapping Quantitative Trait Loci (QTLs) for Hundred-Pod and Hundred-Seed Weight under Seven Environments in a Recombinant Inbred Line Population of Cultivated Peanut (Arachis hypogaea L.).

The cultivated peanut (Arachis hypogaea L.) is a significant oil and cash crop globally. Hundred-pod and -seed weight are important components for peanut yield. To unravel the genetic basis of hundred-pod weight (HPW) and hundred-seed weight (HSW), in the current study, a recombinant inbred line (RIL) population with 188 individuals was developed from a cross between JH5 (JH5, large pod and seed weight) and M130 (small pod and seed weight), and was utilized to identify QTLs for HPW and HSW. An integrated genetic linkage map was constructed by using SSR, AhTE, SRAP, TRAP and SNP markers. This map consisted of 3130 genetic markers, which were assigned to 20 chromosomes, and covered 1998.95 cM with an average distance 0.64 cM. On this basis, 31 QTLs for HPW and HSW were located on seven chromosomes, with each QTL accounting for 3.7-10.8% of phenotypic variance explained (PVE). Among these, seven QTLs were detected under multiple environments, and two major QTLs were found on B04 and B08. Notably, a QTL hotspot on chromosome A08 contained seven QTLs over a 2.74 cM genetic interval with an 0.36 Mb physical map, including 18 candidate genes. Of these, Arahy.D52S1Z, Arahy.IBM9RL, Arahy.W18Y25, Arahy.CPLC2W and Arahy.14EF4H might play a role in modulating peanut pod and seed weight. These findings could facilitate further research into the genetic mechanisms influencing pod and seed weight in cultivated peanut.

SRAP markers as an alternative tool for Alternaria classification

Alternaria is one of the main fungal contaminants of cereal grains worldwide with the potential to produce mycotoxins hazardous to human and animal health. Many studies have been carried out to characterize Alternaria sp.-grp. using traditional morphology or polyphasic approach, but a good correlation between morphological sp.-grp., molecular, and chemotaxonomic groups has not always been achieved. For this reason, this study aimed to investigate the usefulness of a cheaper alternative tool, SRAP markers, in identifying Alternaria sp.-grps. obtained from Argentinean barley grains and to compare it with preliminary characterization using morphological traits, phylogeny, and metabolite profiles. Fifty-three Alternaria isolates from barley grains of the main producing regions of Argentina were analyzed with four combinations of SRAP markers. The UPGMA dendrogram, based on the Simple Matching similarity coefficient, revealed three distinct groups. SRAP markers allowed the separation of Alternaria from Infectoriae sections in agreement with the results of a polyphasic approach previously made. Besides, isolates of A. arborescens sp.-grp. were clustered in a separate group from isolates of A. tenuissima and A. alternata sp.-grp., which were grouped in the same cluster. SRAP markers are a recommended tool for classifying Alternaria isolates because of its simplicity, reliability, and cost-effectiveness compared to other molecular markers.

Genetic Variation and Genomic Constitution in The Spatulata Orchid Hybrids (Dendrobium spp.) Derived from Interspecific Hybridization Using SRAP marker

Dendrobium is the second largest genus in the Orchidaceae family. Dendrobium section Spatulata is widely cultivated in Indonesia due to its ease of cultivation, high economic value and adaptability, and extended flower shelf life. In this study, we have conducted a breeding program for developing new cultivar of Dendrobium section Spatulata through interspecific hybridization. This study is aimed to investigate the genetic variation and genomic constitution of the eight hybrids and their corresponding parental lines resulted from interspecific hybridization using SRAP markers. Dendrobium section Spatulata hybrids produced by interspecific hybridization are genuine hybrids with substantial genetic variability based on flower morphology, including labellum shapes and color intensities, as well as curly horn shapes and color intensities. The SRAP marker, which was utilized to genotype the hybrid and parental lines, exhibited a significant degree of polymorphism, and may be used to distinguish each accession. The UPGMA dendrogram and PCoA biplot showed that all the hybrids were grouped with their corresponding parental lines based on their genetic background and genomic constitution. These findings are critical for genetic improvement of the Spatulata orchid to develop novel varieties.

Assessment of genetic variability among some quinoa (Chenopodium quinoa Willd.) genotypes using ISSR, SRAP and protein markers

Assessment of genetic variability among some quinoa (Chenopodium quinoa Willd.) genotypes using ISSR, SRAP and protein markers