Sequence-related Amplified Polymorphism Research Articles

Exploring sequence-related amplified polymorphism (SRAP) markers for assessing genetic diversity in onion (Allium cepa L.) genotypes and their wild relatives

Exploring sequence-related amplified polymorphism (SRAP) markers for assessing genetic diversity in onion (Allium cepa L.) genotypes and their wild relatives

Determination of genetic diversity of edible-seeded watermelon genotypes using SRAP markers

The watermelon (Citrullus lanatus L.) is one of the most commonly grown and consumed vegetables in the world. Some genotypes of watermelon, which have significant variations, have a snack potential due to their seed characteristics. In this study, SRAP (Sequence Related Amplified Polymorphism) marker technique was used to determine the genetic relationship between some edible-seeded watermelon genotypes. A total of 166 bands were obtained in 24 genotypes and the polymorphism rate was calculated as 97.4%. Four main clusters were observed in the cluster analysis. It was determined that genotypes 2 and 7 clustered separately from the others. Structure analysis revealed that the genotypes consisted of two subpopulations. It was concluded that the edible-seeded watermelon genotypes can be genetically differentiated by the SRAP techniques. The results of this study can be used in breeding strategies for the improvement of the edible-seeded watermelon cultivars.

The development and utilization of two SCAR markers linked to the resistance of banana (Musa spp. AAA) to Fusarium oxysporum f. sp. cubense race 4

Banana (Musa spp.) production worldwide is seriously threatened by Fusarium wilt caused by Fusarium oxysporum f. sp. cubense (Foc). The best way to control this disease is to grow resistant cultivars. However, it requires large-scale field evaluations and labor- and time-consuming to obtain disease-resistant germplasm. Development of early, reliable, and reproducible selection strategies are considered as the efficient approach which could speed up the selection procedure. In this study, two pairs of sequence-related amplified polymorphism (SRAP) primers related to banana Foc resistance/susceptibility were screened from 100 pairs of random primers. Correspondingly, two pairs of sequence characterized amplified region (SCAR) markers (namely SC4-F/SC4-R and SC14-F/SC14-R, respectively) were successfully generated from these two SRAP markers using 30 cultivars either resistant or susceptible to Foc. Both SCAR markers were located in mitochondrion genome and showed discriminatory power of 96.67% and 100%, respectively. Mitochondrial proteins possibly play a very important role in banana resistance to Foc. In additional, these two SCAR markers were employed simultaneously to screen potential resistant germplasm from 53 accessions with unknown resistance to Foc, and the results revealed a consistency of 83.0% with each other, further indicating their high reliability and reproducibility. These results suggest that both SCAR markers could be used in molecular marker-assisted selection for banana germplasm resistant to Fusarium.

Phylogenetic study on some species of Fabaceae using morphological traits and sequence related amplified polymorphism (SRAP) markers

Phylogenetic study on some species of Fabaceae using morphological traits and sequence related amplified polymorphism (SRAP) markers

Genetic analysis of banana cultivars and fidelity testing in somatic embryo derived Ney poovan (Elakki bale) using SRAP (sequence related amplification polymorphism).

Abstract Bananas and plantains are a major staple food in many countries. In the current study, the genetic variability of ten banana cultivars (i.e., Grand naine, Monthan, Nendran, Ney poovan, Rasthali, Robusta, Red banana, Kadali, Musa balbisiana , Calcutta 4) were analyzed using SRAP. SRAP amplification resulted in a total of 6028 strong, clear, and reproducible bands from 10 cultivars using 13 forward and 16 reverse SRAP primers (208 SRAP primer combinations), Of 6028 bands 96.77% were polymorphic and 3.221% were monomorphism. In addition, the fidelity testing of plants derived from somatic embryo was carried out. The 24 SRAP primers were employed for DNA analysis which produced a total of 153 clear, distinct and reproducible amplicons of variable size. Out of 24 SRAP primers, 9 primers produced amplification patterns which are identical between the mother plants and plants derived from somatic embryogenesis. Cluster analysis depicted more than 95% genetic similarity between the somatic embryogenesis derived plants and the mother plants indicating a high degree of genetic fidelity.

Genetic Variation among Aeluropus lagopoides Populations Growing in Different Saline Regions

Aeluropus lagopoides is a halophytic grass growing in different sabkhas of Saudi Arabia. In this study, 14 inter-simple sequence repeat (ISSR) and 15 sequence-related amplified polymorphism (SRAP) molecular markers were selected to investigate the genetic diversity within and among five natural populations of A. Lagopiodes. The genetic diversity varied within and among populations. ISSR markers were slightly more efficient than SRAP markers in evaluating genetic diversity. Average polymorphism information content, effective number of alleles, Nei’s genetic diversity, and Shannon’s information index values of ISSR markers were higher than SRAP. Analysis of molecular variance revealed about 40% genetic variation among the population and 60% within the population. Overall, the genetic diversity was lowest in Jouf (40%), while the Qaseem populations were the highest (60%). Jizan populations were highly dissimilar to other regions. A Mantel test indicated a positive correlation between geographic and genetic distance. The cluster analysis showed three groups; the first group comprises Jouf and Salwa populations, the second group comprises Qareenah and Qaseem, and the third group comprises the Jizan population. This observation matched the geographic distribution of the species. These findings can help in the conservation of a diverse population of A. lagopoides in saline regions as well as rehabilitation of these degraded unique habitats.

The impact of non-environmental factors on the chemical variation of Radix Scrophulariae

Radix Scrophulariae is a commonly used Chinese herb derived from the dried root of Scrophularia ningpoesis Hemsl. (S. ningpoensis). It is difficult to accurately estimate the dosage of Chinese medicinal materials used in the prescription because of the chemical variation caused by various factors. To analyze the non-environmental factors affecting the chemical variation of Radix Scrophulariae, we planted nine different cultivated varieties of S. ningpoensis in the same plantation. Based on sequence-related amplified polymorphism (SRAP), simple sequence repeats (SSR) markers and high-performance liquid chromatography (HPLC) analysis, we found that the materials from the cultivated varieties could be divided into two groups, the Zhejiang group, and the southwest China group. The genetic distance based on molecular data between the two groups was above 0.3882, and the Euclidean distance based on chemical data between the two groups was above 5.312. The correlation analysis between the genetic distance matrix based on SRAP and the Euclidean distance matrix based on 18 HPLC peaks of the whole underground part revealed that the genetic differentiation and chemical variation were positively related, r = 0.7196 (p < 0.05). The genetic background, different part of the roots and the different development of the roots are the three non-environmental factors causing the chemical variation. The coefficient of variation (C.V) of chemical composition of Radix Scrophulariae with different genetic background reached to 93.62 %, the C.V of the chemical composition of Radix Scrophulariae derived from the same variety reached to 64.21 %, the C.V of the chemical composition of Radix Scrophulariae derived from the middle part of the roots of S. ningpoensis from the same variety reached to 45.55 %. The C.V of chemical composition of Radix Scrophulairae produced in the same plantation could be controlled to 38.43 % by using the same variety of roots with the approximate mass derived from the middle part of the roots under 20 g. Our findings provided insights to decrease the chemical variation of Chinese medicinal materials by controlling non-environmental factors.

Sequence-related Amplified Polymorphism and Target Region Amplification Polymorphism Markers-based Profiling of Sodium Azide and Ethyl Methanesulfonate-derived Black Rot-resistant Dendrobium sp. ‘Earsakul’ Mutants from In Vitro Mutagenesis and Selection

To reveal the applicability of sequence-related amplified polymorphism (SRAP) and target region amplification polymorphism (TRAP) markers to mutant genotyping and marker identification for resistance to black rot (Phytophthora palmivora) in orchids (Dendrobium sp. ‘Earsakul’), we fingerprinted four nonmutagenized controls and 12 black rot-resistant mutants obtained with in vitro sodium azide (NaN3) and ethyl methanesulfonate (EMS) mutagenesis and in vitro selection using culture filtrate of P. palmivora. Each of the 20 SRAP and TRAP primer combinations yielded 375 and 384 scorable DNA bands, respectively, of which 94 (24.42%) and 88 (22.91%) were polymorphic, respectively. Mantel’s test cophenetic correlation coefficients of SRAP, TRAP, and SRAP/TRAP were 0.750, 0.921, and 0.861, respectively, indicating the efficiency of these markers, especially TRAP and SRAP/TRAP, for Dendrobium sp. ‘Earsakul’ mutant characterization. Moreover, the correlations between the matrices of cophenetic correlation values for the dendrograms of SRAP with TRAP, SRAP with SRAP/TRAP, and TRAP with SRAP/TRAP were 0.399, 0.566, and 0.793, respectively, and the dendrograms based on SRAP vs. TRAP and SRAP vs. SRAP/TRAP, with lower correlations, had more variations, i.e., the number of clusters, the members of clusters, and the placement of the materials, than the ones based on TRAP vs. SRAP/TRAP. Among the three dendrograms, all nonmutagenized controls were clustered together, whereas all the highly resistant and the most resistant mutants were distributed separately as individuals. Interestingly, the four SRAP and TRAP markers were significantly associated with black rot resistance. Overall, our results will be useful for facilitating future Dendrobium sp. ‘Earsakul’ breeding programs.

Clinacanthus nutans genetic diversity and its association with anti-apoptotic, antioxidant, and anti-bacterial activities

Clinacanthus nutans (Burm. f.) Lindau has been extensively utilized in Thai folk medicine. However, there has been no prior exploration of its genetic diversity or its correlation with biological activity and phytochemical profiles. Herein, a total of 10 samples of C. nutans were collected from different geographic locations in different environments of Thailand, encompassing Northern, Northeastern, and Central regions. The genetic diversity study using sequence-related amplified polymorphism (SRAP) markers showed that all C. nutans samples were closely related, as indicated by UPGMA cluster analysis. When comparing the biological activities of C. nutans extracts, our findings demonstrated that those sourced from Northern Thailand exhibited the most potent activity in reducing lipopolysaccharide-inducing cell death, as accessed by cell viability assay. Furthermore, they showed remarkable antioxidant and antibacterial activities against Staphylococcus epidermidis, Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli. High-performance liquid chromatography (HPLC) analysis of phytochemical profiles revealed consistent chromatography peak patterns across all C. nutans extracts. However, they exhibited varying levels of phenolic contents, as judged by the Folin-Ciocalteu assay, which positively correlated with their observed activities. In conclusion, this study highlights the limited genetic variation within C. nutans population in Thailand. Furthermore, it underscores the association between the biological activity and the total phenolic contents which might be mainly impacted by environmental conditions.

Genetic Diversity of Bananas (Musa spp.) in Pesawaran District, Lampung Province Based on Sequence Related Amplified Polymorphism (SRAP) Marker

Banana (Musa spp.) is a leading commodity that makes a major contribution to national fruit production. One of the districts in Lampung Province which has a significant contribution to Indonesia's banana production is Pesawaran Regency. The molecular marker used in this study is Sequence-Related Amplified Polymorphism (SRAP). This study aims to determine the genetic diversity of bananas, determine the suitable combination of SRAP primers to determine the genetic diversity of bananas and determine the similarity relationship of bananas in the Pesawaran District. The total genomic DNA was extracted using DNeasy Plant Mini Kit (Geneaid) according to the protocol from the manufacturer followed by their amplification using SRAP primers. Similarity analysis was carried out based on similarity index values and dendrogram construction using the NTSYS 2.0 program. Research results show that a total of 204 loci (167 polymorphic loci and 37 monomorphic loci) were obtained from 9 selected primer combinations. The genetic diversity of 19 banana cultivars originating from Pesawaran Regency resulted in low genetic diversity values (0-0.27). Banana kinship based on Sequence Related Amplified Polymorphism (SRAP) markers divided 19 banana cultivar samples and 4 wild banana samples into 2 large clusters with similarity coefficient values between 0.70-0.97.

Genetic Diversity and Structure of Quercus petraea (Matt.) Liebl. Populations in Central and Northern Romania Revealed by SRAP Markers

The genetic variability of five populations of Quercus petraea originating from the Transylvania and Maramureș regions of Romania was investigated in this study to provide insights into the species’ adaptability, population dynamics, and potential for preservation in the face of environmental challenges. To achieve this, sequence-related amplified polymorphism (SRAP) markers, in conjunction with a set of 18 primer combinations, were employed. The outcomes of the analysis revealed a range of polymorphisms spanning from 69.78% to 85.75%. Additionally, the assessment of genetic diversity using Shannon’s information index (I) yielded values ranging between 0.2887 and 0.3955, while Nei’s gene diversity (He) exhibited a spectrum from 0.1833 to 0.2582. The analysis of genetic variability, conducted via molecular variance (AMOVA), unveiled that 9% of the genetic variation was attributable to differences among the populations, while a substantial 91% resided within the populations. A further investigation of the population structure revealed that the construction of a UPGMA dendrogram based on Nei’s genetic distances elucidated the presence of two principal genetic clusters, a finding that was reinforced by a Principal Coordinate Analysis (PCoA). The genetic diversity revealed by Quercus petraea using SRAP molecular markers offers promising potential for upcoming breeding programs to identify optimal genitors, facilitating the development of well-adapted oak populations in the Transylvania and Maramureș regions.

The effect of plant growth regulators on micropropagation of Melientha suavis Pierre. and assessment of genetic fidelity of regenerants based on iPBS and SRAP markers

Abstract. Siringam T, Vanijajiva O. 2023. The effect of plant growth regulators on micropropagation of Melientha suavis Pierre. and assessment of genetic fidelity of regenerants based on iPBS and SRAP markers. Biodiversitas 24: 4628-4634. Melientha suavis Pierre, a significant deciduous edible plant species with high nutritional value and belonging to the Opiliaceae family, holds paramount importance for both agricultural and conservation purposes in its native Southeast Asia. However, the species faces challenges due to habitat fragmentation and negative anthropogenic impacts, leading to a decline in its population. This study aimed to explore the effects of various concentrations of plant growth regulators (cytokinin and auxin) on the shoot and root development of M. suavis, and to assess the genetic stability of micropropagated plants obtained from nodal explants. In vitro shoot regeneration and proliferation were conducted on Murashige and Skoog (MS) semi-solid medium, supplemented with 6-benzylaminopurine (BAP) or kinetin (Kn) at different doses. The optimal shoot length, shoot number, and leaf volume were observed in the modified MS medium with 1.0 mg/L BAP after an 8-week incubation period. Efforts to enhance the rooting of micropropagated shoots included the addition of auxins, such as ?-naphthalene acetic acid (NAA) or indole-3-butyric acid (IBA). However, the species exhibited recalcitrant behavior during the reproduction and rooting stages, as the rooting percentage did not correlate with the increase in auxin concentration. Interestingly, the highest root number and length were achieved in the MS medium without plant growth regulators after 8 weeks of incubation. To ensure genetic fidelity, regenerants were subjected to inter-primer binding site (iPBS) and sequence-related amplified polymorphism (SRAP) marker analysis. The results revealed no genetic variation between the micropropagated plants and the mother trees, confirming the production of genetically stable progeny. Overall, this protocol presents a promising alternative for profitable propagation and establishment of genetically constant progeny of M. suavis, with important implications for sustainable applications and germplasm conservation in Southeast Asia. Addressing the challenges faced by this valuable species through micropropagation and genetic fidelity assessment can contribute significantly to its preservation and utilization for agricultural and conservation initiatives.

Genetic evaluation of F2 and F3 interspecific hybrids of mung bean (Vigna radiata L. Wilczek) using retrotransposon‐based insertion polymorphism and sequence‐related amplified polymorphism markers

Mung bean (Vigna radiata L. Wilczek) is a self‐pollinating and indispensable pulse crop in Indonesia. While low yield productivity is a major concern, genetic improvement is possible through interspecific hybridization. However, interspecific hybridization is relatively infrequent and produces low recombination exchanges, significantly limiting crop breeding efficiency. Thus, a comprehensive study is needed of the selection and genetic diversity evaluation of progenies in advanced generations derived from interspecific hybridization using a specific molecular marker. This study aims to confirm the heterozygosity in the F2 population and assess the genetic diversity in F3 mung bean populations resulting from interspecific hybridization between the mung bean and common bean. We designed the retrotransposon‐based insertion polymorphism (RBIP) marker by identifying the syntenic regions in the flanking sequences of retrotransposon insertion in common bean and mung bean. The RBIP marker can be applied to distinguish the heterozygote progenies from the homozygote progenies. Six combinations of sequence‐related amplified polymorphism (SRAP) primers were used in the genotyping of F3 mung bean progenies. The SRAP marker showed a high degree of polymorphism of up to 100%, while high genetic variation was observed within the population (71%) of mung bean progenies. The F3.4 population had the greatest number of genotypes and displayed the highest number of effective alleles, private alleles, and percentage of polymorphic loci, suggesting the existence of high genetic diversity within this population. These genetic diversity data are exceptionally critical for future genetic research since it has potentially high yield production. The genomic and marker‐assisted selection studies will support the major goals of the mung bean breeding program.

Development of SRAP markers to evaluate the genetic variability in Brachypodium distachyon complex

ABSTRACT Brachypodium distachyon has been accepted as a model grass species for genetics and molecular genomics in cereals since 2001. However, the genetic variability present in Brachypodium spp. continue being the aim of many research. Therefore, the aim of this work was to analyze the genetic variability present in different Brachypodium spp. from different countries and to find different open reading frames (ORFs) among them by using sequence-related amplified polymorphism (SRAP) markers. In our study, a total of 12 Brachypodium spp. accessions were selected from different countries. By using SRAP markers, the genetic variability was evaluated and some fragments were sequenced to obtain differential ORF information among genotypes. SRAP molecular markers revealed high variability among accessions being USA the accession that showed the most variability at the DNA level. The analysis of sequenced SRAP fragments from monomorphic and polymorphic fragments as well as those obtained from new primer combinations targeted coding regions into B. distachyon available genome. SRAP molecular marker showed not only to be an excellent tool for Brachypodium variability studies but also to provide additional information about differential amplification of open reading frames.

High throughput pre-breeding evaluation of Greek oregano (Origanum vulgare L. subsp. hirtum) reveals multi-purpose genotypes for different industrial uses

Origanum vulgare L. subsp. hirtum (commonly known as Greek oregano) is a perennial species of the Lamiaceae family that counts numerous applications in the food and pharmaceutical industry. The exploitation of Greek oregano germplasm lies in its unique diversity in secondary metabolites, which are accumulated in the aerial parts of the plant. For the industrial exploitation of this crop the starting germplasm is of high importance in terms of valorizing well characterized chemotypes with desired and stable agronomic and phytochemical traits. For this reason, a pre-breeding evaluation of twenty-one accessions collected and preserved under the same environmental conditions was performed in order to develop a descriptive database containing: a) morphometric traits, b) the genetic structure, c) the extensive metabolic fingerprint in terms of volatile composition, polyphenolic and triterpenoid content, and d) the ‘bio-activity’ on the embryonic development of Ascaridia galli eggs for highly divergent accessions. This study revealed the existence of essential oil rich chemotypes superior in morphometric characteristics, containing high carvacrol content (> 75%) and traces of thymol (< 5%), according to the requested international standards. Apart from genotypes considered as ‘high yield essential oil-producers’ (> 6%), accessions of highly productivity of ‘green’ raw materials rich in polyphenols and triterpenoids were also identified. According to their rosmarinic acid content, Greek oregano accessions were classified in three groups; 1) those with significantly high concentration (1640–2726 mg 100 g−1 dry weight), 2) those expressing intermediate content (1103–1200 mg 100 g−1 dry weight), and 3) the ones with significantly low content (< 873 mg 100 g−1 dry weight). A total of 118 polymorphic alleles were identified using sequence-related amplified polymorphism (SRAPs) and simple sequence repeat (SSRs) markers, while 2 genetic clusters based on a single data matrix with SRAPs and SSRs alleles, were identified. The presence of private bands in some accessions was also observed, which can be used in future breeding programs for germplasm authentication purposes. As a result this study provides a comprehensive knowledge on metabolic and genetic diversity of Greek oregano accessions native to Greece, as well as powerful tools for the selection of starting genetic materials for subsequent breeding studies to create superior cultivars. The multifaceted approach was developed to exploit the genetic resources of Greek oregano in further breeding programs for subsequent selection of genotypes with desired traits.

Evaluation in Genetic Variation of Krachai by Sequence Related Amplified Polymorphism (SRAP) and Random Amplified Polymorphic DNA (RAPD) Techniques

Krachais are local name of Thai herb which are identified within 2 genera, namely Bosenbergia (white or red krachai) and Kaempferia (black krachai). The rhizome of Bosenbergia rotunda (L.) Mansf. contains major aromatic compounds against COVID19 but its many morphological characteristics such as leaves, stems and rhizome are like other species in same genus or family. In this study, a total of 13 accessions containing 5 samples of B. rotunda, 2 samples of Boesenbergia spp. and 3 samples of Kaempferia parviflora including 3 samples of other species in same family as outgroups were analyzed and clustered using sequence-related amplified polymorphism (SRAP) and random amplified polymorphism DNA (RAPD) markers. The results showed that 8 SRAP primers (M1E1, M1E2, M1E7, M2E10, M3E9, M5E1, M5E2 and M6E10) could generate 79 polymorphism bands with an average of 92.15% whereas a total of 5 RAPD primers (OPY04, OPY02, OPY04, JAT11 and JAT12) could give 64 polymorphisms with 100% as a percentage of the polymorphism band. The PIC of the SRAP marker (0.470) has a higher value than the RAPD marker (0.264). The highest similarity coefficients within genus Boesenbergia of 1.000 and 0.952 were obtained from SRAP and RAPD markers, respectively. The UPGMA dendrogram of SRAP and RAPD information among krachai presented 2 and 4 groups, respectively. The cluster of Boesenbergia was separated from K. parviflora and other species in same family. Furthermore, the results also pointed that Boesenbergia sp. from Phayao is in correct genus and is B. pandurata (Roxb.) Schltr. because of having red leaf while Boesenbergia sp. from Chiang Rai showed confusion between SRAP and RAPD data. It was concluded that SRAP and RAPD have great potential for the study of genetic diversity of Boesenbergia and other species in family Zingiberaceae.

The Use of Wheat Starch as Gelling Agent for In Vitro Proliferation of Blackberry (Rubus fruticosus L.) Cultivars and the Evaluation of Genetic Fidelity after Repeated Subcultures

Micropropagation has an important role in the large-scale production of blackberry plant material, given the high proliferation rates of this species. The aim of the present study was to evaluate the proliferative capacity of blackberry grown in vitro on wheat starch-gelled culture medium compared to classical agar-gelled medium and to assess the genetic fidelity between the proliferated shoots in starch-gelled culture medium and their mother plants. Six blackberry varieties (‘Čačanska Bestrna’, ‘Chester Thornless’, ‘Driscoll’s Victoria’, ‘Loch Ness’, ‘Polar’, and ‘Karaka Black’) were tested. For the in vitro shoots proliferation, Murashige and Skoog (MS) medium supplemented with 0.5 mg dm−3 6-benzyladenine (BA) was used. The conventional medium was gelled with 0.5% plant agar, and wheat starch was used as an alternative gelling agent in a concentration of 5%. The results showed that for all blackberry cultivars, the highest number of shoots/inoculum was obtained in wheat starch-gelled culture medium, with a maximum value of 54.42 ± 4.18 presented by ‘Karaka Black’. Considering the length of the proliferated shoots, all tested cultivars presented outstanding results on the culture medium gelled with 5% wheat starch. The highest values regarding shoots length were observed on the ‘Chester Thornless’ followed by ‘Čačanska Bestrna’, and ‘Loch Ness’ with values of 5.55 ± 0.04 cm, 5.46 ± 0.06 cm, and 5.37 ± 0.09 cm, respectively. The genetic uniformity of the micropropagated shoots in relation to their mother plants was confirmed by sequence-related amplified polymorphism (SRAP) and start codon targeted (SCoT) molecular markers.

Molecular Characterization and Metabolite Profiling of Philippine Allium sativum Linn.: Ilocos Pink

Ilocos Pink garlic (IPG) is a local garlic variety found in Ilocos Norte, Philippines. Recently known for its moderate beta-adrenergic receptor inhibitory activity in vivo, there is still a limited number of studies describing its genetic and metabolite profile to distinguish it from other garlic varieties. In this study, genetic markers of IPG were identified using sequence-related amplified polymorphism (SRAP) analysis. Ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry followed by principal component analysis (PCA) was used to discriminate IPG’s metabolites from Ilocos Native garlic. Based on the degree of brown-stripe pigmentation on their outer skin, IPG samples can be classified into three – light, moderate, and heavy pigmentation. These subgroups were found to share seven SRAP marker pairs – namely,ME1-EM1 (at 300bp), ME1-EM4 (at 400bp), ME2-EM3 (500bp), ME3-EM1 (300bp), ME3-EM2(at 400bp), ME3-EM4 (at 200bp), and ME5-EM2 (at 300bp). Unique SRAP marker pairs were also observed between subgroups. PCA revealed Ilocos Native garlic to be discriminated from the IPG groups, but the marker matrix tool showed mere differences in concentrations except m/z247.129 at RT 1.40. Concentration-wise, nine markers may be proposed to discriminate IPG light from IPG moderate and heavy, seven of which are putatively identified as saponins. These findings suggest that SRAP markers can effectively discriminate IPG into subgroups, whereas metabolite profiling may provide little insight into the differences between IPG and Ilocos Native garlic.

Genetic diversity and structure of the coffee leaf rust fungus Hemileia vastatrix across different coffee management systems in Ethiopia.

Although coffee leaf rust (CLR), caused by Hemileia vastatrix, poses an increasing threat to coffee production in Ethiopia, little is known regarding its genetic diversity and structure and how these are affected by coffee management. Here, we used genetic fingerprinting based on sequence-related amplified polymorphism (SRAP) markers to genotype H. vastatrix samples from different coffee shrubs, across 40 sites, covering four coffee production systems (forest coffee, semi plantation coffee, home garden coffee, and plantation coffee) and different altitudes in Ethiopia. In total, 96 H. vastatrix samples were successfully genotyped with three primer combinations, producing a total of 79 scorable bands. We found 35.44% of amplified bands to be polymorphic, and the polymorphic information content (PIC) was 0.45, suggesting high genetic diversity among our CLR isolates. We also found significant isolation-by-distance across the samples investigated and detected significant differences in fungal genetic composition among plantation coffee and home garden coffee and a marginally significant difference among plantation coffee and forest coffee. Furthermore, we found a significant effect of altitude on CLR genetic composition in the forest coffee and plantation systems. Our results suggest that both spore dispersal and different selection pressures in the different coffee management systems are likely responsible for the observed high genetic diversity and genetic structure of CLR isolates in Ethiopia. When selecting Ethiopian coffee genotypes for crop improvement, it is important that these genotypes carry some resistance against CLR. Because our study shows large variation in genetic composition across relatively short geographical distances, a broad selection of rust isolates must be used for coffee resistance screening.

Genetic diversity analysis and potential suitable habitat of Chuanminshen violaceum for climate change

To provide a scientific basis for the sustainable development of C. violaceum, we correctly identified the different germplasm resources and obtained excellent germplasm resources. In this study, MaxEnt was used to predict the distribution range of C. violaceum in China under current and future climate scenarios and explain the impact of environmental variables on its distribution. An SRAP (sequence-related amplified polymorphism) molecular marker was used to analyse the genetic diversity of the plant. The results showed the areas of the total, most, moderately and poorly suitable habitats of C. violaceum were 69.93 × 104 km2, 7.77 × 104 km2, 12.68 × 104 km2 and 49.49 × 104 km2, respectively. The most suitable habitat was concentrated in central and eastern Sichuan, and scattered in Chongqing and Hubei. Under SS1–2.6, SSP2–4.5 and SSP5–8.5 scenarios in 2050s and 2090s, the area of the most suitable habitat would decrease by 25.13%–34.88%. The centroid of the most suitable habitat would move to the west by 45.44 km (SSP1–2.6), 42.15 km (SSP2–4.5) and 37.72 km (SSP5–8.5) in the future. Annual precipitation (bio12), minimum temperature of the coldest month (bio6), precipitation of coldest quarter (bio19), temperature annual range (bio7), elevation (El) and mean UV-B of highest month (UV-B3) were identified as the dominant environmental variables related to the distribution of C. violaceum. A total of 374 bands were amplified by 37 primer pairs, of which 283 bands were polymorphic, and the polymorphic percentage was 75.67%. The analysis of molecular variance showed higher percentages of genetic variation within the population. All the accessions could be distinguished by SRAP markers. The cluster analysis results showed that 63 accessions were classified into 7 groups, which were correlated with the geographical distribution of the accessions to some degree. The accessions from Langzhong and Qingbaijiang had higher diversity. These results suggest that strategic transplantation of C. violaceum from particular geographic locations could help make the species more resilient to climate change and slow the contraction of the species' distribution.