Polymorphic DNA Markers Research Articles

Association between quantitative morphological traits and RAPD molecular markers in pomegranate (Punica granatum L.).

Pomegranate (Punica granatum L.) is very important in terms of horticulture and food around the world. The present research aimed to identify the random amplified polymorphic DNA (RAPD) markers associated with morphological traits in pomegranate genotypes. Significant differences were observed among the studied genotypes based on the recorded traits. The 18 RAPD primers produced a total of 154 polymorphic fragments among genotypes. Using multiple regression analysis between each of the morphological traits and 154 RAPD polymorphic bands, RAPD markers associated with each of the morphological traits were identified. In total, 11 markers showed significant correlations with fruit weight, 9 markers with 100-aril weight, 11 markers with anthocyanin, and 8 markers with total soluble solids. Some markers were associated with more than one morphological trait, showing that the association of a marker with more than one trait can be caused by the pleiotropic effects of quantitative trait loci related to each other in different traits. For instance, the BA6-1 marker showed positive correlations with fruit weight, fruit crown width, and leaf length. Also, OPG13-3 and BA6-10 markers showed positive correlations with total soluble solids and anthocyanin content. The informative markers identified related to morphological characteristics in pomegranate can be a suitable guide to identify the genotypes with valuable fruit traits. Also, these markers can be used in selecting suitable parents for population generation for mapping purposes.

The potential of gamma irradiation on antioxidant capacity and genomic alterations in Calendula officinalis

There are lines of evidence that ionizing radiations such as gamma rays can cause different biological effects on plants. Marigold (Calendula officinalis L.) is a member of the family Asteraceae. It possesses profound amounts of active ingredients. The aim of this study was to evaluate the changes imposed upon different dose levels of gamma radiation on some features of Calendula officinalis such as antioxidant activity, total phenolic compounds and flavonoid contents, antibacterial activity and genomic alterations. Calendula officinalis seeds were exposed to different doses of Gamma radiation (0, 10, 15, 20 and 25 GY). Total phenolics, flavonoids, antioxidant activity (measured by DPPH assay) using methanolic extracts of plants and antibacterial activity measured by the disc diffusion assay showed significant differences to the control samples. The samples treated with 10 GY gamma rays showed the highest total phenol and flavonoid contents. Antioxidant activity significantly differed between Gamma rays dose levels and it was the highest at 25 GY. Four bacterial strains including E. coli, Bacillus subtilis and Pseudomonas aeroginosa were used for the antibacterial assay. Extracts from plants treated with 25 GY gamma rays showed the highest antibacterial activity against the 4 bacterial strains. Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers were used to study the genetic variation. The polymorphism information content (PIC) for RAPD primers ranged from 3% to 13% and ranged from 6 to 13% for ISSR primers. Results indicated that ISSR markers were more efficient than RAPD markers, as they detected 25.57% polymorphic DNA bands compared to 21.31% polymorphism for RAPD markers.

Analysis genetic diversity of rombeng pines using RAPD markers

The tourism industry in Indonesia continues to grow from year to year, as evidenced by the expansion of tourism villages. In the context of tourism, the term’resources’ refers to everything that has the potential to be developed to directly or indirectly support tourism. The natural potential of the Rombeng pine forest (Pinus sp.) in Bantaeng Regency, South Sulawesi, has become a tourist attraction for the surrounding community and visitors from outside the city. This pine species has a trunk characteristic that distinguishes it from scattered pine in general. This trait is manifested by grayish skin and a reddish hue that can be exfoliated. Based on this, an examination of the genetic diversity of pine species in the Bantaeng district was conducted. Utilizing Random Amplified Polymorphic DNA (RAPD) markers and Darwin 6. 0 as a research methodology. This study indicates that the diversity value (HE) of Pinus species is 0.46, which is relatively high. The near category of based genetic distance is dominated by genetic kinship, and the closest genetic distance is 0.04 while the farthest is 0.80.

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.

Genetic relationships and genome verification of Thai banana cultivars using Random Amplification of Polymorphic DNA (RAPD) markers

Abstract. Boonsrangsom T, Fuenghoi C, Premjet D, Suvittawat K, Ratanasut K, Sujipuli K. 2023. Genetic relationships and genome verification of Thai banana cultivars using Random Amplification of Polymorphic DNA (RAPD) markers. Biodiversitas 24: 3758-3765. Edible bananas and plantains, belonging to the family Musaceae, genus Musa, represent one of the most important fruit crops, with an annual production of more than 65 million tons worldwide. Bananas have several hybrid variations since they are descended from the two species Musa acuminata Colla (AA genome) and Musa balbisiana Colla (BB genome). Different morphological traits divide almost hybrid bananas into various genomic groupings. Banana genome categorization and identification, however, have always been challenging issues. This study aimed to assess the genetic relationships and verify the genomes of Thai banana cultivars using random amplification of polymorphic DNA (RAPD) markers. Using the 15 selected RAPD markers, 149 RAPD bands were found, with sizes ranging from 0.2 to 3.2 kb, and 88.6% were polymorphic. Polymorphic information content (PIC) values ranged from 0.18 to 0.42, averaging 0.30. Based on the Jaccard coefficient, the unweighted pair-group method arithmetic average (UPGMA) analysis showed that the banana samples had a similarity range of 0.27 to 1.00 with a mean of 0.56, demonstrating an abundance of viability across six banana genomes. The dendrogram generated from RAPD data revealed that all 18 Musa samples could be divided into two main groups (Group I and II). Three additional subgroups were created for each primary group (A, B, and C). The accurate identification and genetic data on the available genetic resources for bananas will be beneficial for breeding and conservation programs.

Isolation and characterization of 17 polymorphic microsatellite loci with tri- and tetra-nucleotide repeat motifs for Ayu (Plecoglossus altivelis) using next-generation sequencing.

Ayu or sweetfish, Plecoglossus altivelis, an amphidromous fish ranging in the northwestern Pacific, is economically important inland fisheries and aquaculture resources. Genetic characterization of wild Ayu and derived culture seeds with competent molecular genetic markers is still insufficient for their sustainable use. Microsatellite DNA markers with larger repeat motifs (e.g. tri- and tetra-nucleotide motifs) are convenient and accurate compared with those having mono- and di-nucleotide motifs, but the latter motifs characterized most Ayu microsatellite markers developed previously. Here, we isolated and characterized 17 polymorphic microsatellite DNA markers with tri- and tetra-nucleotide repeat motif using next-generation sequencing. Alleles per locus varied from 6 to 23. The observed and expected heterozygosities ranged from 0.542 to1.000and 0.709to0.951, respectively. Polymorphic information content (PIC) of 15 out of the 17 loci were high (≧ 0.700), suggesting them to be highly informative. Twelve of the 17 loci were used for preliminary assignment test among three collections, and successfully allocated the examined fish to the original populations. The novel polymorphic microsatellite markers developed herein will be useful to examine the genetic diversity and population structure of wild Ayu and the effect of seed transplantation on native populations, providing a tool for conservation and sustainable adaptive management of this species.

DNA Fingerprinting of Crops and Its Significance in Crop Improvement

One of the improvements made possible by the era of genomics is DNA fingerprinting. DNA fingerprinting can be used to detect a variety of genetic changes. In breeding programmes fingerprinting is used to improve productivity and performance. Variety differentiation was relied on morphological characteristics prior to the introduction of genomics and proteomics approaches. Although morphological markers have been used for decades, protein-based markers like isozymes were discovered in the middle of the twentieth century and used for fingerprinting and crop genetic variety assessments. But nowadays, the emergence of genome sequencing has led to the widespread use of genetic markers for crop fingerprinting. The discovery of DNA-based genetic markers has improved genetic research. For genetic diversity estimation, crop evolution, gene mapping and phylogeny, diploid/haploid crop appraisal, heterosis analysis, varietal identification by using marker assisted selection (MAS), highly polymorphic DNA markers are generated. The use of DNA markers for crop fingerprinting started with RFLPs that did not involve PCR and subsequently advanced to PCR amplifiable markers such as AFLPs, RAPDs, SSRs, ISSRs, SNPs, and GBS.This review will provide an outlook on several types of markers and their significance in DNA fingerprinting of crops and possible applications, as well as suggestions for further research.

Evaluation of Wild Almond Genotypes Grown as a Rain-fed Crop in Sulaimani Governorate using RAPD and ISSR Markers

Almond is considered the most common and essential nut grown in the rainfed area. It has many species wildly distributed in the Iraqi Kurdistan region, which are called Chaqala by local people. To understand and improve the characteristics of the cultivated almonds, a comprehensive study of wild almonds in terms of population structure and genetic diversity is needed to transfer new traits into the domesticated almonds. So, twelve different genotypes were collected and analyzed using random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. The results revealed polymorphic bands for both markers, the mean value of 5.8 for the RAPD marker and 7.8 for the ISSR marker was also documented. The polymorphic information content (PIC) values were obtained for RAPD primes that range between (0.64-0.85) and ISSR primers were also verified between (0.53-0.91), which shows the discriminatory power of these markers. “Jaccard similarity coefficients” were obtained between 0.34 (G11 vs. G12) to 0.77 (G1 vs. G10), and clustered into four groups with a mean similarity (0.65) for ten RADP markers. For ten ISSR markers, 0.35 (G8, G10) to 0.79 (G6 vs. G11) were also observed, which is clustered into a mean similarity (0.65). Structure analysis of RAPD and ISSR showed two major groups. Overall, these outcomes showed the diversity between the studied genotypes and among groups which are highly important for future almond breeding and conservation programs.

Genetic diversity of tomato (Solanum lycopersicum) accessions using chloroplast DNA and random amplified polymorphic DNA markers

Information regarding genetic diversity and genetic relationships among different genotypes is invaluable in crop improvement of which its success is largely dependent on genetic variability. As molecular markers continue to be an effective tool for localization of a gene to improvement of plant varieties, the need to establish phylogenetic relationships becomes extremely important for the process of breeding new cultivars. This study reports genetic diversity for Tomato accessions across Nigeria (Six geo-Political Zones) as revealed by chloroplast DNA (cpDNA) and Random Amplified Polymorphic DNA (RAPD) markers. cpDNA data showed a Nucleotide diversity for all accessions of Tomato at 0.302 while the number of segregated sites as well as parsimony informative sites to be 4.0. Data from five Random Amplified Polymorphic DNA (RAPD) primers showed a low Gene diversity (h) which ranged from 0.10 to 0.28, Percentage polymorphism (Pp) ranged from 20 % to 84%. The Unweighted Pair Group Method with Arithmetic Mean (UPGMA) dendrogram grouped the accessions into two groups at similarity coefficient of 72%, with a value of r = 0.98, showing an excellent correlation between the accessions and the values of the initial distances (similarity matrix). Similar results were seen with the dendrogram constructed for genetic relationships of Tomato accessions using RAPD or cpDNA (you have mentioned RAPD up) markers. Split tree analysis equally revealed a 2 structured gene pool for Tomato gene pool in Nigeria. The high homogeneity of species observed in the study signifies a low genetic diversity and limited variability in tomato species in Nigeria. Amongst the consequences of low genetic diversity is the absence of unique variants that can possibly combat disease conditions or adapt to unfavourable environmental changes. The use of both cpDNA and RAPD markers in this study has efficiently shown that continuous cycling/shuffling of species within the narrow gene pool is expected to lead to a continuous reduction in genetic variability. No addition of new variant into the gene pool and in turn leads to inbreeding depression, thus suggesting the need to breed with known wild cultivars to increase genetic variability. Key words: CpDNA, Gene pool, Genetic Diversity, Inbreeding depression, RAPD marker, Tomatoes breeding

Development of Molecular Marker Linked to Seed Hardness in Pomegranate Using Bulked Segregant Analysis.

The pomegranate (Punica granatum L.) is one of the fruit species with the oldest cultural history. There are many traits to determine the quality of pomegranate fruits. Among them, soft-seeded feature of pomegranate fruit is important trait for the market value of the fruit. For this reason, the demand for pomegranate varieties with soft seeds has been increasing, especially in recent years. In this study, molecular markers associated with seed hardness were developed to distinguish pomegranate cultivars with soft-seeded feature based on genomic DNA at the early stages of the pomegranate breeding process. For this purpose, pomegranate genotypes and/or cultivars from the population involved in reciprocal crosses of hard-seeded Ernar, medium-hard-seeded Hicaznar, and soft-seeded Fellahyemez cultivars were grouped as soft-seeded or hard-seeded. Further, leaf samples were collected from individuals belonging to each group. Then, the genomic DNA was isolated from each plant separately, and equal amount of genomic DNA from individuals with the similar seed hardness were mixed for bulked segregant analysis (BSA). The bulked genomic DNAs of opposite characters were analyzed by polymerase chain reaction (PCR) using random decamer primers to develop random amplified polymorphic DNA (RAPD) markers associated with soft-seeded or hard-seeded pomegranates. A total of three RAPD markers were determined to distinguish the individuals having soft- or hard-seeded pomegranate genotypes and/or cultivars. As a result of the comparison of the DNA sequences of these RAPD markers, insertion-deletions (inDels) primers were designed to developed and validate a PCR assay to distinguish the soft- and hard-seeded pomegranate genotypes/cultivars from each other. The molecular markers developed in this study will enable us to distinguish soft-seeded pomegranate types easily in a short time at the early stages of the pomegranate breeding programs.

Random Amplified Polymorphic DNA-Polymerase Chain Reaction Analysis of Four Koi Fish (Cyprinus carpio var. koi) Variants from Yogyakarta, Indonesia

Koi fish (Cyprinus carpio var. koi) is an ornamental fish with many hobbyists because of the beauty of its color pattern. Koi fish are widely cultivated around the world. Indonesia is a country that has many koi fish breeders and hobbyists. Crossbreeding between variants of koi fish can form a new variants. and provide a lot of genetic variation. This study aims to determine the variations and genetic relationships of koi fish that are widely cultivated in Indonesia. This study used 40 koi fish originating from fish farmers in the Special Region of Yogyakarta. Koi fish variants used are Kohaku, Showa, Sanke, and Shiro. This research uses amplification method with Polymerase Chain Reaction (PCR) with Random Amplified Polymorphic DNA (RAPD) marker which is OPA-1 and OPA-9. The results of the RAPD-PCR showed 14 bands from the OPA-1 primer and 5 bands from the OPA-9 primer with a total of 19 bands consisting of 18 polymorphic bands and 1 monomorphic band from the four samples of koi fish variants. The results of the polymorphism analysis showed that the polymorphisms of the Shiro variants is 63.16%, Showa 47.37%, Kohaku 36.84%, and Sanke 31.58%. Genetic distance calculation using the Nei genetic distance shows that the Kohaku variant has a close genetic distance to the Showa variant and the Sanke variant has a close genetic distance to the Shiro variant.

Comparative assessment of ISSR, DAMD and RAPD markers for evaluation of genetic diversity of gerbera (Gerbera jamesonii Bolus ex Hooker f.) cultivars

Genetic diversity is the best way to improve available genetic resources for breeding programs in gerbera. In present study, genetic diversity of 22 gerbera cultivars was investigated using inter-simple sequence repeat (ISSR), directly amplified minisatellite DNA (DAMD), and Random Amplified Polymorphic DNA (RAPD) markers. Average polymorphism information content (PIC) for ISSR, DAMD and RAPD markers was 0.40, 0.41 and 0.40, respectively. Cluster analysis for ISSR, DAMD and RAPD divided the cultivars into three distinct clusters. The comparative analysis of the three markers (ISSR, DAMD and RAPD) showed that DAMD had superiority over RAPD and ISSR in characterization of genetic diversity in Gerbera. To our knowledge, this is the first report of a comparison of performance among DAMD, ISSR and RAPD techniques on a set of gerbera genotypes. Overall, our results showed that DAMD markers well represented different genotypes of gerbera diversity.

RAPD MARKERS BASED GENETIC DIVERSITY ANALYSIS OF ONION (ALLIUM CEPA) GERMPLASM

Onion is one of the most popular spice crop, which is used for seasoning wide range of dishes as well as folk medicine. Assessment of genetic diversity helps to use the onion germplasm as breeding materials for its improvement. Molecular marker based diversity assessment is more powerful, rapid and reliable compared to morphology based genetic diversity assessment. Thirty eight onion germplasm were characterized by using 10 random amplied polymorphic DNA (RAPD) markers for estimating genetic diversity within the germplasm. The germplasm exhibited wide range of variability which could be used in cross breeding for getting superior F1 generation. Out of 10 primers, four gave polymorphism among onion germplasm. Genetic diversity of 38 germplasm was analyzed using variation at 34 RAPD loci, of which 91.89% were polymorphic. The highest pair wise genetic distance was 1.046 and the lowest was 0.056. The mean gene diversity among all the germplasm was 1.54 and Shannon's information index was 0.3188. The UPGMA dendrogram, based on Nei`s genetic diversity showed 6 clusters. The frequency of polymorphic loci ranged from 0.0263 to 1.0000, indicates that there exists a wide genetic diversity among the germplasm and corroborated the usefulness of RAPD markers for estimating genetic diversity in onion.

Genetic differentiation among Batak fish populations (Neolissochilus sumatranus, Tor douronensis, and Tor soro) in North Sumatra, Indonesia revealed by RAPD markers

Abstract. Barus TA, Wahyuningsih H, Simanjuntak BN, Ginting RH, Batubara AS, Hartanto A. 2023. Genetic differentiation among Batak fish populations (Neolissochilus sumatranus, Tor douronensis, and Tor soro) in North Sumatra, Indonesia was revealed by RAPD markers. Biodiversitas 24: 1327-1332. Mahseer or Batak fish species within the genera of Neolissochilus and Tor are highly valued as a source of food for local communities, especially in North Sumatra. Assessment of genetic differentiation of the Batak fish population, namely Tor soro, Tor douronensis, and Neolissochilus sumatranus in the North Sumatra Rivers, has been conducted. The objective of this study was to determine the possible genetic divergence among congeneric fish and supply the genetic information for the design of conservation strategies. Fish specimens were collected from three rivers in North Sumatra Bahorok River (Langkat District), Asahan River (Toba Samosir District), and Batangtoru River (South Tapanuli District). The genetic analysis employed the Random Amplified Polymorphism DNA (RAPD) markers using a set of RAPD primers: OPA-2, OPA-3, OPA-6, OPA-7, OPA-9, OPA-11, and OPA-17. The amplified fragments were analyzed using the Numerical Taxonomy and Multivariate Analysis System (NTSYS) 2.00 program to construct the dendrogram of relationship among accessions. The genetic similarity coefficient among species of T. soro, T. douronensis, and N. sumatranus reached 0.44-0.86, with the lowest similarity at 44%. The cluster analysis indicated that T. douronensis is more closely related to N. sumatranus than T. soro based on the grouping of accessions. There is an indication of natural hybrids occurrence between N. sumatranus and T. soro populations despite the different habitats and locations of sampling. Our study revealed that using RAPD markers may discriminate inter- and intraspecific Batak fish populations in North Sumatra.

Molecular identification of mother trees of four matoa cultivars (Pometia pinnata Forst & Forst) from Pekanbaru City, Indonesia using RAPD markers

Abstract. Zulfahmi, Pertiwi SA, Rosmaina, Elfianis R, Gulnar Z, Zhaxybay T, Bekzat M, Zhaparkulova G. 2023. Molecular identification of mother trees of four matoa cultivars (Pometia pinnata Forst & Forst) from Pekanbaru City, Indonesia using RAPD markers. Biodiversitas 24: 1524-1530. Pekanbaru city has four matoa (Pometia pinnata Forst & Forst) cultivars, i.e. red matoa, yellow matoa, green matoa, and black matoa, but the knowledge of the genetic variation among matoa cultivars is not available. The objective of this study was to assess the genetic variation among matoa cultivars using Random amplified polymorphism DNA (RAPD) markers and to identify the specific marker to distinguish among matoa cultivars. Eighteen primers were initially screened and four matoa cultivars were analyzed with twelve primers using the RAPD marker. The results of this study found that the twelve selected RAPD primers generated 39 fragments, with fragment sizes ranging from 200 to 1500 bp. The percentage of fragment polymorphic was 80.41%, indicating the high genetic variation of the matoa cultivar. The high genetic variation of matoa in this study is caused by cross-pollinated among matoa cultivars in the field. Eleven primers can differentiate four matoa cultivars with specific bands. The obtaining unique bands can be utilized by breeders and farmers as a basis to select the parents for the genetic improvement of Matoa, cultivars or clones protection, detection of seedling purity in a nursery, and to verify the originality of the seedlings that will be cultivated.

Assessment of Biological Activities and Genomic Changes on Microorganisms, Wheat, and Wilding Arise from Poly(pyrazole).

The rapidly growing human population has led to duplicate food production and also reduced product loss. Although the negative effects of synthetic chemicals were recorded, they are still used as agrochemical. The production of non-toxic synthetics makes their use particularly safe. The goal of our research is to evaluate antimicrobial activity of previously synthesized Poly(p-phenylene-1-(2,5-dimethylphenyl)-5-phenyl-1H-pyrazole-3,4-dicarboxy amide) (poly(PDPPD)) against selected Gram-negative, Gram-positive bacteria, and fungus. In addition, the possible genotoxic effects of the poly(PDPPD) were searched on Triticum vulgare and Amaranthus retroflexus seedlings using Random Amplified Polymorphic DNA (RAPD) marker. The binding affinity and binding energies of the synthesized chemical to B-DNA were simulated with AutoDock Vina. It was observed that the poly(PDPPD) affected most of the organisms in a dose-dependent manner. Pseudomonas aeruginosa was the most affected species in tested bacteria at 500 ppm with 21.5 mm diameters. Similarly, a prominent activity was observed for tested fungi. The poly(PDPPD) decreased root and stem length of the Triticum vulgare and Amaranthus retroflexus seedlings and also reduced the genomic template stability (GTS) value of Triticum vulgare more than Amaranthus retroflexus. The binding energy of poly(PDPPD) was found in range of -9.1 and -8.3 kcal/mol for nine residues of B-DNA.

Genetic variation of arta populations ( Calligonum polygonoides subsp. comosum) in Egypt: Genepools for biodiversity and afforestation

Genetic diversity manipulates a prime and vital role in the sustainable use of genetic resources. The data highlighted more insights into the genetic diversity of the arta plant ( Calligonum polygonoides subsp. comosum) populations collected from three localities, Qalabshu ( QQ), Mutubas ( MM) and Gamasa (GG), in Egypt as gene pool for biodiversity conservation and afforestation. Random amplified polymorphic DNA (RAPD) markers investigated the population pattern and structure. A total of 129-amplicons oscillated from 145 to 1505 bp and a total of 19-amplicons were specific markers with an average of nine bands for each population. The Shannon index (I) scored at an average of 0.3. The diversity ( h) oscillated from 0.11 to 0.25. The similarity matrices based on Jaccard coefficient recorded positive values. A higher correlation (r = 0.83) was between the combined Qalabshu (QQ) and Mutubas (MM) matrices using the Mantel test with 1,000 permutations. This species has higher adaptability for their regions. This gene pool is a valuable reservoir for enriching genetic diversity and provides basal information for the biodiversity conservation of a dominant species. The dominant species can be utilised in afforestation in the same region or another region which has the same environmental conditions.

A Genome-Wide Association Study and Genomic Prediction for Fiber and Sucrose Contents in a Mapping Population of LCP 85-384 Sugarcane.

Sugarcane (Saccharum spp. hybrids) is an economically important crop for both sugar and biofuel industries. Fiber and sucrose contents are the two most critical quantitative traits in sugarcane breeding that require multiple-year and multiple-location evaluations. Marker-assisted selection (MAS) could significantly reduce the time and cost of developing new sugarcane varieties. The objectives of this study were to conduct a genome-wide association study (GWAS) to identify DNA markers associated with fiber and sucrose contents and to perform genomic prediction (GP) for the two traits. Fiber and sucrose data were collected from 237 self-pollinated progenies of LCP 85-384, the most popular Louisiana sugarcane cultivar from 1999 to 2007. The GWAS was performed using 1310 polymorphic DNA marker alleles with three models of TASSEL 5, single marker regression (SMR), general linear model (GLM) and mixed linear model (MLM), and the fixed and random model circulating probability unification (FarmCPU) of R package. The results showed that 13 and 9 markers were associated with fiber and sucrose contents, respectively. The GP was performed by cross-prediction with five models, ridge regression best linear unbiased prediction (rrBLUP), Bayesian ridge regression (BRR), Bayesian A (BA), Bayesian B (BB) and Bayesian least absolute shrinkage and selection operator (BL). The accuracy of GP varied from 55.8% to 58.9% for fiber content and 54.6% to 57.2% for sucrose content. Upon validation, these markers can be applied in MAS and genomic selection (GS) to select superior sugarcane with good fiber and high sucrose contents.

Molecular characterization of nine grapevine varieties cultivated in Salahaldin, Iraq by using RAPD-PCR marker

Grapevine (Vitis vinifera L.) is one of important economic fruit crops found in Salahaldin province \ Iraq. To examine the Molecular characterization and genetic relationships among nine grape varieties by using random amplified polymorphic DNA (RAPD) marker. Fifteen RAPD primers produced polymorphic band (71, 56%), while two RAPD primers yielded monomorphic bands only. The size of the fragment ranged between 250-2700 bp, with an average of 5.47 band/primer. A total of 20 unique and absent bands used to identify seven cultivars. This study has found that genetic distance values ranged from 0.092 to 0.277 among studied grape cultivars. The cluster analysis showed there were two main groups (G1 and G2). These results proposed RAPD marker as rapid, easy and power marker for Molecular characterization and genetic analysis among grapevine.

Improvement of morphology, biochemical characters, and molecular changes of local upland rice cv. Sidikalang M3 generation through induction of gamma-ray irradiation

Abstract. Naibaho D, Purba E, Hanafiah DS, Hasibuan S. 2023. Improvement of morphology, biochemical characters, and molecular changes of local upland rice cv. Sidikalang M3 generation through induction of gamma-ray irradiation. Biodiversitas 24: 200-207. Upland rice cultivar Sidikalang is one of the local upland red rice cultivars of North Sumatra, which has the potential to be developed. However, this rice has limited planting area due to factors such as its higher plant height and long duration compared to other rice cultivars. Plant characteristics can be improved through induced mutation using gamma-ray irradiation. This study aimed to determine gamma rays' effect on changes in morphological, biochemical, and molecular characters and to obtain a superior Sidikalang cultivar mutant plant M3 generation. Observations of morphological changes were carried out quantitatively and qualitatively, biochemical analysis (amino acid content) was done using a High Performant Liquid Chromatography analyzer, and molecular analysis was performed using Random Amplified Polymorphism DNA markers. The results showed that 600 Gy gamma-ray irradiation improved quantitative morphological characters (shorter plant height, higher number of tillers and panicles, faster panicle release age) and qualitative morphological characters (flag leaf angle in dwarf mutants became upright) compared to no irradiation. 400 Gy gamma-ray irradiation also increased almost all amino acid content compared to no irradiation. The presence of polymorphic bands in the M3 generation Sidikalang cultivar mutant plant evidenced changes in morphological and biochemical characters.