Highest Polymorphism Information Content Value Research Articles

Molecular characterization of Turkish hazelnut cultivars and genotypes using SSR markers

This study defines the genetic characterization of 16 hazelnut varieties and 64 genotypes. SSR method was used in molecular characterization studies. 18 SSR primers were used. In the SSR method, 118 bands were obtained, and 115 were polymorphic. The similarity coefficient in overall genotypes were between 0.12 and 0.98 in SSR andthe polymorphism rate of the primer pairs used was calculated as 98.0%. The lowest polymorphism information content value (0.542) was obtained from the CAC- C 028 locus, and the highest polymorphism information content value (0.987) was obtained from the CAC- B 113 locus. The average polymorphism information content value was 0.786. The total discrimination power values of SSR loci were determined as 17.98; the lowest (0.748) discrimination power value was obtained from the CAC- B 020 locus, while the highest (1.404) discrimination power value was obtained from the CAC- A 024 b locus. The genotypes’clustering positions across the dendograms were essentially correlated with their geographic origins. This result shows that genetic origin plays an important role in terms of classification of genotypes in hazelnut.

Genetic diversity of maize resources revealed by different molecular markers

AbstractMaize (Zea mays L.) is the third most important cereal crop in the world because of its nutritional value and industrial benefits. Molecular markers are used mainly by the breeders to study the genetic variability of genotypes and its application in the breeding process. Two types of molecular markers, 10 random amplified polymorphic DNA (RAPD) primers and 10 start codon target (SCoT) primers, were assayed to determine the genetic diversity of 25 Slovak maize lines and 25 maize cultivars. A high level of polymorphism was found with both RAPD and SCoT markers, which was confirmed by high average polymorphism information content (PIC) values using both techniques. The efficiency of individual marker techniques in the detection of genotype diversity can be compared by calculating the marker index (MI), detecting diversity index (DDI), discriminating power, resolving power (RP) and other indices. A higher MI (11.788), DDI (2.358) and RP (53.08) value was achieved by the SCoT technique compared to the RAPD method. Three joint dendrograms and PCoA plots constructed based on RAPD, SCoT and both methods combined confirmed the unambiguous separation of maize lines and cultivars from each other. The results obtained from the RAPD and SCoT analysis can be used for the selection of potentially suitable biological sources for further marker-assisted breeding.

Genetic Relatedness in Elite Cultivars of Moth Bean using Morpho-agronomic and Molecular Markers

Background: Moth bean is a very nutritive and hardy crop, especially for resource poor-arid agriculture. The limited use of cultivars in moth bean breeding resulted into narrow genetic base. This study aimed to diversify the conical genetic base and developimproved cultivars, through molecular (RAPD) and morpho-agronomic characterization of commercially elite moth bean cultivars. Methods: Elite moth bean cultivars (15) were evaluated for 11 morpho-agronomic traits. Eleven RAPD markers were used to amplify genomic DNA and perform molecular characterization.Clustering approach was used for grouping of the cultivars. Result: RAPD markers revealed high polymorphism in 15 elite moth bean cultivars. The polymorphism information content (PIC) values varied within the range of 0.45 to 0.88, with an average of 0.77. The number of alleles at different loci ranged from 4 to 16, with an average of 10 alleles per locus. When employing UPGMA-based cluster analysis, utilizing 11 morpho-agronomic traits, the cultivars were grouped into four clusters. However, when RAPD markers were used, the cultivars were grouped into five clusters. The Jaccard’s similarity coefficient and Manhattan dissimilarity coefficient fell within the ranges of 0.18 to 0.70 and 0.02 to 0.42, respectively. These values signify the degree of genetic variability within the cultivars. Furthermore, a Mantel test was conducted to examine the correlation between agronomic traits and the RAPD-based matrix. The results showed a negative correlation, but it was not statistically significant.The high PIC values and the successful amplification of multiple loci demonstrate the efficacy of RAPD markers in assessing genetic diversity in moth beans. The study revealed enormous genetic variation among cultivars and crosses can be attempted between cultivars of different groups to create better recombinants in moth bean breeding programmes.

Genetic diversity and population structure of Anatolian Hair goats, an ancient breed

Abstract. This study aimed to investigate the genetic characterization and diversity of Hair goats from 10 regions using 20 microsatellite markers. A total of 522 alleles were observed. The INRA0023 locus exhibited the greatest number of alleles (48), while the DRBP1 locus had the highest effective allele number (16.27), and the BM1818 and DRBP1 loci had the highest polymorphic information content value (0.94). The expected heterozygosity value ranged from 0.85 (ILSTS011) to 0.94 (BM1818, SRCRSP15, and DRBP1). The Hair goat populations in Konya and Hatay displayed the lowest and highest allele numbers, with values of 10.40 and 16.25, respectively. The fixation index (FIS) values are significant in defining population structures and determining the extent of heterozygosity losses. The FIS values exhibited a range of 0.031 in Muǧla to 0.226 in Burdur. A total of 107 unique alleles were identified in Hair goat populations. However, it is noteworthy that, out of all the alleles, only 25 had a frequency exceeding 5 %. The results indicate that the microsatellite markers utilized demonstrate sufficient levels of polymorphism, making them appropriate for efficiently investigating the genetic variability of Hair goat populations.

Microsatellite-Based Genetic Diversity Analysis and Population Structure of Proso Millet (Panicum miliaceum L.) in Kazakhstan

Proso millet is an important allotetraploid cereal crop; however, it is the least studied species of the Poaceae family, as it is an under-utilized crop. Genomic resources for proso millet are very limited compared to major crops. An understanding of the genetic relationships among germplasm resources is important for future breeding endeavors. In the present study, simplesequence repeat (SSR) markers were employed to assess the polymorphism and genetic diversity of 100 millet accessions from different countries, which were tested in the dry steppe zone conditions of the Akmola region from 2020 to 2022. The use of 20 SSR markers detected a total of 47 alleles, with an average allele number of 2.35 per locus among these proso accessions. Nine of them were polymorphic among the genotypes, which suggests that these SSR markers can be used for genetic studies. The results showed a moderate level of polymorphism information content (PIC) that averaged at 0.424, ranging from 0.125 to 0.795. The markers SSR-67, SSR-82, SSR-85 and SSR-109 showed high PIC values of 0.536, 0.756, 0.795 and 0.758, respectively. Markers SSR 85 and SSR 86 significantly correlated to agronomic traits, such as productive tillering (PT) and grain yield (GY). The genetic structure, UPGMA cluster and PCoA assay indicated that the accessions that originated from Central Asia had higher genetic diversity. Based on structure (K = 3), all the accessions were divided into three groups, where the gene pool that originated from Central Asia wasdetected in all three clusters. Based on a principal component analysis (PCA), the accessions of Central Asian origin were genetically closer to the North Asian group.

Assessment of Genetic Diversity and Protein Content of Scandinavian Peas (Pisum sativum)

We produced homogeneous lines of 227 pea accessions from the Nordic Genetic Resource Center via single seed descent. The genetic diversity among these, mostly Scandinavian accessions, was investigated using three microsatellite markers, A9, AC58 and AA5. The microsatellites were highly informative and separated 153 of 194 accessions on a Neighbor Joining topology. The high polymorphism information content (PIC) values between 0.87 and 0.91 indicated that the gene bank material contains a large number of pea accessions with different breeding histories. The peas were grown in the field for two years and seed protein content showed variation between 9.3% and 34.1% over the years and accessions, respectively. The mean thousand seed weight was 152.05 g. More than 10 accessions had a protein content above 28%, showing that the collection has potential as breeding nursery for high-protein pea cultivars.

Efficiency of RAPD and SCoT Markers in the Genetic Diversity Assessment of the Common Bean.

Knowledge about the genetic diversity of the available common bean germplasm can help breeders properly direct the choice of genetic material in the breeding process. The aim of the present work was to estimate the usefulness of 10 RAPD and 10 SCoT markers in genetic diversity detection among 33 common bean genotypes. Both molecular marker systems were able to generate high levels of polymorphism in the genetic material, which was supported by the relatively high polymorphic information content (PIC) values observed for the used markers. The Diversity Detection Index (DDI) and Marker Index (MI) were used to compare the effectiveness of RAPD and SCoT markers. For both techniques, high values of MI and DDI were calculated, representing their effectivity. The SCoT markers showed higher values of the parameters used (MI = 7.474, DI = 2.265) than the RAPD markers (MI = 5.323, DDI = 1.612), indicating their higher efficiency in the detection of molecular variability. Three constructed dendrograms and PCoA plots were created using RAPD and SCoT, and both methods combined confirmed sufficient separation of the bean genotypes from each other. At the same time, a higher efficiency of SCoT markers compared to RAPD markers in the detection of the genetic diversity of beans was also proven. The results may be of future interest in the choice of genetically distant material for breeding purposes.

GENETIC PURITY AND DIVERSITY ASSESSMENT OF PARENTAL CORN INBRED LINES USING SSR MARKERS FOR PHILIPPINE HYBRID BREEDING

Accurate data and relevant insights on parental corn inbred lines' and hybrids’ genetic purity and diversity are essential for hybrid development and seed production. Here, the genetic purity and diversity of 19 parental yellow corn inbred lines were assessed using SSR markers. A total of 91 SSR markers were utilized, of which 61 were highly polymorphic and had high polymorphism information content value (PIC = 0.379). Genetic purity and diversity parameters were calculated from the generated SSR marker data. Observed pairwise genetic distances ranging from 0.257 to 0.808 implied high genetic dissimilarities among the accessions. Cluster analysis separated the parental lines into three distinct subclusters, which can potentially be a basis for generating heterotic groupings among the parental lines. Eight (8) out of the 19 parental lines showed considerable residual heterozygosity of ≤10%. Inbred line CML 431 displayed complete homozygosity across all 61 SSR markers. Inbred lines that have residual heterozygosity of >15% need purification through further breeding and selection. Out of the resultant F1 hybrids analyzed, only four (4) showed genetic impurity of ≤10%. It may be attributed to the intrinsic genetic impurity of parental line CML 452 (21.67%). In contrast, hybrids generated from two genetically pure parents (e.g., CML 431 and CML 575) showed low to no off-types. Overall, genetic purity and diversity determination of promising parental lines can be valuable for future yellow corn breeding programs in the Philippines.

Assessment of Genetic Diversity of Local Coffee Populations in Southwestern Saudi Arabia Using SRAP Markers

Coffea arabica, a member of the Rubiaceae family, is the most commercially important species of the genus Coffea. It has been grown on the mountain terraces of southwestern Saudi Arabia for centuries. At present, the species is subject to increased genetic erosion due to the abandonment of many gardens by their owners and the increasingly dry climate. The current study was carried out to determine the genetic diversity of 56 local coffee accessions collected from the southern regions of Saudi Arabia using 30 sequence-related amplified polymorphism (SRAP) markers. Six SRAP markers showed polymorphism among the 56 accessions. A total of 1125 bands, with an average of 187.5, was produced from all six SRAP primers. The polymorphic information content (PIC) ranged from 74.8 to 97.7, with an average of 91.4 for all studied SRAP markers. The high polymorphism percentage seen in this study, along with the high number of alleles produced and the high PIC values of the primers used, demonstrate that the SRAP approach was an effective molecular technique for assessing genetic diversity in the studied populations. The structural analysis showed a sharp peak, with no ambiguity, demonstrating the highest delta K value at K = 3 and K = 6, and the coffee accessions could be grouped into three and six main populations, respectively. The PCoA, cluster analysis, and structural population analysis results suggest considerable genetic diversity among coffee populations growing on the southwestern mountain terraces of Saudi Arabia. The 56 accessions were segregated into five groups, mostly according to geographic distribution. The accessions from the southern districts of Jazan region mostly clustered in groups 2 and 4, while the accessions from the northern districts of Al-Baha and Assir regions formed separate groups. Based on these analyses, accessions KSA1R, KSA6R, KSA21, KSA25, KSA37, KSA38, KSA42, KSA59, KSA60, KSA62, and KSA63 were the most divergent. The genotypes should be conserved for use in coffee-breeding programs to improve the agronomic value of the crop, broaden the genetic base of C. arabica in Saudi Arabia and increase environmental resilience. Additional molecular and functional genomics studies are necessary to further elucidate how this germplasm has evolved and enhance the value of local Arabica coffee diversity in the Kingdom.

Molecular Characterization of Different Soybean [Glycine max (L). Merril] genotypes by RAPD Markers

The present investigation was carried out on molecular characterization of different soybean genotypes by using RAPD markers. Genetic diversity of 10 soybean genotypes was studied using Random Amplified polymorphic DNA (RAPD). 12 RAPD primers were used for screening 10 soybean genotypes from which total 334 fragments were amplified. It was observed that 41.10% bands were polymorphic and 58.88% were monomorphic. The percent of polymorphic amplicons in banding pattern was calculated and it was highest in OPA-01 (67.85%) followed by OPA-11 (66.66%). Polymorphism information content (PIC) was calculated and highest PIC value was observed in OPA-01 (0.26) and lowest was observed in OPA-08 and OPA-05 (0.03). Maximum amplicons were produced in OPA-01 (56) and minimum in OPA-08 (11). Genetic relationship between soybean genotypes was determined on the basis of Jaccard’s pair wise similarity coefficient values and dendrogram was generated by UPGMA (Unweighted Pair Group Method with Arithmetic Mean) cluster analysis using dice’s similarity matrix through NT-SYS pc software. The dendrogram of RAPD analysis shows 8 clusters and sub clusters were revealed. The value of similarity coefficient ranged from 0.19 to 0.71. The maximum similarity percentage i.e. 71% was found between KDS-726 and KDS-922 genotypes. The minimum similarity i.e. 19% was found between IVT-33 and IVT-13. According to this information it is concluded that the KDS-726 and KDS-922 genotypes showed minimum genetic diversity as compare to the IVT-33 and IVT-13 genotypes. Therefore, understanding the genetic diversity of soybean genotypes is essential to broaden the genetic base and to further utilize in the MAS breeding program.

Genetic Diversity and Population Structure of Normal Maize Germplasm Collected in South Sudan Revealed by SSR Markers.

Maize is one of the leading global cereals, and in South Sudan maize cultivation occurs in nearly all of the country’s agro-ecological zones. Despite its widespread cultivation, farmers in South Sudan depend on undeveloped varieties, which results in very low yields in the field. In the current study, 27 simple sequence repeat (SSR) markers were used to investigate genetic diversity and population structures among 37 landrace maize accessions collected from farmers’ fields in South Sudan. In total, 200 alleles were revealed with an average of 7.4 alleles per locus and a range from 3.0 to 13.0 alleles per locus. The observed heterozygosity values ranged from 0.06 to 0.91 with an average of 0.35. High polymorphic information content (PIC) values were identified with a mean of 0.69, which indicates the informativeness of the chosen SSR loci. Genetic structure analysis revealed a moderate genetic differentiation among the maize populations with a fixation index of 0.16, while there was very high genetic differentiation within the groups of populations of three regions with a mean fixation index (F) of 0.37. An unweighted pair group method with an arithmetic mean (UPGMA) dendrogram clustered the 37 maize accessions into three groups with 43% genetic similarity. The clustering pattern of the maize accessions was moderately consistent with their collection area. The findings of this study will provide maize breeders with a better understanding of maize diversification as well as a reserve of genetic resources for use in the selection of advantageous and useful resources for the development of maize varieties in South Sudan.

Molecular Characterization of Land Races of Rice by Using SSR Markers (Oryza sativa L.)

The study was conducted to use thirty one rice land races for characterized the genetic diversity analysis at Seed Unit, UAHS, Shivamogga. The SSR markers (25 SSR markers) were used for the assessment of genetic diversity and relatedness among 31 rice landraces and all of them were found polymorphic.  Twenty five SSR markers revealed 50 alleles in the 31 land races, the number of alleles per locus with an average of 2 per locus. Major allele frequency ranged from 0.58 (RM 25) to 0.94 (RM 229) with an average of 0.74 per marker. The PIC (polymorphism information content) value ranged from 0.12 (RM 229) to 0.66 (RM 481 and RM 25) with an average of 0.36 per marker. The PIC value of each marker, which was evaluated on the basis of its alleles, varied greatly all tested SSR loci-from 0.58 to 0.94 with an average of 0.74. The highest PIC value 0.49 was obtained for RM481 and RM25, followed by RM443 (0.47), RM224 (0.46) RM 159, RM 1054, RM226 and RM24 (0.44). Remaining markers were showed less PIC value. Lower PIC value result of closely related landraces and higher PIC values result of diverse landraces. The dendrogram based on UPGMA grouped the 31landraces into 10 clusters that were demarcated at a similarity coefficient of 0.68. Cluster III was the largest including 13 land races followed by cluster VI and II each of which had four and three land races respectively. The remaining clusters had one and two landraces each.

CgSSR marker-based genome-wide association study identified genomic regions for panicle characters and yield in rice (Oryza sativa L.).

To improve production efficiency, positive alleles corresponding to yield-related attributes must be accumulated in a single elite background. We designed and used cgSSR markers, which are superior to random SSR markers in genome-wide association study, to identify genomic regions that contribute to panicle characters and grain yield in this study. As evidenced by the high polymorphic information content value and gene diversity coefficient, the new cgSSR markers were determined to be highly informative. These cgSSR markers were employed to generate genotype data for an association panel evaluated for four panicle characters and grain yield over three seasons. For five traits, 17 significant marker-trait associations on six chromosomes were discovered. The percentage of phenotypic variance that could be explained ranged from 4% to 13%. Unrelated gene-derived markers had a strong association with target traits as well. Trait-associated cgSSR markers derived from corresponding or related genes ensure their utility in direct allele selection, while other linked markers aid in allele selection indirectly by altering the phenotype of interest. Through a marker-assisted breeding approach, these marker-trait associations can be leveraged to accumulate favourable alleles for yield enhancement in rice. © 2022 Society of Chemical Industry.

Genetic Diversity of Eight Native Indonesian Chicken Breeds on Microsatellite Markers

Indonesia has diversity in native chickens based on phenotypes. This diversity is utilized for economic purposes such as meat, eggs, fancy, crowing, and fighting. This study aimed to determine the genetic structure of eight native Indonesian chicken breeds with microsatellite markers, the genetic distance, and inbreeding coefficient of each breed of chicken used for crossbreeding programs to obtain a positive heterosis effect for selection programs. The samples used were Arab, Merawang, Pelung, Sentul, Cemani, KUB, Black Kedu and White Kedu. Broiler chickens (Cobb) were used as the outgroup in this study. A total of 192 DNA samples from eight breeds were used in this study. A total of 24 microsatellite markers were used in this study to observe the genetic diversity of 8 native breeds. The POPGENE, Cervus, and FSTAT were used to generate the observed number of alleles, the effective number of alleles, observed heterozygosity value, expected heterozygosity value, the heterozygote deficit within the breed (FIS), gene flow (Nm), Hardy-Weinberg equilibrium, Polymorphism Information Content (PIC), and UPGMA tree. The principal component analysis (PCA) was performed using adegenet package of R software. Bayesian clustering assignments were analyzed using the STRUCTURE program. This study revealed a very close genetic relationship between seven native chickens and broilers. We also found Arab chickens separated from other Indonesian native chickens and no inbreeding in eight native Indonesian chicken breeds. In conclusion, we found two clusters among eight native Indonesian chicken breeds. Twenty microsatellite markers have a high PIC value in this study.

DNA marker based diversity across rice genotypes and advanced breeding lines bred for temperate regions of North-West India.

Characterization and evaluation of plant genetic resources play an important role for their utilization in the crop improvement programmes. This study involves the agro-morphological and cooking quality besides, molecular characterization of 51 genotypes/advance breeding lines of rice from Kashmir Himalayas. Significant variability was observed for all agro-morphological and cooking quality traits among all the studied genotypes. Cluster analysis using UPGMA method divided the genotypes into two major clusters having 15 and 36 genotypes. Thirty eight genotypes screened using 24 SSR markers detected 48 alleles with 2.0 alleles for each locus with average polymorphism information content (PIC) of 0.37. High polymorphism information content (PIC) values was observed for the primers RM263 (0.67), RM159 (0.59) and RM333 (0.50). Furthermore, out of 38 SSR markers screened on 192 temperate rice germpalsm lines, R4M17 accurately differentiated indica and temperate japonica genotypes amplifying 220bp and 169bp, respectively. Accordingly, 15 genotypes were reported as indica and 28 temperate japonica in addition to 149 genotypes as intermediate types. The information on marker-based diversity and performance based on cooking quality and agronomic traits helped to select the most divergent lines for crossing. Also the analysis was useful to classify the temperate germplasm into indica and temperate japonica. The classification could be helpful to devise a strategy for inter-sub species hybridization to breed for improved rice varieties.

​Cross Genera Marker Transferability and Genetic Diversity Analysis in Elite Cultivars of Mungbean [Vigna radiata (L.) Wilczek]

Backgrounds: To increase the accessibility of molecular markers for germplasm evaluation, genetic analysis and new cultivar development in mung bean, cross genera transferability of microsatellites (SSR) was studied. Methods: Forty simple sequence repeat markers developed for adzuki bean were used to amplify genomic DNA extracted from 70 diverse elite cultivars of greengram. Result: All SSR markers (100%) generated repeatable and clear products, signifying a high genomic homology between two species of Vigna. Among the 40 amplified markers, only 11 (28%) were highly polymorphic in 70 diverse elite cultivars of greengram. The polymorphism information content (PIC) ranged between 0.64 to 0.88 with an average of 0.81, while number of alleles ranged with 6 to 12 with an average of 9.27 alleles per locus. The multiple locus amplification and high PIC values indicated the effectiveness of the transferable SSRs in mungbean. Cluster analysis based on UPGMA grouped the studied genotypes into eleven clusters. The Jaccard’s similarity coefficient ranged from 0.17 to 0.46 indicating the extent of transitional amount of genetic variability within the tested genotypes.

SSR Marker Based Genetic Diversity and Fusarium Wilt Resistance Screening of Tomato (Solanum lycopersicum L.) Genotypes

Fusarium oxysporum is one of the devastating diseases of tomato (Solanum lycopersicum L.) causing high yield losses in fields and commercial greenhouses, inferring necessity for development of disease resistance. An research experiment was laid out with 23 diverse genotypes including susceptible check at research farm during wet season-2018 for screening of tomato genotypes for fusarium wilt resistance. Phenotypic screening of 23 genotypes revealed varied disease resistance as highly resistant (AVTO1219 and EC631), resistant (Pant bahar, EC620428, EC620378, EC631369 and EC620503), moderately resistant (EC615055, EC620389, EC620394, EC620422, EC620406 and AVTO9803) and moderately susceptible (PKM1, EC620382, EC620427 and EC620395) over the highly susceptible checks (Pusa Ruby, Arka Vikas). Employing 95 SSRs for molecular profiling resulted in 33 polymorphic markers, 58 monomorphic markers and remaining 4 markers as unamplified. A total of 74 alleles were detected using 33 polymorphic markers with an average allele number of 2.24 for each marker. Two markers viz., TES60 and TGS633 produced maximum (4) alleles. The polymorphic information content (PIC) value ranged from 0.28 to 0.76 with an average of 0.53 and marker TGS633 was found to be the most suitable marker with the highest PIC value. Cluster analysis through UPGMA method classified twenty three genotypes into five clusters and the coefficient among 23 genotypes was varied from 0.5 to 0.86. Over all, EC631379, EC631369, EC620428, EC620378 and EC620503 were identified as new resistant genetic resources against Fusarium wilt at both phenotypic and genotypic level with the presence of I-2 gene loci. Based on the results, the identified genotypes can be further tested and be used in Marker Assisted Selection or gene pyramiding programs to develop disease resistant commercial cultivars.

Analysis of genetic variability in F2 interspecific hybrids of mung bean (Vigna radiata) using inter-retrotransposon amplified polymorphism marker system

Abstract. Fatmawati Y, Setiawan AB, Purwantoro A, Respatie DW, Teo CH. 2021. Analysis of genetic variability in F2 interspecific hybrids of mung bean (Vigna radiata) using inter-retrotransposon amplified polymorphism marker system. Biodiversitas 22: 4880-4889. Mung bean (Vigna radiata L. Wilczek) categorized as one of the pivotal annual crops of Vigna genera is commonly cultivated in rotation with the cereal crops during the drought season. Conversely, to ameliorate its stunted productivity, the interspecific hybridization technique has been introduced between the mung bean and the common bean to promote genetic improvement with the breeding projects in Indonesia. However, since mung bean is a self-pollinated crop and has a narrow genetic base, the selection and improvement of a specific trait using marker-assisted selection is more challenging. Hence, a precautionary investigation is imperative to evaluate the progenies resulting from interspecific hybridization using an ideal marker. This study aimed to investigate the genetic variability of the F2 population of the interspecific mung bean hybrids using retrotransposon-based markers, particularly Inter-Retrotransposon Amplified Polymorphism (IRAP) markers. In this study, we identified retrotransposon from the mung bean genome and determined the Long Terminal Repeat (LTR) sequence using the LTR Finder. The IRAP primers were designed from a conserved region of the LTR sequence. One hundred of the F2 interspecific hybrids generated from the crossing between mung bean and common bean were successfully discriminated by IRAP markers. The IRAP marker showed high heterozygosity and moderate Polymorphic Information Content (PIC) values. The IRAP markers were able to detect genetic variability in the F2 progenies resulting from the interspecific hybridization. Cluster analysis showed that 100 of the F2 progenies were grouped into three clusters. This study demonstrated that retrotransposon-based markers can offer an effective approach for evaluating the segregation in the F2 population of intercross hybrids in the mung bean.

Genetic diversity of eucalypts for germplasm conservation in Forest Area with the Special Purpose of Mount Bromo, Karanganyar, Indonesia

Abstract. Rahayu, Fatimah, Wiwoho J, Firdaus SU, Pujiyono, Marimin, Arianto DP, Pramono A. 2021. Genetic diversity of eucalypts for germplasm conservation in Forest Area with the Special Purpose of Mount Bromo, Karanganyar, Indonesia. Biodiversitas 22: 4223-4235. As a repository of a gene pool, eucalypts germplasm enriches biodiversity, maintains ecosystem sustainability, and aids in conservation. Therefore, this study aims to analyze the genetic diversity of eucalypts (Corymbia and Eucalyptus) for the development of germplasm conservation in Forest Area with the Special Purpose (KHDTK) Bromo Forest, Karanganyar, Indonesia. In this study, 14 simple sequence repeat (SSR) markers were used to assess the genetic diversity among 20 accessions (Corymbia and 5 Eucalyptus species) from Central and West Java. Subsequently, the genetic parameters were measured and a phylogenetic tree was constructed. The result showed that the SSR markers have high variability, although they belong to different genera. Furthermore, the genetic diversity showed 49 alleles with an average of 3 alleles per locus, while the polymorphism information content (PIC) values were 0.55. There were 4 SSR markers (EMBRA13, EMBRA8, EMCRC11, and EMBRA2) with high PIC value, while the gene diversity (He) of Corymbia and 5 Eucalyptus showed a low level of genetic diversity. The genetic relationship and population structure were divided into genera Corymbia and Eucalyptus. For further application, the eucalypt cultivated in the KHDTK Bromo Forest can contribute as a reference set and 14 SSR markers as a potential marker in combination with morphological characterization to generate a database for germplasm management and conservation.

Association analysis, genetic diversity and population structure of barley (Hordeum vulgare L.) under heat stress conditions using SSR and ISSR markers linked to primary and secondary metabolites.

Barley is one of the major cereal crops, which can provide a significant source of genes for stress tolerance due to its high diversity and adaptability. Metabolite traits are considered to be significant for adaptation of barley to heat stress. In the present study, genetic relationships between 120 barley genotypes were determined with 50 simple sequence repeat (SSR) and 26 inter simple sequence repeat (ISSR) markers under heat stress and non-stress conditions. Moreover, genetic diversity of barley accessions was investigated using the studied markers covering 7 chromosomes of barley. In general, 153 and 85 polymorphic alleles were detected for SSR and ISSR and number of the observed polymorphic allele varied between 2-9 and 2-6, with an average of 3.26 and 3.26 alleles per locus, respectively. Markers of Bmag0223, GBMS180/180, HVM7, ISSR22, ISSR25, and ISSR48 were the most informative due to their high polymorphism information content value demonstrating that putative techniques utilized in this research can be powerful and valuable tools in breeding program of barley. Association analysis was performed between 9 important traits and SSR and ISSR markers using four statistical models. The results revealed that the model containing both population structure (Q) and general similarity in genetic background arising from shared kinship (K) factors reduced false positive associations between markers and phenotypes. According to the results, some of markers related to more than one trait under normal conditions (ISSR31-2, HVM62, and GBMS180/180) and heat stress conditions (ISSR20-5, EBmac635, HVM14, and ISSR37-3) were determined, which can be considered to be the most interesting candidates for further studies and simultaneously will provide a useful target for the future breeding programs, such as marker-assisted selection (MAS).