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

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 variability and relationship among different accessions of Froriepia subpinata Bail (Gijavash) an endangered medicinal plant from Iran revealed by ISSR and IRAP markers

The genetic variability of Froriepia subpinata Ledeb. Bail., an endangered Iranian endemic species, has been estimated with a total of 52 accessions using 20 markers including ISSR and IRAP. The results showed the polymorphic band produced by primers was 82.3%. The best mean values of genetic diversity parameters observed in ISSRs markers, being UBC873, UBC811, and UBC873 the best primers tested. The similarity range among accessions was 34.45% to 93.3%. The cluster analysis classified the accessions into five main groups that in totally, accessions with similarity in region generally were clustered in the same group. Overall, present study could provide elementary information for formulation of conservation strategies and invaluable elementary genetic information for next breeding or designing conservation programs.

Identification of Sakura interspecific hybrids in Prunus collections

The use of IRAP and ISSR markers for the genetic analysis of Cerasus and Padus samples from the NCFRCHVW collection made it possible to establish the collection genetic structure and identify interspecific hybrids of cherry trees. Clustering of genotyped samples revealed 4 main clusters: 1) Bird cherry; 2) Cherries; 3) Interspecific hybrids of sakura; 4) Sakura. Most of the hybrid forms of sakura and cherries have formed a separate group, which is different from both sour and sweet cherry varieties, and from the classic sakura varieties. Also, some samples were identified that were assigned to groups that were not typical for them. These samples include the genotype of the Sibirskaya krasavitsa bird cherry, AI72 rootstock, Podbelskaya cherry, Polskaya sakura and ornamental cherry Rexii. In general, ISSR and IRAP markers have demonstrated their effectiveness as tools for genetic analysis of Prunus collections and identification of genotypes arising in the course of interspecific hybridization.

Genotypic variability and relationships of Sorghum bicolor accessions from Java Island, Indonesia based on IRAP markers

Martiwi INA, Nugroho LH, Daryono BS, Susandarini R. 2020. Genotypic variability and relationships of Sorghum bicolor accessions from Java Island, Indonesia based on IRAP markers. Biodiversitas 21: 5637-5643. Sorghum (Sorghum bicolor (L.) Moench) is a multifunctional crop with high adaptability to various habitats and thus it is important to assess the genotypic variability of this crop species. This study aimed to reveal the genotypic variability and relationships of sorghum accessions using inter-retrotransposon amplified polymorphism (IRAP) molecular markers. Twenty-three sorghum accessions were collected from smallholder farmers in three provinces of Java Island during the 2019 planting season. The IRAP profiles generated using 10 primer combinations produced 233 scorable bands, with degree of polymorphism 75-96.9%. Cluster analysis using the neighbor-joining (NJ) method showed the formation of three groups corresponds to geographic origin of samples. The NJ dendrogram structure indicated high genotypic variability, and was supported by distribution pattern of accessions on the scatterplot constructed using principal coordinate analysis. The grouping of accessions did not correspond to classification of botanical races. Each group recognized from cluster analysis and principal coordinate analysis consisted of various races namely Bicolor, Guinea, Caudatum, and Kaffir. The fact that each group consisted of various botanical races indicated local adaptation and the maintenance of genotypic identity through farmers’ selection in traditional cultivation practices. It could be concluded, therefore, that geographical proximity and the practice of seed exchange between different regions showed considerable influence on the genotypic relationships of sorghum accessions.

Population differentiation and gene flow in Rrodium cicutarium: A potential medicinal plant

Erodium (Geranaiceae) species are distributed in different habitats of Iran. Some species are of medicinal importance while some are well known weeds. In arid and semi-arid regions, E. cicutarium has had some importance as a forage plant and is an important grazing plant and source of protein supplements to straw for ruminants in semi deserts and wastelands of the Middle East. There is no information on its population genetic structure, genetic diversity, and morphological variability in Iran. Due to the medicinal importance of this species, a genetic variability and populations? structure study is performed studying 15 geographical populations of E. cicutarium Therefore, we used six inter-retrotransposon amplified polymorphism (IRAP) markers and 15 combined IRAP markers to reveal within and among population genetic diversity in this plant. AMOVA test produced significant genetic difference (PhiPT = 0.39, P = 0.010) among the studied populations and also revealed that, 55% of total genetic variability was due to within population diversity while, 45% was due to among population genetic differentiation. Mantel test showed positive significant correlation between genetic distance and geographical distance of the studied populations. Networking, STRUCTURE analyses and population assignment test revealed some degree of gene flow among these populations. PCoA plot of populations based on morphological characters was in agreement with MDS plot of molecular data. These results indicated that geographical populations of E. cicutarium are well differentiated both in genetic content as well as morphological characteristics. Consensus tree based on morphological and genetic data separated some of these populations from the others suggesting the existence of ecotypes within this species.

Search of effective IRAP markers for sakura genotyping

The aim of this study is to find and use effective IRAP markers for DNA genotyping of representatives of sakura species (ornamental cherries). The work demonstrates the results of testing ISSR markers on the genotypes of the species P. serrulata. Also, based on the testing data, the selection of effective IRAP markers was carried out. The selected IRAP markers were used in the genetic analysis of 12 sakura genotypes.

Development and Deployment of High-Throughput Retrotransposon-Based Markers Reveal Genetic Diversity and Population Structure of Asian Bamboo

Bamboo, a non-timber grass species, known for exceptionally fast growth is a commercially viable crop. Long terminal repeat (LTR) retrotransposons, the main class I mobile genetic elements in plant genomes, are highly abundant (46%) in bamboo, contributing to genome diversity. They play significant roles in the regulation of gene expression, chromosome size and structure as well as in genome integrity. Due to their random insertion behavior, interspaces of retrotransposons can vary significantly among bamboo genotypes. Capitalizing this feature, inter-retrotransposon amplified polymorphism (IRAP) is a high-throughput marker system to study the genetic diversity of plant species. To date, there are no transposon based markers reported from the bamboo genome and particularly using IRAP markers on genetic diversity. Phyllostachys genus of Asian bamboo is the largest of the Bambusoideae subfamily, with great economic importance. We report structure-based analysis of bamboo genome for the LTR-retrotransposon superfamilies, Ty3-gypsy and Ty1-copia, which revealed a total of 98,850 retrotransposons with intact LTR sequences at both the ends. Grouped into 64,281 clusters/scaffold using CD-HIT-EST software, only 13 clusters of retroelements were found with more than 30 LTR sequences and with at least one copy having all intact protein domains such as gag and polyprotein. A total of 16 IRAP primers were synthesized, based on the high copy numbers of conserved LTR sequences. A study using these IRAP markers on genetic diversity and population structure of 58 Asian bamboo accessions belonging to the genus Phyllostachys revealed 3340 amplicons with an average of 98% polymorphism. The bamboo accessions were collected from nine different provinces of China, as well as from Italy and America. A three phased approach using hierarchical clustering, principal components and a model based population structure divided the bamboo accessions into four sub-populations, PhSP1, PhSP2, PhSP3 and PhSP4. All the three analyses produced significant sub-population wise consensus. Further, all the sub-populations revealed admixture of alleles. The analysis of molecular variance (AMOVA) among the sub-populations revealed high intra-population genetic variation (75%) than inter-population. The results suggest that Phyllostachys bamboos are not well evolutionarily diversified, although geographic speciation could have occurred at a limited level. This study highlights the usability of IRAP markers in determining the inter-species variability of Asian bamboos.