Genetic diversity analysis of yardlong bean genotypes (Vigna unguiculata subsp. sesquipedalis) based on IRAP marker

Widyawan MH, Wulandary S, Taryono. 2020. Genetic diversity analysis of yardlong bean genotypes (Vigna unguiculata subsp. sesquipedalis) based on IRAP marker. Biodiversitas 21: 1101-1107. Inter-Retrotransposon Amplified Polymorphism (IRAP) marker is a PCR-based molecular marker that detects polymorphism between retrotransposon sites. This marker has been utilized and successfully assessed genetic diversity in many crop species. Yardlong bean (Vigna unguiculata subsp. sesquipedalis) was an important vegetable legume crop that grown mainly for its fresh pod that rich in nutritional benefits for humans, ultimately dietary fiber and protein. Trends of people awareness to nutritional content of food are increasing, therefore breeding for quality traits is important. Genetic diversity analysis is an important and elementary step in breeding programs in order to determine the breeding strategy. The aims of this research are to perform an optimization of IRAP marker and applied it for genetic diversity analysis in 16 yardlong bean genotypes. Seven primers were used as marker in a pair or single combination and resulted in 11 optimized markers that able to be used for genetic diversity analysis. Sixteen yardlong bean genotypes consisting of commercial cultivars and local genotypes from Indonesia were genotyped using eleven IRAP markers. Marker polymorphism and diversity parameters from each marker i.e. Percentage of Polymorphic Loci (PPL), Expected Heterozygosity (He), Polymorphic Information Content (PIC), Effective Multiplex Ratio (EMR), Marker Index (MI), Discriminating Power (D), and Resolving Power (RP) were calculated. Based on those values, several markers used in this study were considered as informative and efficient in terms of analyzing genetic diversity in yardlong bean. Jaccard's method was used to measure genetic similarity and it is revealed that there is high level of similarity between yardlong bean genotypes used in this study. Thus, it is implied that there is a narrow genetic diversity of yardlong bean genotypes used in this study. Cluster analysis was performed to construct dendrogram based on genetic similarity and classified 16 yardlong genotypes into 4 clusters. Interestingly, majority of the clusters formed were not able to classified genotypes based on their origin. The result of cluster analysis then confirmed by Principal Coordinate Analysis (PCoA) that able to explain 47.76 % of total variation. The results of this study provide a foundation for the genetic diversity analysis based on IRAP marker and genetic improvement in yardlong bean.

Genome Classification of Banana Cultivars Found in Manipur, India using IRAP and RAPD

The genome groups of 34 wild and cultivated banana samples collected from 9 districts of Manipur, India were analyzed using IRAP and RAPD. IRAP-PCR analysis of the banana genome revealed that 32 out of 34 banana samples have shown presence of multiple polymorphic bands in amplified products. There were 5 genome specific bands (2 for B genome and 3 for A genome) in all the samples analyzed by using IRAP marker. Analysis of A and B genome among plant samples using RAPD-PCR generated a total of 1425 polymorphic bands by six primers (OPF-6, OPX-6, OPK-12, RAPD-6, RAPD-14 and RAPD-17). The highest number of bands was generated by OPK12 (318) followed by RAPD6 (308 bands), OPX6 (263 bands), RAPD 17 (215 bands), RAPD 14 (165 bands) and OPF6 (156 bands) respectively. Among these primers, RAPD 14 displayed specific bands per sample thereby showing higher delineating power than other primers.

Genetic Diversity in Ficus Sycomorus L. Species (Moraceae) Using Rapd and Irap Markers

This study was conducted in order to assess accuracy, repeatability and reproducibility of the RAPD and IRAP techniques for determining the genetic variability in 10 Ficus sycomorus L. genotypes grown in the coastal regions of Syria. Thirty-six RAPD primers applied gave 352 discernible loci, of which 252 (71.59%) were polymorphic. Polymerase chain reaction (PCR) amplification with 36 RAPD primers gave an average of 9.778 selected markers/primers, with a maximum of 21 (OPA18) and a minimum of five (OPG11, OPK12 and OPT18). The amplification with 22 IRAP primers (single or combination) generated 178 bands, of which 151 (84.83%) were polymorphic, with an average of 11.125 selected markers/ primer, with a maximum of 17 (IRAP-TDK11F) and a minimum of seven (BREP1F+BREP1R, IRAP-TDK1F+IRAP- TDK1R and IRAP-TDK2F+IRAP-TDK2R). In the present investigation, the IRAP marker was more efficient than the RAPD assay, where the latter exhibited a lower marker index (MI) average (1.629) compared with the IRAP technique (2.941). Otherwise, F. sycomor4 genotype showed the highest dissimilarity compared with other genotypes studied in this investigation. Based upon the estimated percent disagreement values (PDV), we can suggest that there are three subspecies present among the 10 samples tested.