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

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MUHAMMAD HABIB WIDYAWAN
SRI WULANDARY
TARYONO

Abstract

Abstract. 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.

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References
Basirnia A, Darvishzadeh R, Mandoulkani BA. 2016. Retrotransposon insertional polymorphism in sunflower (Helianthus annuus L.) lines revealed by IRAP and REMAP markers. Plant Biosys. 150: 641-651.
Branco CJS, Vieira EAm Malone G, Kopp MM, Malone E, Bernarndes A, Mistura CC, Carvalho FIF, Oliveira CA. 2007. IRAP and REMAP assessments of genetic similarity in rice. J. Appl. Genet. 48:
Govindaraj M, Vetriventhan M, Srinivasan M. 2015. Importance of genetic diversity assessment in crop plants and its recent advances: an overview of its analytical perspectives. Genet. Res. Int. 2015: 1-14.
Gupta M, Chyi YS, Romero-Severson J, Owen JL. 1994. Amplification of DNA markers from evolutionarily diverse genomes using single primers of simple sequence repeats. Theor. Appl. Genet. 89: 998-1006.
Howley PM, Israel MF, Law M, Martin MA. 1979. A rapid method for detecting and mapping homology between heterologous DNAs. Evaluation of polyomavirus genomes. J. Biol. Chem. 154: 4876-4883.
Kalendar R, Grob T, Regina M, Suoniemi A, Schulman A. 1999. IRAP and REMAP: two retrotransposon-absed DNA fingerprinting techniques. Theor. Appl. Genet. 98: 704-711.
Kalendar R, Shculman AH. 2006. IRAP and REMAP for retrotransposon-based genotyping and fingerprinting. Nat. Prot. 5: 2478-2484.
Korbie DJ, Mattick S. 2008. Touchdown PCR for increased specificity and sensitivity in PCR amplification. Nat. Prot. 3: 1452-1456.
Lee S, Kim N. 2014. Transposable elements and genome size variations in plants. Genomics Inform. 12: 87-97.
Li G, Quiros CF. 2001. Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theor. Appl. Genet. 103: 455-461.
Lorenz TC. 2012. Polymerase chain reaction: basic protocol plus troubleshooting and optimization strategies. J. Vis. Exp. 63: 1-15.
Mandoulakani BA, Piri Y, Darvishzadeh R, Bernoosi I, Jafari M. 2012. Retroelement insertional polymorphism and genetic diversity in Medicago sativa populations revealed by IRAP and REMAP markers. Plant Mol. Biol. Rep. 30: 286-296.
Mandoulakani BA, Sadigh P, Azizi H, Piri Y, Nasri S, Arzahang S. 2015. Comparative assessment of IRAP, REMAP, ISSR, and SSR markers for evaluation of genetic diversity of alfalfa (Medicago sativa L.). J. Agr. Sci. Tech. 17: 999-1010.
Marmur J, Doty P. 1962. Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J. Mol. Biol 5: 109-118.
Murray MG, Thompson WF. 1980. Rapid isolation of high molecular weight DNA. Nuc. Acid. Res. 8: 4321-4325.
Otwe EP, Agyirifo DS, Galyuon IK, Heslop-Harrison JS. 2017. Molecular diversity in some Ghanaian cowpea [Vigna unguiculata L. (Walp)] accessions. Tropical Plant Biol. 10: 57-67.
Rychlik W, Spencer WJ, Rhoads RE. 1990. Optimization of the annealing temperature for DNA amplification in vitro. Nuc. Acids Res. 18: 6409-6412.
SantaLucia J, Allawi HT, Seneviratne PA. 1996. Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 15: 3555-3562.
Sergeant MJ, Constantinidou C, Cogan T, Penn CW, Pallen MJ. 2012. Hight-throughput sequencing of 16s rRNA gene amplicons: effects of extraction procedure, primer length, and annealing temperature. Plos One 7: e38094.
Sheidai M, Riazifar M, Hoordadian A, Alishah O. 2018. Genetic fingerprinting of salt and drought tolerant cotton cultivars (Gossypium hirsutum) by IRAP-REMAP and SRAP molecular marker. Plant Gene 14: 12-19.
Shiokai S, Kitashiba H, Nishio T. 2010. Prediction of the optimum hybridization conditions of dot-blot SNP analysis using estimated melting temperatures of oligonucleotides probes. Plant Cell. Rep. 29: 829-834.
Singh BD, Singh AK. 2015. Marker-assisted plant breeding: principle and practices. Springer, New Delhi.
Taheri MT, Alavi-Kia SS, Mohammadi SA, Vahed MM. 2018. Assessment of genetic diversity and relationships among Triticum urartu and Triticum boeoticum populations from Iran using IRAP and REMAP markers. Genet. Resour. Crop. Evol 65:1867-1878.
Teo CH, Tan SH, Ho CL, Faridah QZ, Othman YR, Heslop-Harrison JS, Kalendar R, Schulman AH. 2005. Genome constitution and classification using retrotransposon-based marker in the orphan crop banana. J. Plant Biol. 48: 96-105.
Todorovska E. 2007. Retrotransposons and their role in plant-genome evolution. Biotechnol. Biotechnol. Eq. 21: 294-305.
Vos P, Hogers R, Bleeker M, Reijans M, Lee T, Hornes M, Friters A, Pot J, Paleman J, Kuiper M, Zabeau. 1995. AFLP: a new technique for DNA fingerprinting. Nuc. Acid Res. 23: 4407-4414.
Williams JG, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV. 1990. DNA polymorphism amplified by arbitrary primers are useful as genetic marker. Nuc. Acids Res. 25:6531-6535.

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