Genome evaluation of banana cultivars based on morphological character and Inter-Simple Sequence Repeat (ISSR) molecular marker

Abstract

Abstract. Wahyudi D, Rifliyah K, Uslan. 2020. Genome evaluation of banana cultivars based on morphological character and Inter-Simple Sequence Repeat (ISSR) molecular marker. Biodiversitas 21: 2982-2990. This study aims to evaluate the genome group and to investigate the genetic variability of banana cultivar using morphological character and ISSR molecular marker. Fourteen banana cultivars with genomic group AA, AAA, AAB, ABB, and BB was used. All samples were Identified morphologically based on minimal descriptors for bananas issued by the International Plant Genetic Resources Institute (IPGRI). Total genomic DNA was extracted using DNA Isolation Kit Promega Wizard®. ISSR primer was used in this study, including UBC834, UBC835, UBC843, UBC848, and UBC855. Clustering analysis was used to evaluate genome grouping of the banana cultivar. Clustering analysis of morphological character was performed using the unweighted pair group method with arithmetic mean (UPGMA) algorithm and Bray-Curtis coefficient similarity using Paleontological Statistics (PAST) software. Morphological and ISSR was successfully differentiate banana cultivars and relatively similar to previous genome grouping. However, pisang Triolin (AAB) must be evaluated since it belongs to AAA group. The identification of cultivars and classification of their genome groups based on morphological characteristics and proved by molecular markers will strengthen the establishment of Musa improvement strategy especially in Indonesia and ease the breeder to identify desirable traits of progenitor to be included in the breeding program.

Genetic diversity of eight maize (Zea mays) cultivars from East Nusa Tenggara (Indonesia) based on inter simple sequence repeat markers

“…GelAnalyzer ver.19.1 was used to assess DNA bands based on band migration distances on gels for ISSR molecular markers analysis, and the gels were scored for the presence or absence of bands, resulting in a binary matrix. Jaccard's similarity coefficient was calculated to evaluate genetic distances and tree construction among accessions (Wahyudi et al 2020b). Later, the Unweighted Pair-Group Method Using Arithmetic Average (UPGMA) with MVSP ver.3.1 was used to represent genetic distances and build dendrogram among samples.…”

“…Moreover, Uslan and Pharmawati (2020) noted that DNA extraction method, DNA concentration and purity, primers, and inhibitors such as proteins, phenols, RNA, and other compounds in cells can influence the success of DNA amplification. According to Wahyudi et al (2020b), the absence of DNA bands may potentially be attributable to primers that do not match the template DNA, resulting in insufficient amplification. A difference in a single base pair is sufficient to cause a mismatch in the mold, resulting in ineffective amplification.…”

“…The detection methods of genetic diversity using molecular markers are commonly categorized into three groups: DNA sequence-based (Nikmah et al 2016), hybridization-based, andPCR-based (Wahyudi et al 2020b). Several DNA molecular methods are frequently used to understand genetic characteristics (Govindaraj et al 2015), such as Restriction Fragment Length Polymorphism (RFLP) (Hapsari et al 2015), Random Amplified Polymorphic DNA (RAPD) (Uslan and Pharmawati 2020), Variable Number Tandem Repeats (VNTR) (Hermenegildo et al 2021), and Sequence-Related Amplified Polymorphism (Wahyudi et al 2020b). One of the approaches, Inter Simple Sequence Repeat (ISSR), is thought to be more robust than others and generates more polymorphism bands than RAPD (Das et al 2018;Poerba et al 2018).…”

Short Communication: Genetic polymorphism of registered and popularly cultivated coffee (Coffea spp.) in the Philippines using inter-simple sequence repeats markers

“…Genomic DNA samples were extracted from silicadried coffee leaves using the Dneasy Plant Mini Kit (Qiagen, Germany) according to the manufacturer's protocol. The quality and quantity of the extracted DNA were estimated using lambda (λ) DNA as standard (Grativol et al 2010) in 1% agarose gel (Wahyudi et al 2020).…”

“…In some cases, ISSR markers, which are dominant, generated more polymorphism than when using RAPD and SSR (Lal et al 2014). Inter-simple sequence repeats had been used to evaluate the genome group and genetic variability of some economically important crops (Aguilera et al 2011;Carrasco et al 2012;Esmailnia et al 2015;Raghavendra et al 2016;Wahyudi et al 2020). However, there have been no reports on genetic diversity analysis of coffee using ISSR in the Philippines.…”