Genetic Diversity Analysis in Family Zingiberaceae Accessed by RAPD-PCR and PCR-RFLP

Yap, Lo Shan (2021) Genetic Diversity Analysis in Family Zingiberaceae Accessed by RAPD-PCR and PCR-RFLP. Final Year Project (Bachelor), Tunku Abdul Rahman University College.

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Abstract

Zingiberaceae (ginger) is the largest families of the plant kingdom comprising 53 genera and over 1200 species. It has been used in condiments, food additives, and spice in cuisine for many years. The rhizome has wide spectrum of and medicinal properties such as antitumorigenic, anti-oxidant, anti-inflammatory, and anti-hyperglycemic activities. This herbaceous plant is widely distributed and cultivated in tropical Asia and Africa, especially in Indonesia-Malaysia. However, it is quite challenging to distinguish among ginger cultivators depending on only phenotypic characteristics. Despite its significant importance in therapeutic effect and health benefits, there is limited characterization at genotypic level and lack of availability of appropriate genetic markers. The purpose of this study was to accessed the genetic relationships of 4 genera in this family: Alpinia, Curcuma, Kaempferia, and Zingiber using cross-amplification of rice microsatellite markers as RAPD markers and PCR-RFLP analysis. In RAPD analysis, 8 rice SSR markers yielded 141 bands with 140 (99.5%) polymorphic bands across 14 genotypes; another 36 rice SSR markers yielded 181 bands with 165 (91.2%) polymorphic bands across 12 genotypes. Although the sequence analysis of these bands confirmed that there was no target repeat motif, the amplification of a large number of polymorphic bands provided a basis for genetic diversity analysis. In PCR-RFLP analysis, 10 chloroplast gene regions digested with different restriction enzymes yielded 335 fragments with 285 (85%) were polymorphic across 22 accessions. The gene region trnS-trnfM displayed intrageneric variability in most species and HinfI was the most useful restriction enzyme because it digested all of the gene regions assayed. However, the relative efficiency of different restriction enzymes depends on the gene region and genus investigated. Overall, the present study indicated that the rice microsatellite primers and chloroplast DNA exhibit high degree of polymorphism were useful for depicts the relative diverse genetic profile among genera in the family Zingiberaceae.