Optimization of Annealing Cycle and Temperature SNAP T12 Primer Distinguishing Markers for Male, Female and Hermaphrodite Plants in Papaya (Carica papaya L)

Abstract

Papaya has three types of efflorescense which are male flowers, female flowers, hermaphrodite. That was difficult to determine in advance for the type of flower that appear. The molecular technology approach is an effort to quickly predict the types of flowers that will appear. SNAP primers were designed based on SNP on genomic sequences of male papaya and hermaphrodite DNA. This research aimed to found the specific cycle and annealing temperature for PCR. The research was conducted at the in Indonesia Tropical Fruit Research Institute from January to March 2020. The SNAP primer used was T12, The plants used were papaya varieties of Pomegranate and local cultivar from male and hermaphrodite aged 8 months trees. The results showed that an annealing temperature of 59°C with a cycle of 28 times as effective in producing male DNA amplification on SNAP T2 reverse (R) primers and hermaphrodite DNA amplification plants appeared on alternate SNAP T12 primers (A) with a product size is 430 bp, while female plants did not occur. Amplification according to the SNAPT12 primer.

Morpho-anatomical characterization and DNA barcoding of Achillea millefolium L.

“…Annealing is the most important step in the PCR process, because at this stage an optimum temperature is required so that the DNA band is well amplified and also to facilitate DNA analysis (Nurjayadi et al 2019) and at this stage, the primer is also attached to the DNA strand. In addition to primers and annealing, DNA concentration is also a factor supporting the success of PCR (Noflindawati et al 2021). The sequencing results of the rbcL gene showed 496 bp in replicates 1, 495 bp in replicates 2, and 494 bp in replicates 3.…”

Genetic similarity among Dendrobium species from Indonesia using RAPD markers

“…Setting the annealing temperature is an important step in PCR amplification. According to (Noflindawati et al 2021), the primer attaches to the target DNA sequence at annealing temperature. The calculated temperature refers to the melting temperature value of each primer.…”