Development of TRAP primers for Ricinus communis L.

Abstract

ABSTRACT. The objective of this article was to develop TRAP (target region amplification polymorphism) primers for castor bean, with the goal of making functional markers available for genetic studies about the species. To do this, oligonucleotides were designed based on ESTs, obtained from the NCBI (National Center for Biotechnology Information) databank, which code enzymes involved in metabolic routes of fatty acid synthesis, ricin synthesis, and resistance to castor bean pathogens. The forward primers were designed with the help of the Primer3 software and, for the reverse, six arbitrary primers were used. To standardize the amplification reactions, the following criteria were used to select the primers: sizes between 18 and 20 bp, guanine/ cytosine (GC) in the range of 40 to 60%, and average annealing temperature between 55° and 62°C. The design quality of the primers was verified using the Net Primer application. Fifty-six primers were designed, which had an average GC percentage of 53.2%. A total of 336 combinations were obtained using the 56 fixed and 6 arbitrary primers. Based on polymerase chain reaction, 330 combinations (89%) presented good amplification patterns for the genomic DNA of castor bean. The size of the fragments amplified varied between 50 and 2072 bp. The TRAP primers designed and validated in this study are the first for castor bean and represent a significant increase in the molecular markers for this species.

Evaluation of the genetic variability of faba bean (Vicia faba L.) genotypes using agronomic traits and molecular markers

“…The greater degree of polymorphism proved the genetic diversity among the 18 genotypes and makes the SRAP marker a perfect system for studying genetic variability among closely related genotypes. The number of amplified loci, for the 330 TRAP combinations of the primers with castor bean genotypes, varied from 2 to15 with an average of 1.22 loci per combination (Simões et al 2017).…”

Research Article Genetic divergence in elite castor bean lineages based on TRAP markers.

“…These markers have also been used to study the following: genetic maps of wheat (Liu et al, 2005), germplasm in spinach (Hu et al, 2007), and sugarcane (Suman et al, 2012); polymorphisms in cassava (Carmo et al, 2015); and the design and optimization of castor bean (Simões et al, 2017). The elite lineages used in this study were obtained from crossing parents (BRS Nordestina, Sipeal, EBDA MPA-17, Mirante, and Paraguaçu) developed by the genetic improvement program at the Núcleo de Melhoramento Genético e Biotecnologia in the Universidade Federal do Recôncavo da Bahia (NBIO-UFRB), in the city of Cruz das Almas, Bahia, Brazil.…”