Genomic screening in dioecious “yerba mate” tree (Ilex paraguariensis A. St. Hill., Aquifoliaceae) through representational difference analysis

Abstract

The "yerba mate" tree, Ilex paraguariensis, is a functionally dioecious crop species with economic relevance in several South American countries. We report a genomic screening accomplished through representational difference analysis (RDA) in male and female I. paraguariensis trees. The aim of the present paper was to investigate the occurrence of sex-related genomic differences in order to develop an early gender detection molecular method that could help reducing energy inputs during the "yerba mate" processing and that could be suitable for breeding programs. An intra-experiment redundancy was detected via SSCP analysis and sequence characterization. Taking together both reciprocal RDA assays, fragments isolated can be discriminated into three main categories. The first category of fragments shows spurious affinities with available deposited sequences and could be considered as specific to I. paraguariensis. The second category comprises sequences identified as organellar or ribosomal plant DNA. Sequences grouped in the third category involve clones akin to conserved domains of retrotransposons (RNaseH, integrases and/or chromodomains) from at least two distinct lineages of Ty3/Gypsy retrotransposons and one from Ty1/Copia retroelements, which in addition are associated to sex determination regions of the Solanaceae, Caricaceae and Salicaceae. A contig sequence was assembled that codes for an integrase core domain and a chromodomain. The phylogenetic analysis of the so-called IPRE (for I. paraguariensis retroelement) integrase domain indicates that it belongs to the Del lineage of the Chromoviridae. This is the first report of mobile elements isolated and detected from the "yerba mate" tree. Although RDA derived fragments, so far tested, have been retrieved from both sexes with similar sequences, association to sex related regions cannot be completely discarded. Implications of present results are further discussed.

Exploring the Genes of Yerba Mate (Ilex paraguariensis A. St.-Hil.) by NGS and De Novo Transcriptome Assembly

“…Several transposable elements (TE) were identified by sequence homology in yerba mate. In the literature, only a few sequences have been recently reported corresponding to yerba mate TE fragments obtained by DNA based methods [14] , [36] , hence this is the first report describing actively yerba mate TEs. As expected for a transcriptional library, most of the sequences corresponded to Retro-Transposon elements, mainly Group Antigen polyprotein (GAG-Pol), reverse-transcriptase and RNAse H domain hits of Gypsy-like and Copia-like retro-elements.…”

“…The identification of transcripts related to sex identity, such as miR156 and SPL gene families, is of special interest in yerba mate. In this diclino-dioecious crop, plants cannot be recognized as male or female prior to their first blooming, which occurs between 3 and 10 years post seedling emergence [14] , delaying considerably the selection of parentals for breeding purposes. So, a cost-effective early sex determination system would be promising for the yerba mate breeding programs.…”

“…However, apart from this trait, very little is known about agronomically important loci on the limited available germplasm of this species. Moreover, yerba mate plants cannot be recognized as male or female prior to their first blooming, which takes 3 to 10 years post seed germination [14] , delaying the selection of parentals for breeding purposes. Likewise, knowledge of sequences of interesting genes is needed to achieve genetic improvement based on molecular tools, a valuable information that is lacking in yerba mate.…”

Phytochemistry and biology of Ilex pharmaceutical resources

“…Representational difference analysis (RDA) was adopted to screen I. paraguariensis genomes (Gottlieb and Poggio, 2010). The occurrence of sex-related genomic differences was studied to develop an early gender detection molecular method that could help reduce energy inputs during the mate tea processing and that could be helpful in…”

Unraveling the genetic complexity of a cultivated breeding population of “yerba mate” (Ilex paraguariensis St. Hil.)

“…Variation in consumer´s preferences at regional and international markets had fostered producer´s renewed interest in developing new varieties (Marx et al 2003, Scherer et al 2006. Notably, current breeding programs had relied purely on phenotypic traits, and although it is well established that genetic characterizations produce more stable and valuable information to implement modern conservation and improvement programs (Picca et al 2004), records on the genetic variation of Argentinean "yerba mate" germplasms are restricted to a small number of individuals (Gottlieb et al 2005, Gottlieb & Poggio 2010 due to a near elimination of natural forests. In contrast, the knowledge on Brazilian genetic resources is centered on the survey of their natural populations (Gauer & Cavalli-Molina 2000, Neuman-Wendt et al 2007, 2009, Pereira et al 2013.…”