Genome-Wide Identification and Expression Profiling Analysis of WOX Family Proteins Encoded Genes in Triticeae Plant Species
Abstract Background: Genotype dependence of plant regeneration is an important factor restricting the genetic improvement of Triticeae plant species. The WUSCHEL-related homeobox (WOX) is a group of plant specific transcription factor, which play an important role in plant growth and development, and cell division and differentiation. Recent studies revealed that the application of regeneration-related genes such as WOX and BABY BOOM (BBM) could improve plant regeneration. The application of WOX genes is one of the ways to improve the genetic transformation system of Triticeae and other species, but there are rare studies in this area.Results: From the available genome sequence database, in total 136 WOX transcripts were identified for the Triticeae plants, including 43 in Triticum aestivum, 30 in Triticum turgidum, 25 in Triticum dicoccoides, 17 in Hordeum vulgare, 13 in Aegilops tauschii, and 8 in Triticum urartu. All of the WOX family genes were distributed on the chromosomes of homologous groups 1 to 5 in the six Triticeae species, part of which were confirmed by their specific PCR markers using a set of T. durum-T. aestivum genome D substitution lines. All of the WOX proteins in the six Triticeae species could be grouped into three clades, similar to those in rice (Oryza sativa L.) and Arabidopsis. WOX family members were conserved among these Triticeae plants, all of them contained the conserved HOX DNA-binding homeodomain, and WUS clade members contained the characteristic WUS motif, while only TaWUS and TaWOX9 in all the six Triticeae plant species contained the ERF-associated amphiphilic repression (EAR) motif. The expression profiles of TaWOX genes by quantitative real-time PCR (qPCR) showed obvious difference among WOX family members.Conclusions: Totally 130 WOX genes were identified in the six Triticeae plant species. The WOX family genes were located on the chromosomes in the five homologous groups except groups 6 and 7 in the Triticeae species, and their expression profiles were different in different tissues, indicating that each of them had diverse function. The findings in this study could provide a basis for evolution and functional investigation and practical application of the WOX family genes in Triticeae plant species.