Genome-wide identification and transcriptional analyses of MATE transporter genes in root tips of wildCicerspp. under aluminium stress

Abstract

26Chickpea is an economically important legume crop with high nutritional value in human diets. 27 Aluminium-toxicity poses a significant challenge for the yield improvement of this increasingly 28 popular crop in acidic soils. The wild progenitors of chickpea may provide a more diverse gene pool 29 for Al-tolerance in chickpea breeding. However, the genetic basis of Al-tolerance in chickpea and its 30 wild relatives remains largely unknown. Here, we assessed the Al-tolerance of six selected wild 31 Cicer accessions by measuring the root elongation in solution culture under control (0 µM Al 3+ ) and 32 Al-treatment (30 µM Al 3+ ) conditions. Al-treatment significantly reduced the root elongation in all 33 target lines compared to the control condition after 2-day's growth. However, the relative 34 reduction of root elongation in different lines varied greatly: 3 lines still retained significant root 35 growth under Al-treatment, whilst another 2 lines displayed no root growth at all. We performed 36 genome-wide identification of multidrug and toxic compound extrusion (MATE) encoding genes in 37 the Cicer genome. A total of 56 annotated MATE genes were identified, which divided into 4 major 38 phylogeny groups (G1-4). Four homologues to lupin LaMATE (> 50% aa identity; named CaMATE1-39 4) were clustered with previously characterised MATEs related to Al-tolerance in various other 40 plants. qRT-PCR showed that CaMATE2 transcription in root tips was significantly up-regulated 41 upon Al-treatment in all target lines, whilst CaMATE1 was up-regulated in all lines except Bari2_074 42 and Deste_064, which coincided with the lines displaying no root growth under Al-treatment. 43 Transcriptional profiling in five Cicer tissues revealed that CaMATE1 is specifically transcribed in the 44 root tissue, further supporting its role in Al-detoxification in roots. This first identification of MATE-45 encoding genes associated with Al-tolerance in Cicer paves the ways for future functional 46 characterization of MATE genes in Cicer spp., and to facilitate future design of gene-specific 47 markers for Al-tolerant line selection in chickpea breeding programs.48

A Systematic Phylogenomic Classification of the Multidrug and Toxic Compound Extrusion Transporter Gene Family in Plants

“…This is because the number of MATEs we identified for species differs from existing data in some instances, which we believe reflects likely differences in the use of genome assemblies/annotations, selection criteria, and data download sources. For example, our CarMATEs count ( n = 48) is relatively low compared to that reported by Zhang et al (2020) , who identified 56 CarMATEs using the reference genome of the CDC Frontier available in the NCBI database (BioProject: PRJNA190909 ). At the same time, compared with previous studies, we identified comparable numbers of MATEs in the dicot model Arabidopsis ( Arabidopsis thaliana ; n = 57) and the monocot model rice ( Oryza sativa ; n = 55; Huang et al, 2019 ; Qiao et al, 2020 ), which further validates our identification strategy based on the MATE-domain based hmm profile search.…”