Comprehensive Analysis and Expression Profiling of the OsLAX and OsABCB Auxin Transporter Gene Families in Rice (Oryza sativa) under Phytohormone Stimuli and Abiotic Stresses

Abstract

The plant hormone auxin regulates many aspects of plant growth and developmental processes. Auxin gradient is formed in plant as a result of polar auxin transportation by three types of auxin transporters such as OsLAX, OsPIN, and OsABCB. We report here the analysis of two rice auxin transporter gene families, OsLAX and OsABCB, using bioinformatics tools, publicly accessible microarray data, and quantitative RT-PCR. There are 5 putative OsLAXs and 22 putative OsABCBs in rice genome, which were mapped on 8 chromosomes. The exon-intron structure of OsLAX genes and properties of deduced proteins were relatively conserved within grass family, while that of OsABCB genes varied greatly. Both constitutive and organ/tissue specific expression patterns were observed in OsLAXs and OsABCBs. Analysis of evolutionarily closely related "gene pairs" together with organ/tissue specific expression revealed possible "function gaining" and "function losing" events during rice evolution. Most OsLAX and OsABCB genes were regulated by drought and salt stress, as well as hormonal stimuli [auxin and Abscisic Acid (ABA)], which suggests extensive crosstalk between abiotic stresses and hormone signaling pathways. The existence of large number of auxin and stress related cis-regulatory elements in promoter regions might account for their massive responsiveness of these genes to these environmental stimuli, indicating complexity of regulatory networks involved in various developmental and physiological processes. The comprehensive analysis of OsLAX and OsABCB auxin transporter genes in this study would be helpful for understanding the biological significance of these gene families in hormone signaling and adaptation of rice plants to unfavorable environments.

Keywords: ABA; auxin transport; drought; gene expression; salinity.

Figure 1

Phylogenetic analysis of LAXs (A) and ABCBs (B) auxin transporter protein families from rice, Arabidopsis, sorghum, and maize. The protein sequences of sorghum and maize were retrieved from Phytozome (v10.3) based on recent publications (Shen et al., ; Yue et al., 2015). The phylogenetic trees were constructed using Mega5.2 program (Tamura et al., 2011).

Figure 2

Chromosomal distribution of OsLAXs and OsABCBs. The position of each gene was determined based on the start position of each gene.

Figure 3

Phylogenetic analysis and gene structures of OsLAXs (A) and OsABCBs (B).

Figure 4

Tissue/organ specific gene expression patterns of OsLAXs and OsABCBs. The heat map was constructed using publicly available microarray data of rice (Jain et al., ; Patel et al., 2012). RT, roots; ML, mature leaves; YL, young leaves; SA, shoot apical meristem; YI, young inflorescence; I2–I6, inflorescence from stage 2 to stage 6; S1–S5, developing seed from stage1 to stage5.

Figure 5

Expression profiles of OsLAXs and OsABCBs under drought and salinity stresses. (A) Fold change of OsLAXs and OsABCBs gene expression in shoots and roots under drought and salinity stresses. Data presented here are means of fold changes of qRT-PCR under moderate and severe drought, and salinity stress with biological triplicates and two technical replicates. MDL, moderate drought stressed leaves; MDR, moderate drought stressed roots; SDL, severe drought stressed leaves; SDR, severe drought stressed roots; SL-1h, leaves at 1 h after imposition of salinity stress; SL-5h, leaves at 5 h after imposition of salinity stress; SL-1d, leaves at 1day after imposition of salinity stress; SL-2d, leaves at 2 days after imposition of salinity stress; SR-1h, roots at 1 h after imposition of salinity stress; SR-5h, roots at 5 h after imposition of salinity stress; SR-1d, roots at 1 day after imposition of salinity stress; SR-2d, roots at 2 days after imposition of salinity stress. (B) Venn diagram analysis of data in (A). Summary of OsLAXs and OsABCBs gene expression in shoots and roots under drought and salinity stresses.

Figure 6

Expression profiles of OsLAXs and OsABCBs under IAA and ABA stimuli. (A) Fold change of OsLAXs and OsABCBs gene expression in shoots and roots under auxin and ABA treatments. Data presented here are means of fold changes of qRT-PCR under auxin (10 μM IAA) and ABA (200 μM) treatments with biological triplicates and two technical replicates. IAA-L, IAA treated leaves; IAA-R; IAA treated roots; ABA-L, ABA treated leaves; ABA-R, ABA treated roots. (B) Venn diagram analysis of data in (A). Summary of OsLAXs and OsABCBs gene expression in shoots and roots under auxin and ABA treatments.

Figure 7

Analysis of auxin responsive and stress-related cis-regulatory elements in the 2-kb promoter regions of OsLAXs and OsABCBs.