Genome-Wide Identification and Functional Analysis of the Calcineurin B-like Protein and Calcineurin B-like Protein-Interacting Protein Kinase Gene Families in Turnip (Brassica rapa var. rapa)

Abstract

The calcineurin B-like protein (CBL)–CBL-interacting protein kinase (CIPK) complex has been identified as a primary component in calcium sensors that perceives various stress signals. Turnip (Brassica rapa var. rapa) has been widely cultivated in the Qinghai–Tibet Plateau for a century as a food crop of worldwide economic significance. These CBL–CIPK complexes have been demonstrated to play crucial roles in plant response to various environmental stresses. However, no report is available on the genome-wide characterization of these two gene families in turnip. In the present study, 19 and 51 members of the BrrCBL and BrrCIPK genes, respectively, are first identified in turnip and phylogenetically grouped into three and two distinct clusters, respectively. The expansion of these two gene families is mainly attributable to segmental duplication. Moreover, the differences in expression patterns in quantitative real-time PCR, as well as interaction profiles in the yeast two-hybrid assay, suggest the functional divergence of paralog genes during long-term evolution in turnip. Overexpressing and complement lines in Arabidopsis reveal that BrrCBL9.2 improves, but BrrCBL9.1 does not affect, salt tolerance in Arabidopsis. Thus, the expansion of the BrrCBL and BrrCIPK gene families enables the functional differentiation and evolution of some new gene functions of paralog genes. These paralog genes then play prominent roles in turnip's adaptation to the adverse environment of the Qinghai–Tibet Plateau. Overall, the study results contribute to our understanding of the functions of the CBL–CIPK complex and provide basis for selecting appropriate genes for the in-depth functional studies of BrrCBL–BrrCIPK in turnip.

Genome-Wide Identification and Expression Analysis of the Cation Diffusion Facilitator Gene Family in Turnip Under Diverse Metal Ion Stresses

“…Compared with Arabidopsis , gene family expansion occurred in the BrrMTP gene family. This might be because the polyploidization events occurred in the evolutionary history of Brassica rapa ( Yin et al, 2017 ). These events were followed by chromosomal reduction and rearrangement and numerous gene losses ( Yin et al, 2017 ).…”

BrrICE1.1 is associated with putrescine synthesis through regulation of the arginine decarboxylase gene in freezing tolerance of turnip (Brassica rapa var. rapa)

“…qRT-PCR was conducted in triplicate with different cDNAs synthesized from different treatments using FastStart Universal SYBR Green Master (Rox, Roche, Indianapolis, IN, USA) and a 7500 Sequence Detection System (Applied Biosystems, USA). The reaction parameters for thermal cycling were as follows: 95 °C for 10 min, followed by 40 cycles of 94 °C for 5 s and 60 °C for 15 s. B. rapa tubulin beta-2 chain-like (LOC103873913) was ampli ed as an internal control [25]. The primers used for qRT-PCR are listed in Table S1.…”

BrrICE1.1 is associated with putrescine synthesis through regulation of the arginine decarboxylase gene in freezing tolerance of turnip (Brassica rapa var. rapa)

“…Total RNA extraction, cDNA synthesis and qRT-PCR analysis were performed as described previously [25]. The primers used for qRT-PCR are listed in Table S1.…”

“…A. tumefaciens EHA105 carrying the construct of interest was in ltrated into N. benthamiana leaves. Fluorescence images were obtained as described previously [25]. The primers used are listed in Table S1.…”