Elucidating Quadruplication Event of IPHO1/I Gene: A Key Regulator of Plant Phosphate Translocation in IBrassica rapa/I

• Published in: Horticulturae 2023-07, Vol.9 (7)
• Main Authors: Shahbuddin, Dahlia, Rusly, Rosazlina, Shuid, Ahmad Naqib, Ahmad Khair, Ahmad Bukhary
• Format: Article
• Language: English
• Subjects: Brassica; Environmental aspects; Genetic aspects; Phosphates; Physiological aspects; Plant translocation
• ISSN: 2311-7524; 2311-7524
• DOI: 10.3390/horticulturae9070845

In response to Pi deprivation, phosphate 1 (PHO1) is a significant regulator at trans-eQTL hotspots in Brassica rapa. Brassica rapa short-read sequencing data analysis revealed four PHO1 paralog genes, PHO1_A, PHO1_B, PHO1_C, and PHO1_D, placed in tandem with very high sequence similarity. However, based on short-read genomic sequence data, only three transcripts are accessible. Five bacterial artificial chromosomes (BACs) can be sequenced using a long-read sequencer, which improves de novo assembly and identifies structural variants. The PHO1 gene’s quadruplicating tandem positions in the genomic sequence were confirmed by an analysis of long-read data. Transcript analysis identified only three groups of PHO1 paralogs (ortholog AT1G14040 in Arabidopsis), i.e., PHO1_A, PHO1_B, and PHO1_D, expressed in B. rapa leaf tissues under Pi deficiency. PHO1_A, with transcript ID XM_009150437.2, has five different splice variants found. These splice variants’ truncated proteins demonstrated PHO1_A’s function in P control as opposed to protein encoding.