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Article|17 May 2022|OPEN
Integrated multi-omics analysis provides insights into genome evolution and phosphorus deficiency adaptation in pigeonpea (Cajanus cajan)
Chun Liu1,2,3 ,† , Yuling Tai4 ,† , Jiajia Luo1 , Yuanhang Wu2 , Xingkun Zhao2 , Rongshu Dong1 , Xipeng Ding1 , Shancen Zhao3 and Lijuan Luo2 , , Pandao Liu1 , Guodao Liu,1 ,
1Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
2College of Forestry & College of Tropical Crops, Hainan University, Haikou 570228, China
3BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen 518120, China
4School of Life Science, Anhui Agricultural University, Hefei 230036, China
*Corresponding author. E-mail:,
Both authors contributed equally to the study.

Horticulture Research 9,
Article number: uhac107 (2022)
Views: 350

Received: 09 Dec 2021
Accepted: 23 Apr 2022
Published online: 17 May 2022


Pigeonpea (Cajanus cajan) is an important legume food crop and plays a crucial role in a secure food supply in many developing countries. Several previous studies have suggested that pigeonpea has great potential for phosphorus (P) deficiency tolerance, but little is known about the underlying mechanism. In this study, the physiological and molecular responses of pigeonpea roots to phosphate (Pi) starvation were investigated through integrating phenotypic, genomic, transcriptomic, metabolomic, and lipidomic analyses. The results showed that low-Pi treatment increased total root length, root surface area, and root acid phosphatase activity, and promoted the secretion of organic acids (e.g. citric acids, piscidic acids, and protocatechuic acids) and the degradation of phospholipids and other P-containing metabolites in the roots of pigeonpea. Consistent with the morphological, physiological, and biochemical changes, a large number of genes involved in these Pi-starvation responses were significantly upregulated in Pi-deficient pigeonpea roots. Among these Pi-starvation response genes upregulated by low-Pi treatment, four gene families were expanded through recent tandem duplication in the pigeonpea genome, namely phosphate transporter 1 (PHT1), phosphoethanolamine/phosphocholine phosphatase (PECP), fasciclin-like arabinogalactan protein (FLA), and glutamate decarboxylase (GAD). These gene families may be associated with Pi uptake from the soil, phospholipid recycling, root morphological remodeling, and regulation of organic acid exudation. Taken together, our results suggest that pigeonpea employs complex Pi-starvation responses to strengthen P acquisition and utilization during low-Pi stress. This study provides new insights into the genome evolution and P deficiency adaptation mechanism of pigeonpea.