Proofing Direct-Seeded Rice with Better Root Plasticity and Architecture

Abstract

The underground reserve (root) has been an uncharted research territory with its untapped genetic variation yet to be exploited. Identifying ideal traits and breeding new rice varieties with efficient root system architecture (RSA) has great potential to increase resource-use efficiency and grain yield, especially under direct-seeded rice, by adapting to aerobic soil conditions. In this review, we tried to mine the available research information on the direct-seeded rice (DSR) root system to highlight the requirements of different root traits such as root architecture, length, number, density, thickness, diameter, and angle that play a pivotal role in determining the uptake of nutrients and moisture at different stages of plant growth. RSA also faces several stresses, due to excess or deficiency of moisture and nutrients, low or high temperature, or saline conditions. To counteract these hindrances, adaptation in response to stress becomes essential. Candidate genes such as early root growth enhancer PSTOL1, surface rooting QTL qSOR1, deep rooting gene DRO1, and numerous transporters for their respective nutrients and stress-responsive factors have been identified and validated under different circumstances. Identifying the desired QTLs and transporters underlying these traits and then designing an ideal root architecture can help in developing a suitable DSR cultivar and aid in further advancement in this direction.

Keywords: direct-seeded rice; genes; quantitative trait loci; root plasticity; root system architecture.

Figure 1

Major benefits of direct-seeded rice (DSR) system over transplanted rice (TPR) system.

Figure 2

Ideal DSR root system with root-specific traits and genes/QTLs at different stages of growth. The varying growth stages have different requirements of root morphology and associated genes/QTLs depicted in the Figure. (1) The germinating seed requires AG genes for germination: qEUE11.1 and qEVV9.1 for early high seedling vigor and qSOR1 for better surface rooting. (2) From the nutrient perspective, the seedling stage would require OsPT1 and OsPT8 for P uptake, OsZIP genes for Zn uptake, and TOND1 for nitrogen deficiency tolerance, supplemented with PSTOL1 (a root growth enhancer). (3) The vegetative stage needs DRO genes that articulate the roots working in complementation with SOR, OsNRT, and OsAMT genes for nitrogen transport efficiency, expansin genes (such as OsEXP) for growth of root hair and increased root length, and most of the roots are ideally at a 45° angle with each other measured from the base. (4) The reproductive stage needs better anchorage and root spread, higher silicon deposition on culm supplemented with qLDG genes for lodging tolerance, higher nutrient and moisture uptake compensated with more fine roots, new roots and root cap development, high N uptake, and C accumulation. * The genes/QTLs for these attributes are yet to be identified.

Figure 3

A schematic representation of the root growth zone and types of roots illustrated with necessary genes/QTLs for the DSR root system and their interaction with soil nutrients. The right side (A) indicates the essential nutrients and their transporters, and left side (B) indicates the specific root attributed traits along with their regulating genes/QTLs under the DSR system of rice cultivation, and the main center (C) indicates the hormonal regulation in development of different types of roots (CRD: Crown root development; SRD: Surface root development; RHE: Root hair elongation; ADR: Adventitious roots; and T&DR: Thick and deeper roots. Immobile nutrients (surface layer of the soil) Zn, Mn, Fe, and P are acquired by the crown roots, surface roots, and lateral roots. PSTOL1, qSOR1, and DRO1 help in surface root development, whereas WOX, CRL1, and NAL genes and OsARM1,2 stimulate crown root and lateral root growth. These roots proliferate when auxin levels are low in the plant, unlike deep roots that require a higher auxin level. Thick roots are developed with the help of gene STA1 and when the abscisic acid level is high. Besides Zn and Fe transporters, phytosiderophores (root exudates) and YSLs play a role in Zn and Fe uptake. AMF colonizes in the roots, enhancing P uptake by the plant along with the respective transporters. [PS: phytosiderophores; AMF: arbuscular mycorrhizal fungi; OsPT1 and OsPT8: phosphorus transporters; OsZIP1, OsZIP3, OsZIP4, and OsZIP5: zinc transporters; OsIRT1 and OsIRT2: iron transporters; OsAMT: nitrogen (ammonium) transporter; OsNRT: nitrogen (nitrate) transporter; YSL: yellow stripe-like protein; TOND1: tolerance of nitrogen deficiency 1; PSTOL1: phosphorus starvation tolerance 1; qSOR1: soil surface rooting 1; DRO1: deeper rooting 1; WOX: Wuschel-related homeobox gene; CRL1: crown rootless 1; NAL: narrow-leaf; OsARM1,2: armadillo proteins; STA1: stele transversal area 1; AUX: auxin; CTY: cytokinin; ABA: abscisic acid]. Arrows indicate the increasing/decreasing concentration of growth hormones and their involvement in root development.

Figure 4

Depicted diagram of the genomic regions of root system architecture (RSA) traits associated with QTLs and genes in all chromosomes. The left bar numeric values indicate the genomic position (in Mb), and the names of QTLs and genes are on the right side. The blue color represents the important QTLs and genes used in improving RSA traits in DSR conditions, whereas the black color represents the QTLs and genes collected from the comprehensive literature survey on RSA traits under DSR conditions.