Breeding Resilience: Exploring Lodging Resistance Mechanisms in Rice

doi:10.1016/j.rsci.2024.08.002

Abstract

Abstract:

Lodging is more than just plants falling over; it incurs significant economic losses for farmers leading to a decrease in both yield and quality of the final produce. Human management practices, such as dense sowing, excessive nitrogen fertilizer applications, inappropriate sowing dates, and upland rice cultivation, exacerbate the risk of lodging in rice. While breeders have developed high-yielding rice varieties utilizing the sd1 gene, relying solely on this gene is insufficient to enhance lodging resistance. Identifying the traits that contribute to lodging resistance is crucial. Key factors include biochemical, anatomical, and morphological traits, such as the levels of lignin, cellulose, hemicellulose, silicon, and potassium, along with the number and area of vascular bundles and the thickness, diameter, and length of the culm. Moreover, markers associated with lodging-related genes, like SCM2, SCM3, SCM4, and prl4, can be utilized effectively in marker-assisted backcrossing to develop rice varieties with desirable culm traits. This literature review aims to aid rice breeders in addressing the issue of lodging by examining traits that influence lodging resistance, developing phenotyping strategies for these traits, identifying suitable instrumentation, exploring methods for screening lodging-resistant plants, understanding the mathematical relationships involved, and considering molecular breeding aspects for pyramiding genes related to lodging.

Key words: rice, lodging resistance, breaking and bending type lodging, culm strength, SCM gene, prl gene, lignin, cellulose

Durga Prasad Mullangie, Kalaimagal Thiyagarajan, Manonmani Swaminathan, Jagadeesan Ramalingam, Sritharan Natarajan, Senthilkumar Govindan. Breeding Resilience: Exploring Lodging Resistance Mechanisms in Rice[J]. Rice Science, 2024, 31(6): 659-672.

Figures/Tables 5

Table 1. Phenotyping for biochemical estimation.

Biochemical	Staining	Wet estimation technique	Reference
Non-reducing sugars	Iodine staining	Anthrone test-glucose	de Bruyn et al, 1968
Pectin	Ruthenium red staining; 0.02% unesterified pectin; de-esterified with 0.1 mol/L Na₂CO₃ overnight at 4^ofollowed by staining	Carbazole method (galacturonic is standard); FTIR; HPLC	Hou et al, 1999; Kyriakidis and Psoma, 2001
Suberin	Sudan red staining	Vapor osmometry; FTIR	Lopes et al, 2000; Rao, 2011
Lignin	Weisner staining (Phloroglucinol staining); Toluidine staining	Karlson lignin; thioglycolic acid; acetyl bromide; DFRC, FTIR, HPLC, AIL, and ASL	Sjöberg et al, 2004; Liljegren, 2010; Pradhan Mitra and Loqué, 2014; Dampanaboina et al, 2021a
Silicon	Digestion with octyl-alcohol, H₂O₂, and NaOH, and determination by ICP-OES; FTIR		Kraska and Breitenbeck, 2010
Potassium	Digestion with H₂O₂ and H₂SO₄ followed by measured through plasma spectrometer		Yue et al, 2023
Cellulose	Calcofluor staining by the use of fluorescent microscope	Updergraff’s method; modified Updergraff’s method; FTIR	Bauer and Ibáñez, 2014; Wu et al, 2017; Dampanaboina et al, 2021b

Fig. 1. Mechanics of lodging resistance in rice. A, Section modulus (a1 and b1, the major and minor outer diameters; a2 and b2, the major and minor inner diameters). B, Universal Testing Machine (UTM), used to measure bending stress or load and deflection. C, Plant lodging tester, not as bulky as the UTM used to measure bending stress or load and deflection and elastic modulus. D and E, Deflection of a weak culm is more (D), but a stiff culm is less (E). F and G, Bending moment at breaking (BMB) with leaf sheath (MWLS, F) and without leaf sheath (MWOLS, G) used to measure degree of leaf sheath reinforcement (DLSR) to evaluate the contribution of leaf sheath for lodging resistance. H, Understanding bending-type lodging, less plant height leads to reduced lodging index. I, Prostrate tester utilized to measure bending resistance of the canopy (Pushing resistance reading/tiller number per plant) and culm strength. Δσ, Change in stress; Δε, Change in strain; YM, Young modulus; FL, Load × fulcrum distance; FR, Flexural rigidity; SM, Section modulus; τ, Torque; F, Force; r, Distance from the pivot point; θ, The angle between the force and the lever arm; LI, Lodging index; PH, Plant height; FW, Fresh weight of culm; BS, Bending stress; CS, Culm strength; PR, Pushing resistance; PRL, Pushing resistance of lower internode; TN, Tiller number. The rice image is generated using Meta AI (Llama 3.1).

Fig. 2. Comparisons for understanding lodging resistance. A, High section modulus, i.e., less area in the medullary region/lacuna, generally leads to lodging resistance, while low section modulus, i.e., more area in the medullary region, leads to lodging susceptibility. B, Dark pink phloroglucinol stain suggests the presence of more lignin, while light stain signifies the presence of less lignin. C, Powdered X-ray diffraction (XRD) is used to determine cellulose crystallinity. A sharp peak at 22.5º indicates highly crystalline cellulose. Peaks at 22.5º and 18.0º on the X axis are checked for a rough estimation of cellulose crystallinity (sengal method). D, Genotype with high bending stress is observed withstand a load of 18.6 N before breaking, and the genotype with comparatively lower bending stress is observed withstand a load of 6.2 N load before breaking (y-axis, Load; x-axis, Time in seconds).

Table 2. Genes associated with lodging resistance.

Gene	Chr.	Marker	Mapping population	Remark	Reference
qCD1.1, qCS1.1	1	Id10019973-Id1006772	Swarna × Moroberekan^♂ (BIL)	Lead to an increase in culm diameter and culm strength	Yadav et al, 2017
qLR1, qLR8	1	BIN1-161-BIN1-162 BIN8-32-BIN8-33	93-11 × O. longistaminata^♂ (BIL)	An increase in CD and breaking strength pleiotropic effect qLR1 and qLR8 is seen for lodging resistance	Long et al, 2020
OsCYPq1	1	RM12285-RM212	Cheongcheong^♂ × Nagdong (DH)	The candidate gene identified controls basal internode length and mutations in it led to reduced internode elongation and also showed pleiotropic effect by increasing yield	Zhao et al, 2021
Gnla	1	N321-RM10316	R498^♂ × R3551 (RIL and CSSL)	Increase in CD and crown root development hence can also deal with root lodging	Tu et al, 2022
SCM1	1	RM562-RM5	Habataki^♂ × Sasanishiki (CSSL)	Increases culm wall thickness	Yang et al, 2023
qSCM4	2	SSR1-RM5511	LTH^♂ × Shennong265 (F₂ and RIL)	Increase in CWT, CD, and culm folding resistance	Yang et al, 2023
SCM3	3	RM15761-RM15782 SNPV318_03-RM15767	Koshihikari × Chugoku 117^♂ (BIL)	Improves CD, SM, and BMB	Yano et al, 2015
prl4	4	RM5749	Nona Bokra^♂ × Koshihikari (CSSL)	Pushing resistance, and accumulates NSC in basal culm	Kashiwagi, 2022
prl5	5	C1081	Nipponbare × Kasalath^♂ (NIL)	Delays leaf senescence, PR, NSC content, starch reaccumulation, and high YM	Kashiwagi et al, 2006
SCM2	6	RM20546-RM20562	Sasanishiki × Habataki^♂ (CSSL and NIL)	Increases CWT and affects yield because it increases the number of spikelets per panicle	Ookawa et al, 2010a
qTyM6, qTyH6	6	RM3343-20318	Cheongcheong^♂ × Nagdong (DH)	Resistance reported in Typhoons, as it reduces plant height and lowers plant thrust resistance	Zhao et al, 2023
sdm8	8	C10122	Kasalath^♂ × Nipponbare (CSSL)	Increases in CD, CWT, culm stiffness, and heavy lower part of the plant	Kashiwagi et al, 2008
BSUC11	11	G44 and G257	Kasalath^♂ × Koshihikari (CSSL)	Increases content of holocellulose in upper culm; thickening of cortical fiber tissue in internode 1	Kashiwagi et al, 2016

Table 2. Genes associated with lodging resistance.

Gene	Chr.	Marker	Mapping population	Remark	Reference
qCD1.1, qCS1.1	1	Id10019973-Id1006772	Swarna × Moroberekan^♂ (BIL)	Lead to an increase in culm diameter and culm strength	Yadav et al, 2017
qLR1, qLR8	1	BIN1-161-BIN1-162 BIN8-32-BIN8-33	93-11 × O. longistaminata^♂ (BIL)	An increase in CD and breaking strength pleiotropic effect qLR1 and qLR8 is seen for lodging resistance	Long et al, 2020
OsCYPq1	1	RM12285-RM212	Cheongcheong^♂ × Nagdong (DH)	The candidate gene identified controls basal internode length and mutations in it led to reduced internode elongation and also showed pleiotropic effect by increasing yield	Zhao et al, 2021
Gnla	1	N321-RM10316	R498^♂ × R3551 (RIL and CSSL)	Increase in CD and crown root development hence can also deal with root lodging	Tu et al, 2022
SCM1	1	RM562-RM5	Habataki^♂ × Sasanishiki (CSSL)	Increases culm wall thickness	Yang et al, 2023
qSCM4	2	SSR1-RM5511	LTH^♂ × Shennong265 (F₂ and RIL)	Increase in CWT, CD, and culm folding resistance	Yang et al, 2023
SCM3	3	RM15761-RM15782 SNPV318_03-RM15767	Koshihikari × Chugoku 117^♂ (BIL)	Improves CD, SM, and BMB	Yano et al, 2015
prl4	4	RM5749	Nona Bokra^♂ × Koshihikari (CSSL)	Pushing resistance, and accumulates NSC in basal culm	Kashiwagi, 2022
prl5	5	C1081	Nipponbare × Kasalath^♂ (NIL)	Delays leaf senescence, PR, NSC content, starch reaccumulation, and high YM	Kashiwagi et al, 2006
SCM2	6	RM20546-RM20562	Sasanishiki × Habataki^♂ (CSSL and NIL)	Increases CWT and affects yield because it increases the number of spikelets per panicle	Ookawa et al, 2010a
qTyM6, qTyH6	6	RM3343-20318	Cheongcheong^♂ × Nagdong (DH)	Resistance reported in Typhoons, as it reduces plant height and lowers plant thrust resistance	Zhao et al, 2023
sdm8	8	C10122	Kasalath^♂ × Nipponbare (CSSL)	Increases in CD, CWT, culm stiffness, and heavy lower part of the plant	Kashiwagi et al, 2008
BSUC11	11	G44 and G257	Kasalath^♂ × Koshihikari (CSSL)	Increases content of holocellulose in upper culm; thickening of cortical fiber tissue in internode 1	Kashiwagi et al, 2016

Fig. 3. Pleiotropic action of SCM3, SCM2 and depiction of other genes involved in lodging resistance. Gn1a is expressed in culm, roots, inflorescence meristem, and leaves (grey dots). The null allele gn1a in the roots leads to well-developed crown roots, and this allele leads to an increase in grain number. The Gn1a allele SCM1 increases culm diameter and strength. The allele of APO1 (SCM2) increases spikelet number and culm diameter (blue dots). SCM3 decreases tiller number but increases spikelet number (pink dots). The prl4 allele leads to an increase in the bending resistance of the lower internode. GA-inactive (#), GA-active (*), and GA-inactive GA (##) [conversions from active gibberellic acid (GA) to inactive GA alleles SD1 (GA20 oxidase) and SBI (GA2 oxidase)] lead to a reduction in GA levels, leading to dwarfism, prl5 is a gene associated with late senescence, and the orange boxes represent genes involved in lignin and cellulose biosynthesis.The rice image is generated using Meta AI (Llama 3.1).

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