Association between root growth angle and root length density of a near-isogenic line of IR64 rice with DEEPER ROOTING 1 under different levels of soil compaction

Figures & data

Figure 1. Diagrams of (a) the size and geometry of the baskets used in the root basket method for counting root numbers from 0° to 45° (shallow angles) and 45° to 90° (deep angles); (b) a seedling raised in a nursery cell tray and transplanted into a basket in the field at one of the three soil compaction levels (no compaction, moderate compaction, and hard compaction); and (c) placement of the basket and the position of the corers used to obtain samples at depths of 0 to 30 cm and 30 to 60 cm.

Figure 2. Daily minimum and maximum air temperatures (°C) in the (a) 2013 and (b) 2014 experiments, and daily rainfall (mm) and daily cumulative solar radiation (MJ m⁻²) in the (c) 2013 and (d) 2014 experiments.

Figure 3. Profile of soil strength (resistance to penetration) in the three soil compaction treatments on (a) 30 May (33 DAS), (b) 21 August (116 DAS), and (c) 7 October (163 DAS) 2014. Bars indicate standard error.

Figure 4. Time course of soil-water potential in no compaction (NC), moderate compaction (MC) and hard compaction (HC) treatments from 26 June to 6 October 2014.

Figure 5. Profile of root length density (RLD) at a depth from 30 to 60 cm for the three genotypes (IR64, Dro1-NIL, and Kinandang Patong [KP]) on 19 October (126 DAS) 2013. IR64 and Dro1-NIL were significantly different (t-test, n = 3, p < .05); KP could not be compared with the other genotypes because it was not replicated. Values are mean ± standard deviation.

Table 1. Total numbers of roots in the two growth angle categories (0° to 45° and 45° to 90° from the horizontal) and proportions of the total in these categories for IR64, Dro1-NIL, and Kinandang Patong on 19 September (140 DAS) (2013 (mean ± standard error). We calculated the least-significant difference at p < .05 (LSD_.05).

Genotype	Stem number	Total number of roots	Number of roots with a shallow angle (0°–45°)	Number of roots with a deep angle (45°–90°)	Proportion of roots with a shallow root angle (0°–45°)	Proportion of roots with a deep root angle (45°–90°)
IR64	30 ± 2.93 b	189 ± 43.31 a	165 ± 40.44 a	24 ± 3.90 a	.87 ± .03 c	.13 ± .03 a
Dro1-NIL	34 ± 3.01 b	225 ± 9.23 a	147 ± 4.31 a	79 ± 7.77 b	.65 ± .02 b	.35 ± .02 b
Kinandang Patong	8 ± 2.17 a	129 ± 12.15 a	61 ± 7.13 a	67 ± 9.15 b	.48 ± .04 a	.52 ± .04 c
Average	24	181	124	57	.66	.34
CV	.53	.35	.51	.49	.26	.51
LSD.05	8.6***	88.6*	86.7*	25.4**	.12**	.12**

Notes: Values labeled with different letters differ significantly among genotypes (p < .05, Tukey’s LSD test).

* p < .05

** p < .01

*** p < .001.

Table 2. Root numbers and proportions of the total for the two growth angle categories (0° to 45° for shallow angles, 45° to 90 for deep angles) for IR64, Dro1-NIL, and Kinandang Patong in the three compaction treatments: no compaction, moderate compaction, and hard compaction (mean ± standard error). We calculated the least-significant difference at p < .05 (LSD_.05). (a) 23 July 2014 (around maximum tillering).

Treatment	Genotype	Number of stems	Total number of roots	Number of roots with a shallow angle (0°–45°)			Number of roots with a deep angle (45°–90°)	Proportion of roots with a shallow root angle (0°–45°)	Proportion of roots with a deep root angle (45°–90°)
No compaction	IR64	24 ± 2.19 b	126 ± 12.50 a	111 ± 8.84 b			15 ± 7.22 a	.88 ± .05 b	.12 ± .05 a
	Dro1-NIL	23 ± .49 b	157 ± 18.52 a	103 ± 10.6 b			54 ± 13.00 a	.66 ± .05 a	.34 ± .05 b
	Kinandang Patong	5 ± .67 a	97 ± 11.89 a	46 ± 3.53 a			50 ± 8.41 a	.48 ± .02 a	.52 ± .02 b
	CV	.56	.27	.38			.60	.27	.58
Moderate compaction	IR64	29 ± 1.76 b	188 ± 28.11 a	160 ± 24.26 a			28 ± 6.35 a	.85 ± .03 c	.15 ± .03 a
	Dro1-NIL	36 ± .88 c	195 ± 34.28 a	143 ± 29.31 a			52 ± 4.98 ab	0.73 ± 0.02 b	.27 ± .02 b
	Kinandang Patong	9 ± .67 a	162 ± 7.17 a	81 ± 2.91 a			80 ± 7.31 b	.50 ± .03 a	.50 ± .03 c
	CV	.49	.23	.38			.46	.23	.51
Hard compaction	IR64	30 ± 1.45 b	216 ± 17.34 a	194 ± 13.42 a			21 ± 5.24 a	.90 ± .02 b	.10 ± .02 a
	Dro1-NIL	37 ± 3.21 b	198 ± 26.69 a	169 ± 21.53 a			29 ± 5.17 a	.85 ± .01 b	.15 ± .01 a
	Kinandang Patong	10 ± 2.33 a	203 ± 31.63 a	133 ± 32.42 a			70 ± 6.23 b	.64 ± .06 a	.36 ± .06 b
	CV	.50	.19	.27			.60	.16	.65
Average of genotypes
	IR64	27 B	177 A		155 B		21 A	.88 C	.12 A
	Dro1-NIL	32 C	183 A		138 B		45 B	.75 B	.25 B
	Kinandang Patong	8 A	154 A		87 A		67 C	.54 A	.46 C
Average of treatments
No compaction		17 X	127 X		87 X		40 X	.68 X	.32 Y
Moderate compaction		25 Y	182 XY		128 XY		53 Y	.69 X	.31 Y
Hard compaction		25 Y	205 Y		165 Y		40 XY	.80 Y	.20 X
LSD test
LSD.05 for genotype (G)		3.65***	45.02 ns		37.25**		14.33***	.06***	.06***
LSD.05 for treatment (T)		3.02***	45.12***		36.87***		10.53*	.06***	.06***
LSD.05 for G × T		5.54 ns	70.89 ns		58.49 ns		21.4*	.10 ns	.10 ns
Analysis of variance for IR64 versus Dro1-NIL (excluding Kinandang Patong)
P for genotype (G)		*	ns		ns		**	***	***
P for treatment (T)		**	*		*		ns	*	*
P for G × T		ns	ns		ns		ns	*	*
(b) 6 October 2014 (around maturity)
No compaction	IR64	45 ± 3.71 b	250 ± 35.27 a	205 ± 37.95 a		44 ± 3.51 a		.82 ± .04 a	.18 ± .04 a
	Dro1-NIL	46 ± 10.40 b	272 ± 29.06 a	179 ± 34.82 a		93 ± 14.50 b		.66 ± .08 a	.34 ± .08 a
	Kinandang Patong	13 ± 1.76 a	322 ± 14.19 a	166 ± 17.46 a		156 ± 5.77 c		.51 ± .03 a	.49 ± .03 a
	CV	.54	.19	.27		.52		.23	.45
Moderate compaction	IR64	42 ± 3.21 b	190 ± 31.18 a	163 ± 27.14 b		26 ± 4.10 a		.86 ± .00 b	.14 ± .00 a
	Dro1-NIL	66 ± 7.22 c	271 ± 20.81 b	179 ± 10.04 b		92 ± 21.67 b		.66 ± .05 b	.34 ± .05 a
	Kinandang Patong	16 ± 1.15 a	202 ± 4.06 a	81 ± 6.69 a		121 ± 3.79 b		.40 ± .03 a	.60 ± .03 b
	CV	.55	.23	.37		.58		.32	.58
Hard compaction	IR64	64 ± 3.51 b	252 ± 31.13 a	203 ± 27.84 a		48 ± 3.38 a		.81 ± .01 b	.19 ± .01 a
	Dro1-NIL	53 ± 8.09 b	202 ± 37.90 a	149 ± 31.56 a		53 ± 6.74 a		.74 ± .02 b	.26 ± .02 a
	Kinandang Patong	18 ± 2.31 a	240 ± 29.21 a	110 ± 7.64 a		130 ± 22.36 b		.46 ± .03 a	.54 ± .03 b
	CV	.49	.24	.36		.58		.24	.48
Average of genotypes
	IR64	50 B	230 A	191 B		40 A		.83 C	.17 A
	Dro1-NIL	55 B	248 A	169 AB		79 B		.68 B	.32 B
	Kinandang Patong	16 A	255 A	119 A		136 C		.46 A	.54 C
Average of treatments
No compaction		35 X	281 X	183 X		98 X		.66 X	.34 X
Moderate compaction		41 X	221 X	141 X		80 X		.64 X	.36 X
Hard compaction		45 X	231 X	154 X		77 X		.67 X	.33 X
LSD test
LSD.05 for genotype (G)		8.92***	48.22 ns	48.5*		19.95***		.08***	.08***
LSD.05 for treatment (T)		11.89 ns	79.54 ns	49.86 ns		36.82 ns		.06 ns	.06 ns
LSD.05 for G × T		15.33*	91.63 ns	76.83 ns		4.49 ns		.12 ns	.12 ns
Analysis of variance for IR64 versus Dro1-NIL (excluding Kinandang Patong)
Significance for genotype (G)		ns	ns	ns		**		**	**
Significance for treatment (T)		ns	ns	ns		ns		ns	ns
Significance for G × T		*	ns	ns		*		ns	ns

Notes: Values labeled with different lower-case letters differ significantly within a treatment (p < .05, Tukey’s LSD test); values labeled with different capital letters differ significantly among genotypes and treatments in the combined analysis. Analysis of variance was also conducted separately for IR64 and Dro1-NIL to assess the effects of DRO1 and its interaction with the compaction treatment.

* p < .05

** p < .01

*** p < .001; ns, not significant.

Figure 6. Comparison of the root length density (RLD) at a depth from 30 to 60 cm among the three genotypes (IR64, Dro1-NIL, and Kinandang Patong [KP]) in the three soil compaction treatments: no compaction, moderate compaction, and hard compaction. Data were obtained on 2 September (128 DAS) 2014. Values are mean ± standard deviation (n = 3). For a given compaction treatment, bars labeled with the same letter differ significantly (p < .05, Tukey’s LSD test.

Figure 7. (a) Relationships between the number of roots around maximum tillering and at maturity for roots with shallow (s) and deep (d) angles in the no compaction (NC), moderate compaction (MC), and hard compaction (HC) treatments. (b) Relationship between proportion of roots with a deep angle around maximum tillering and root length density (RLD) at a depth of 30 to 60 cm. (c) Relationship between the proportion of roots with a deep angle around maximum tillering and the proportion of total RLD at a depth of 30 to 60 cm. Values are for both 2013 and 2014, for all three rice genotypes (IR64, Dro1-NIL, and Kinandang Patong [KP]) across the three compaction levels in 2014 and in the no compaction treatment in 2013. Only statistically significant linear regression lines are shown. **p < .01; ns, not significant; n = 12.

Table 3. Values of Pearson’s correlation coefficient (r) for the relationships between root length density (RLD) measured by core sampling and root number and angle measured in 2014 by the basket method around (a) maximum tillering and (b) maturity.

	Total RLD from 0 to 60 cm	RLD from 0 to 30 cm	RLD from 30 to 60 cm	Proportion of total RLD from 30 to 60 cm
(a) Basket measurement around maximum tillering
Total number of roots	.514 ns	.587 ns	−.166 ns	−.423 ns
No. of roots with a shallow angle (0°–45°)	.324 ns	.459 ns	−.573 ns	−.800**
No. of roots with a deep angle (45°–90°)	.235 ns	.086 ns	.887**	.905**
Proportion of roots with a deep root angle (45°–90°)	−.004 ns	−.161 ns	.829**	.972**
(b) Basket measurement around maturity
Total number of roots	.042 ns	−.007 ns	.282 ns	.321 ns
No. of roots with a shallow angle (0°–45°)	−.025 ns	.077 ns	−.550 ns	−.627*
No. of roots with a deep angle (45°–90°)	.063 ns	−.078 ns	.773*	.881**
Proportion of roots with a deep root angle (45°–90°)	.064 ns	−.081 ns	.792*	.891**

* p < .05

** p < .01

ns: not significant.

Table 4. Summary of previous studies of rice root growth angles.

Citation	Genetic material used	Definition of root growth angle	Soil or growth medium	Growth stage	Range of proportions of roots with a deep angle	Major findings about treatment effects
Kato et al. (2006)	12 cultivars (upland and lowland cultivars)	>50° plastic hemispherical steel basket with 13- and 5-cm open top and bottom diam. and 7-cm depth in 2004, versus 22, 8, and 5 cm, respectively, in 2005	Irrigated upland field	Seedling to tillering stages (30 to 60 DAS)	6–31%	Cultivar variation in root growth angle was identified in upland field
Norton and Price (2009)	134 lines (F6 recombinant inbred lines [RILs]) for Azucena and Bala	Degree of bending of the growing seminal root when rotated by 90° in a Perspex case (25 cm × 20 cm × 1 cm)	Hydroponics	Seedling stage (9 DAS)	9–19%	QTLs for a response of seminal roots to gravity were identified, all co-located with known root-growth QTLs
					(degree of bending)
Uga et al. (2009)	59 rice accessions (lines)	>50° plastic hemispherical basket with 15- and 8.5-cm open top and bottom diam. and 6-cm depth	Rainfed upland field	Tillering stage (49 DAS)	10–64%	59 accessions were divided into japonica, indica-I, and indica-II’ the proportion of roots with a deep angle was largest in indica-I and least in indica-II
Uga et al. (2011)	117 F6 RILs of IR64 and Kinandang Patong (KP)	>50° stainless-steel mesh hemispherical basket with a 7.5-cm open top diam. and 5-cm depth	Well watered soil in a greenhouse	Seedling stage (39 DAS)	12% IR64	QTL Dro1 (Deeper rooting 1) for the proportion of roots with a deep growth angle was mapped between markers RM24393 and RM7424 on chromosome 9, and explained 66.6% of total phenotypic variance
					78% Dro1-NIL
					93% KP
Uga et al. (2012)	124 F6 RILs of Gemdjah Beton and Sasanishiki	Proportion of surface roots in a small cylindrical cup with a diam. of 3.7 cm and a depth of 4 cm, and the angle between the soil surface and the shallowest root	Soil flooded to a depth of 2 cm (saturated) in a greenhouse	seedling stage (18 DAS)	0–56%	QTL for SOIL SURFACE ROOTING 1 (qSOR1) was identified between markers RM21941 and RM21976 on chromosome 7, and explained 32.5% to 53.6% of total phenotypic variance
					(proportion of surface rooting)
Uga et al. (2013a)	BC4F4 Dro1-near-isogenic lines	≥50° stainless-steel mesh hemispherical basket with a 7.5-cm open top diam. and 5-cm depth	Well watered soil in a greenhouse	Seedling stage (35 to 42 DAS)	13% IR64	DEEPER ROOTING 1 (DRO1) was cloned. DRO1 is negatively regulated by auxin and is involved in cell elongation in the root tip to cause responses to gravity. Higher expression of DRO1 increased the root growth angle and increased growth in a more downward direction. The introduction of DRO1 improved yield under droughted upland conditions
					60% Dro1-NIL
Uga et al. (2013b)	3 mapping popul-ations from Kinandang Patong crossed with ARC5955, Pinulupot1, and Tupa729	>50° stainless-steel mesh hemispherical basket with a 7.5-cm open top diam. and 5-cm depth	Well watered soil in a greenhouse	Seedling stage (39 DAS)	16–27% ARC5955, Pinulupot1, Tupa729	A new QTL for root growth angle (DRO2) was identified on chromosome 4
					80% KP
Uga et al. (2015)	26 Chromosome segment substitution lines (CSSLs) from IR64 and Kinandang Patong (KP)	>50° stainless-steel mesh hemispherical basket with a 7.5-cm open top diam. and 5-cm depth	Well watered soil in a greenhouse	Seedling stage (35 to 42 DAS)	8% IR64	A new QTL for root growth angle (DRO3) was identified on chromosome 7, and was involved in the DRO1 genetic pathway
					53% Dro1-NIL
					74% KP
Kitomi et al. (2015)	3 mapping populations from Kinandang Patong crossed with Momiroman, Yumeaoba, and Tachisugata, all with the functional allele of DRO1	>50° and >70° stainless-steel mesh hemispherical basket with a 7.5-cm open top diam. and 5-cm depth	Well watered soil in a greenhouse	Seedling stage (42 DAS)	33–97% (>50°)	New QTLs for root growth angle DRO4, DRO5 were identified on chromosomes 4, 2, and 6 (respectively) from three mapping populations deriving from Kinandang Patong
					2–56% (>70°)

Kato, Y., Abe, J., Kamoshita, A., & Yamagishi, J. (2006). Genotypic variation in root growth angle in rice (Oryza sativa L.) and its association with deep root development in upland fields with different water regimes. Plant Soil, 287, 117–129.10.1007/s11104-006-9008-4

 Web of Science ®Google Scholar

Norton, G. J., & Price, A. H. (2009). Mapping of quantitative trait loci for seminal root morphology and gravitropic response in rice. Euphytica, 166, 229–237.10.1007/s10681-008-9833-z

 Web of Science ®Google Scholar

Uga, Y., Ebana, K., Abe, J., Morita, S., Okuno, K., & Yano, M. (2009). Variation in root morphology and anatomy among accessions of cultivated rice (Oryza sativa L.) with different genetic backgrounds. Breeding Science, 59, 87–93.10.1270/jsbbs.59.87

 Web of Science ®Google Scholar

Uga, Y., Okuno, K., & Yano, M. (2011). Dro1, a major QTL involved in deep rooting of rice under upland field conditions. Journal of Experimental Botany, 62, 2485–2494.10.1093/jxb/erq429

 PubMed Web of Science ®Google Scholar

Uga, Y., Hanzawa, E., Nagai, S., Sasaki, K., Yano, M., & Sato, T. (2012). Identification of qSOR1, a major rice QTL involved in soil-surface rooting in paddy fields. Theoretical Applied Genetics, 124, 75–86.10.1007/s00122-011-1688-3

 PubMed Web of Science ®Google Scholar

Uga, Y., Sugimoto, K., Ogawa, S., Rane, J., Ishitani, M., Hara, N., … Yano, M. (2013a). Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions. Nature Genetics, 45, 1097–1102.10.1038/ng.2725

 PubMed Web of Science ®Google Scholar

Uga, Y., Yamamoto, E., Kanno, N., Kawai, S., Mizubayashi, T., & Fukuoka, S. (2013b). A major QTL controlling deep rooting on rice chromosome 4. Scientific Reports, 3, 3040. doi:10.1038/srep030401

 PubMed Web of Science ®Google Scholar

Uga, Y., Kitomi, Y., Yamamoto, E., Kanno, N., Kawai, S., Mizubayashi, T., & Fukuoka, S. (2015). A QTL for root growth angle on rice chromosome 7 is involved in the genetic pathway of DEEPER ROOTING 1. Rice, 8, 8.10.1186/s12284-015-0044-7

 Web of Science ®Google Scholar

Kitomi, Y., Kanno, N., Kawai, S., Mizubayashi, T., Fukuoka, S., & Uga, Y. (2015). QTLs underlying natural variation of root growth angle among rice cultivars with the same functional allele of DEEPER ROOTING 1. Rice, 8, 16. doi:10.1186/s12284-015-0049-2

 Web of Science ®Google Scholar