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QTL Analysis for Lodging Resistance in Rice Using a DH Population under Lowland and Upland Cultural Conditions

Ping Mu, Zi-chao Li1, Chun-ping Li, Hong-liang Zhang and Xiang-kun Wang

Key Lab of Crop Genomics and Genetic Improvement, Ministry of Agriculture and Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, 100094, P.R .China
1
Author for correspondence; E-mail: lizichao@cau.edu.cn

Abstract

A DH (doubled haploid) population, derived from a cross between Japonica upland rice IRAT109 and Japonica paddy rice Yuefu, was used in this study. Three culm traits, basal culm thickness(BCT), culm length (CL) and culm strength (CS), of DH lines and their parents under upland and lowland cultural conditions at milk stage were evaluated. Data from upland and lowland cultural conditions were analyzed based on a constructed molecular linkage map(including 94 RFLP markers and 71 SSR markers and covering 1535.1cM )and the software QTLmapper version 1.0. QTLs and QTLenvironment interactions for BCT, CL and CS were obtained. A total of six additive QTLs and eight pairs of epistatic QTLs associated with these traits were found. There was only one additive QTL performed significant interactions with environment. Two pairs of epistatic QTLs associated with CS were detected with a high general contribution of 24.01% and 36.45% respectively.

Media summary

QTLs associated with lodging resistance traits in rice were revealed and marker aided selection strategy for lodging resistance in rice was also proposed.

Key words

Lodging resistance; Basal culm thickness; Culm length; Culm strength; QTLEnvironment

Introduction

Lodging is one of the most important factors for grain yield reduction. The culm physical characteristic is the main factor for crop lodging. Culm strength is the most important select index for lodging resistance breeding (Xiao et al, 2002). Basal culm thickness, culm length and culm strength are all correlated with lodging resistance (Zhang et al, 1999). Rice lodging resistance could be improved by means of shortening the length of basal internodes, strengthening the hardness of the basal culm (Liang et al, 2000a). Crop lodging resistance is also affected by plant height (culm length). Thirteen QTLs were found for wheat lodging resistance (Keller et al, 1999). But to our knowledge no QTL for lodging resistance have been localized in rice.

The objective of this study was to identify QTLs governing these traits, to obtain the contributions of QE interaction for these traits in different environments and to provide guidelines for lodging resistance breeding and marker aided selection.

Materials and Methods

1.1Materials and cultural conditions

A population comprising 116 DH lines derived from a cross between Yuefu (a Japonica lowland variety) and IRAT109 (a Japonica upland variety) was used in this study.

This experiment was conducted in China Agricultural University in 2002.Two cultural conditions, i.e, upland and lowland cultural conditions were set up in this experiment. DH lines and the parents were planted in a randomized complete design with 2 replications under upland and lowland cultural conditions. The seeds of each DH line with chemical dressing were sown directly in lowland and upland fields (N 150 kg/ha, P2O5 150 kg/ ha and K2O 150 kg/ ha combined fertilizer were practiced) in early May 5, 2002. Thirty plants of each DH line were sown in each row. The distance between rows was 30 cm and that between seeds was 5 cm. For lowland cultural condition, 2—10 cm layer of water was kept during the growth period. Three times of irrigation were practiced during the growth period under upland condition.

1.2 Measurements of traits

Basal culm thickness (mm, in diameter) was measured using a vernier caliper in the field at ten randomly selected strong tillers in the middle of the first above ground internode at milk development to dough ripe stage. Culm length (cm) was calculated from plant height minus spike length. Culm strength (g/stem) was assessed using a prostrate tester(DIK-7400 Daiki Soil & Moisture made in Japan)in the field at the second below spike internode by pushing the plant at an angle of 45from the vertical(Xiao et al, 2002).

1.3 QTL analysis

QTL analysis including additive QTLs, epistatic QTLs and QTLEnvironment interactions was achieved by mixed linear model approaches conducted with QTL mapper version 2.0 (Wang et al., 1999). A threshold probability of P≤0.005 and P≤0.001 was used for additive and epistatic QTLs respectively.

Results

2.1 Phenotypic traits analysis of DH population and its parents

Table1 Phenotype value of DH lines and the parents for culm traits under upland and lowland cultural conditions

Traits

Cultural conditions

IRAT109

Yuefu

DH mean

Range

BCT (mm)

lowland

6.11

4.14

5.18

3.95 -7.03

BCT (mm)

Upland

5.85

3.46

4.56

3.34 -5.87

CL (cm)

lowland

76.30

86.60

77.30

52.00 - 101.20

CL (cm)

Upland

86.00

69.00

77.20

31.30 - 100.90

CS (g/stem)

Upland

29.68

15.63

25.37

7.48 - 84.58

BCT=Basal culm thickness, CL=Culm length, CS=Culm strength

The phenotypic means and ranges of the population and its parents for culm traits were summarized (Table1). IRAT109 had bigger BCT as compared to Yuefu both under upland and lowland cultural conditions. Mean BCT across the DH lines declined to 88% under upland condition. Mean CL did not show any variation. While IRAT109 was increased 9.7 cm, Yuefu showed 17.6 cm reduction under stress. Mean CS of DH population was in the middle of IRAT109 and Yuefu under upland ecosystem. The CS range of DH lines varied from infirmness to strength ( strength≥55.1g/stem,medium 25.1~55 g/stem, infirmness≤25 g/stem).

2.3 Identification of QTLs for BCT, CL and CS

A list of putative QTLs for BCT, CL and CS flanked by the RFLP/SSR markers along with their chromosome number, effects, LOD score and phenotypic variance were presented in table 2. Six additive QTLs and eight pairs of epistasis QTLs were detected for BCT, CL and CS. All the QTLs for BCT and CL (except QTL flanked by C39-RM214 on chromosome7) were both detected under upland and lowland cultural conditions.

Table 2 Interval, site, LOD score, effects(A/AA) and general contributions(H2A/AA, H2AAE) of QTLs and QTLenvironment interaction associated with culm traits

Traits

Chr.

No

Interval

Site (M) a

Chr.

No

Interval

Site (M) a

LOD

A/AAb

H2A/AAc

AAEd1

H2AAEc

BCT

7

C39-RM214

0.36

     

3.57

-0.126

2.60

0.151

7.48

 

8

OSR30-RM152

0.12

     

2.73

0.133

2.90

   
 

1

C904-RM306

0.04

8

OSR30-RM152

0.02

4.23

0.0187

4.27

   
 

2

R3393-C747

0.08

11

C3-R2918

0.02

5.03

0.237

6.86

   
 

2

G1327-RM263

0.28

5

RM161-R521

0.00

2.89

0.150

2.75

   
 

2

RM208-RM48

0.00

3

RM231-RM175

0.12

5.39

0.185

4.18

   

CL

2

G204-G1327

0.02

     

3.20

-4.38

12.76

   
 

3

RM231-RM175

0.04

     

2.86

-2.94

5.75

   
 

5

RM146-R569

0.14

     

4.23

-3.45

7.89

   
 

5

C282-R1838

0.06

     

3.77

4.10

11.17

   
 

4

R738-C513

0.00

7

RM47-RM172

0.30

4.46

2.09

2.09

   
 

6

C1004-R1962

0.00

7

RM346-RM10

0.08

3.06

2.49

3.00

   

CS

1

RM5-RM302

0.26

10

RM311-RM216

0.02

4.04

-0.28

24.01

   
 

5

R521-R566

0.00

12

R617-S826

0.10

3.80

0.35

36.45

   

a: The distance from the left marker to the putative QTL. b: A negative value meant that minus effect was derived from Yuefu. c: H2A/AA,HAAE was the contribution from additive QTL, epistasis QTL and QTLenvironment interaction respectively. d:E1:Environment of lowland ecosystem , E2: Environment of upland ecosystem.AAE1= -AAE2

QTLs for BCT: Two additive QTLs and four pairs of epistasis QTLs were detected for BCT and explained 5.5% and 18.1% phenotypic variation respectively. All the QTLs (except QTL flanked by C39-RM214 on chromosome7) had positive effects. The value ranged from 0.0187to 0.237. There was a pair of epistasis QTLs flanked by R3393-C747 on chromosome 2 and C3-R2918 on chromosome 11 with large effect (0.237) and high general contribution (6.86%).

QTLs for CL: For CL, four additive QTLs and two pairs of epistatic QTLs on chromosome2, 3, 4, 5, 6 and 7 respectively were detected. The general contribution ranged from 2.09% to 12.76%. The QTLs were all common QTLs across upland and lowland cultivated conditions. There were two QTLs (flanked by G204-G1327 on chromosome2 and C282-R1838 on chromosome 5) having large effects (4.38cm and 4.10cm) and high general contributions (12.76% and 11.17%).

QTLs for CS: For CS, two pairs of epistatic QTLs on chromosome 1-10 and 5-12 respectively were detected. These 2 pairs of common QTLs had high general contribution of 24.01% and 36.45% respectively.

For all the 3 traits examined, epistatic QTLs were all detected. The general contributions of epistatic QTLs for BCT,CL, and CS were 18%,5%,and 60.5% respectively. So it was important of epistasis QTLs for BCT and CS. But for CL, more additive QTLs were detected than epistasis QTLs.

2.4 Correlations between QTLs conferring different traits

QTLs locations across different traits were compared in this study. Some QTLs controlling different traits were mapped to similar chromosome regions or the same chromosomes. For example, QTLs controlling BCT and CS on chromosome1, QTLs controlling BCT and CL on chromosome2, chromosome3 and chromosome7, QTLs controlling BCT, CL and CS on chromosome 5 were all correlative QTLs. This result was in accordance with the correlations between the phenotypic values of culm traits.

Discussion

In the present study, QTLs conferring BCT, CL and CS under upland and paddy cultivated conditions were obtained. No QTLEnvironment interaction was detected for CL and only one QE interaction QTL was found for BCT. The difference between upland and lowland cultural conditions was very large. This result indicted that the inheritance of CL and BCT were high. This result was in accordance with Wons results (Won et al, 1998) Therefore, BCT and CL might be selected in early generations in breeding program. Marker assisted selection (MAS) for BCT and CL may be used in lodging resistance breeding.

QTLs of additive and epistatic effects for culm traits were obtained based on mixed linear model approaches. The result showed that epistasis was an important genetic component underlying BCT, CL and CS. But the general contributions of epistatic QTLs controlling various traits were different. So different marker assisted selection strategies for CL and CS should be adopted. Closely linked markers with additive effect QTLs for CL are emphasized. But for CS, epistatic QTLs should be considered firstly.

Acknowledgements

This work was supported by the Hi-Tech Research of China (Grant No. 2003AA207040) and 948”project (Grant No. 2001-204) of Ministry of Agriculture of China.

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