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Research Article

Identification of Quantitative Trait Loci Associated with Grain Shape Using Cheongchenong/Nagdong Double Haploid Lines in Rice

Plant Breeding and Biotechnology 2016;4(2):188-197.
Published online: May 31, 2016

1Department of Food Security and Agricultural Development, College of Agriculture and Life Science, Kyungpook National University, Daegu 41566, Korea

2Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu 41566, Korea

*Corresponding author: Kyung-Min Kim, kkm@knu.ac.kr, Tel: +82-53-950-5711, Fax: +82-53-958-6880
• Received: March 21, 2016   • Revised: May 4, 2016   • Accepted: May 5, 2016

Copyright © 2016 The Korean Society of Breeding Science

This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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    Physiology and Molecular Biology of Plants.2024; 30(7): 1145.     CrossRef
  • Combined Linkage Mapping and Genome-Wide Association Study Identified QTLs Associated with Grain Shape and Weight in Rice (Oryza sativa L.)
    Ju-Won Kang, Nkulu Rolly Kabange, Zarchi Phyo, So-Yeon Park, So-Myeong Lee, Ji-Yun Lee, Dongjin Shin, Jun Hyeon Cho, Dong-Soo Park, Jong-Min Ko, Jong-Hee Lee
    Agronomy.2020; 10(10): 1532.     CrossRef

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Identification of Quantitative Trait Loci Associated with Grain Shape Using Cheongchenong/Nagdong Double Haploid Lines in Rice
Plant Breed. Biotech.. 2016;4(2):188-197.   Published online May 31, 2016
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Identification of Quantitative Trait Loci Associated with Grain Shape Using Cheongchenong/Nagdong Double Haploid Lines in Rice
Plant Breed. Biotech.. 2016;4(2):188-197.   Published online May 31, 2016
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Identification of Quantitative Trait Loci Associated with Grain Shape Using Cheongchenong/Nagdong Double Haploid Lines in Rice
Image Image
Fig. 1 Frequency distributions of five traits associated with grain appearance in Cheongcheong/Nagdong doubled haploid population. ‘C’ and ‘N’ indicate mean values of Cheongcheong and Nagdong in 2013 and 2014, respectively.
Fig. 2 The genetic regions associated with the grain length for 2 years in Cheongcheong/Nagdong doubled haploid. cM: centiMorgans, GL: grain length, GW: grain width, GT: grain thickness, GR: Ratio of grain length/width, TGW: 1,000-grain weight.
Identification of Quantitative Trait Loci Associated with Grain Shape Using Cheongchenong/Nagdong Double Haploid Lines in Rice

The grain phenotypes of 120 DH lines from a cross of Cheongcheong and Nagdong.

Grain trait Year Parent DHz) population


Cheongcheong Nagdong Range Mean Heritability
Grain length (mm) 2014 5.74±0.15 4.91±0.09 4.27–7.26 5.41±0.18 98.0
2013 5.88±0.14 4.92±0.12 4.75–7.37 5.31±0.16 100.0
Grain width (mm) 2014 2.66±0.15 2.80±0.09 2.14–3.05 2.66±0.11 100.0
2013 2.71±0.07 2.87±0.07 2.12–3.15 2.74±0.09 99.4
Grain thickness (mm) 2014 1.96±0.07 2.00±0.10 1.61–2.19 1.90±0.09 95.0
2013 1.99±0.06 2.04±0.05 1.65–2.22 1.94±0.08 98.2
Ratio of length to width (%) 2014 2.16±1.63 1.75±1.49 1.59–3.32 2.05±1.93 99.5
2013 2.17±0.02 1.71±0.54 1.57–3.17 2.04±1.76 97.8
Grain weight (g) 2014 23.50±0.41 21.00±1.26 15.00–26.50 20.94±3.13 94.0
2013 23.83±0.29 22.0±0.50 29.50–16.50 22.37±2.86 100.0

Values are presented as mean±standard deviation, range, or percentage only.

z)DH: double haploid.

Correlation analysis among five grain traits of 120 DH lines from CNDH from a cross Cheongcheong and Nagdong.

Grain trait GLz) GW GT GR TGW





2014 2013 2014 2013 2014 2013 2014 2013 2014 2013
GL 1.00 1.00
GW −0.425** 0.441** 1.00 1.00
GT −0.255** 0.337** 0.767** 0.784** 1.00 1.00
GR 0.864** 0.859** −0.811** 0.827** −0.563** −0.632** 1.00 1.00
TGW 0.317** 0.367** 0.583** 0.558** 0.677** 0.603** −0.110 −0.080 1.00 1.00

**These marks mean significant at the 1% level.

z)DH: double haploid, GL: grain length, GW: grain width, GT: grain thickness, GR: ratio of length to width, TGW: thousand grain weight.

The main effect quantitative trait loci (QTLs) of the grain appearance for 2 years in Cheongcheong/Nagdong doubled haploid population.

Characteristic QTLs Chromosome Peak closed markerz) LODy) Add (%)x) R2 (%)w) Increasingv) effect
Grain length qGL2 2 RM1211 3.17 17 50 Cheongcheong
qGL5 5 RM5311 10.11 24 64 Cheongcheong
qGL7 7 RM21582 7.86 21 63 Cheongcheong
qGL9 9 RM23914 3.34 −13 62 Nagdong
Grain width qGW1 1 RM12285 3.44 −7 50 Nagdong
qGW2 2 RM12895 6.64 −24 −31 Nagdong
qGW3 3 RM15448 3.59 −8 55 Nagdong
qGW10 10 RM24934 3.01 −6 51 Nagdong
Grain thickness qGT2 2 RM12895 3.36 −4 −33 Nagdong
qGT10 10 RM12895 3.36 −4 33 Nagdong
Ratio of grain length/width qGR1 1 RM12285 6.39 9 68 Cheongcheong
qGR2 2 RM12895 49.33 22 69 Cheongcheong
qGR3 3 RM15063 12.84 11 69 Cheongcheong
qGR4 4 RM16429 3.34 −4 61 Nagdong
qGR6 6 RM527 3.53 4 63 Cheongcheong
qGR7 7 RM21582 16.15 8 61 Cheongcheong
qGR8 8 RM223 11.49 9 68 Cheongcheong
qGR9 9 RM24002 3.45 6 62 Cheongcheong
qGR10 10 RM25128 5.50 5 63 Cheongcheong
qGR11 11 RM167 6.96 5 63 Cheongcheong
qGR12 12 RM8216 7.72 6 63 Cheongcheong
Thousand grain weight qTGW1 1 RM1297 4.23 −1.07 48 Nagdong
qTGW2 2 RM6 3.94 1.0 45 Cheongcheong
qTGW8 8 RM23230 4.04 0.99 41 Cheongcheong

z)Those within the significance threshold on each border of the quantitative trait locus (QTL) range.

y)Logarithm of odds deviation.

x)Positive values of the additive effect indicate that alleles from Cheongcheong are in the direction of increasing the traits.

w)R2 the proportion of evaluated phenotype variation attributable a particular QTL was estimated by the coefficient of determination.

v)Increase allele is the source of the allele causing an increase in the measured trait.

Table 1 The grain phenotypes of 120 DH lines from a cross of Cheongcheong and Nagdong.

Values are presented as mean±standard deviation, range, or percentage only.

DH: double haploid.

Table 2 Correlation analysis among five grain traits of 120 DH lines from CNDH from a cross Cheongcheong and Nagdong.

These marks mean significant at the 1% level.

DH: double haploid, GL: grain length, GW: grain width, GT: grain thickness, GR: ratio of length to width, TGW: thousand grain weight.

Table 3 The main effect quantitative trait loci (QTLs) of the grain appearance for 2 years in Cheongcheong/Nagdong doubled haploid population.

Those within the significance threshold on each border of the quantitative trait locus (QTL) range.

Logarithm of odds deviation.

Positive values of the additive effect indicate that alleles from Cheongcheong are in the direction of increasing the traits.

R2 the proportion of evaluated phenotype variation attributable a particular QTL was estimated by the coefficient of determination.

Increase allele is the source of the allele causing an increase in the measured trait.