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Research Article

Characterization of Selected Rice Varieties Adapted in Africa

Plant Breeding and Biotechnology 2016;4(3):297-305.
Published online: August 31, 2016

1Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea

2Department of Plant Science, Collage of Agriculture and Environmental Science, Arsi University, Asella, Ethiopia

*Corresponding author: Hee-Jong Koh, heejkoh@snu.ac.kr, Tel: +82-2-880-4541, Fax: +82-2-873-2056
• Received: July 26, 2016   • Revised: August 12, 2016   • Accepted: August 13, 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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  • QTL Analysis of Rice Grain Size Using Segregating Populations Derived from the Large Grain Line
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  • Development and application of indica–japonica SNP assays using the Fluidigm platform for rice genetic analysis and molecular breeding
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Characterization of Selected Rice Varieties Adapted in Africa
Plant Breed. Biotech.. 2016;4(3):297-305.   Published online August 31, 2016
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Plant Breed. Biotech.. 2016;4(3):297-305.   Published online August 31, 2016
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Characterization of Selected Rice Varieties Adapted in Africa
Image Image Image
Fig. 1 UPGMA Dendrogram of 40 varieties based on 11 agronomic traits. The colour of each germplasm corresponds to three subpopulations (G1, blue; G2, green; G3, red).
Fig. 2 STRUCTURE analysis of 40 varieties based on 96 single nucleotide polymorphisms. (A) plot of Ln P(D), (B) plot of Delta k with K=1–10, (C) population structure of 40 germplasms at K=2.
Fig. 3 UPGMA dendrogram based on CS Chord (1967) genetic distance using 96 single nucleotide polymorphism markers. The colour of each germplasm corresponds to subpopulation assignment by STRUCTURE (indica type, red; japonica type, green; admixed ancestry, grey; Reference cultivars are 38, 39, and 40).
Characterization of Selected Rice Varieties Adapted in Africa

List of 40 varieties used in this study.

Code Variety Origin Seed source
1 AAI R 4 India EIARz)
2 AD 04022 India EIAR
3 AMOL 1 Iran EIAR
4 CB04-110 India EIAR
5 CB05-501 India EIAR
6 CB06-505 India EIAR
7 CB06-541 India EIAR
8 CB06-550 India EIAR
9 IET 21119 India EIAR
10 MTU-1098 India EIAR
11 MTU-1115 India EIAR
12 OM 5628 Vietnam EIAR
13 OMCF 6 Vietnam EIAR
14 BRRI dhan 48 Bangladesh EIAR
15 BR7232-6-2-3 Bangladesh EIAR
16 TAK RATIA Pakistan EIAR
17 TOOR THULLA Pakistan EIAR
18 IR10N105 IRRIz) EIAR
19 ESMET101 ARCz) EIAR
20 ESMET102 ARC EIAR
21 ESMET103 ARC EIAR
22 ESMET106 ARC EIAR
23 ESMET107 ARC EIAR
24 ESMET110 ARC EIAR
25 ESMET114 ARC EIAR
26 ESMET115 ARC EIAR
27 ESMET116 ARC EIAR
28 ESMET118 ARC EIAR
29 ESMET120 ARC EIAR
30 ESMET121 ARC EIAR
31 ESMET122 ARC EIAR
32 ESMET126 ARC EIAR
33 IR70031-4B-R-9-3-1 IRRI EIAR
34 NERICA4 ARC EIAR
35 CG14 Senegal EIAR
36 NERICA L-16 ARC EIAR
37 NERICA L-19 ARC EIAR
38 IR64 IRRI SNUz)
39 Nipponbare Japan SNU
40 Malagkit Sninaguing Philippines SNU

z)IRRI: International Rice Research Institute, ARC: Africa Rice Center, EIAR: Ethiopian Institute of Agricultural Research, SNU: Seoul National University.

Eleven agronomic traits of 40 rice varieties tested in 2014.

PNz) PH (cm) PL (cm) PB SB SP SPF (%) KGW (g) GL (mm) GW (mm) GS
Average 13.32** 111.02** 24.28** 12.08** 35.62** 189.18** 74.54** 24.71** 7.68** 2.90** 2.71**
SD 3.83 19.29 2.59 1.48 13.85 62.74 11.82 5.73 0.92 0.41 0.51
Min. 5.00 82.33 17.33 9.33 14.00 87.67 48.27 14.27 6.27 2.29 1.90
Max. 21.67 176.00 32.67 15.67 67.67 340.67 97.31 42.88 10.23 4.09 3.92
CV % 29.14 17.60 10.83 12.43 39.42 33.58 16.06 23.46 12.09 14.31 19.00

**This marks indicates significant difference at P<0.01 level.

z)PN: panicle number per plant, PH: plant height, PL: panicle length, PB: number of primary branch, SB: number of secondary branch, SP: number of spikelet per panicle, SPF: spikelet fertility, KGW: 1,000 grain weight, GL: grain length, GW: grain width, GS: grain shape, SD: standard deviation, Min.: minimum, Max.: maximum, CV %: coefficient of variance in percentage, (SD/average)×100.

Correlation matrix among the eleven agronomic traits of 40 varieties.

Traits PNz) PH PL PB SB SP SPF KGW GW GL
PH 0.29
PL 0.27 0.55**
PB −0.19 0.20 0.17
SB −0.29 −0.13 0.10 0.63**
SP −0.30 −0.11 0.09 0.69** 0.97**
SPF 0.31 0.20 −0.08 −0.24 −0.55** −0.52**
KGW −0.01 0.25 0.11 −0.14 −0.64* −0.62** 0.50**
GW −0.20 0.19 0.22 −0.08 −0.23 −0.23 0.34* 0.65**
GL 0.24 0.10 −0.03 0.08 −0.56** −0.53** 0.11 0.48** −0.22
GS 0.29 −0.09 −0.20 −0.01 −0.19 −0.16 −0.15 −0.15 −0.81** 0.74**

Level of significance ** is significant at P<0.01, *Significant at P<0.05.

z)PN: panicle number per plant, PH: plant height, PL: panicle length, PB: number of primary branch, SB: number of secondary branch, SP: number of spikelet per panicle, SPF: spikelet fertility, KGW: 1,000 grain weight, GW: grain width, GL: grain length, GS: grain shape.

Average values and SD of each group clustered based on the eleven agronomic traits.

Group PNz) PH (cm) PL (cm) PB SB SP SPF (%) KGW (gm) GL (mm) GW (mm) GS
G1 (n=9) Average 12.22a 106.67b 24.11a 13.56a 56.78a 287.26a 64.24c 18.51c 6.85b 2.73b 2.55a
SD 4.05 9.50 2.24 1.22 5.58 33.93 12.87 4.48 0.61 0.35 0.41
G2 (n=25) Average 13.81a 106.71b 24.47a 11.85b 32.12b 171.69b 75.29b 25.39b 7.91a 2.84b 2.85a
SD 3.27 17.43 2.56 1.31 6.95 28.19 9.32 3.39 0.82 0.33 0.54
G3 (n=6) Average 12.94a 135.47a 23.69a 10.78b 18.44c 114.95c 86.84a 31.17a 7.97a 3.39a 2.38a
SD 6.02 23.03 3.70 0.81 5.71 19.34 7.78 7.30 1.13 0.52 0.37

Averages within columns with the same letters were not significantly different at P<0.05. Significance was calculated using Duncan’s multiple range test. The number in parenthesis indicates the number of germplasms included in subgroup.

z)PN: panicle number per plant, PH: plant height, PL: panicle length, PB: number of primary branch, SB: number of secondary branch, SP: number of spikelet per panicle, SPF: spikelet fertility, KGW: 1,000 grain weight, GL: grain length, GW: grain width, GS: grain shape, SD: standard deviation.

Average values and standard (SD) of each group clustered based on 96 single nucleotide polymorphisms.

Group PNz) PH (cm) PL (cm) PB SBz) SP SPF (%) KGW (gm) GL (mm) GW (mm) GS
japonica type (n=4) Average 10.17 124.71 22.33 11.58 22.00 140.84 80.05 30.12 8.24 3.25 2.55
SD 3.87 34.25 3.62 1.23 9.64 47.59 10.61 8.59 1.35 0.48 0.30
indica type (n=35) Average 13.68 109.50 24.49 12.13 37.13 194.56 73.92 24.11 7.62 2.86 2.73
SD 3.77 17.35 2.46 1.53 13.70 63.30 12.09 5.24 0.87 0.40 0.53

This mark indicates significance between japonica-type and indica-type at 5% level by unpaired Student’s t-test. The number in parenthesis indicates the number of germplasms included in subgroup.

z)PN: panicle number per plant, PH: plant height, PL: panicle length, PB: number of primary branch, SB: number of secondary branch, SP: number of spikelet per panicle, SPF: spikelet fertility, KGW: 1,000 grain weight, GL: grain length, GW: grain width, GS: grain shape.

Table 1 List of 40 varieties used in this study.

IRRI: International Rice Research Institute, ARC: Africa Rice Center, EIAR: Ethiopian Institute of Agricultural Research, SNU: Seoul National University.

Table 2 Eleven agronomic traits of 40 rice varieties tested in 2014.

This marks indicates significant difference at P<0.01 level.

PN: panicle number per plant, PH: plant height, PL: panicle length, PB: number of primary branch, SB: number of secondary branch, SP: number of spikelet per panicle, SPF: spikelet fertility, KGW: 1,000 grain weight, GL: grain length, GW: grain width, GS: grain shape, SD: standard deviation, Min.: minimum, Max.: maximum, CV %: coefficient of variance in percentage, (SD/average)×100.

Table 3 Correlation matrix among the eleven agronomic traits of 40 varieties.

Level of significance ** is significant at P<0.01, *Significant at P<0.05.

PN: panicle number per plant, PH: plant height, PL: panicle length, PB: number of primary branch, SB: number of secondary branch, SP: number of spikelet per panicle, SPF: spikelet fertility, KGW: 1,000 grain weight, GW: grain width, GL: grain length, GS: grain shape.

Table 4 Average values and SD of each group clustered based on the eleven agronomic traits.

Averages within columns with the same letters were not significantly different at P<0.05. Significance was calculated using Duncan’s multiple range test. The number in parenthesis indicates the number of germplasms included in subgroup.

PN: panicle number per plant, PH: plant height, PL: panicle length, PB: number of primary branch, SB: number of secondary branch, SP: number of spikelet per panicle, SPF: spikelet fertility, KGW: 1,000 grain weight, GL: grain length, GW: grain width, GS: grain shape, SD: standard deviation.

Table 5 Average values and standard (SD) of each group clustered based on 96 single nucleotide polymorphisms.

This mark indicates significance between japonica-type and indica-type at 5% level by unpaired Student’s t-test. The number in parenthesis indicates the number of germplasms included in subgroup.

PN: panicle number per plant, PH: plant height, PL: panicle length, PB: number of primary branch, SB: number of secondary branch, SP: number of spikelet per panicle, SPF: spikelet fertility, KGW: 1,000 grain weight, GL: grain length, GW: grain width, GS: grain shape.