1. Biotechnology and Genetic Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; 2. Key Lab of Crop Genomics and Genetic Improvement of Ministry of Agriculture, Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing 100094, China; 3. Supervision and Testing Center for Farm Products Quality, Ministry of Agriculture of the People’s Republic of China, Kunming 650223, China; 4. Yunnan Agricultural University, Kunming 650201, China
Yunnan is one of the largest centers of genetic diversity in the world. Allele size of microsatellites associated with phenotypic traits of rice landraces in Yunnan, Southwest China, was investigated based on 20 SSR markers and 23 phenotypic traits, as well as eight mineral elements in brown rice within the core collection of 629 accessions; and there was a significant correlation for 182 (r = 0.083*-0.438**) of 620 pairs among these markers and traits, as well as elements. Surprisingly, there was a significant correlation for 94 of 180 pairs between the allele size of microsatellites and grain traits, and 48 of 160 pairs between allele size of microsatellites and panicle traits. In these rice landraces, 309 alleles were detected, with an average of 15.5 alleles per marker, ranging from 5 (RM60) to 40 (RM257). There was a significant correlation between the allele size of 20 SSR markers and some phenotypic traits, such as the significant correlation of 17 (r = -0.085*--0.438**) pairs between the allele size of RM224 and 23 phenotypic traits, as well as eight elements. The allele size of microsatellites was more associated with grain or panicle traits than that of plant traits or element contents in brown rice. Grain length/width ratio and 1-2 internode length, as indica-japonica classification traits, in which two traits were closely associated with the allele size of 14 SSR markers ranging from 0.089* to -0.438**. Therefore, allele size of SSRs was associated with phenotypic traits (especially in grain traits), as well as elemental contents in brown rice.
Corresponding Author(s):
ZENG Yawen,Email:zengyw1967@126.com; LI Zichao,Email:lizichao@cau.edu.cn
引用本文:
. Correlation between allele sizes of microsatellites and phenotypic variations in rice landraces[J]. Frontiers of Agriculture in China, 2009, 3(2): 130-139.
Yawen ZENG, Shuming YANG, Juan DU, Xiaoying PU, Hongliang ZHANG, Zichao LI, Luxiang WANG, Jiafu LIU, Fenghui XIAO. Correlation between allele sizes of microsatellites and phenotypic variations in rice landraces. Front Agric Chin, 2009, 3(2): 130-139.
percent head rice, amylase content, alkali spreading score, protein content, grain length, grain length /width ratio, days to maturity, heading date, awn length
Xiao et al., 1996; Linh et al., 2006
RM18
12
150-172
(GA)4AA(GA)(AG)16
frizzle panicle, grain yield, tillers per plant, grains per panicle, heading date
Duan et al., 2003
RM234
17
110-170
(CT)25
days to heading, days to maturity, maximum root length
Thomson et al., 2003; Miyata et al., 2007
RM223
17
137-170
(CT)20
panicle per plant, days to heading, panicle length;
Pradeep et al., 2005; Miyata et al., 2007
RM257
40
123-210
(CT)24
cold resistance, heading date
Miyata et al., 2007
RM244
9
149-164
(CT)4(CG)3C(CT)6
fertility restorer genes
Jing et al., 2000
RM258
13
131-152
(GA)21(GGA)3
spikelet fertility, 1000-grain weight, tiller number, heading date
Cui et al., 2004; Miyata et al., 2007
RM224
18
124-162
(AAG)8(AG)13
plant height, tillers per plant, panicle length, root-shoot ratio
Miyata et al., 2007
RM235
18
95-137
(CT)24
panicles per plant
Thomson et al., 2003
RM247
28
124-184
(CT)16
phosphorus deficiency, plant height
Thomson et al., 2003
Tab.1
markers
P
K
Ca
Mg
Fe
Zn
Cu
Mn
RM5
-0.011
0.087*
0.080
-0.022
-0.017
-0.001
0.036
-0.013
RM81A
-0.144**
-0.086*
-0.014
0.003
0.003
0.076
-0.129**
0.033
RM211
-0.049
0.002
-0.043
0.015
-0.026
0.008
0.036
0.029
RM263
0.002
0.001
-0.058
0.035
0.001
0.064
0.076
0.042
RM60
0.012
-0.028
0.046
0.024
0.042
-0.061
-0.096*
-0.091*
RM232
0.101*
-0.018
0.007
0.042
-0.015
0.006
0.001
-0.002
RM241
0.001
0.006
-0.047
-0.012
-0.056
0.007
0.012
0.046
RM255
0.060
0.074
0.091*
0.047
-0.005
0.023
-0.023
0.051
RM249
-0.041
0.036
0.018
-0.022
-0.051
-0.037
-0.062
-0.066
RM225
-0.075
-0.087*
-0.059
-0.101*
-0.083*
0.037
-0.027
-0.093*
RM253
-0.104*
-0.092*
-0.009
-0.063
0.024
0.015
-0.103*
0.002
RM18
0.035
-0.021
0.025
0.088*
-0.013
0.017
-0.013
0.033
RM234
0.096*
-0.026
0.042
-0.020
0.007
-0.006
-0.047
0.014
RM223
0.019
0.052
0.044
0.019
-0.009
0.002
0.027
-0.025
RM257
-0.002
0.037
-0.052
-0.010
-0.020
0.028
-0.024
-0.046
RM244
-0.092*
-0.085*
0.016
-0.091*
-0.030
-0.002
-0.065
-0.011
RM258
0.076
-0.036
-0.031
0.020
-0.012
0.039
0.028
-0.004
RM224
-0.034
0.006
-0.024
-0.034
0.009
0.033
0.042
-0.034
RM235
0.053
0.110**
-0.007
0.058
0.024
0.036
-0.042
0.047
RM247
0.029
0.059
0.101*
0.047
0.051
0.010
-0.084*
0.041
Tab.2
markers
chromosome
plant height
tillers per plant
panicles per plant
days to heading
flagleaf length
flagleaf width
RM5
1
-0.019
-0.089*
0.037
0.054
0.037
0.064
RM81A
1
0.042
0.059
0.057
0.013
0.137
-0.047
RM211
2
-0.052
-0.023
0.012
-0.019
-0.001
0.012
RM263
2
-0.085*
-0.028
-0.015
-0.036
-0.049
-0.098*
RM60
3
-0.109**
-0.002
0.022
-0.084*
0.058
-0.020
RM232
3
0.057
0.043
0.066
0.143**
0.070
-0.043
RM241
4
0.039
-0.070
0.058
0.078
0.021
0.006
RM255
4
0.029
0.070
0.042
0.071
0.065
0.009
RM249
5
0.044
0.033
-0.100*
0.0423
0.047
0.005
RM225
6
-0.140**
-0.015
-0.001
-0.0275
-0.031
0.042
RM253
6
0.012
-0.028
0.077
0.0641
0.033
-0.010
RM18
7
0.045
0.095*
0.055
0.0275
0.068
-0.078
RM234
7
0.022
-0.022
-0.077
-0.0104
0.037
0.043
RM223
8
0.037
-0.008
-0.068
0.2001**
0.052
-0.053
RM257
9
0.028
0.126**
0.006
0.0417
0.138**
0.055
RM244
10
0.042
0.076
0.053
0.0501
0.058
0.008
RM258
10
-0.039
-0.026
-0.108**
0.0114
-0.043
0.008
RM224
11
-0.151**
-0.085*
-0.042
-0.1134**
-0.086*
0.021
RM235
12
0.023
-0.052
0.044
0.0228
-0.032
-0.048
RM247
12
-0.006
0.082*
0.049
-0.0140
0.047
-0.012
Tab.3
markers
1000-grainweight
grain length
grain width
grain length/width ratio
grain thickness
rice length
ricewidth
rice thickness
shattering
RM5
-0.089*
0.273**
-0.195**
0.294**
-0.130**
0.148**
-0.220**
-0.133**
-0.134**
RM81A
0.059
0.189**
-0.186**
0.233**
-0.029
0.010
-0.194**
-0.209**
-0.187**
RM211
-0.080
-0.121**
0.101*
-0.134**
0.025
-0.134**
0.079
-0.032
0.092*
RM263
-0.183**
-0.287**
0.127**
-0.246**
0.077
-0.224**
0.194**
0.052
0.070
RM60
-0.079
-0.045
-0.068
0.019
0.016
-0.078
-0.025
-0.024
-0.010
RM232
-0.028
-0.020
-0.053
0.027
-0.045
0.025
-0.048
-0.026
-0.045
RM241
0.001
0.064
-0.089*
0.089*
-0.041
0.050
-0.067
-0.066
-0.013
RM255
0.057
0.180**
-0.162**
0.212**
-0.125**
0.073
-0.178**
-0.134**
-0.089*
RM249
-0.008
0.041
-0.056
0.066
0.024
-0.023
-0.069
-0.047
-0.092*
RM225
-0.141**
-0.155**
0.103*
-0.174**
0.025
-0.126**
0.124**
0.028
-0.011
RM253
-0.069
-0.056
-0.001
-0.035
0.011
-0.087*
0.035
-0.019
0.030
RM18
0.046
0.198**
-0.148**
0.221**
-0.079
0.148**
-0.166**
-0.028
-0.051
RM234
-0.073
-0.079
0.014
-0.060
0.074
-0.079
0.068
0.006
0.090*
RM223
0.013
-0.032
0.037
-0.026
-0.012
0.012
0.055
0.033
-0.012
RM257
0.009
0.214**
-0.239**
0.291**
-0.144**
0.138**
-0.241**
-0.151**
0.085*
RM244
0.037
0.210**
-0.159**
0.230**
-0.142**
0.116**
-0.159**
-0.109**
-0.135**
RM258
-0.151**
-0.226**
0.135**
-0.216**
-0.032
-0.152**
0.160**
0.049
0.067
RM224
-0.190**
-0.424**
0.242**
-0.420**
0.173**
-0.349**
0.348**
0.189**
0.113**
RM235
-0.027
-0.129**
0.236**
-0.239**
0.143**
-0.052
0.209**
0.167**
0.086*
RM247
0.027
0.244**
-0.188**
0.265**
-0.089*
0.176**
-0.190**
-0.087*
-0.068
Tab.4
markers
1-2 internode length
panicle length
awn length
filled grainsper panicle
blighted grains per panicle
total grains per panicle
seedsetting rate
graindensity
RM5
-0.251**
-0.013
-0.055
-0.039
0.022
-0.035
-0.013
-0.029
RM81A
-0.369**
0.098*
-0.130**
0.005
0.045
0.055
-0.029
0.010
RM211
0.156**
-0.021
0.041
-0.114**
0.129**
0.019
-0.120**
0.010
RM263
0.298**
-0.045
0.061
-0.035
0.088*
0.050
-0.035
0.085*
RM60
-0.016
-0.013
0.019
-0.057
0.016
-0.075
-0.047
-0.019
RM232
0.017
0.039
-0.020
-0.009
0.070
0.015
-0.061
0.049
RM241
-0.049
-0.001
-0.025
-0.016
-0.043
-0.003
0.042
-0.057
RM255
-0.262**
0.036
-0.093*
0.029
-0.009
0.022
0.039
0.009
RM249
-0.074
0.038
0.009
-0.009
-0.015
-0.010
0.054
-0.025
RM225
0.113**
-0.035
0.046
-0.158**
0.133**
0.044
-0.149**
0.006
RM253
0.006
0.035
-0.039
0.022
0.045
0.042
-0.027
0.036
RM18
-0.259**
-0.011
-0.036
0.015
-0.066
-0.025
-0.082*
-0.057
RM234
0.052
0.020
0.061
-0.036
0.039
0.043
-0.028
-0.004
RM223
0.094*
0.100*
0.059
-0.074
0.088*
-0.005
-0.110**
-0.031
RM257
-0.285**
0.036
-0.111**
0.046
-0.042
0.060
0.090*
-0.023
RM244
-0.293**
0.032
-0.055
0.062
-0.041
0.033
0.046
0.023
RM258
0.279**
0.003
0.130**
-0.054
0.099*
-0.072
-0.087*
0.044
RM224
0.438**
-0.057
0.090*
-0.040
0.098*
0.071
-0.072
0.086*
RM235
0.303**
-0.005
0.070
-0.080
0.135**
0.055
-0.134**
0.030
RM247
-0.257**
0.083*
-0.101*
0.060
-0.034
0.025
0.056
-0.005
Tab.5
1
Abdelkhalik A F, Shishido R, Nomura K, Ikehashi H (2005). QTL-based analysis of heterosis for grain shape traits and seedling characteristics in an indica-japonica hybrid in rice (Oryza sativa L.). Breeding Science , 55(1): 41-48 doi: 10.1270/jsbbs.55.41
2
Andersen J R, Lübberstedt T (2003). Functional markers in plants. Trends in Plant Science , 8(11): 554-560 doi: 10.1016/j.tplants.2003.09.010
3
Bassam B J, Caetano-Anolles G, Gresshoff P M (1991). Fast and sensitive silver staining of DNA in polyacrylamide gels. Analytical Biochemistry , 196(1):80-83 doi: 10.1016/0003-2697(91)90120-I
4
Chang T T (1976). The origin, evolution, cultivation, dissemination and diversification of Asian and African rices. Euphytica , 25(1): 425-441 doi: 10.1007/BF00041576
5
Cui K H, Peng S B, Ying Y Z, Yu S B, Xu C G (2004). Molecular dissection of the relationships among tiller number, plant height and heading date in rice. Plant Production Science , 7(3): 309-318 doi: 10.1626/pps.7.309
6
Doyle J J, Doyle J L (1990). Isolation of plant DNA from fresh tissue. Focus , 12(1): 13-15
7
Duan Y L, Li W M, Wu W R, Pan R S, Zhou Y C, Qi J M, Lin L H, Chen Z W, Mao D M, Liu H Q, Zhang D F, Xue Y B (2003). Genetic analysis and mapping of gene fzp(t) controlling spikelet differentiation in rice. Science in China (Series C) , 46(4): 328-334
8
Gao L Z, Ge S, Hong D Y, Lin R S, Tao G D, Xu Z F (2002). Allozyme variation and conservation genetics of common wild rice (Oryza rufipogon Griff.) in Yunnan, China. Euphytica , 124(4): 273-281 doi: 10.1023/A:1015740331079
9
Jiang H, Guo L B, Qian Q (2007). Recent progress on rice genetics in China. Journal of Integrative Plant Biology , 49(6): 776-790 doi: 10.1111/j.1744-7909.2007.00492.x
10
Jing R C, Li X M, Yi P, Zhu Y G (2001). Mapping fertility-restoring genes of rice WA cytoplasmic male sterility using SSLP markers. Botanical Bulletin of Academia Sinica , 42(3): 167-171
11
Lawson M J, Zhang L Q (2006). Distinct patterns of SSR distribution in the Arabidopsis thaliana and comment rice genomes. Genome Biology , 7(2): R14 doi: 10.1186/gb-2006-7-2-r14
12
Li Y C, Korol A B, Fahima T, Nevo E (2004). Microsatellites within genes: structure, function and evolution. Molecular Biology and Evolution , 21(6): 991-1007 doi: 10.1093/molbev/msh073
13
Liang F S, Deng Q Y, Wang Y Q, Xiong Y D, Jin D M, Li J M, Wang B (2004). Molecular marker-assisted selection for yield-enhancing genes in the progeny of “9311×O. rufipogon” using SSR. Euphytica , 139(2): 159-165 doi: 10.1007/s10681-004-2560-1
14
Linh L H, Jin F X, Kang K H, Lee Y T, Kwon S J, Ahn S N (2006). Mapping quantitative trait loci for heading date and awn length using an advanced backcross line from a cross between Oryza sativa and O. minuta. Breeding Science , 56(4): 341-349 doi: 10.1270/jsbbs.56.341
15
Ma J F, Tamai K, Yamaji N, Mitani N, Konishi S, Katsuhara M, Murata Y, Yano M, Ishiguro M (2006). A silicon transporter in rice. Nature , 440(30): 688-691 doi: 10.1038/nature04590
16
McCouch S R, Teytelman L, Xu Y, Lobos K B, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q F, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L (2002). Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Research , 9(6): 199-207 doi: 10.1093/dnares/9.6.199
17
Miyata M, Yamamoto T, Komori T, Nitta N (2007). Marker-assisted selection and evaluation of the QTL for stigma exsertion under japonica rice genetic background. Theoretical and Applied Genetics , 114(3): 539-548 doi: 10.1007/s00122-006-0454-4
18
Panaud O, Chen X, McCouch S R (1996). Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Molecular General Genetics , 252(5): 597-607
19
Pradeep R M, Sarla N, Laminaratana V R, Siddiq E A (2005). Identification and mapping of yield and yield related QTLs from an Indian accession of Oryza rufipogon. BMC genetics , 6: 33
20
Ramakrishna W, Davierwala A P, Gupta V S, Ranjekar P K (1998). Expansion of a (GA) dinucleotide at a microsatellite locus associated with domestication in rice. Biochemical Genetics , 36(9-10): 323-327 doi: 10.1023/A:1018793328896
21
Septiningsih E M, Trijatmiko K R, Moeljopawiro S, McCouch S R (2003). Identification of quantitative trait loci for grain quality in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon. Theoretical and Applied Genetics , 107(8): 1433-1441 doi: 10.1007/s00122-003-1376-z
22
Shen Y J, Jiang H, Jin J P, Zhang Z B, Xi B, He Y Y, Wang G, Wang C, Qian L, Li X, Yu Q B, Liu H J, Chen D H, Gao J H, Huang H, Shi T L, Yang Z N (2004). Development of genome-wide DNA polymorphism database for map-based cloning of rice genes. Plant Physiology , 135(3): 1198-1205 doi: 10.1104/pp.103.038463
23
Tan L B, Liu F X, Xue W, Wang G J, Ye S, Zhu Z F, Fu Y C, Wang X K, Sun C Q (2007). Development of Oryza rufipogon and O. sativa introgression lines and assessment for yield-related quantitative trait loci. Journal of Integrative Plant Biology , 49(6): 871-884 doi: 10.1111/j.1744-7909.2007.00497.x
24
Thomson M J, Tai T H, McClung A M, Lai X H, Hinga M E, Lobos K B, Xu Y, Martinez C P, McCouch S R (2003). Mapping quantitative trait loci for yield, yield components and morphological traits in an advanced backcross population between Oryza rufipogon and the Oryza sativa cultivar Jefferson. Theoretical and Applied Genetics , 107(3): 479-493 doi: 10.1007/s00122-003-1270-8
25
Xiao J, Grandillo S, Ahn S A, McCouch S R, Tanksley S D, Li J, Yuan L (1996). Genes from wild rice improve yield. Nature , 384: 223-224 doi: 10.1038/384223a0
26
Xu J L, Yu S B, Luo L J, Zhong D B, Mei H W, Li Z K (2004). Molecular dissection of the primary sink size and its related traits in rice. Plant Breeding , 123(1): 43-50 doi: 10.1046/j.1439-0523.2003.00936.x
27
Xue W Y, Xing Y Z, Weng X Y, Zhao Y, Tang W J, Wang L, Zhou H J, Yu S B, Xu C G, Li X H, Zhang Q F (2008). Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nature Genetics , 40: 761-767 doi: 10.1038/ng.143
28
Yoshida S, Ikegami M, Kuze J, Sawada K, Hashimoto Z, Ishii T, Nakamura C, Kamijima O (2002). QTL analysis for plant and grain characters of sake-brewing rice using a doubled haploid population. Breeding Science , 52(4): 309-317 doi: 10.1270/jsbbs.52.309
29
Zeng Y W, Liu J F, Wang L X, Du J, Pu X Y, Yang S M, Zhang H L (2006). Ecogeographic difference and variation pattern of mineral contents for Yunnan rice landraces. Acta Agronomica Sinica , 32(8): 1166-1173
30
Zeng Y W, Shen S Q, Li Z C, Yang Z Y, Wang X K, Zhang H L, Wen G S (2003). Ecogeographic and genetic diversity based on morphological characters of indigenous rice (Oryza sativa L.) in Yunnan, China. Genetic Resources and Crop Evolution , 50(6): 566-577
31
Zeng Y W, Shen S Q, Wang L X, Liu J F, Pu X Y, Du J, Gui M (2005). Correlation of plant morphological and grain quality traits with mineral element contents in Yunnan rice. Rice Science , 12(2): 101-106
32
Zeng Y W, Wang L X, Sun Z H, Yang S M, Du J, Li Q W, Pu X Y, Du W, Xiao F H (2008). Determination of mineral elements of brown rice in near-isogenic lines poputation for japonica rice by ICP-AES. Spectroscopy and Spectral Analysis , 28(12): 2966-2969 (in Chinese)
33
Zeng Y W, Xu F R, Shen S Q, Deng J Y (2000). Correlation of indica-japonica classification and morphological character of Yunnan nuda rice cultivars. Chinese Journal of Rice Science , 14(2): 115-118 (in Chinese)
34
Zeng Y W, Zhang H L, Li Z C, Shen S Q, Sun J L, Wang M X, Liao D Q, Liu X, Wang X K, Xiao F H, Wen G S (2007). Evaluation of genetic diversity in the rice landraces (Oryza sativa L.) in Yunnan, China. Breeding Science , 57(2): 91-99 doi: 10.1270/jsbbs.57.91
35
Zhang H L, Sun J L, Wang M X, Liao D Q, Zeng Y W, Shen S Q, Yu P, Mu P, Wang X K, Li Z C (2006). Genetic structure and phylogeography of rice landraces in Yunnan, China, revealed by SSR. Genome , 50(1): 72-83 doi: 10.1139/G06-130
