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Frontiers of Agriculture in China

ISSN 1673-7334

ISSN 1673-744X(Online)

CN 11-5729/S

Front Agric Chin    2009, Vol. 3 Issue (2) : 130-139     DOI: 10.1007/s11703-009-0033-y
RESEARCH ARTICLE |
Correlation between allele sizes of microsatellites and phenotypic variations in rice landraces
Yawen ZENG1(), Shuming YANG1, Juan DU1, Xiaoying PU1, Hongliang ZHANG2, Zichao LI2(), Luxiang WANG3, Jiafu LIU3, Fenghui XIAO4
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
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Abstract  

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.

Keywords allele size of microsatellite      phenotypic traits      mineral elements      correlation      rice landraces     
Corresponding Authors: ZENG Yawen,Email:zengyw1967@126.com; LI Zichao,Email:lizichao@cau.edu.cn   
Issue Date: 05 June 2009
URL:  
http://academic.hep.com.cn/fag/EN/10.1007/s11703-009-0033-y     OR     http://academic.hep.com.cn/fag/EN/Y2009/V3/I2/130
markers629 accessionsrepeat motif*linking traits of microsatellites from http://www.shigen.nig.ac.jp/ rice/oryzabase/update/htmlmain references
no. allelesize of allele/bp
RM511103-121(GA)14yield-enhancing, grains per panicle, percent germination, head rice grain, grain length/width ratioXiao et al., 1996; Thomson et al., 2003; Liang et al., 2004
RM81A12101-120(TCT)10grain yield per plant, 1000-grain weight, plant heightCui et al., 2004
RM2118142-162(TC)4T3C3(TC)(CT)2yield-improving, grain width, days to headingMiyata et al., 2007
RM26317149-197(CT)34broken rice grain, crushed rice grain, 1000-grain weight, spotted leafSeptiningsih et al., 2003; Xu et al., 2004
RM605160-168(AATT)5AATCT(AATT)high-tillering dwarf 1, days to heading, shatteringThomson et al., 2003; Septiningsih et al., 2003
RM23215137-164(CT)241000-grain weight, panicles per plant, panicle length, grains per panicle, grain yield per plant, cracked grainTan et al., 2007;Yoshida et al., 2002
RM24121111-148(GA)31Panicles per plant, plant heightThomson et al., 2003; Cui et al., 2004
RM25515112-159(AGG)5(AG)2(GA)161000-grain weight, panicle size, panicles per plant, panicle neck diameterXu et al., 2004;Yoshida et al., 2002
RM24911121-166(AG)5A2(AG)14tillers per plant, panicles per plant, grains number per plant, grain thickness, 1000-grain weight, panicle lengthPradeep et al., 2005; Miyata et al., 2007;Abdelkhalik et al., 2005
RM22512124-151(CT)18nitrogen use efficiency, grain breadthhttp://www.cropscience.org.au/icsc2004/poster/3/4/1/1296_senthilvels.htm
RM2532298-187(GA)25percent head rice, amylase content, alkali spreading score, protein content, grain length, grain length /width ratio, days to maturity, heading date, awn lengthXiao et al., 1996; Linh et al., 2006
RM1812150-172(GA)4AA(GA)(AG)16frizzle panicle, grain yield, tillers per plant, grains per panicle, heading dateDuan et al., 2003
RM23417110-170(CT)25days to heading, days to maturity, maximum root lengthThomson et al., 2003; Miyata et al., 2007
RM22317137-170(CT)20panicle per plant, days to heading, panicle length;Pradeep et al., 2005; Miyata et al., 2007
RM25740123-210(CT)24cold resistance, heading dateMiyata et al., 2007
RM2449149-164(CT)4(CG)3C(CT)6fertility restorer genesJing et al., 2000
RM25813131-152(GA)21(GGA)3spikelet fertility, 1000-grain weight, tiller number, heading dateCui et al., 2004; Miyata et al., 2007
RM22418124-162(AAG)8(AG)13plant height, tillers per plant, panicle length, root-shoot ratioMiyata et al., 2007
RM2351895-137(CT)24panicles per plantThomson et al., 2003
RM24728124-184(CT)16phosphorus deficiency, plant heightThomson et al., 2003
Tab.1  Allele size of microsatellites in Yunnan rice landraces and its linking gene or traits
markersPKCaMgFeZnCuMn
RM5-0.0110.087*0.080-0.022-0.017-0.0010.036-0.013
RM81A-0.144**-0.086*-0.0140.0030.0030.076-0.129**0.033
RM211-0.0490.002-0.0430.015-0.0260.0080.0360.029
RM2630.0020.001-0.0580.0350.0010.0640.0760.042
RM600.012-0.0280.0460.0240.042-0.061-0.096*-0.091*
RM2320.101*-0.0180.0070.042-0.0150.0060.001-0.002
RM2410.0010.006-0.047-0.012-0.0560.0070.0120.046
RM2550.0600.0740.091*0.047-0.0050.023-0.0230.051
RM249-0.0410.0360.018-0.022-0.051-0.037-0.062-0.066
RM225-0.075-0.087*-0.059-0.101*-0.083*0.037-0.027-0.093*
RM253-0.104*-0.092*-0.009-0.0630.0240.015-0.103*0.002
RM180.035-0.0210.0250.088*-0.0130.017-0.0130.033
RM2340.096*-0.0260.042-0.0200.007-0.006-0.0470.014
RM2230.0190.0520.0440.019-0.0090.0020.027-0.025
RM257-0.0020.037-0.052-0.010-0.0200.028-0.024-0.046
RM244-0.092*-0.085*0.016-0.091*-0.030-0.002-0.065-0.011
RM2580.076-0.036-0.0310.020-0.0120.0390.028-0.004
RM224-0.0340.006-0.024-0.0340.0090.0330.042-0.034
RM2350.0530.110**-0.0070.0580.0240.036-0.0420.047
RM2470.0290.0590.101*0.0470.0510.010-0.084*0.041
Tab.2  Correlation coefficients between allele size of microsatellites and mineral concentration contents
markerschromosomeplant heighttillers per plantpanicles per plantdays to headingflagleaf lengthflagleaf width
RM51-0.019-0.089*0.0370.0540.0370.064
RM81A10.0420.0590.0570.0130.137-0.047
RM2112-0.052-0.0230.012-0.019-0.0010.012
RM2632-0.085*-0.028-0.015-0.036-0.049-0.098*
RM603-0.109**-0.0020.022-0.084*0.058-0.020
RM23230.0570.0430.0660.143**0.070-0.043
RM24140.039-0.0700.0580.0780.0210.006
RM25540.0290.0700.0420.0710.0650.009
RM24950.0440.033-0.100*0.04230.0470.005
RM2256-0.140**-0.015-0.001-0.0275-0.0310.042
RM25360.012-0.0280.0770.06410.033-0.010
RM1870.0450.095*0.0550.02750.068-0.078
RM23470.022-0.022-0.077-0.01040.0370.043
RM22380.037-0.008-0.0680.2001**0.052-0.053
RM25790.0280.126**0.0060.04170.138**0.055
RM244100.0420.0760.0530.05010.0580.008
RM25810-0.039-0.026-0.108**0.0114-0.0430.008
RM22411-0.151**-0.085*-0.042-0.1134**-0.086*0.021
RM235120.023-0.0520.0440.0228-0.032-0.048
RM24712-0.0060.082*0.049-0.01400.047-0.012
Tab.3  Correlation coefficients between allele size of microsatellites and plant traits
markers1000-grainweightgrain lengthgrain widthgrain length/width ratiograin thicknessrice lengthricewidthrice thicknessshattering
RM5-0.089*0.273**-0.195**0.294**-0.130**0.148**-0.220**-0.133**-0.134**
RM81A0.0590.189**-0.186**0.233**-0.0290.010-0.194**-0.209**-0.187**
RM211-0.080-0.121**0.101*-0.134**0.025-0.134**0.079-0.0320.092*
RM263-0.183**-0.287**0.127**-0.246**0.077-0.224**0.194**0.0520.070
RM60-0.079-0.045-0.0680.0190.016-0.078-0.025-0.024-0.010
RM232-0.028-0.020-0.0530.027-0.0450.025-0.048-0.026-0.045
RM2410.0010.064-0.089*0.089*-0.0410.050-0.067-0.066-0.013
RM2550.0570.180**-0.162**0.212**-0.125**0.073-0.178**-0.134**-0.089*
RM249-0.0080.041-0.0560.0660.024-0.023-0.069-0.047-0.092*
RM225-0.141**-0.155**0.103*-0.174**0.025-0.126**0.124**0.028-0.011
RM253-0.069-0.056-0.001-0.0350.011-0.087*0.035-0.0190.030
RM180.0460.198**-0.148**0.221**-0.0790.148**-0.166**-0.028-0.051
RM234-0.073-0.0790.014-0.0600.074-0.0790.0680.0060.090*
RM2230.013-0.0320.037-0.026-0.0120.0120.0550.033-0.012
RM2570.0090.214**-0.239**0.291**-0.144**0.138**-0.241**-0.151**0.085*
RM2440.0370.210**-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**0.0490.067
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**-0.0520.209**0.167**0.086*
RM2470.0270.244**-0.188**0.265**-0.089*0.176**-0.190**-0.087*-0.068
Tab.4  Correlation coefficients between allele size of microsatellites and grains traits
markers1-2 internode lengthpanicle lengthawn lengthfilled grainsper panicleblighted grains per panicletotal grains per panicleseedsetting rategraindensity
RM5-0.251**-0.013-0.055-0.0390.022-0.035-0.013-0.029
RM81A-0.369**0.098*-0.130**0.0050.0450.055-0.0290.010
RM2110.156**-0.0210.041-0.114**0.129**0.019-0.120**0.010
RM2630.298**-0.0450.061-0.0350.088*0.050-0.0350.085*
RM60-0.016-0.0130.019-0.0570.016-0.075-0.047-0.019
RM2320.0170.039-0.020-0.0090.0700.015-0.0610.049
RM241-0.049-0.001-0.025-0.016-0.043-0.0030.042-0.057
RM255-0.262**0.036-0.093*0.029-0.0090.0220.0390.009
RM249-0.0740.0380.009-0.009-0.015-0.0100.054-0.025
RM2250.113**-0.0350.046-0.158**0.133**0.044-0.149**0.006
RM2530.0060.035-0.0390.0220.0450.042-0.0270.036
RM18-0.259**-0.011-0.0360.015-0.066-0.025-0.082*-0.057
RM2340.0520.0200.061-0.0360.0390.043-0.028-0.004
RM2230.094*0.100*0.059-0.0740.088*-0.005-0.110**-0.031
RM257-0.285**0.036-0.111**0.046-0.0420.0600.090*-0.023
RM244-0.293**0.032-0.0550.062-0.0410.0330.0460.023
RM2580.279**0.0030.130**-0.0540.099*-0.072-0.087*0.044
RM2240.438**-0.0570.090*-0.0400.098*0.071-0.0720.086*
RM2350.303**-0.0050.070-0.0800.135**0.055-0.134**0.030
RM247-0.257**0.083*-0.101*0.060-0.0340.0250.056-0.005
Tab.5  Correlation coefficients between allele size of microsatellites and panicle traits
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