Correlation between allele sizes of microsatellites and phenotypic variations in rice landraces

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

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Acknowledgements

This research was supported by the National Natural Science Foundation of China (Grant Nos. 30660092 and 30260060), the National Basic Research Program of China (also called “973” Program, No. 2004CB117201) and Yunnan Introduction and Foster Talent, China (No. 2005PY01-14), Cooperation Program between Province and Zhejiang University from Yunnan Provincial Scientific and Technology Department, China (No. 2006YX12). We are grateful to Professor Talekar N S of Yunnan Agricultural University for his suggestions and assistance in manuscript preparation and Shen Shiquan for his help in experiments.

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2014 Higher Education Press and Springer-Verlag Berlin Heidelberg