Association and structure analysis of some of rice (Oryza sativa L.) genetic resources based on microsatellite markers

Document Type : Research Paper

Authors

1 Ph. D. Graduated, Dept. of Agronomy and Plant Breeding, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran

2 Assist. Prof., Dept. of Agronomy and Plant Breeding, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran

3 Prof., Dept. of Agronomy and Plant Breeding, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran

4 Research Assist. Prof., Dept. of Seed Improvement, Rice Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Rasht, Iran

Abstract

The economic value of cultivar depends on different characteristics. Thus detailed knowledge on genetic behavior and identification of genomic loci involved in control of these traits could help to breeder to improve plant cultivars. In this investigation, relation and linkage among 25 microsatellite markers with some of important agromorphological traits in 121 different rice cultivars and lines were evaluated based on GLM and MLM association models using the Structure and Tassel software. Based on the 25 microsatellite markers used in this study, population genetic structure divided into five subpopulations (K=5) that barplat results also confirmed it. In association analysis based on GLM and MLM models, 26 and 30 loci showed significant relations with the evaluated traits, respectively, and confirmed considerable variations of this studied traits. In the present study, identified common markers between of some of assayed traits such as significant relation of RM5 marker with flag leaf length and width traits and RM3355 with days to 50% flowering and plant height traits can be due to pleiotropic effects or linkage between of genomic regions involved in these traits. Also RM190 and RM6080 markers with higher R2 were related to paddy length and grain yield, respectively, that these related region could be saturated and sequenced after complementary experiments and confirmation for identification of coding genes of these traits.

Highlights

Agrama, H. A., Eizenga, G. C. and Yan, W. 2007. Association mapping of yield and its components in rice cultivars. Molecular Breeding 19: 341-356.##Allahgholipour, M., Mohammad Salehi, M. S. and Ebadi, A. A. 2004. An evaluation of genetic diversity, and classification of rice varieties. Iranian Journal of Agricultural Science 35 (4):
973- 981. (In Persian with English Abstract).##Al-Maskri, A. H., Sajjad, M. and Khan, S. H. 2012. Association mapping: A step forward to discovering new alleles for crop improvement. International Journal of Agriculture and Biology 14: 153-160.##Andersen, J. R., Zein, I., Wenzel, G., Krützfeldt, B., Eder, J., Ouzunova, M. and Lübberstedt, T. 2007. High levels of linkage disequilibrium and associations with forage quality at a phenylalanine ammonia-lyase locus in European maize (Zea mays L.) inbreds. Theoretical and Applied Genetics 114: 307-319.##Anderson, J. A., Churchill, G. A., Autrique, J. E. and Tanksley, S. D. 1993. Optimizing parental selection for genetic linkage maps. Genome 36: 181-186.##Breseghello, F. and Sorrells, M. E. 2006. Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172: 1165-1177.##Ching, A., Caldwell, K. S., Jung, M., Dolan, M., Smith, O. S., Tingey, S., Morgante, M. and Rafalski, A. J. 2002. SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genetics 3: 19.##Das, B., Sengupta, S., Parida, S. K., Roy, B., Gosh, M., Prasad, M. and Ghose, T. K. 2013. Genetic diversity and population structure of rice landraces from Eastern and North Eastern States of India. BMC Genetics 14: 71.##DeWan, A., Liu, M., Hartman, S. and Zhang, S. S. M. 2006. HTRA1 promoter polymorphism in wet age-related macular degeneration. Science 314 (5801): 989-992.##Doerge, R. W. 2002. Mapping and analysis of quantitative trait loci in experimental populations. Nature Reviews Genetics 3 (1): 43-52.##Evanno, G., Regnaut, S. and Goudet, J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Molecular Ecology 14 (8): 2611-2620.##FAO. 2013. Food and agriculture organization of the United States. Available online at: http://faostat.fao.org/.##Gupta, P. K., Rustgi, S. and Kulwal, P. L. 2005. Linkage disequilibrium and association studies in higher plants: Present status and future prospects. Plant Molecular Biology 57: 461-485.##IRRI. 2002. Standard evaluation system for rice. International Rice Research Institute, Manilla, Philippines.##Jia, L. M., Yan W. G., Zhu, C. S., Agrama, H. A., Jackson, A., Yeater, K., Li, X. B., Huang, B. H., Hu, B. L., McClung, A. and Wu, D. X. 2012. Allelic analysis of sheath blight resistance with association mapping in rice. PLoS One 7: e32703.##Jin, L., Lu, Y., Xiao, P., Sun, M., Corke, H. and Bao, J. S. 2010. Genetic diversity and population structure of a diverse set of rice germplasm for association mapping. Theoretical and Applied Genetics 121: 475-487.##Jun, T. H., Van, K., Kim, M. Y., Lee, S. H. and Walker, D. R. 2008. Association analysis using SSR markers to find QTL for seed protein content in soybean. Euphytica 62: 179-191.##Kiani, Gh. and Nematzadeh, Gh. 2012. Assessment of genetic variability of rice fertility restorer lines based on morphological traits. Journal of Research and Development 97: 122-130. (In Persian with English Abstract).##Kovi, M. R., Hu, Y., Bai, X. and Xiang, Y. 2015. QTL mapping for thermo-sensitive heading date in rice. Euphytica 205: 51-62.##Liu, L., Wang, L., Yao, J., Zheng, Y. and Zhao, C. 2010. Association mapping of six agronomic traits on chromosome 4A of Wheat (Triticum aestivum L.). Molecular Plant Breeding 1 (5): 1-10.##Maccaferri, M., Sanguineti, M. C., Demontis, A. and El-Ahmed, A. 2010. Association mapping in durum wheat grown across a broad range of water regimes. Journal of Experimental Botany 14: 287-293.##Mackay, T. F., Stone, E. A. and Ayroles, J. F. 2009. The genetics of quantitative traits: Challenges and prospects. Nature Reviews Genetics 10 (8): 565-577.##Mardani, Z., Rabiei, B., Sabouri, H. and Sabouri, A. 2013. Mapping of QTLs for Germination Characteristics under Non-stress and Drought Stress in Rice. Rice Science 20 (6): 391-399.##Mauricio, R. 2001. Mapping quantitative trait loci in plants: Uses and caveats for evolutionary biology. Nature Reviews Genetics 2 (5): 370-381.##Mokrani, L., Gentzbittel, L., Azanza, F., Fitamant, L., Al-Chaarani, G. and Sarrafi, A. 2002. Mapping and analysis of quantitative trait loci for grain oil content and agronomic traits using AFLP and SSR in sunflower (Helianthus annuus L.). Theoretical and Applied Genetics 106 (1): 149-156.##Pasam, R. K., Sharma, R., Malosetti, M. and Van Eeuwijk, F. A. 2012. Genome-wide association studies for agronomical traits in a world wide spring barley collection. BMC Plant Biology 12 (1): 16.##Pritchard, J. K. and Donnelly, P. 2001. Case-control studies of association in structured or admixed populations. Theoretical Population Biology 60: 227-237.##Pritchard, J. K., Stephens, M. and Donnelly, P. 2000. Inference of population structure using multilocus genotype data. Genetics 155 (2): 945-959.##Rahimi, M., Rabiei, B., Ramezani, M. and Movafegh, S. 2010. Evaluation of agronomical traits and variables determination for yield improvement of rice. Iranian Journal of Field Crops Research 8 (1): 111-119. (In Persian with English Abstract).##Remington, D. L., Thornsberry, J. M., Matsuoka, Y., Wilson, L. M., Whitt, S. R., Doebley, J., Kresovich, S., Goodman, M. M. and Buckler, E. S. 2001. Structure of linkage disequilibrium and phenotypic associations in the maize genome. PNAS 98: 11479-11484.##Rogers, S. O. and Bendich, A. J. 1985. Extraction of DNA from milligram amounts of fresh, herbarium and mummified plant tissues. Plant Molecular Biology 5 (2): 69-76.##Sabouri, A., Rabiei, B., Toorchi, M., Aharizad, S. and Moumeni, A. 2012. Mapping quantitative trait loci (QTL) associated with cooking quality in rice (Oryza sativa L.). Australian Journal of Crop Science 6 (5): 808-814.##Semagn, K., Bjørnstad, A. and Xu, Y. 2010. The genetic dissection of quantitative traits in crops. Electronic Journal of Biotechnology 13 (5): 1-45.##Slatkin, M. 1994. An exact test for neutrality based on the Ewens snampling distribution. Genetic Research 64: 71-74.##Spataro, G., Tiranti, B., Arcaleni, P. and Bellucci, E. 2011. Genetic diversity and structure of a worldwide collection of Phaseolus coccineus L. Theoretical and Applied Genetics 122 (7):
1281-1291.##Triphati, K. K., Govila, O. P., Warreir, R. and Ahuja, V. 2011. Biology of Oryza sativa L. (Rice). Ministry of Environment and Forests Government of India. Department of Biotechnology, Ministry of Science and Technology Government of India. pp: 1-63.##Tuberosa, R., Gill, B. S. and Quarrie, S. A. 2002. Cereal genomics: Ushering in a brave new world. Plant Molecular Biology 48 (5): 445-449.##Vanniarajan, C., Vinod, K. K. and Pereira, A. 2012. Molecular evaluation of genetic diversity and association studies in rice (Oryza sativa L.). Genetics 91: 1-11.##Wen, W., Mei, H., Feng, F., Yu, S., Huang, Z., Wu, J., Chen, L., Xu, X. and Luo, L. 2009. Population structure and association mapping on chromosome 7 using a diverse panel of Chinese germplasm of rice (Oryza sativa L.). Theoretical and Applied Genetics 119: 459-470.##Yu, J. and Buckler, E. S. 2006. Genetic association mapping and genome organization of maize. Current Opinion in Biotechnology 17 (2): 155-160.##Yu, J. M., Pressoir, G., Briggs, W. H. and Bi, I. V. 2006. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Natural Genetics 38: 203-208.##Zheng, H., Wang, J., Zhao, H., Liu, H., Sun, J., Guo, L. and Zou, D. 2015. Genetic structure, linkage disequilibrium and association mapping of salt tolerance in japonica rice germplasm at the seedling stage. Molecular Breeding 35: 152. https://doi.org/10.1007/s11032-015-0342-1.##Zhu, J., Gale, M. D., Quarrie, S., Jackson, M. T. and Bryan, G. J. 1998. AFLP markers for the study of rice biodiversity. Theoretical and Applied Genetics 96: 602-611.##Zietkiewicz, E., Rafalski, A. and Labuda, D. 1994. Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20 (2): 176-183.

Keywords

References

Agrama, H. A., Eizenga, G. C. and Yan, W. 2007. Association mapping of yield and its components in rice cultivars. Molecular Breeding 19: 341-356.##Allahgholipour, M., Mohammad Salehi, M. S. and Ebadi, A. A. 2004. An evaluation of genetic diversity, and classification of rice varieties. Iranian Journal of Agricultural Science 35 (4):
973- 981. (In Persian with English Abstract).##Al-Maskri, A. H., Sajjad, M. and Khan, S. H. 2012. Association mapping: A step forward to discovering new alleles for crop improvement. International Journal of Agriculture and Biology 14: 153-160.##Andersen, J. R., Zein, I., Wenzel, G., Krützfeldt, B., Eder, J., Ouzunova, M. and Lübberstedt, T. 2007. High levels of linkage disequilibrium and associations with forage quality at a phenylalanine ammonia-lyase locus in European maize (Zea mays L.) inbreds. Theoretical and Applied Genetics 114: 307-319.##Anderson, J. A., Churchill, G. A., Autrique, J. E. and Tanksley, S. D. 1993. Optimizing parental selection for genetic linkage maps. Genome 36: 181-186.##Breseghello, F. and Sorrells, M. E. 2006. Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172: 1165-1177.##Ching, A., Caldwell, K. S., Jung, M., Dolan, M., Smith, O. S., Tingey, S., Morgante, M. and Rafalski, A. J. 2002. SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genetics 3: 19.##Das, B., Sengupta, S., Parida, S. K., Roy, B., Gosh, M., Prasad, M. and Ghose, T. K. 2013. Genetic diversity and population structure of rice landraces from Eastern and North Eastern States of India. BMC Genetics 14: 71.##DeWan, A., Liu, M., Hartman, S. and Zhang, S. S. M. 2006. HTRA1 promoter polymorphism in wet age-related macular degeneration. Science 314 (5801): 989-992.##Doerge, R. W. 2002. Mapping and analysis of quantitative trait loci in experimental populations. Nature Reviews Genetics 3 (1): 43-52.##Evanno, G., Regnaut, S. and Goudet, J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Molecular Ecology 14 (8): 2611-2620.##FAO. 2013. Food and agriculture organization of the United States. Available online at: http://faostat.fao.org/.##Gupta, P. K., Rustgi, S. and Kulwal, P. L. 2005. Linkage disequilibrium and association studies in higher plants: Present status and future prospects. Plant Molecular Biology 57: 461-485.##IRRI. 2002. Standard evaluation system for rice. International Rice Research Institute, Manilla, Philippines.##Jia, L. M., Yan W. G., Zhu, C. S., Agrama, H. A., Jackson, A., Yeater, K., Li, X. B., Huang, B. H., Hu, B. L., McClung, A. and Wu, D. X. 2012. Allelic analysis of sheath blight resistance with association mapping in rice. PLoS One 7: e32703.##Jin, L., Lu, Y., Xiao, P., Sun, M., Corke, H. and Bao, J. S. 2010. Genetic diversity and population structure of a diverse set of rice germplasm for association mapping. Theoretical and Applied Genetics 121: 475-487.##Jun, T. H., Van, K., Kim, M. Y., Lee, S. H. and Walker, D. R. 2008. Association analysis using SSR markers to find QTL for seed protein content in soybean. Euphytica 62: 179-191.##Kiani, Gh. and Nematzadeh, Gh. 2012. Assessment of genetic variability of rice fertility restorer lines based on morphological traits. Journal of Research and Development 97: 122-130. (In Persian with English Abstract).##Kovi, M. R., Hu, Y., Bai, X. and Xiang, Y. 2015. QTL mapping for thermo-sensitive heading date in rice. Euphytica 205: 51-62.##Liu, L., Wang, L., Yao, J., Zheng, Y. and Zhao, C. 2010. Association mapping of six agronomic traits on chromosome 4A of Wheat (Triticum aestivum L.). Molecular Plant Breeding 1 (5): 1-10.##Maccaferri, M., Sanguineti, M. C., Demontis, A. and El-Ahmed, A. 2010. Association mapping in durum wheat grown across a broad range of water regimes. Journal of Experimental Botany 14: 287-293.##Mackay, T. F., Stone, E. A. and Ayroles, J. F. 2009. The genetics of quantitative traits: Challenges and prospects. Nature Reviews Genetics 10 (8): 565-577.##Mardani, Z., Rabiei, B., Sabouri, H. and Sabouri, A. 2013. Mapping of QTLs for Germination Characteristics under Non-stress and Drought Stress in Rice. Rice Science 20 (6): 391-399.##Mauricio, R. 2001. Mapping quantitative trait loci in plants: Uses and caveats for evolutionary biology. Nature Reviews Genetics 2 (5): 370-381.##Mokrani, L., Gentzbittel, L., Azanza, F., Fitamant, L., Al-Chaarani, G. and Sarrafi, A. 2002. Mapping and analysis of quantitative trait loci for grain oil content and agronomic traits using AFLP and SSR in sunflower (Helianthus annuus L.). Theoretical and Applied Genetics 106 (1): 149-156.##Pasam, R. K., Sharma, R., Malosetti, M. and Van Eeuwijk, F. A. 2012. Genome-wide association studies for agronomical traits in a world wide spring barley collection. BMC Plant Biology 12 (1): 16.##Pritchard, J. K. and Donnelly, P. 2001. Case-control studies of association in structured or admixed populations. Theoretical Population Biology 60: 227-237.##Pritchard, J. K., Stephens, M. and Donnelly, P. 2000. Inference of population structure using multilocus genotype data. Genetics 155 (2): 945-959.##Rahimi, M., Rabiei, B., Ramezani, M. and Movafegh, S. 2010. Evaluation of agronomical traits and variables determination for yield improvement of rice. Iranian Journal of Field Crops Research 8 (1): 111-119. (In Persian with English Abstract).##Remington, D. L., Thornsberry, J. M., Matsuoka, Y., Wilson, L. M., Whitt, S. R., Doebley, J., Kresovich, S., Goodman, M. M. and Buckler, E. S. 2001. Structure of linkage disequilibrium and phenotypic associations in the maize genome. PNAS 98: 11479-11484.##Rogers, S. O. and Bendich, A. J. 1985. Extraction of DNA from milligram amounts of fresh, herbarium and mummified plant tissues. Plant Molecular Biology 5 (2): 69-76.##Sabouri, A., Rabiei, B., Toorchi, M., Aharizad, S. and Moumeni, A. 2012. Mapping quantitative trait loci (QTL) associated with cooking quality in rice (Oryza sativa L.). Australian Journal of Crop Science 6 (5): 808-814.##Semagn, K., Bjørnstad, A. and Xu, Y. 2010. The genetic dissection of quantitative traits in crops. Electronic Journal of Biotechnology 13 (5): 1-45.##Slatkin, M. 1994. An exact test for neutrality based on the Ewens snampling distribution. Genetic Research 64: 71-74.##Spataro, G., Tiranti, B., Arcaleni, P. and Bellucci, E. 2011. Genetic diversity and structure of a worldwide collection of Phaseolus coccineus L. Theoretical and Applied Genetics 122 (7):
1281-1291.##Triphati, K. K., Govila, O. P., Warreir, R. and Ahuja, V. 2011. Biology of Oryza sativa L. (Rice). Ministry of Environment and Forests Government of India. Department of Biotechnology, Ministry of Science and Technology Government of India. pp: 1-63.##Tuberosa, R., Gill, B. S. and Quarrie, S. A. 2002. Cereal genomics: Ushering in a brave new world. Plant Molecular Biology 48 (5): 445-449.##Vanniarajan, C., Vinod, K. K. and Pereira, A. 2012. Molecular evaluation of genetic diversity and association studies in rice (Oryza sativa L.). Genetics 91: 1-11.##Wen, W., Mei, H., Feng, F., Yu, S., Huang, Z., Wu, J., Chen, L., Xu, X. and Luo, L. 2009. Population structure and association mapping on chromosome 7 using a diverse panel of Chinese germplasm of rice (Oryza sativa L.). Theoretical and Applied Genetics 119: 459-470.##Yu, J. and Buckler, E. S. 2006. Genetic association mapping and genome organization of maize. Current Opinion in Biotechnology 17 (2): 155-160.##Yu, J. M., Pressoir, G., Briggs, W. H. and Bi, I. V. 2006. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Natural Genetics 38: 203-208.##Zheng, H., Wang, J., Zhao, H., Liu, H., Sun, J., Guo, L. and Zou, D. 2015. Genetic structure, linkage disequilibrium and association mapping of salt tolerance in japonica rice germplasm at the seedling stage. Molecular Breeding 35: 152. https://doi.org/10.1007/s11032-015-0342-1.##Zhu, J., Gale, M. D., Quarrie, S., Jackson, M. T. and Bryan, G. J. 1998. AFLP markers for the study of rice biodiversity. Theoretical and Applied Genetics 96: 602-611.##Zietkiewicz, E., Rafalski, A. and Labuda, D. 1994. Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20 (2): 176-183.
Cereal Research
Volume 7, Issue 1
June 2017
Pages 1-16

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