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United States Department of Agriculture

Agricultural Research Service

Title: Genetic Diversity Analyzed by Microsatellite Markers among Rice (Oryza Sativa L.) Genotypes with Different Adaptations to Saline Soils

Authors
item Zeng, Linghe
item Kwon, Taek-Ryoun - NAT INS AG BIOTEC S.KOREA
item Liu, Xuan
item Wilson, Clyde
item Grieve, Catherine
item Gregorio, Glenn - INT RICE INS, PHILIPPINES

Submitted to: Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 5, 2004
Publication Date: April 20, 2004
Citation: Zeng, L., Kwon, T.-R., Liu, X., Wilson, C., Grieve, C.M., Gregorio, G.B. 2004. Genetic diversity analyzed by microsatellite markers among rice genotypes with different adaptations to saline soils. Plant Science. 166:1275-1285.

Interpretive Summary: The success of salt tolerance breeding programs employing traditional approaches has been limited in the past decades. However, crosses between parental lines with maximized genetic distance can increase the success in salt tolerance breeding. This study was designed to characterize a subset of rice germplasm with different adaptations to saline soils for their genetic diversity using DNA markers (microsatellites). Thirty-three rice genotypes, consisted of breeding lines, commercial cultivars and land races, were grown in sand tanks under greenhouse condition and irrigated with nutrient solutions. Plants were treated with sodium chloride and calcium chloride of 6:1 molar ratio (6.5 dS/m). A great amount of genetic diversity was identified using 25 microsatellite markers among the rice genotypes. The genetic similarity among the germplasm was calculated based on microsatellite markers using the NTSYS-pc statistical package. A dendrogram of 33 rice genotypes was created by using a cluster method, UPGMA, based on the genetic similarity. The rice genotypes grouped into five clusters in the dendrogram. Among the clusters, a few closely related sister breeding lines could be distinguished at 80% similarity. Thirty percent of the genetic variations detected in twenty breeding lines were not identified in the commercial cultivars analyzed. These variations may provide favorable genetic combinations if the breeding lines are used for improving salt tolerance. These results support the contention that microsatellite marker systems can distinguish genetically close breeding lines and cultivars, thereby providing a powerful tool to design crossing schemes in salt tolerance breeding programs. However, there was a lack of significant relation between the genetic similarity of microsatellite markers and the similarity described by salt tolerance related morphological characters. The scientific explanation for this phenomenon has been discussed. We suggest that both evaluation of morphological characters for salt tolerance and characterization of genetic similarity among genotypes are necessary for selection of parents in the designs of crossing schemes.

Technical Abstract: The success of salt tolerance breeding programs employing traditional screening and selection has been limited in the past decades. However, intermating between parental genotypes with maximized genetic distance can increase the probability of identifying salt tolerant recombinants in segregating populations. This study was designed to characterize a subset of rice germplasm with different adaptations to saline soils for their genetic diversity using microsatellite markers. Plants of 33 genotypes were grown in sand tanks under greenhouse condition and irrigated with Yoshida nutrient solutions. Two salt levels were imposed with electrical conductivities of 0.9 dS/m (control) and 6.5 dS/m (6:1 molar ratio of NaCl and CaCl2). A total of 123 alleles were generated at 25 microsatellite loci among the 33 genotypes. Genotypes of ssp. japonica grouped into three clusters, A1, A2 and A3 and those of ssp. indica grouped into two clusters, B1 and B2, based on the microsatellite markers. Among them, a few closely related sister breeding lines could be distinguished at 80% similarity. These genotypes grouped into three clusters, Clusters 1, 2 and 3, based on the morphological characters related to salt tolerance. Morphological characters under salt stress were diversified among the clusters by microsatellite markers. Thirty percent of the alleles detected in twenty breeding lines were not identified in the cultivars analyzed. These alleles may provide favorable allelic combinations if the breeding lines are used for intermating crosses. These results support the contention that microsatellite marker systems can distinguish genetically close breeding lines and cultivars, thereby providing a powerful tool to design crossing schemes that maximize genetic variation in breeding populations. There was a lack of significant relation between the genetic similarity at microsatellite loci and the similarity described by salt tolerance related morphological characters. We suggest that both evaluation of morphological characters for salt tolerance and characterization of genetic similarity among genotypes are necessary for selection of parents in the designs of crossing schemes.

Last Modified: 7/28/2014
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