Association mapping of salinity and alkalinity tol

Authors: Di Cui Changying Xu Chungang Yang Qixing Zhang Junguo Zhang Xiaoding Ma Yongli Qiao Guilan Cao Sanyuan Zhang Longzhi Han

Publish Date: 2014/09/27

Volume: 62, Issue: 4, Pages: 539-550

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Abstract

Salinity and alkalinity seriously threaten global rice production As a consequence elucidation of the genetic basis of salinity and alkalinity tolerance is crucial for rice breeding To identify genetic marker loci/QTLs associated with salinity and alkalinity tolerance we performed association mapping based on different statistical models using 347 rice accessions from all over the world Salinity tolerance for all traits was evaluated on saline land along the seashore of Hebei while alkalinity tolerance at the seedling stage was assessed in the alkaline soil of paddy fields in Jilin A total of 148 SSRs were used for genotyping Within the entire population 641  of SSR locus pairs were in significant linkage disequilibrium LD P  005 Most of this LD was due to the overall population structure as the percentage of locus pairs in LD was much lower within each subpopulation ranging from 212 to 324  LD decayed with genetic distance indicating that linkage was a main cause of LD Model comparisons indicated that the Q + K model which controls for both population structure Q and relative kinship K performed better than other models A total of 40 markers were identified 25 related to salinity tolerance and 15 related to alkalinity tolerance Of the identified markers 17 were located either in or near regions in which QTLs for salinity and alkalinity tolerance have been previously reported Furthermore we identified three of these markers—RM475 RM567 and RM505—in rice under both salinity and alkalinity stress conditions These results highlight target regions for fine mapping cloning and molecular breeding by design for rice salinity and alkalinity toleranceWe thank the Chinese National Germplasm Bank for providing the improved japonica rice seeds This work was supported by the National Key Technology Research and Development Program of China 2013BAD01B022 the Project of 973 2010CB1259045 Science and Technology Innovation Project of CAAS and The platform of National Crop Germplasm Resources the Protective Program of Crop Germplasm of China NB201321301352501 the Basic Work Project of the Ministry of Science and Technology 2007FY11050012 International Cooperation Project PJ008685

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