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Partnerships for enhanced engagement in research (PEER) SCIENCE
Cycle 2 (2012 Deadline)

Validation of salt tolerance determinants in rice (Oryza sativa L. indica) landrace Horkuch and its segregating population by 2b-RAD sequencing and RNA-seq analysis under stress

PI: Zeba I. Seraj (University of Dhaka), with co-PI Abdelbagi Ismail (International Rice Research Institute)
U.S. Partner: Thomas Juenger (University of Texas at Austin)
Project Dates: August 2013 to October 2015

Bangladesh is the world’s fourth-largest rice-producing country and is an enriched germplasm reservoir with 6,500 varieties of wild accessions, landraces, and modern varieties. Salt-tolerant rice landraces are of particular interest as donors of salt tolerance traits. The Bangladesh Rice Research Institute has released six slightly to moderately tolerant modern rice varieties, but for various reasons most have not be widely adopted by farmers. In view of the predicted increase in salinity levels in Bangladesh, more tolerant varieties are needed. Horkuch is a rice landrace popular with some farmers in the southwestern coastal areas in Satkhira, but it has low yields. Farmers in this area cannot grow modern high-yielding varieties due to salinity in the soil. Horkuch has been identified as salt tolerant at the seedling stage, and subsequently its yield-related traits under stress were also found to be superior. In order to determine exactly which genes from Horkuch could be integrated most productively into existing rice varieties, intensive study of the Horkuch landrace is essential.

Bangladesh Partnership Picture 1 The rice plants are set up for F2 phenotyping (Photo courtesy Zeba Seraj).

Bangladesh Partnership Picture 2 During the phenotyping of F3 plants, the research team measures SES values (Photo courtesy Zeba Seraj).

As part of this project, next-generation sequencing methods will be used to map a population of several hundred individual plants in weeks rather than the usual months or years required. The ultimate goal will be to develop a list of candidate genes to be targeted for introgression into popular but sensitive varieties of rice to make them more salt tolerant. If these determinants can be identified and introduced into more sensitive rice varieties, this will result in the production of salt-tolerant rice for the coastal areas of Bangladesh. Even a modest increase in rice production in the moderate saline zones would go a long way toward ensuring food security for the local landless farmers in the saline zone.

Summary of Recent Activities
February 2014 saw the completion of extended research and training visits to the University of Texas by two research assistants from the University of Dhaka, Samsad Razzaque and Taslima Haque. Samsad spent five months and Taslima two learning Next Generation Sequencing (NGS) techniques for wet lab experiments and computational analysis. PI Zeba Seraj also visited U.S. partner Thomas Juenger’s lab for a month in January-February for NGS training and participation in the ongoing research efforts.  Along with another visiting scholar from Dhaka, Sabrina Elias, the visitors prepared and sequenced more than 1,200 DNA and RNA samples from rice seedlings from various cross populations being evaluated for their tolerance to salt stress. They also  resequenced the parent rice genomes Horkuch and IR29, generating a more suitable reference map for subsequent genotyping and expression analysis.
Now that they are back at Dhaka University, Samsad and Taslima are working under Dr. Seraj’s supervision to analyze the large amount of data generated during their visit. Sabrina is currently continuing her phenotyping and validation efforts on the project while visiting the University of Nebraska. A data connection has been established between UT and DU, with RNASeq analysis being carried out using the supercomputer facilities at the Texas Advanced Computing Center. Internet connectivity problems initially presented some challenges, but a dedicated line installed at DU has now resolved the issues. In addition to data analysis, field experiments with seedlings will continue at the Bangladesh Rice Research Institute in the coming months. Samsad and Taslima plan to return to UT for about three months of training beginning in October 2014, and Dr. Seraj will visit in November. They hope to participate in the 2nd Annual Symposium on Rice Functional Genomics in Tucson, November 16-19, 2014.
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