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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.
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

Since the commencement of PEER study activities, the research team has bred two generations of horkuch rice seedlings under some degree of salt stress. The DNA from these plants has been isolated and about 200 samples taken. The RNA of these plants has been isolated from three identified groups of plants—most tolerant of salt stress, most sensitive to salt stress, and an intermediate response. The RNA has been isolated at both seedling and reproductive stages under control and stress conditions and has yielded 1,020 samples. These have been sent to the University of Texas, Austin for analysis. Research assistants Samsad Razzaque and Taslima Haque have been preparing the samples there. 


  Bangladesh Partnership Picture 1 Experiment setup for F2 phenotyping (Photo courtesy Zeba Seraj).

  Bangladesh Partnership Picture 2 During the phenofyping of F3 plants, the research team measures SES values (Photo courtesy Zeba Seraj).
Future plans include library preps and sequencing at the University of Texas. Dr. Seraj is expected to visit Austin from mid-January to mid-February, after which Mr. Razzaque and Ms. Haque are expected to return to Dhaka University. Working with MBBISP scholar Sabrina Elias, who is temporarily based at the University of Nebraska, they will commence data analysis, a process expected to take the better part of a year. While this is going on, a follow-on generation of rice seedlings bred from the first generation will be planted at the Bangladesh Rice Research Institute in July 2014 to form recombinant inbred lines. These plants are expected to be useful in the validation of results obtained by DNA and RNA sequencing. Dr. Elias is expected to start large-scale phenotyping of promising individual plant lines at the University of Nebraska.

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