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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
 
This PEER project has four key objectives and, during the summer of 2014, Dr. Seraj and her team were able to make progress on all four. The team resequenced both salt-tolerant and salt-sensitive parent populations, and while this proved insufficient to identify unique variations in the parents due to certain constraints, the team has reached out to Hudson Alpha, JGI, and Dr. Rod Wing's group to sequence the parent populations in much greater detail. Similarly, the team identified 1,200 markers that will be used to establish a linkage map among the second generation progeny (F2) of the parent plants. Once the linkage map is ready, it will be used to detect characterizations that are associated with seedling stage tolerance phenotypes.

The project PI visited UT Austin from mid-November through mid-December 2014, and two of her research associates, Taslima Haque and Samsad Razzaque, made their second extended research visit to Austin from mid-October 2014 though January 2015. For part of their stay they were also joined by Dr. Seraj's PhD student Sabrina Elias, who is usually based at the University of Nebraska. Once the linkage map is done and chromosomal loci linked to salt tolerance traits identified, these will be fine mapped using the RNA sequence data. Once specific genes linked to salt tolerance are identified, they will be further validated in advanced F4 populations. Both DNA and RNA from selected F4 progenies have been isolated at DU and transported to UT Austin. Moreover F3 and F4 seeds have been sent to Lincoln, Nebraska, where there is a system for rice to be grown. Presence of specific alleles/markers in tolerant/sensitive F4 progenies and transcript abundance of specifically identified genes will be investigated. Ideas for manuscript/s will also be discussed and formulated.