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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 May 2016

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
During the final quarter of 2014, Dr. Seraj and her team were able to make significant progress in identifying the salt tolerance traits in multiple strains of rice. The team built off their previous work by preparing and submitting DNA samples for sequencing from two strains of rice, namely: salt tolerant Horkuch and non-salt tolerant IR29. This expanded the existing dataset and filled in gaps from previous work. This work also aided in identifying the genetic variation associated with salt tolerance and allowed the team to create a framework for reliably identifying plants that are descended from each particular strain. While the team is still searching for the particular genes that influence salt tolerance in adult stage rice, they did generate a map of all genetic variation in the genomes of the two rice strains and, from this, they have identified the likely location of the salt tolerance gene in infant stage rice known as the quantitative trait locus (QTL).

In the coming months, Dr. Seraj’s team will complete an accurate sequencing map for Horkuch and IR29 from the sequence information and use it to fine tune the linkage map obtained from broad gene searches this quarter. The team will also build QTL maps for both seedling and reproductive rice stages and validate them using an advanced reciprocal population.