What's happening at IRRI

PB & GB Joint Division Seminar

Wednesday, April 26, 2017, 02:00pm - 03:00pm


PB and GB Joint Division Seminar
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Title: A rice multi-approach study to discover new loci associated with traits contributing to
salinity stress under controlled and field conditions

Soil salinity is a major constraint to rice production worldwide. Thus, to feed 9 billion people by 2050, we need to increase rice production while facing the challenges of rapid global environmental changes. To meet some of these challenges, there is a vital requirement to significantly increase rice production in salinized land.
Here we present a genome-wide association study (GWAS) with the aim to discover new genes associated with traits contributing to rice salinity tolerance under both controlled and field conditions. Our multi-approach study includes high-throughput phenotyping, field trials and dynamic QTL analysis. We used two diversity panels- indica and aus, which were established within the ‘Phenomics of Rice Adaptation and Yield Potential’ (PRAY) project. First, both panels were grown in controlled waterlogged conditions, and used to quantify the effects of salinity on growth and transpiration traits using high-throughput phenotyping. Second, the indica panel alone was cultivated under irrigated field conditions in Senegal, to investigate the effects of salinity stress on yield and yield components. The use of the same indica panel in both experiments may uncover new sources of salinity tolerance by discovering novel loci associated with growth, transpiration, and yield. Moreover, to clearly identify genes only responsive to salinity stress, we are using an association model- the interaction model- that takes into account the interaction between treatment (control and salt) and genetic marker. This model allowed the identification of loci affecting transpiration use efficiency on chromosome 11, in the indica panel, and associated with the early responses of rice to salinity. Furthermore, we observed that some loci are present exclusively during the early time intervals after salt exposure while others only occur in the later time intervals. This dynamic and complex response of rice to salinity stress led us to develop a 3D visualization software- the 3D-QTL. This software analyzes longitudinal association data, and can be used in any type of species (e.g rice), time-interval (e.g. different years of field trials) and population (e.g. nested association mapping).
We will present the field data preliminary analyses, and we will discuss how we can tie and correlate the obtained GWAS results under both field and controlled conditions. Our final goal is to further explore the genetic diversity present in the PRAY indica panel, and to develop salt-tolerant rice varieties.

Dr. Sonia S. Cabrita-Negrao
Research Scientist
King Abdullah University of Science and Technology, Jedda, Saudi Arabia


DL Umali room A