Harnessing the Wild Relatives of Rice for Novel Adaptive Phenotypes: Genetics and breeding for agricultural sustainability beyond the Green Revolution

View the project final report

Commodities

• Agronomic: rice

Practices

• Crop Production: crop improvement and selection, plant breeding and genetics

Salinity is a major yield-limiting factor in rice production across the southern USA, especially in the Gulf Coast region, due to poor-quality irrigation water and intrusion of seawater. This study supports a breeding paradigm based on a holistic view of genomic interaction that explores the cryptic genetic contributions hidden in the wild progenitors of cultivated rice. The project will maximize the full combining potential of wild genetic sources to create novel adaptive traits for sustainable production of rice under salinity-affected environments. We will utilize Chromosome Segment Substitution Lines (CSSL) of Oryza sativa (cv. Curinga) harboring introgression for almost the entire complement of genomic segments from Oryza rufipogon and Oryza meridionalis in the context of their effects in the creation of non-parental physiological attributes for salinity tolerance. The direct outcome of this research will be the identification of novel salinity tolerant introgression lines that can be used for cultivation in the Southern USA and will also serve as donors for subsequent breeding of salinity tolerance in elite cultivars for sustainable production under marginal environments. Using genomic technologies, we seek to reveal the mechanism that underpins tolerance in CSSLs, identify genetic variations that may serve as markers for salinity tolerance, and identify critical gene pathways connected to salinity tolerance. We are moving to develop a cost-effective PCR (polymerase chain reaction) toolkit useful for marker-assisted breeding of salinity tolerance. 

1) To perform a comprehensive physio-morphometric evaluation of two populations of chromosome segment substitution lines (CSSL) of Oryza sativa cv. Curinga harboring introgression for the almost entire complement of genomic segments from Oryza rufipogon and Oryza meridionalis in the context of tolerance to salinity. This study is designed to uncover novel stress tolerance attributes configured by wild chromosome segment introgression in certain CSSLs.

2) To perform comparative transcriptomics to shed light on the mechanism responsible for the novel salt stress tolerance from wild chromosome segment introgression in certain CSSLs.  This study will uncover global patterns of genetic reconfiguration, physiological, and/or biochemical enriched pathways in superior transgressive individuals. Outcomes are expected to facilitate the understanding of the gain or loss of stress tolerance attributes at the whole-plant level. This analysis will help identify genetic markers associated with the enriched pathways contributing to the tolerant phenotype. The identified makers will be used to develop a cost-effective PCR-based genotyping platform employing KASP^TM (Kompetitive Allele-Specific PCR) technology.

3) To study the inheritance pattern of the novel genomic attributes and validation of KASP^TM markers in recurrent crossed generations. An F2 mapping population, derived from the cross between specific CSSL(s) and recurrent parent (Oryza sativa cv. Curinga), will be used to validate the KASP^TM markers. We will also perform qPCR (quantitative real-time PCR) analysis of the specific F2 lines to check the differential gene expression of specific genes.