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 maximized the full combining potential of wild genetic sources to create novel adaptive traits for sustainable production of rice under salinity-affected environments. We utilized the Chromosome Segment Substitution Lines (CSSL) of Oryza sativa (cv. Curinga) harboring introgression for almost the entire complement of genomic segments from Oryza rufipogon in the context of their effects in the creation of non-parental physiological attributes for salinity tolerance. This study led to the identification of novel salinity-tolerant inter-species introgression lines that can be utilized as donors for subsequent breeding of cultivars suitable to the limiting agroecology of the Southern USA’s rice industry. By exploring the cryptic genetic variation in O. rufipogon using a library of CSSLs, we identified novel salinity-tolerant phenotypes and their underlying genetic mechanisms by integrating genomics and transcriptomics datasets. Additionally, we mined the O. rufipogon genome for novel genes and alleles (nine novel genes and alleles for the BTB/POZ protein family) with potential application in wide introgression breeding. In conclusion, this study revealed the untapped cryptic genetic functions and novelties from the wild relatives of cultivated rice. The outcome of this project establishes the groundwork for widening the genetic base of the pre-breeding germplasm of rice that can be effectively used to supplement the inherent capacity of current cultivars for traits related to climate resilience and adaptation to marginal environments.

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.