Designing climate-resilient rice with ideal grain quality suited for high-temperature stress

Abstract

To ensure rice food security, the target outputs of future rice breeding programmes should focus on developing climate-resilient rice varieties with emphasis on increased head rice yield coupled with superior grain quality. This challenge is made greater by a world that is increasingly becoming warmer. Such environmental changes dramatically impact head rice and milling yield as well as increasing chalkiness because of impairment in starch accumulation and other storage biosynthetic pathways in the grain. This review highlights the knowledge gained through gene discovery via quantitative trait locus (QTL) cloning and structural-functional genomic strategies to reduce chalk, increase head rice yield, and develop stable lines with optimum grain quality in challenging environments. The newly discovered genes and the knowledge gained on the influence of specific alleles related to stability of grain quality attributes provide a robust platform for marker-assisted selection in breeding to design heat-tolerant rice varieties with superior grain quality. Using the chalkiness trait in rice as a case study, we demonstrate here that the emerging field of systems genetics can help fast-track the identification of novel alleles and gene targets that can be pyramided for the development of environmentally robust rice varieties that possess improved grain quality.

Keywords: Chalk; functional genomics; genetics; grain quality; milling and head rice yield; stress tolerance; systems biology; systems genetics..

Fig. 1.

The ontology of seed development covering import phase transitions. High temperature stress-induced perturbations occurring during seed development affect the grain quality, cooking quality, and eating quality of rice.

Fig. 2.

The grain quality QTL hotspot in rice chromosome 6 and the effect of gene perturbation in the starch biosynthesis pathway. (A) Selected QTLs for grain quality traits on japonica chromosome 6 located in syntenic regions between indica and japonica reference genomes. Chromosome 6 is a grain quality hotspot as multiple grain quality QTLs related to amylose, chalk, head rice yield, gel consistency, gelatinization temperature, and grain dimensions and shape are co-located on both arms of the chromosome. The accession IDs of these grain quality QTLs are listed in Supplementary Table S1 at JXB online. (B) Gene perturbation in the starch metabolism pathway. Perturbations in the starch metabolism pathway involving starch synthase III and starch branching enzyme IIa and IIb lead to alterations in amylose–amylopectin composition and starch structure variation (Butardo, 2011). The proposed molecular and physiological mechanisms of chalk formation are a complex system associated with source–sink disturbances. However, the initial genetic evidence points to the disturbance of the storage pathways in developing seeds.

Fig. 3.

Synteny between japonica chromosome 5 (OsJ5) and related chromosomes in indica (OSI1 and OSI5). This figure shows the syntenic blocks between chromosome 5 of O. sativa japonica with chromosomes 1 and 5 of indica (innermost section of the figure). The bar plot shows SNP density in the genomic region based on SNPs common to five indica re-sequenced genomes. Blue lines represent SNP densities ≥5 per kb, while orange lines represent SNP densities <5 per kb. SNP density was calculated separately for every 100kb. Mapped grain quality QTLs are shown next to the SNP density bar plots. Mapped QTLs whose lengths are between 1Mb and 5Mb are represented as lines, while fine-mapped QTLs (size <1Mb) are represented as triangles. Genomic hotspots that have the highest SNP densities can be found on chromosomes 1 and 5 of indica as well as japonica. These hotspots coincide with several grain quality QTLs, including the recently cloned chalk gene H ⁺ -translocating pyrophosphatase.

Fig. 4.

The gene regulatory networks derived from co-expression data of seed development-specific genes. (A) The gene regulatory networks of the endosperm-specific H ⁺ -translocating pyrophosphatase gene cloned for chalkiness in rice derived using the PLANET database (Mutwil et al., 2011) seem to control the selective proteolysis pathway (E3.SCF) during 3–5 DAF (Supplementary Table S2 at JXB online). (B) On the other hand, its orthologue in wheat (Ta.1322.1.S1_x_at) regulates thousands of genes involved in starch biosynthesis and protease inhibitors during seed filling. These divergent expression patterns of H ⁺ -translocating pyrophosphatase genes between rice and triticale members are likely to trigger functional divergence during seed development.

Fig. 5.

Schematic representation of the systems genetics approach to explore the potential of existing intraspecific variation for various grain quality traits on a genetic map using GWAS/QTL. Unravelling a holistic view of grain quality perturbation under stress requires the integration of knowledge from systems biology (regulatory networks and flux balance analysis), systems genetics, and comparative genomics to explore the perspectives of a genomics revolution in breeding to develop climate-resilient lines with superior grain quality.