Genomics and molecular markers for rice grain quality: a review

Rice grain quality is a benchmark of rice breeding success. Current rice breeding programs consider grain characteristics that are preferred by consumers in the rice value chain. Specific traits of quality that suit the demands of stakeholders must be targeted before, during and after breeding of new varieties. Therefore, screening tools that are environmentally independent, cheap, robust and easy to use, such as molecular markers, are needed to facilitate timely and accurate selection of traits. As a multifaceted overall phenotype and consisting of several parameters ranging from physical, textural, aroma and increasingly nutritional properties, the selection for quality has not only become about which trait(s) to focus on but is rather an issue of the combination of traits that can be incorporated into a dream variety. The more traits that are available, the more markers we need to capture these traits and feed them into the breeding and selection pipelines. This chapter reviews progress made on genomics and the molecular markers developed for quality traits of rice grains. In addition, this chapter presents the increasing need for novel phenotypes in the form of metabolites that can be traced back to the genome of rice

Metabotyping of 30 maize hybrids under early-sowing conditions reveals potential marker-metabolites for breeding

Introduction: In Northern Europe, maize early-sowing used to maximize yield may lead to moderate damages of seedlings due to chilling without visual phenotypes. Genetic studies and breeding for chilling tolerance remain necessary, and metabolic markers would be particularly useful in this context. Objectives: Using an untargeted metabolomic approach on a collection of maize hybrids, our aim was to identify metabolite signatures and/or metabolites associated with chilling responses at the vegetative stage, to search for metabolites differentiating groups of hybrids based on silage-earliness, and to search for marker-metabolites correlated with aerial biomass. Methods: Thirty genetically-diverse maize dent inbred-lines (Zea mays) crossed to a flint inbred-line were sown in a field to assess metabolite profiles upon cold treatment induced by a modification of sowing date, and characterized with climatic measurements and phenotyping. Results: NMR- and LC-MS-based metabolomic profiling revealed the biological variation of primary and specialized metabolites in young leaves of plants before flowering-stage. The effect of early-sowing on leaf composition was larger than that of genotype, and several metabolites were associated to sowing response. The metabolic distances between genotypes based on leaf compositional data were not related to the genotype admixture groups, and their variability was lower under early-sowing than normal-sowing. Several metabolites or metabolite-features were related to silage-earliness groups in the normal-sowing condition, some of which were confirmed the following year. Correlation networks involving metabolites and aerial biomass suggested marker-metabolites for breeding for chilling tolerance. Conclusion: After validation in other experiments and larger genotype panels, these marker-metabolites can contribute to breeding.MetaboHUBPHENOMEAMAIZINGAgence Nationale de la Recherch

Wild Oryza for quality improvement

Rice consumers demand a wide range of attributes in the different types of rice produced in different regions. Wild Oryza species provide an extensive gene pool that could be used to breed rice varieties with desirable quality characteristics. More than 20 Oryza species are found around the tropical world in diverse environments and have a wide range of grain properties. Traits influencing grain appearance, nutritional value, functional quality (e.g., cooking characteristics), and processing performance may be sourced from wild species. The useful genes available include many controlling grain size and shape, grain color, and starch properties. Advances in genomic technology are making this genetic diversity more readily available for use in the genetic improvement of rice beyond just advancing yield