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Analysing Rice Genome Networks to Boost Biomass Accumulation in Roots and Shoots

Genome studies have allowed scientists to create association networks that reveal the correlations between various root and shoot traits of rice plants to optimise high-biomass rice breeding.

As the most commonly cultivated food crop in the world, Oryza sativa L., also known as Asian rice, is a crucial staple cereal that feeds nearly half of the world’s population. In fact, the average person in Asia consumes 90 to 181kg of rice annually. Given its importance, many farmers and scientists have ventured into developing methods to maximise agricultural yield and optimise rice quality.

In recent years, researchers have begun investigating the genetic makeup of rice plants in an attempt to genetically develop rice with high biomass. However, designing superior rice cultivars with high biomass, specifically high root biomass, has remained a challenge for scientists as it is difficult to pinpoint the effects of specific genes in rice with different genetic backgrounds. In-depth knowledge of the natural variation in genes that underlie root and shoot biomass accumulation is also needed.

To better understand how roots and shoots coordinate the development of rice plants at a molecular level, researchers from China Agricultural University, Shandong Agricultural University, and the Rice Research Institute of Guangxi Academy of Agricultural Sciences have joined together to conduct genetic studies and construct an association network to illustrate the synergistic biomass accumulation of roots and shoots of rice plants.

Using 666 rice accessions identified from genome-wide association study, the team explored six traits that are likely to be responsible for root and shoot biomass accumulation – root weight, shoot weight, and the ratio of root-to-shoot mass, and sub-traits like root length, root thickness, and shoot length of rice. They proposed the use of a top-to-bottom genetic regulation approach to examine the association between high priority pathways for root weight, shoot weight, and the ratio of root-to-shoot mass, and identify how they relate to the low priority pathways for sub-traits.

The team first conducted a hydroponic culture experiment of different rice species to phenotype the six traits for root and shoot biomass accumulation. They later compared the biomass of two main rice subspecies, indica and japonica. The results suggested that indica was more capable of accumulating plant biomass, while japonica exhibited a greater tendency to accumulate root biomass.

Upon analysing the links between traits, it was reported that root weight and shoot weight were highly correlated in both indica and japonica rice populations. This finding led the team to conclude that there are superior genes or networks that contribute to the collaborative development of roots and shoots. These genes are hypothesised to regulate subordinate genes or networks associated with root length, root thickness and shoot length.

With this knowledge, the team further investigated the genes related to shoot biomass accumulation and analysed the genetic basis of variation in rice biomass accumulation, from which the team identified a new common association signal for root weight and shoot weight at Chr5_25405785 in japonica. This link is suspected to be responsible for the regulation of coordinated development of roots and shoots. They validated the loci by comparing the results of their genomic study with known quantitative trait locus of rice genes.

To illustrate the relationship between the six traits, association networks were constructed using Cytoscape 3.5.1. Their network detected 37 enriched genome clusters with more than two association signals and revealed that the relationship among the six traits could be linked to linkage and pleiotropy. With the network, they distinguished pleiotropy and linkage disequilibrium at a sequencing level by analysing the known pleiotropy gene, OsPTR9, for root weight, the ratio of root-to-shoot mass, and root length.

While the predominant genetic basis underlying synergistic biomass accumulation of roots and shoots remains largely elusive, the team’s experiments have successfully dissected the genetic architecture of the roots and shoots biomass accumulation, and shed light on the underlying mechanisms of synergistic root and shoot development. Their model is expected to advance future developments in high-biomass rice breeding. [APBN]

Source: Zhao et al. (2021). Genetic basis and network underlying synergistic roots and shoots biomass accumulation revealed by genome-wide association studies in rice. Scientific Reports, 11, 13769.