Genome-wide association study identifies loci and candidate genes for root traits in rice grown in Brazil

Rice is a staple food for more than half of the world's population. In Brazil, this crop plays an important role in terms of consumption, production and economy. Root system is a key trait for rice yield, as it is responsible for water uptake, absorption, transportation of nutrients from soil, and other vital functions. Root dry weight (RDW) and root length (RL) are related to crop yields. Understanding molecular basis of root traits in rice is a strategy to help breeders develop genotypes with greater yield. However, few studies using Brazilian germplasm have been developed. Therefore, the objective of this research was to map genome regions responsible for root dry weight and length in adult rice plants grown in Southern of Brazil. Genome-wide association study (GWAS) was applied using 7098 single nucleotide polymorphism (SNPs) markers and a collection of 188 rice genotypes. Seven SNP markers for root length and four markers for root dry weight were detected. Genes encoding myeloblastosis (MYB) transcription factor, Cinnamyl alcohol dehydrogenase, Cyclin-dependent protein kinase (Cdk)-activating kinase, Similar to Auxin/Indole-3-Acetic Acid (IAA11), among others, were found associated to root length. Amidst the genes related to root dry weight, those encoding Cellulose synthase, Lipid transfer protein, Receptor-like cytoplasmic kinase and CCCH-type zinc finger protein associated to drought tolerance were identified. This study provides insights of genetic control of rice root traits considering a panel composed mainly of Brazilian genotypes. The rice breeders can apply this knowledge to guide for further research and develop new cultivars in Brazil.