Genomics and Transcriptomics for Root System Architecture in Bread Wheat

Abstract

Root system architecture (RSA) of a plant is primary organ for absorption of water and nutrients from soil and is vital for survival, growth and development. Herein, we performed RNA-seq from leaf and root tissues of 24 historical spring wheat cultivars. We identified 97 genes related to RSA in wheat and their differential expression was observed in leaf and root tissues in a collection of 24 wheat cultivars. The Pearson’s coefficients of correlation indicated significant correlations between leaf and root gene expression and various root and yield-related traits. In second experiment, we developed a simple, robust and cost-effective platform for phenotyping root system architecture (RSA) and phenotyped a panel of 58 diverse bread wheat cultivars from Pakistan under water-limited and well-watered conditions. Under water-limited conditions, a significant positive correlation was found between root depth and yield-related traits. We also investigated the effects of dwarfing genes and some phenology-related genes on RSA and identified significant associations of these genes with important root traits. Of these genes, expression analysis of DRO1 and TaMOR was performed using RNA-seq and results were validated using qRT-PCR. In third experiment, we developed and optimized a simple and high-throughput method for root hair (RH) phenotyping using portable Dinolite™ edge microscope. Using this method, we measured root hair length (RHL) and root hair density (RHD) of a set of 24 historical spring wheat cultivars under optimal conditions. Agronomic and physiological traits collected from five different environments and their best linear unbiased predictions (BLUPs) were correlated with RHL and RHD. The expression patterns of TaRSL4, a gene controlling root hair length in wheat, were analyzed using RNA-seq and the results were validated using qRT PCR. The order of gene expression in roots was TaRSL4-2D>TaRSL4-2A>TaRSL4-2B whereas expression in leaves was observed only in B-homoeologue. In fourth experiment, we characterized a set of 113 historical spring wheat cultivars for RHL and RHD under low and high phosphorous. The panel was genotyped using 66836 genome-wide single nucleotide polymorphisms (SNPs) from 50 K SNP array data and genome-wide association study (GWAS) was carried out to identify significant loci associated with RHL/D under P treatment. A total of 67 significant loci were found associated with RHL and RHD. The maximum number of SNPs (41) linked to RHL/D were observed under high-P levels, and 25 loci identified under low-P conditions. A total of six genes linked to SNPs causing missense mutations were identified and their expression patterns in diverse wheat cultivars were DRSML QAU xx investigated. Conclusively, a historic change was observed in post-1965 cultivars that is attributed to genetic factors linked with favored RSA traits which may be implicated in selection breeding. Our work provided a first insight into genetic loci linked to RHL/D in bread wheat which could be valuable source for further functional investigation.