Root-associated microbiomes in 12 wheat varieties

Engineering root-associated microbiomes in crop breeding is a promising strategy to improve crop production and maintain agriculture sustainability. However, the beneficial root-associated microbiome leverageable characteristics in wheat varieties are still unclear. Here, we characterized root-associated bacterial and fungal microbiomes of 12 wheat varieties grown at three sites for two consecutive years using a high-throughput amplicon sequencing. We also evaluated a scalable sampling method (root zone pencil cores collected using a soil sampler probe) applicable to breeding plots. Environmental factors (i.e., site and year) were the main drivers of microbial community structure. The effect of wheat varieties on microbial communities was modified by environmental factors and wheat varieties retained a core microbiome across six station years. The core bacteria were largely plant growth-promoting rhizobacteria, but the core fungi were largely plant pathogens. A select bacterial and fungal community were closely associated with wheat yield performance. The pencil core sampling has comparable statistical power to the root sampling and the rhizosphere sampling in retaining varietal effect on microbiome communities and predicting the yield performance of the wheat varieties.