Plants are rife with bacteria and fungi that colonize roots and shoots both externally and internally. By providing novel nutritional and defense pathways and influencing plant biochemical pathways, microbes can fundamentally alter plant phenotypes. Here we review the widespread nature of microbially mediated plant functional traits. We highlight that there is likely fitness conflict between hosts and symbionts and that fitness outcomes can depend on partner genotypes and ecological factors. Microbes may influence ecosystems through their effects on the functional trait values and population dynamics of their plant hosts. These effects may feed back on symbiont evolution by altering transmission rates of symbionts and scale up to ecosystem processes and services. We end by proposing new avenues of research in this emerging field.

Zero hunger and good health could be realized by 2030 through effective conservation, characterization and utilization of germplasm resources¹. So far, few chickpea (Cicerarietinum) germplasm accessions have been characterized at the genome sequence level². Here we present a detailed map of variation in 3,171 cultivated and 195 wild accessions to provide publicly available resources for chickpea genomics research and breeding. We constructed a chickpea pan-genome to describe genomic diversity across cultivated chickpea and its wild progenitor accessions. A divergence tree using genes present in around 80% of individuals in one species allowed us to estimate the divergence of Cicer over the last 21 million years. Our analysis found chromosomal segments and genes that show signatures of selection during domestication, migration and improvement. The chromosomal locations of deleterious mutations responsible for limited genetic diversity and decreased fitness were identified in elite germplasm. We identified superior haplotypes for improvement-related traits in landraces that can be introgressed into elite breeding lines through haplotype-based breeding, and found targets for purging deleterious alleles through genomics-assisted breeding and/or gene editing. Finally, we propose three crop breeding strategies based on genomic prediction to enhance crop productivity for 16 traits while avoiding the erosion of genetic diversity through optimal contribution selection (OCS)-based pre-breeding. The predicted performance for 100-seed weight, an important yield-related trait, increased by up to 23% and 12% with OCS- and haplotype-based genomic approaches, respectively.