Genetic control of rhizosphere microbiome of cotton plant under field conditions

Abstract Background Understanding the extent of heritability of plant-associated microbiome (phytobiome) is critical for exploitation of phytobiome in agriculture. Two crosses were made between pairs of cotton cultivars with differential resistance to the Verticillium wilt. F 2 plants were grown together with the four parents to study the heritability of cotton rhizosphere microbiome. Amplicon sequencing was used to profile bacterial and fungal communities. Results F 2 hybrid offspring of both crosses had higher alpha diversity indices as well as greater variability than the two parents. Two types of data were used generated to study the heritability of rhizosphere microbiome: principal components (PCs) and individual top microbial OTUs. For the L1×Z49 cross, the variance among the 100 progeny genotypes ( V T ) was significantly greater than the random variability ( V E ) for 12 and 34 out of top 100 fungal and bacterial PCs, respectively. For the Z2×J11 cross, the corresponding values were 10 and 20 PCs. Out of the top 100 OTUs, 29 fungal OTUs and 10 bacterial OTUs had V T that was significantly greater than V E for the L1×Z49 cross; the corresponding value for the Z2×J11 cross were 24 and one. The estimated heritability was mostly in the range of 40–60%. Conclusions These results suggested the existence of genetic control in terms of rhizosphere microbiome in cotton.