Chickpea shows genotype-specific nodulation responses across soil nitrogen environment and root disease resistance categories

Abstract

Background: The ability of chickpea to obtain sufficient nitrogen via its symbiotic relationship with Mesorhizobium ciceri is of critical importance in supporting growth and grain production. A number of factors can affect this symbiotic relationship including abiotic conditions, plant genotype, and disruptions to host signalling/perception networks. In order to support improved nodule formation in chickpea, we investigated how plant genotype and soil nutrient availability affect chickpea nodule formation and nitrogen fixation. Further, using transcriptomic profiling, we sought to identify gene expression patterns that characterize highly nodulated genotypes.

Results: A study involving six chickpea varieties demonstrated large genotype by soil nitrogen interaction effects on nodulation and further identified agronomic traits of genotypes (such as shoot weight) associated with high nodulation. We broadened our scope to consider 29 varieties and breeding lines to examine the relationship between soilborne disease resistance and the number of nodules developed and real-time nitrogen fixation. Results of this larger study supported the earlier genotype specific findings, however, disease resistance did not explain differences in nodulation across genotypes. Transcriptional profiling of six chickpea genotypes indicates that genes associated with signalling, N transport and cellular localization, as opposed to genes associated with the classical nodulation pathway, are more likely to predict whether a given genotype will exhibit high levels of nodule formation.

Conclusions: This research identified a number of key abiotic and genetic factors affecting chickpea nodule development and nitrogen fixation. These findings indicate that an improved understanding of genotype-specific factors affecting chickpea nodule induction and function are key research areas necessary to improving the benefits of rhizobial symbiosis in chickpea.

Keywords: Genotype specificity; Nodulation regulation; Nodule nitrogen production; Rhizobia; Root disease resistance; Soil N environment; Transcriptomic analysis.

Fig. 1

Chickpea shoot dry weight and soil N environment account for the number of nodules per plant. Linear regression plot of shoot dry weight (DW) for the six genotypes of chickpea grown with three levels of available N (HN (paddock soil + N), MN (paddock soil—N) and LN (sand:soil 2:1)) as predictors of the numbers of nodules per plant, r² = 71.9, standard error of observations 9.97

Fig. 2

Number of nodules formed per plant varies by genotype but is not linked to root disease resistance categories. A Average number of nodules formed per g root for 29 genotypes of chickpea, with SED, LSD and P values presented, N = 5 per genotype. Genotypes in bold were selected for further transcriptomic study. B Genotype root disease resistance categories by the average number of nodules per plant for 22 lines with differing Fusarium wilt (FW) resistance categories (MR moderately resistant, R resistant, AS asymptomatic) and seven lines with differing Phytophthora root rot (PRR) resistance (S susceptible, MS moderately susceptible, MR moderately resistant). Two FW MR genotypes also have resistance to Dry Root Rot (DRR) and two FW AS genotypes also have resistance to Botrytis Grey Mould (BGM). The LSD value of 21.7 is presented as an error bar, N = 5. All specific genotypes values in each figure are provided in Supplementary Table SM2

Fig. 3

Six chickpea genotypes with differing nodulation ability have similar transcriptomic profiles. A PCA plot of normalized and rlog transformed RNAseq count data for the roots of 6 chickpea genotypes grown in sterile soil. 95% confidence ellipses for each genotype are shown. B-D Normalized gene expression for genes known to be involved in B the common symbiotic signaling pathway (CSSP), C nitrogen transport and D flavonoid biosynthesis pathways in the roots of six chickpea genotypes grown in sterile soil. Genes indicated with arrows are (i) DMI1 (ii) high-affinity nitrate transporters, (iii) chalcone-synthase homologues or (iv) a flavonoid methyltransferase

Fig. 4

Six chickpea genotypes with differing nodulation ability have inconsistent changes in gene expression in known nodulation pathways after inoculation with rhizobia. A Simplified schematic of early signalling events and interactions upon perception of rhizobia by legume roots. B-D Log2 fold change in gene expression for genes involved in B the common symbiotic signalling pathway (CSSP) and autoregulation of nodulation (AON), C cytokinin and auxin hormone responses and D flavonoid biosynthesis pathways in the roots of six chickpea genotypes 3 days after inoculation with M. ciceri

Fig. 5

A subset of genes expressed in chickpea roots after inoculation with Mesorhizobium ciceri differentiate varieties with high nodule formation from those with low nodule formation. A PLS-DA plot of normalized and rlog transformed RNAseq count data for the roots of 6 chickpea genotypes 3 days after inoculation with M. ciceri, with groupings assigned based on nodulation ability (high or low). 95% confidence ellipses for each nodulation level are shown. B Plot of loadings values from A for all expressed genes. Genes having coordinates with r > 0.013 were considered to contribute to the separation of high or low nodulation varieties