Candidate genes expression profiling during wilting in chickpea caused by Fusarium oxysporum f. sp. ciceris race 5

Abstract

Chickpea production may be seriously threatened by Fusarium wilt, a disease caused by the soil-borne fungus Fusarium oxysporum f. sp. ciceris. F. oxysporum race 5 is the most important race in the Mediterranean basin. Recently, the region responsible for resistance race 5 has been delimited within a region on chromosome 2 that spans 820 kb. To gain a better understanding of this genomic region, we used a transcriptomic approach based on quantitative real-time PCR to analyze the expression profiles of 22 selected candidate genes. We used a pair of near-isogenic lines (NILs) differing in their sensitivity to Fusarium race 5 (resistant vs susceptible) to monitor the transcriptional changes over a time-course experiment (24, 48, and 72 hours post inoculation, hpi). Qualitative differences occurred during the timing of regulation. A cluster of 12 genes were induced by the resistant NIL at 24 hpi, whereas a second cluster contained 9 genes induced by the susceptible NIL at 48 hpi. Their possible functions in the molecular defence of chickpea is discussed. Our study provides new insight into the molecular defence against Fusarium race 5 and demonstrates that development of NILs is a rich resource to facilitate the detection of candidate genes. The new genes regulated here may be useful against other Fusarium races.

Breeding, Genetics, and Genomics Approaches for Improving Fusarium Wilt Resistance in Major Grain Legumes

“…Differential gene expression analysis at 24 h post inoculation (hpi) suggested two known candidate genes LOC101499873 (encoding chaperonin) and LOC101490851 and three novel candidate genes (LOC101509359, LOC101495941, and LOC101510206 encoding MADS-box transcription factor, MATE family protein and serine hydroxymethyl-transferase, respectively) to be related to defense activity against FW. Likewise, nine genes viz., LOC101503802, LOC101505941, LOC101506693 had significantly higher expression in FW sensitive NIL at 48 hpi than the FW resistant NIL (Caballo et al, 2019a). Transcriptome analysis of JG 62 and WR 315 in response to FW (race 1) infection uncovered abundance of differentially expressed transcripts related to various TFs, cellular transporters, sugar metabolism contributing to activate defense signaling against FW in chickpea (Gupta et al, 2013a; see Table 4).…”

“…The underlying genomic region containing these SNPs and indels was predicted to be associated with defense related activity. Caballo et al (2019a) functionally validated the genomic region controlling Foc (race 5) resistance in chickpea from resistant and sensitive NILs developed from the cross ILC 3279 × WR 315. Differential gene expression analysis at 24 h post inoculation (hpi) suggested two known candidate genes LOC101499873 (encoding chaperonin) and LOC101490851 and three novel candidate genes (LOC101509359, LOC101495941, and LOC101510206 encoding MADS-box transcription factor, MATE family protein and serine hydroxymethyl-transferase, respectively) to be related to defense activity against FW.…”

Genomic Regions Associated with Fusarium Wilt Resistance in Flax

“…These loci were discovered in a population of double haploid lines developed from crosses between flax wilt-resistant and susceptible parents. Overall, this plethora of information could be further used in follow-up experiments to decipher resistance mechanisms [33] or in breeding programs for the development of superior cultivars [34].…”

Aldehyde Dehydrogenase 3 Is an Expanded Gene Family with Potential Adaptive Roles in Chickpea

“…Although no regulation of most of the ALDH candidates seems to be induced in our material, the LOC101511819 (CaALDH3F3) is clearly upregulated in infected roots of the susceptible and resistant NILs at 24 and 72 hpi, respectively (Figure 5). This is interesting because the appropriate timing of gene regulation that leads to Foc5 pathogen recognition has been suggested as a distinct feature of the NIL pair [49]. The encoded protein by LOC101511819 is highly conserved among other legumes and shares >80% identity at the amino acid level with the homologue of M. truncatula, L. angustifolius, G. max, A. hypogaea and P. vulgaris, among others.…”

“…Plant material and treatment have been described in detail elsewhere [49]. Briefly, a pair of near isogenic lines RIP8-94-5 resistant (R)/RIP8-94-11 susceptible (S)-segregant to Fusarium oxysporum race 5 resistance were grown in controlled conditions under a temperature regime of 25 and 22 • C and 12 h photoperiod under fluorescent light.…”