Homoeologous chromosome exchange explains the creation of a QTL affecting soil‐borne pathogen resistance in tobacco

Abstract

Summary Crop plant partial resistance to plant pathogens controlled by quantitative trait loci (QTL) is desirable in cultivar development programmes because of its increased durability. Mechanisms underlying such resistance are difficult to study. We performed RNA‐seq analyses for tobacco (Nicotiana tabacum) nearly isogenic lines (NILs) with and without favourable allele(s) at Phn7.1, a major QTL influencing partial resistance to the soil‐borne pathogens Phytophthora nicotianae and Ralstonia solanacearum. Based upon combined analyses of transcriptome‐based sequence variation and gene expression profiles, we concluded that allelic variability at the Phn7.1 locus was likely generated from homoeologous exchange, which led to deletion of low‐expressing members of the SAR8.2 gene family and duplication of high‐expressing SAR8.2 genes from a different subgenome of allotetraploid tobacco. The high expression of endogenous Phn7.1‐associated SAR8.2 genes was correlated with observed resistance to P. nicotianae. Our findings suggest a role for genomic rearrangements in the generation of favourable genetic variability affecting resistance to pathogens in plants.

Naringenin confers defence against Phytophthora nicotianae through antimicrobial activity and induction of pathogen resistance in tobacco

“…To examine whether naringenin induces basal pathogen resistance, we analysed the expression of PR1 and SAR8.2 genes in tobacco after naringenin treatment using RT-qPCR. The SAR8.2 gene is a gene that controls plant resistance to P. nicotianae (Shi et al, 2022). As expected, the expression levels of PR1 and SAR8.2 with naringenin treatment were approximately 1.4-fold and 3.5-fold higher than those of the control, respectively (Figure 3e,f).…”

“…The SAR8.2 gene is a gene that controls plant resistance to P . nicotianae (Shi et al, 2022). As expected, the expression levels of PR1 and SAR8.2 with naringenin treatment were approximately 1.4‐fold and 3.5‐fold higher than those of the control, respectively (Figure 3e,f).…”

“…Furthermore, SAR8.2 , a gene in tobacco that regulates plant resistance to P . nicotianae (Shi et al, 2022), was substantially up‐regulated by treatment with naringenin. These results indicate that naringenin induces plant‐pathogen resistance.…”

“…We also found that genes regulating SA biosynthesis, SA signalling and basal pathogen resistance were enhanced at the transcriptional level by treatment with naringenin . Furthermore, SAR8.2, a gene in tobacco that regulates plant resistance to P. nicotianae (Shi et al, 2022), was substantially up-regulated by treatment with naringenin. These results indicate that naringenin induces plant-pathogen resistance.…”

Effects of homoeologous exchange on gene expression and alternative splicing in a newly formed allotetraploid wheat

“…This suggests HE‐underpinned genetic variants have been selected for during domestication and crop improvement. Indeed, it was documented that HE confers high adaptability and generates a wide range of morphophysiological variations desired in crops (Pires et al., 2004; Raman et al., 2021; Shi et al., 2021; Stein et al., 2017). It was also posited that under natural settings HE plays important parts in generating major evolutionary novelty, accelerating diploidization and facilitating species diversification (Edger et al., 2018; Mason & Wendel, 2020).…”