SNPs, InDels, and Microsatellites within and near to Rice NBS-LRR Resistance Gene Candidates

Plant resistance genes (R-genes) drive the immune responses of crops against specific pathotypes of disease-causing organisms. Over time, genetic diversity in R-genes and R-pseudogenes has arisen among different rice varieties. This bioinformatics study was carried out to (i) predict the full sets of candidate nucleotide-binding site leucine-rich repeat (NLR) R-genes present in six rice genomes; (ii) detect variation within candidate R-genes; (iii) identify potential selectable markers within and near to LRR genes among 75 diverse indica rice genomes. Four high quality indica genomes, plus the standard japonica and indica reference genomes, were analysed with widely available bioinformatic tools to identify candidate R-genes and R-pseudogenes. They were detected in clusters, consistent with previous studies. BLAST analysis of cloned protein sequences of 31 R-gene loci gave confidence in this approach for detection of cloned NLR R-genes. Approximately 10% of candidate R-genes were located within 1 kb of a microsatellite (SSR) marker. Sequence comparisons among indica rice genomes detected SNPs or InDels in 334 candidate rice R-genes. There were significantly more SNPs and InDels within the identified NLR R-gene candidates than in other types of gene. The genome-wide locations of candidate R-genes and their associated markers are presented here for the potential future development of improved disease-resistant varieties. Limitations of in silico approaches used for R-gene discovery are discussed.

The cinnamyl alcohol dehydrogenase gene family is involved in the response to Fusarium oxysporum in resistant and susceptible flax genotypes

Flax (Linum usitatissimum L.) is used for the production of textile, oils, pharmaceuticals, and composite materials. Fusarium wilt, caused by the fungus Fusarium oxysporum f. sp. lini, is a very harmful disease that reduces flax production. Flax cultivars that are resistant to Fusarium wilt have been developed, and the genes that are involved in the host response to F. oxysporum have been identified. However, the mechanisms underlying resistance to this pathogen remain unclear. In the present study, we used transcriptome sequencing data obtained from susceptible and resistant flax genotypes grown under control conditions or F. oxysporum infection. Approximately 250 million reads, generated with an Illumina NextSeq instrument, were analyzed. After filtering to exclude the F. oxysporum transcriptome, the remaining reads were mapped to the L. usitatissimum genome and quantified. Then, the expression levels of cinnamyl alcohol dehydrogenase (CAD) family genes, which are known to be involved in the response to F. oxysporum, were evaluated in resistant and susceptible flax genotypes. Expression alterations in response to the pathogen were detected for all 13 examined CAD genes. The most significant differences in expression between control and infected plants were observed for CAD1B, CAD4A, CAD5A, and CAD5B, with strong upregulation of CAD1B, CAD5A, and CAD5B and strong downregulation of CAD4A. When plants were grown under the same conditions, the expression levels were similar in all studied flax genotypes for most CAD genes, and statistically significant differences in expression between resistant and susceptible genotypes were only observed for CAD1A. Our study indicates the strong involvement of CAD genes in flax response to F. oxysporum but brings no evidence of their role as resistance gene candidates. These findings contribute to the understanding of the mechanisms underlying the response of flax to F. oxysporum infection and the role of CAD genes in stress resistance.

Discovery of powdery mildew resistance gene candidates from Aegilops biuncialis chromosome 2Mb based on transcriptome sequencing

Powdery mildew is one of the most widespread diseases of wheat. Breeding resistant varieties by utilization of resistance genes is considered as the most economic and effective method of controlling this disease. Previous study showed that the gene(s) at 2Mb in Chinese Spring (CS)-Aegilops biuncialis 2Mb disomic addition line TA7733 conferred high resistance to powdery mildew. In this study, 15 Bgt isolates prevalent in different regions of China were used to further test the resistance spectrum of TA7733. As a result, TA7733 was high resistance to all tested isolates, indicating that the gene(s) on chromosome 2Mb was broad-spectrum powdery mildew resistance. In order to mine resistance gene candidates and develop 2Mb-specific molecular markers to assist the transfer resistance gene(s) at chromosome 2Mb, RNA-seq of TA7733 and CS was conducted before and after Bgt-infection, generating a total of 158,953 unigenes. Of which, 7,278 unigenes were TA7733-specific which were not expressed in CS, and 295 out of these 7,278 unigenes were annotated as R genes. Based on Blastn against with CS Ref Seq v1.0, 61 R genes were further mapped to homoeologous group 2. Analysis of R gene-specific molecular markers designed from R gene sequences verified 40 out of 61 R genes to be 2Mb specific. Annotation of these 40 R genes showed most genes encoded nucleotide binding leucine rich repeat (NLR) protein, being most likely resistance gene candidates. The broad-spectrum powdery mildew resistance gene(s), disease resistance gene candidates, and functional molecular markers of 2Mb-specific in present study will not only lay foundations for transferring disease resistance gene(s) from 2Mb to common wheat by inducing CS-Ae. biuncialis homoeologous recombination, but also provide useful candidates for isolating and cloning resistance gene(s) and dissecting molecular and genetic mechanisms of disease resistance from 2Mb.