Patterns of stress response and tolerance based on transcriptome profiling of rice crown tissue under zinc deficiency.

Zinc (Zn) deficiency is the most prevalent micronutrient disorder in rice and leads to delayed development and decreased yield. Several studies have investigated how rice plants respond to Zn deficiency and examined the differences between Zn-efficient (ZE) and Zn-inefficient (ZI) genotypes. ZE genotypes reallocate more Zn to roots and are better at maintaining crown root development than ZI genotypes in response to Zn deficiency. However, little is known about the molecular mechanisms controlling these differences. Moreover, the role of the crown, the part of the stem from which crown roots emerge, has yet to be examined. In this study we highlight the molecular mechanisms triggered by early Zn deficiency in crown tissue through RNA sequencing of two contrasting groups of several ZE and ZI genotypes. This method allowed us to (i) identify several novel and well-known Zn transporters involved in Zn retranslocation from the crown to the shoot and roots in response to Zn deficiency; (ii) determine that Zn deficiency triggers the conversion of soluble sugars into starch; and (iii) detect several candidate genes possibly conferring Zn efficiency, including a monosaccharide transporter, a Zn finger domain-containing protein, a gibberellin-stimulated family protein and a plasma membrane polypeptide family protein.

Identification of a stem rust resistance locus effective against Ug99 on wheat chromosome 7AL using a RAD-Seq approach.

KEY MESSAGE: A locus of major effect for stem rust resistance, effective against Ug99 and possibly a target of a suppressor on chromosome arm 7DL in wheat cultivar Canthatch, was mapped to 7AL. Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is responsible for major production losses around the world. The development of resistant cultivars is an effective and environmentally friendly way to manage the disease, but outbreaks can occur when new pathogen races overcome the existing host resistance genes. Ug99 (race TTKSK) and related Pgt races are virulent to the majority of existing cultivars, which presents a potential threat to global wheat production. The hexaploid wheat cultivar Canthatch has long been known to carry a suppressor of stem rust resistance on chromosome arm 7DL. Multiple "non-suppressor" mutants of Canthatch are reported to have gained resistance to Pgt races, including Ug99 (TTKSK) and related races TTKST and TTTSK. To genetically map the suppressor locus, a mapping population was developed from a cross between the susceptible cultivar Columbus, thought to possess the suppressor, and Columbus-NS766, a resistant, near-isogenic line believed to contain a mutant non-suppressor allele introgressed from Canthatch. Genetic mapping using a 9K SNP genotyping assay and restriction site-associated DNA sequencing (RAD-Seq) on bulked segregants led to the identification of markers linked to a locus of stem rust resistance. Surprisingly, genomic sequence information revealed the markers to be located on 7AL instead of 7DL, indicating that the resistance phenotype was due to a new resistance locus, rather than the inactivated suppressor. We suggest that the 7AL locus of resistance is most likely suppressed by the 7DL suppressor.

Stem rust resistance in wheat is suppressed by a subunit of the mediator complex.

Stem rust is an important disease of wheat that can be controlled using resistance genes. The gene SuSr-D1 identified in cultivar 'Canthatch' suppresses stem rust resistance. SuSr-D1 mutants are resistant to several races of stem rust that are virulent on wild-type plants. Here we identify SuSr-D1 by sequencing flow-sorted chromosomes, mutagenesis, and map-based cloning. The gene encodes Med15, a subunit of the Mediator Complex, a conserved protein complex in eukaryotes that regulates expression of protein-coding genes. Nonsense mutations in Med15b.D result in expression of stem rust resistance. Time-course RNAseq analysis show a significant reduction or complete loss of differential gene expression at 24 h post inoculation in med15b.D mutants, suggesting that transcriptional reprogramming at this time point is not required for immunity to stem rust. Suppression is a common phenomenon and this study provides novel insight into suppression of rust resistance in wheat.

Contrasting development of lysigenous aerenchyma in two rice genotypes under phosphorus deficiency.

OBJECTIVES: Phosphorus (P) deficiency is a major limitation to plant growth. Under several abiotic stresses, including P deficiency, upland cereal crops, such as maize, are well known to develop lysigenous aerenchyma, a root tissue containing gas spaces. Contrary to upland species, rice develops aerenchyma constitutively. Nevertheless, aerenchyma in rice is also enhanced by several abiotic stresses, including P deficiency. However, studies are limited and genotypic differences are not clear. RESULTS: The formation of inducible aerenchyma in response to P deficiency was evaluated in two rice genotypes, DJ123 and Nerica4. Whole root porosity increased for both genotypes in low P conditions, but was more pronounced in DJ123. Direct aerenchyma measurements, at 20 and 30 mm from the seminal root tip, revealed that aerenchyma in low P conditions was only enhanced in DJ123. These results confirm that P deficiency in rice induces the formation of aerenchyma, and further show that genotypic differences exist. Interestingly, DJ123 is considered tolerant to P deficiency, whereas Nerica4 is sensitive, pointing towards a potential role of aerenchyma in tolerance to P deficiency.

Cellular and molecular characterization of a stem rust resistance locus on wheat chromosome 7AL.

BACKGROUND: Wheat stem rust, caused by Puccinia graminis f. sp. tritici, is a major wheat disease which is mainly controlled through the release of resistant cultivars containing one or several resistance genes. Considerable effort has been put into the discovery of new resistance genes, but knowledge of their mechanisms of action is often lacking. In this study, the mechanism of resistance conferred by a recently discovered stem rust resistance locus on wheat chromosome 7AL was investigated through microscopic observations and RNA-sequencing, using the susceptible line Columbus and the independent, backcrossed, resistant lines Columbus-NS765 and Columbus-NS766. RESULTS: Microscopic observations of infected leaves revealed that the resistance conferred by the 7AL resistance locus was initiated 2 days post-inoculation, upon the fungus entry into the plant through the stoma. Resistance was manifested by death of guard and epidermal cells adjacent to an infection site. Occasionally, similar observations were made in the susceptible line, suggesting that the resistance response was the same in all genotypes, but enhanced in the resistant lines. Transcriptomic analysis, combined with assignment of genes to wheat chromosomes, revealed a disproportionately high number of differentially expressed genes were located on chromosomes 7AL and 6A. A number of genes annotated as cysteine-rich receptor-like kinases were located on chromosome 7AL. Closer investigation indicated that the encoded proteins were in fact putative receptor-like cytoplasmic kinases. One of the putative RLCK genes contained a SNP marker previously shown to co-segregate with the 7AL resistance locus. The results also indicated the presence of a large introgression on chromosome 6A in both resistant lines, but whether it has any role in the resistance response is unclear. CONCLUSIONS: This study represents the first investigation on the resistance mechanism conferred by the wheat 7AL stem rust resistance locus. The resistance response was associated with pre-haustorial cell death, and the transcriptome analysis suggested putative receptor-like cytoplasmic kinases as candidate resistance genes for further investigation.