Plant Defensins NaD1 and NaD2 Induce Different Stress Response Pathways in Fungi

Nicotiana alata defensins 1 and 2 (NaD1 and NaD2) are plant defensins from the ornamental tobacco that have antifungal activity against a variety of fungal pathogens. Some plant defensins interact with fungal cell wall O-glycosylated proteins. Therefore, we investigated if this was the case for NaD1 and NaD2, by assessing the sensitivity of the three Aspergillus nidulans (An) O-mannosyltransferase (pmt) knockout (KO) mutants (AnDpmtA, AnDpmtB, and AnDpmtC). AnDpmtA was resistant to both defensins, while AnDpmtC was resistant to NaD2 only, suggesting NaD1 and NaD2 are unlikely to have a general interaction with O-linked side chains. Further evidence of this difference in the antifungal mechanism was provided by the dissimilarity of the NaD1 and NaD2 sensitivities of the Fusarium oxysporum f. sp. lycopersici (Fol) signalling knockout mutants from the cell wall integrity (CWI) and high osmolarity glycerol (HOG) mitogen-activated protein kinase (MAPK) pathways. HOG pathway mutants were sensitive to both NaD1 and NaD2, while CWI pathway mutants only displayed sensitivity to NaD

Molecular characterisation and genetic mapping of candidate genes for qualitative disease resistance in perennial ryegrass (Lolium perenne L.)

<p>Abstract</p> <p>Background</p> <p>Qualitative pathogen resistance in both dicotyledenous and monocotyledonous plants has been attributed to the action of resistance (R) genes, including those encoding nucleotide binding site – leucine rich repeat (NBS-LRR) proteins and receptor-like kinase enzymes. This study describes the large-scale isolation and characterisation of candidate R genes from perennial ryegrass. The analysis was based on the availability of an expressed sequence tag (EST) resource and a functionally-integrated bioinformatics database.</p> <p>Results</p> <p>Amplification of R gene sequences was performed using template EST data and information from orthologous candidate using a degenerate consensus PCR approach. A total of 102 unique partial R genes were cloned, sequenced and functionally annotated. Analysis of motif structure and R gene phylogeny demonstrated that <it>Lolium </it>R genes cluster with putative ortholoci, and evolved from common ancestral origins. Single nucleotide polymorphisms (SNPs) predicted through resequencing of amplicons from the parental genotypes of a genetic mapping family were validated, and 26 distinct R gene loci were assigned to multiple genetic maps. Clusters of largely non-related NBS-LRR genes were located at multiple distinct genomic locations and were commonly found in close proximity to previously mapped defence response (DR) genes. A comparative genomics analysis revealed the co-location of several candidate R genes with disease resistance quantitative trait loci (QTLs).</p> <p>Conclusion</p> <p>This study is the most comprehensive analysis to date of qualitative disease resistance candidate genes in perennial ryegrass. SNPs identified within candidate genes provide a valuable resource for mapping in various ryegrass pair cross-derived populations and further germplasm analysis using association genetics. In parallel with the use of specific pathogen virulence races, such resources provide the means to identify gene-for-gene mechanisms for multiple host pathogen-interactions and ultimately to obtain durable field-based resistance.</p

High-Density Mapping of Triple Rust Resistance in Barley Using DArT-Seq Markers

The recent availability of an assembled and annotated genome reference sequence for the diploid crop barley (Hordeum vulgare L.) provides new opportunities to study the genetic basis of agronomically important traits such as resistance to stripe [Puccinia striiformis f. sp. hordei (Psh)], leaf [P. hordei (Ph)], and stem [P. graminis f. sp. tritici (Pgt)] rust diseases. The European barley cultivar Pompadour is known to possess high levels of resistance to leaf rust, predominantly due to adult plant resistance (APR) gene Rph20. We developed a barley recombinant inbred line (RIL) population from a cross between Pompadour and the leaf rust and stripe rust susceptible selection Biosaline-19 (B-19), and genotyped this population using DArT-Seq genotyping by sequencing (GBS) markers. In the current study, we produced a high-density linkage map comprising 8,610 (SNP and in silico) markers spanning 5957.6 cM, with the aim of mapping loci for resistance to leaf rust, stem rust, and stripe rust. The RIL population was phenotyped in the field with Psh (Mexico and Ecuador) and Ph (Australia) and in the greenhouse at the seedling stage with Australian Ph and Pgt races, and at Wageningen University with a European variant of Psh race 24 (PshWUR). For Psh, we identified a consistent field QTL on chromosome 2H across all South American field sites and years. Two complementary resistance genes were mapped to chromosomes 1H and 4H at the seedling stage in response to PshWUR, likely to be the loci rpsEm1 and rpsEm2 previously reported from the cultivar Emir from which Pompadour was bred. For leaf rust, we determined that Rph20 in addition to two minor-effect QTL on 1H and 3H were effective at the seedling stage, whilst seedling resistance to stem rust was due to QTL on chromosomes 3H and 7H conferred by Pompadour and B-19, respectively

Identification of quantitative trait loci for dynamic and steady-state photosynthetic traits in a barley mapping population

Enhancing the photosynthetic induction response to fluctuating light has been suggested as a key target for improvement in crop breeding programmes, with the potential to substantially increase whole-canopy carbon assimilation and contribute to crop yield potential. Rubisco activation may be the main physiological process that will allow us to achieve such a goal. In this study, we assessed the phenotype of Rubisco activation rate in a doubled haploid (DH) barley mapping population [131 lines from a Yerong/Franklin (Y/F) cross] after a switch from moderate to saturating light. Rates of Rubisco activation were found to be highly variable across the mapping population, with a median activation rate of 0.1 min−1 in the slowest genotype and 0.74 min−1 in the fastest genotype. A unique quantitative trait locus (QTL) for Rubisco activation rate was identified on chromosome 7H. This is the first report on the identification of a QTL for Rubisco activation rate in planta and the discovery opens the door to marker-assisted breeding to improve whole-canopy photosynthesis of barley. This also suggests that genetic factors other than the previously characterized Rubisco activase (RCA) isoforms on chromosome 4H control Rubisco activity. Further strength is given to this finding as this QTL co-localized with QTLs identified for steady-state photosynthesis and stomatal conductance. Several other distinct QTLs were identified for these steady-state traits, with a common overlapping QTL on chromosome 2H, and distinct QTLs for photosynthesis and stomatal conductance identified on chromosomes 4H and 5H, respectively. Future work should aim to validate these QTLs under field conditions so that they can be used to aid plant breeding efforts

Assessment of Molecular Diversity and Population Structure of Pakistani Mulberry Accessions Using Retrotransposon-Based DNA Markers

Both morphological and molecular markers have been extensively used to evaluate genetic diversity; however, molecular markers are considered more reliable and can lead to improved reproductive efficiency. This study utilized inter-primer binding site (iPBS) markers to examine the genetic diversity and population structure of thirty mulberry accessions from the districts of Sahiwal and Faisalabad, Pakistan. These mulberry accessions belonged to three species: Morus nigra (n = 13), Morus alba (n = 12), and Morus rubra (n = 5). The use of nine iPBS primers in this study provided a comprehensive understanding of genetic diversity among the selected mulberry accessions. Nine iPBS primers were used in the study and generated 431 bands with allelic frequencies ranging from 21 to 75 and band sizes from 200 to 1500 base pairs. The primer 2230 showed the highest polymorphic information content (PIC) value of 0.47 and the highest Shannon’s information index (I = 0.53). The Morus nigra accessions had the highest levels of expected heterozygosity (He = 0.30), unbiased expected heterozygosity (µHe = 0.33), and Shannon’s information index (I = 0.45). The molecular variance analysis (AMOVA) revealed a high degree of genetic variation, as estimated by the pairwise PhiPT value of 0.21, which was significant at the p < 0.001 *** level. The neighbor joining tree, principal coordinate analysis, and structure analysis grouped the 30 mulberry accessions into four main clusters. The distinct grouping of accessions SWLS14, SWLS6, FSDS30, and SWLS7 validated their notable genetic distinctiveness. Overall, these findings contribute valuable insights into the genetic landscape of mulberry accessions, which are essential for conservation and breeding strategies

Characterisation of Rph24: A gene conferring adult plant resistance to Puccinia hordei in barley

We identified Rph24 as a locus in barley (Hordeum vulgare L.) controlling adult plant resistance (APR) to leaf rust, caused by Puccinia hordei. The locus was previously reported as a quantitative trait locus in barley line ND24260-1 and named qRphND. We crossed ND24260-1 to the leaf rust susceptible standard Gus and determined inheritance patterns in the progeny. For the comparative marker frequency analysis (MFA), ‘resistant’ and ‘susceptible’ tails of the F2 were genotyped with Diversity Arrays Technology genotyping-by-sequencing (DArT-Seq) markers. The Rph24 locus was positioned at 55.5 cM on chromosome 6H on the DArT-Seq consensus map. Evaluation of F2:3 families confirmed that a single locus from ND24260-1 conferred partial resistance. The haploblock strongly associated with the Rph24 locus was used to estimate the allele frequency in a collection of 282 international barley cultivars. Rph24 was frequently paired with APR locus Rph20 in cultivars displaying high levels of APR to leaf rust. The markers identified in this study for Rph24 should be useful for marker-assisted selection

Genetic Variability and Population Structure of Pakistani Potato Genotypes Using Retrotransposon-Based Markers

Molecular germplasm characterization is essential for gathering information on favorable attributes and varietal improvement. The current study evaluated the genetic divergence and population structure of 80 potato genotypes collected from Punjab, Pakistan, using polymorphic retrotransposon-DNA-based markers (iPBS). A total of 11 iPBS primers generated 787 alleles with a mean value of 8.9 alleles per primer, of which ~95% were polymorphic across the 80 genotypes. Different variation attributes, such as mean expected heterozygosity (H = 0.21), mean unbiased expected heterozygosity (µHe = 0.22), and mean Shannon’s information index (I = 0.32), showed the existence of sufficient genetic diversity in the studied potato genotypes. Analysis of molecular variance (AMOVA) showed that genetic variation within the population was higher (84%) than between populations (16%). A neighbor-joining tree was constructed based on the distance matrices that arranged the 80 genotypes into five distinct groups, and the genotypes FD61-3 and potato 2 had the highest genetic distance. A STRUCTURE analysis corroborated the dendrogram results and distributed the 80 genotypes also into five clusters. Our results determined that retrotransposon-based markers are highly polymorphic and could be used to evaluate genetic diversity between local and exotic potato genotypes. The genotypic data and population structure dissection analysis reported in this study will enhance potato varietal improvement and development