Tracking costs of virulence in natural populations of the wheat pathogen, Puccinia striiformis f.sp.tritici

<p>Abstract</p> <p>Background</p> <p>Costs of adaptation play an important role in host-parasite coevolution. For parasites, evolving the ability to circumvent host resistance may trade off with subsequent growth or transmission. Such costs of virulence (<it>sensu </it>plant pathology) limit the spread of all-infectious genotypes and thus facilitate the maintenance of genetic polymorphism in both host and parasite. We investigated costs of three virulence factors in <it>Puccinia striiformis </it>f.sp.<it>tritici</it>, a fungal pathogen of wheat (<it>Triticum aestivum</it>).</p> <p>Results</p> <p>In pairwise competition experiments, we compared the fitness of near-isogenic genotypes that differed by a single virulence factor. Two virulence factors (<it>vir4</it>, <it>vir6</it>) imposed substantial fitness costs in the absence of the corresponding resistance genes. In contrast, the <it>vir9 </it>virulence factor conferred a strong competitive advantage to several isolates, and this for different host cultivars and growing seasons. In part, the experimentally derived fitness costs and benefits are consistent with frequency changes of these virulence factors in the French pathogen population.</p> <p>Conclusion</p> <p>Our results illustrate the variation in the evolutionary trajectories of virulence mutations and the potential role of compensatory mutations. Anticipation of such variable evolutionary outcomes represents a major challenge for plant breeding strategies. More generally, we believe that agro-patho-systems can provide valuable insight in (co)evolutionary processes in host-parasite systems.</p

QTL Mapping Combined With Comparative Analyses Identified Candidate Genes for Reduced Shattering in Setaria italica

Setaria (L.) P. Beauv is a genus of grasses that belongs to the Poaceae (grass) family, subfamily Panicoideae. Two members of the Setaria genus, Setaria italica (foxtail millet) and S. viridis (green foxtail), have been studied extensively over the past few years as model species for C4-photosynthesis and to facilitate genome studies in complex Panicoid bioenergy grasses. We exploited the available genetic and genomic resources for S. italica and its wild progenitor, S. viridis, to study the genetic basis of seed shattering. Reduced shattering is a key trait that underwent positive selection during domestication. Phenotyping of F2:3 and recombinant inbred line (RIL) populations generated from a cross between S. italica accession B100 and S. viridis accession A10 identified the presence of additive main effect quantitative trait loci (QTL) on chromosomes V and IX. As expected, enhanced seed shattering was contributed by the wild S. viridis. Comparative analyses pinpointed Sh1 and qSH1, two shattering genes previously identified in sorghum and rice, as potentially underlying the QTL on Setaria chromosomes IX and V, respectively. The Sh1 allele in S. italica was shown to carry a PIF/Harbinger MITE in exon 2, which gave rise to an alternatively spliced transcript that lacked exon 2. This MITE was universally present in S. italica accessions around the world and absent from the S. viridis germplasm tested, strongly suggesting a single origin of foxtail millet domestication. The qSH1 gene carried two MITEs in the 5′UTR. Presence of one or both MITEs was strongly associated with cultivated germplasm. If the MITE insertion(s) in qSH1 played a role in reducing shattering in S. italica accessions, selection for the variants likely occurred after the domestication of foxtail millet

Molecular markers for tracking the origin and worldwide distribution of invasive strains of <i>Puccinia striiformis</i>

Investigating the origin and dispersal pathways is instrumental to mitigate threats and economic and environmental consequences of invasive crop pathogens. In the case of Puccinia striiformis causing yellow rust on wheat, a number of economically important invasions have been reported, e.g., the spreading of two aggressive and high temperature adapted strains to three continents since 2000. The combination of sequence-characterized amplified region (SCAR) markers, which were developed from two specific AFLP fragments, differentiated the two invasive strains, PstS1 and PstS2 from all other P. striiformis strains investigated at a worldwide level. The application of the SCAR markers on 566 isolates showed that PstS1 was present in East Africa in the early 1980s and then detected in the Americas in 2000 and in Australia in 2002. PstS2 which evolved from PstS1 became widespread in the Middle East and Central Asia. In 2000, PstS2 was detected in Europe, where it never became prevalent. Additional SSR genotyping and virulence phenotyping revealed 10 and six variants, respectively, within PstS1 and PstS2, demonstrating the evolutionary potential of the pathogen. Overall, the results suggested East Africa as the most plausible origin of the two invasive strains. The SCAR markers developed in the present study provide a rapid, inexpensive, and efficient tool to track the distribution of P. striiformis invasive strains, PstS1 and PstS2

Deciphering resistance to Zymoseptoria tritici in the Tunisian durum wheat landrace accession ‘Agili39’

Septoria tritici blotch (STB), caused by Zymoseptoria tritici (Z. tritici), is an important biotic threat to durum wheat in the entire Mediterranean Basin. Although most durum wheat cultivars are susceptible to Z. tritici, research in STB resistance in durum wheat has been limited. Results: In our study, we have identified resistance to a wide array of Z. tritici isolates in the Tunisian durum wheat landrace accession ‘Agili39’. Subsequently, a recombinant inbred population was developed and tested under greenhouse conditions at the seedling stage with eight Z. tritici isolates and for five years under field conditions with three Z. tritici isolates. Mapping of quantitative trait loci (QTL) resulted in the identification of two major QTL on chromosome 2B designated as Qstb2B_1 and Qstb2B_2. The Qstb2B_1 QTL was mapped at the seedling and the adult plant stage (highest LOD 33.9, explained variance 61.6%), conferring an effective resistance against five Z. tritici isolates. The Qstb2B_2 conferred adult plant resistance (highest LOD 32.9, explained variance 42%) and has been effective at the field trials against two Z. tritici isolates. The physical positions of the flanking markers linked to Qstb2B_1 and Qstb2B_2 indicate that these two QTL are 5 Mb apart. In addition, we identified two minor QTL on chromosomes 1A (Qstb1A) and chromosome 7A (Qstb7A) (highest LODs 4.6 and 4.0, and explained variances of 16% and 9%, respectively) that were specific to three and one Z. tritici isolates, respectively. All identified QTL were derived from the landrace accession Agili39 that represents a valuable source for STB resistance in durum wheat. Conclusion: This study demonstrates that Z. tritici resistance in the ‘Agili39’ landrace accession is controlled by two minor and two major QTL acting in an additive mode. We also provide evidence that the broad efficacy of the resistance to STB in ‘Agili 39’ is due to a natural pyramiding of these QTL. A sustainable use of this Z. tritici resistance source and a positive selection of the linked markers to the identified QTL will greatly support effective breeding for Z. tritici resistance in durum wheat

Investigations into Physiological, Biochemical, and Histological Modifications in a Vine Decline Associated with Biotic and Abiotic Factors

Tunisian table grape production has significantly increased since two decades due to vineyards regional expansion and yield improvement. But, since several years, decline symptoms on Vitis vinifera have been recorded in some areas. A study case of a vineyard in Naassen area (near to Tunis) was chosen to investigate the disease origin and the physiological, biochemical, and histological modifications associated with vine decline. The investigation revealed characteristic symptoms on leaves, old and young shoots similar to decline symptoms of Grapevine Trunk Diseases. Based on cultural characteristics, laboratory investigations revealed the presence of Phaeomoniella chlamydospora and Phaeoacremonium spp., Diplodia seriata and Botryosphaeria dothidea, from root and shoot samples, respectively. These fungi are known as the main pathogens responsible for the Esca, Black dead arm and Excoriose. Molecular analysis confirmed the identification of Diplodia seriata. Beside morphological alterations on leaves and shoots, symptomatic vines presented significant reductions of 30 and 20% in trunk diameter and bud break rate, respectively, and delayed spring growth compared to healthy ones. Furthermore, roots and stems from declined vines contained 3 times more starch than those from asymptomatic ones. Decline survey revealed a heterogeneous dispersion of symptoms in the vineyard in accordance with water supply. The vines along the edge of vineyards are usually less watered and show more decline symptoms. Decline dynamics in time and space scales have to be considered in order to develop effective management strategies

Adaptation et structuration spatiale des populations méditerranéennes de rouille jaune du blé (Puccinia striiformis f.sp. tritici)

En France, la population de rouille jaune du blé P. striiformis f.sp. tritici (PST) est structurée en deux sous-populations : une population Nord qui provoque des épidémies tous les 3-4 ans, évolue rapidement et présente des pathotypes dotés de nombreuses virulences, et une population Sud plus sporadique et dominée par un pathotype simple (6E16-Av9). Malgré la sensibilité des variétés de blé du Sud de la France aux races du Nord et le potentiel migratoire de PST, cette structuration de la population se maintient. Pour expliquer cette structuration, nous avons testé si (i) les pathotypes du Nord subissent une diminution d agressivité du fait du nombre élevé de virulences qu ils portent, (ii) le pathotype 6E16-Av9 présente une adaptation aux conditions méditerranéennes. Parallèlement, nous nous sommes intéressés à décrire le lien entre cette population du Sud de la France et le reste de la zone méditerranéenne. Les tests de compétition de pathotypes ne différant que par une virulence ont révélé l existence d une moindre fitness chez les pathotypes porteurs d une avirulence inutile. Néanmoins, pour trois cas sur huit, une plus forte agressivité des virulents est observée, nuançant ainsi l importance de l effet d un coût des virulences sur la structuration observée. Des expériences de compétition au champ ont parallèlement confirmé la meilleure adaptation du pathotype 6E16-Av9 à hautes températures (thèse M. Mboup, 2008). L étude génétique de PST autour du Bassin Méditerranéen (AFLP et SSR) confirme l appartenance de la population du Sud à une population Ouest Méditerranéenne et illustre l importance des migrations de spores du Maghreb vers le Sud de l Europe. L identification au Maghreb du gène de résistance Yr8 dans les principales variétés de blé cultivées explique l importance de la virulence correspondante v8 dans les populations méditerranéennes, et l avirulence des pathotypes du Nord (Av8) sur variétés du Sud. L étude d un échantillonnage de PST sur le reste du Bassin Méditerranéen révèle la proximité génétique de la population de l Ouest avec celle du Moyen Orient, dont elle est probablement issue par migration. Ces analyses montrent aussi une diversité supérieure des populations de PST encore plus à l Est, au Pakistan, où la diversité des conditions environnementales biotiques et abiotiques contribuent à l existence et la différentiation de populations contrastées de PST. Les relations phylogénétiques entre les différentes populations échantillonnées et le gradient de diversité Ouest-Est observé apportent des indications sur l origine et la diversification des populations de rouille jaune sur le contient eurasien.The wheat yellow rust is structured in two sub-populations in France : a North population responsible for recurrent epidemics (every 3-4 years) due to pathotypes with complex virulence patterns, and a South population, sporadic and dominated by one simple pathotype (6E16-Av9). Despite the high susceptibility of southern France cultivars to the Northern pathotypes and the presence of spore exchanges between the two areas, this spatial structure is steady over time. In order to explain this structure, we tested if (i) the Northern pathotypes present a fitness penalty due to the unnecessary virulence genes carried; (ii) the southern population has a fitness advantage under Mediterranean conditions. In addition we studied the genetic relationship of the South France PST population with populations from the Mediterranean area. Competition tests between pathotypes differing by one virulence revealed a higher fitness of avirulent isolates. However, for three pairs over eight, an higher aggressiveness was observed for virulent isolates, limiting the impact of the virulence cost in the observed PST structure. Field competitions confirmed the best fitness of 6E16-Av9 pathotype at high temperatures (Mboup PHD, 2008). The genetic study of PST in Mediterranean area (AFLP and SSR) confirmed the belonging of South isolates to a Mediterranean population and highlined the importance of spore migration from North Africa to southern Europe. The identification of the resistance gene Yr8 in the prevalent wheat cultivars in North Africa explains the high frequency of the corresponding virulence v8 in the Mediterranean area, as well as the incapacity of northern pathotypes (Av9) to develop in that area. A complementary sampling revealed the genetic proximity of Mediterranean population with Middle East population, from which it probably originated. An even greatest genetic diversity is depicted, in Pakistan, where probably biotic and abiotic environmental diversities contribute to the existence and the differentiation of contrasted populations. Phylogenetic relations between the populations studied bring some indications on the origin and diversification of PST in the Eurasian continent.ORSAY-PARIS 11-BU Sciences (914712101) / SudocSudocFranceF

Wheat yellow rust dynamics in Tunisia since 2013 and resistance genes in durum wheat

Wheat yellow rust epidemics, caused by Puccinia striiformis f. sp. tritici (PST) have increased worldwide with the emergence in Western Europe and North Africa of an aggressive strain and tolerant to high temperature (PstS2) since 2004 and exotic strains (Triticale 2006, 2015, Warrior and Kranich) recently. Even though resistant varieties bring to agriculture effective solutions to reduce the use of pesticides, races of the pathogen quickly overcome introduced resistance genes. In this study we determined the virulence combinations using the European and world differential sets and the simple sequence repeat diversity of 94 PST isolates collected in Tunisia since 2013 from the major wheat growing areas. In addition, 39 local Tunisian durum wheat accessions and 109 recombinant inbred lines RILs (F9) were evaluated at the seedling stage against old and new races of PST in order to identify resistant genotypes and markers associated with resistance genes. The results underlined the rapid change in wheat yellow rust population where 3 predominant races, Warrior1 (W1), Warrior- (W-) and Triticale 2006 were detected since 2013. In addition, 10% of the durum wheat accessions were resistant to W1, W- and PstS2. The evaluation of the RILs issued from a cross between Tunisian durum wheat Khiar and Agili39 revealed one major resistance gene against W1 and two minor genes against PstS2. The use of these genes in breeding can improve durability of the genetic control against PS

Development of a Co-Dominant Cleaved Amplified Polymorphic Sequences Assay for the Rapid Detection and Differentiation of Two Pathogenic Clarireedia spp. Associated with Dollar Spot in Turfgrass

Dollar spot is one of the most destructive diseases in turfgrass. The causal agents belong to the genus Clarireedia, which are known for causing necrotic, sunken spots in turfgrass that coalesce into large damaged areas. In low tolerance settings like turfgrass, it is of vital importance to rapidly detect and identify the pathogens. There are a few methods available to identify the genus Clarireedia, but none of those are rapid enough and characterize down to the species level. This study produced a co-dominant cleaved amplified polymorphic sequences (CAPS) test that differentiates between C. jacksonii and C. monteithiana, the two species that cause dollar spot disease within the United States. The calmodulin gene (CaM) was targeted to generate Clarireedia spp. specific PCR primers. The CAPS assay was optimized and tested for specificity and sensitivity using DNA extracted from pure cultures of two Clarireedia spp. and other closely related fungal species. The results showed that the newly developed primer set could amplify both species and was highly sensitive as it detected DNA concentrations as low as 0.005 ng/µL. The assay was further validated using direct PCR to speed up the diagnosis process. This drastically reduces the time needed to identify the dollar spot pathogens. The resulting assay could be used throughout turfgrass settings for a rapid and precise identification method in the US