Fine mapping quantitative resistances to downy mildew in lettuce revealed multiple sub-QTLs with plant stage dependent effects reducing or even promoting the infection
Boer, E. den; Zhang, N. ; Pelgrom, K.T.B. ; Visser, R.G.F. ; Niks, R.E. ; Jeuken, M.J.W. - \ 2013
Theoretical and Applied Genetics 126 (2013)12. - ISSN 0040-5752 - p. 2995 - 3007.
backcross inbred lines - trait locus qtl - bremia-lactucae - leaf rust - durable resistance - stripe rust - genetic dissection - disease resistance - nonhost resistance - wild lettuce
Previous studies on the genetic dissection of the complete resistance of wild lettuce, Lactuca saligna, to downy mildew revealed 15 introgression regions that conferred plant stage dependent quantitative resistances (QTLs). Three backcross inbred lines (BILs), carrying an individual 30–50 cM long introgression segment from L. saligna in a cultivated lettuce, L. sativa, background, reduced infection by 60–70 % at young plant stage and by 30–50 % at adult plant stage in field situations. We studied these three quantitative resistances in order to narrow down their mapping interval and determine their number of loci, either single or multiple. We performed recombinant screenings and developed near isogenic lines (NILs) with smaller overlapping L. saligna introgressions (substitution mapping). In segregating introgression line populations, recombination was suppressed up to 17-fold compared to the original L. saligna × L. sativaF2 population. Recombination suppression depended on the chromosome region and was stronger suppressed at the smallest introgression lengths. Disease evaluation of the NILs revealed that the resistance of all three BILs was not explained by a single locus but by multiple sub-QTLs. The 17 L. saligna-derived sub-QTLs had a smaller and plant stage dependent resistance effect, some segments reducing; others even promoting downy mildew infection. Implications for lettuce breeding are outlined.
QTLs for resistance to the false brome rust Puccinia brachypodii in the model grass Brachypodium distachyon L.
Barbieri, M. ; Marcel, T.C. ; Niks, R.E. ; Francia, E. ; Pasquariello, M. ; Mazzamurro, V. ; Garvin, D.F. ; Pecchioni, N. - \ 2012
Genome 55 (2012)2. - ISSN 0831-2796 - p. 152 - 163.
agrobacterium-mediated transformation - quantitative trait loci - genetic-linkage map - one major locus - leaf rust - disease resistance - globodera-pallida - powdery mildew - barley genome - stripe rust
The potential of the model grass Brachypodium distachyon L. (Brachypodium) for studying grass–pathogen interactions is still underexploited. We aimed to identify genomic regions in Brachypodium associated with quantitative resistance to the false brome rust fungus Puccinia brachypodii. The inbred lines Bd3-1 and Bd1-1, differing in their level of resistance to P. brachypodii, were crossed to develop an F2 population. This was evaluated for reaction to a virulent isolate of P. brachypodii at both the seedling and advanced growth stages. To validate the results obtained on the F2, resistance was quantified in F2-derived F3 families in two experiments. Disease evaluations showed quantitative and transgressive segregation for resistance. A new AFLP-based Brachypodium linkage map consisting of 203 loci and spanning 812 cM was developed and anchored to the genome sequence with SSR and SNP markers. Three false brome rust resistance QTLs were identified on chromosomes 2, 3, and 4, and they were detected across experiments. This study is the first quantitative trait analysis in Brachypodium. Resistance to P. brachypodii was governed by a few QTLs: two acting at the seedling stage and one acting at both seedling and advanced growth stages. The results obtained offer perspectives to elucidate the molecular basis of quantitative resistance to rust fungi
Compatible Puccinia hordei infection in barley induces basal defense to subsequent infection by Blumeria graminis
Aghnoum, R. ; Niks, R.E. - \ 2012
Physiological and Molecular Plant Pathology 77 (2012)1. - ISSN 0885-5765 - p. 17 - 22.
f-sp-hordei - systemic acquired-resistance - erysiphe-graminis - induced accessibility - powdery mildew - leaf rust - papilla formation - spring barley - cell-death - inaccessibility
Rusts and powdery mildews employ different strategies to suppress defense during penetration. We observed that a compatible interaction of barley-Puccinia hordei induced increased penetration resistance to a challenge infection by powdery mildew. This induced resistance is local and its level is not determined by the virulence spectrum of the challenger isolate. Our data suggest that the inducer effect is due to rust-stoma communication during penetration, to the presence of the rust hyphae in the apoplast, or to penetration resistance mounted by the rust attacked mesophyll cells. We hypothesized that the rust “primes” the basal defense prior to the mildew infection
An eQTL analysis of partial resistance to Puccinia hordei in barley
Chen, Xinwei ; Hackett, C.A. ; Niks, R.E. ; Hedley, P.E. ; Booth, C. ; Druka, A. ; Marcel, T.C. ; Vels, S.A. ; Bayer, M. ; Milne, I. ; Morris, J. ; Ramsay, L. ; Marshall, D. ; Cardle, L. ; Waugh, R. - \ 2010
PLoS ONE 5 (2010)1. - ISSN 1932-6203 - 15 p.
quantitative trait locus - density consensus map - false discovery rate - gene-expression - powdery mildew - leaf rust - flowering-time - stem rust - basal defense - arabidopsis
Background - Genetic resistance to barley leaf rust caused by Puccinia hordei involves both R genes and quantitative trait loci. The R genes provide higher but less durable resistance than the quantitative trait loci. Consequently, exploring quantitative or partial resistance has become a favorable alternative for controlling disease. Four quantitative trait loci for partial resistance to leaf rust have been identified in the doubled haploid Steptoe (St)/Morex (Mx) mapping population. Further investigations are required to study the molecular mechanisms underpinning partial resistance and ultimately identify the causal genes.Methodology/Principal Findings - We explored partial resistance to barley leaf rust using a genetical genomics approach. We recorded RNA transcript abundance corresponding to each probe on a 15K Agilent custom barley microarray in seedlings from St and Mx and 144 doubled haploid lines of the St/Mx population. A total of 1154 and 1037 genes were, respectively, identified as being P. hordei-responsive among the St and Mx and differentially expressed between P. hordei-infected St and Mx. Normalized ratios from 72 distant-pair hybridisations were used to map the genetic determinants of variation in transcript abundance by expression quantitative trait locus (eQTL) mapping generating 15685 eQTL from 9557 genes. Correlation analysis identified 128 genes that were correlated with resistance, of which 89 had eQTL co-locating with the phenotypic quantitative trait loci (pQTL). Transcript abundance in the parents and conservation of synteny with rice allowed us to prioritise six genes as candidates for Rphq11, the pQTL of largest effect, and highlight one, a phospholipid hydroperoxide glutathione peroxidase (HvPHGPx) for detailed analysis.Conclusions/Significance - The eQTL approach yielded information that led to the identification of strong candidate genes underlying pQTL for resistance to leaf rust in barley and on the general pathogen response pathway. The dataset will facilitate a systems appraisal of this host-pathogen interaction and, potentially, for other traits measured in this population
Basal host resistance of barley to powdery mildew: connecting quantitative trait loci and candidate genes
Aghnoum, R. ; Marcel, T.C. ; Johrde, A. ; Pecchioni, N. ; Schweizer, P. ; Niks, R.E. - \ 2010
Molecular Plant-Microbe Interactions 23 (2010)1. - ISSN 0894-0282 - p. 91 - 102.
heterologous rust fungi - head blight resistance - defense-related genes - hordeum-vulgare l - pisum-sativum l. - disease-resistance - leaf rust - nonhost resistance - puccinia-hordei - spring barley
The basal resistance of barley to powdery mildew (Blumeria graminis f. sp. hordei) is a quantitatively inherited trait that is based on nonhypersensitive mechanisms of defense. A functional genomic approach indicates that many plant candidate genes are involved in the defense against formation of fungal haustoria. It is not known which of these candidate genes have allelic variation that contributes to the natural variation in powdery mildew resistance, because many of them may be highly conserved within the barley species and may act downstream of the basal resistance reaction. Twenty-two expressed sequence tag or cDNA clone sequences that are likely to play a role in the barley-Blumeria interaction based on transcriptional profiling, gene silencing, or overexpression data, as well as mlo, Ror1, and Ror2, were mapped and considered candidate genes for contribution to basal resistance. We mapped the quantitative trait loci (QTL) for powdery mildew resistance in six mapping populations of barley at seedling and adult plant stages and developed an improved high-density integrated genetic map containing 6,990 markers for comparing QTL and candidate gene positions over mapping populations. We mapped 12 QTL at seedling stage and 13 QTL at adult plant stage, of which four were in common between the two developmental stages. Six of the candidate genes showed coincidence in their map positions with the QTL identified for basal resistance to powdery mildew. This co-localization justifies giving priority to those six candidate genes to validate them as being responsible for the phenotypic effects of the QTL for basal resistance
Three Combined Quantitative Trait Loci from Nonhost Lactuca saligna Are Sufficient to Provide Complete Resistance of Lettuce Against Bremia lactucae
Zhang, N. ; Pelgrom, K.T.B. ; Niks, R.E. ; Visser, R.G.F. ; Jeuken, M.J.W. - \ 2009
Molecular Plant-Microbe Interactions 22 (2009)9. - ISSN 0894-0282 - p. 1160 - 1168.
barley stripe rust - alleles determining resistance - backcross inbred lines - hypersensitive response - fungal pathogens - wild lettuce - leaf rust - mildew - qtl - wheat
The nonhost resistance of wild lettuce (Lactuca saligna) to downy mildew (Bremia lactucae) is based on at least 15 quantitative trait loci (QTL), each effective at one or more plant developmental stages. We used QTL pyramiding (stacking) to determine how many of these QTL from L. saligna are sufficient to impart complete resistance towards B. lactucae to cultivated lettuce, L. sativa. The alleles of four of the most promising QTL, rbq4, rbq5, rbq6+11, and rbq7 are effective at both the young and adult plant stages. Lines with these four QTL in all possible combinations were generated by crossing the respective backcross inbred lines (BIL). Using the 11 resulting lines (combiBIL), we determined that combinations of three QTL, rbq4, rbq5, and rbq6+11, led to increased levels of resistance; however, one QTL, rbq7, did not add to the resistance level when combined with the other QTL. One line, tripleBIL268, which contains the three QTL rbq4, rbq5, and rbq6+11, was completely resistant to B. lactucae at the young plant stage. This suggests that these three QTL are sufficient to confer the complete resistance of the nonhost L. saligna and any additional QTL in L. saligna are redundant. Histological analysis of B. lactucae infection in L. saligna, the BIL, and the combiBIL 48 h after inoculation revealed different microscopical phenotypes of resistance. The QTL differed with respect to the stage of the infection process with which they interfered
High diversity of genes for nonhost resistance of barley to heterologous rust fungi
Jafary, H. ; Albertazzi, G. ; Marcel, T.C. ; Niks, R.E. - \ 2008
Genetics 178 (2008)4. - ISSN 0016-6731 - p. 2327 - 2339.
puccinia-hordei - leaf rust - linkage map - iii effector - defense - plants - pathogens - qtls - identification - accumulation
Inheritance studies on the nonhost resistance of plants would normally require interspecific crosses that suffer from sterility and abnormal segregation. Therefore, we developed the barley¿Puccinia rust model system to study, using forward genetics, the specificity, number, and diversity of genes involved in nonhost resistance. We developed two mapping populations by crossing the line SusPtrit, with exceptional susceptibility to heterologous rust species, with the immune barley cultivars Vada and Cebada Capa. These two mapping populations along with the Oregon Wolfe Barley population, which showed unexpected segregation for resistance to heterologous rusts, were phenotyped with four heterologous rust fungal species. Positions of QTL conferring nonhost resistance in the three mapping populations were compared using an integrated consensus map. The results confirmed that nonhost resistance in barley to heterologous rust species is controlled by QTL with different and overlapping specificities and by an occasional contribution of an R-gene for hypersensitivity. In each population, different sets of loci were implicated in resistance. Few genes were common between the populations, suggesting a high diversity of genes conferring nonhost resistance to heterologous pathogens. These loci were significantly associated with QTL for partial resistance to the pathogen Puccinia hordei and with defense-related genes
Relative ratio of mature pustules: a simple method to assess partial resistance of barley to Puccinia hordei
Jiang, Guo-Liang ; Marcel, T.C. ; Martinez, F. ; Niks, R.E. - \ 2007
Plant Disease 91 (2007)3. - ISSN 0191-2917 - p. 301 - 307.
leaf rust - parameters - components - field - qtls
In plant breeding and germplasm evaluation, large-scale assessment of quantitative resistance is desirable. but feasible only if a simple and accurate measure is available. In several plant-pathogen systems. latent period (LP) is a parameter that is well correlated with the level of partial resistance observed in field trials. However, measuring LP or relative LP (RLP), i.e., relative to the reference accessions, is laborious. We investigated the value of relative ratio of mature pustules (RRMP. relative to the susceptible control) as a simple and rapid alternative to replace LP estimation in barley to barley leaf rust (Puccinia hordei). A set of 103 F-9 recombinant inbred lines (RILs) derived from a cross L94 x Vada was sown in a greenhouse compartment, and was inoculated at the seedling stage with isolate Uppsala or 24, and at the adult plant stage with isolate 24. In demarcated sections of leaves, the number of mature pustules was counted several times after inoculation. The ratio of mature pustules (RMP) and LP50 were calculated to assess RRMP and RLP. respectively, and to identify the quantitative trait loci (QTLs) contributing to the genetic variation. The contrasts in RRMP among accessions were highest when the susceptible reference line had developed 70 to 90% mature orange pustules, the immature infection sites being visible as pale flecks. At this optimal time of observation, the correlation between RRMP and RLP in both the seedling stage and the adult plant stage was highly significant (r = -0.82 similar to -0.98). Compared with RLP, RRMP was much easier and simpler to measure and still showed good correspondence with RLP in the identification of QTLs for partial resistance. In another experiment at the seedling stage with 25 barley cultivars and lines inoculated with isolate 1.2.1, the coefficient of correlation between RRMP and RLP was -0.98. Therefore, we conclude that RRMP should have great application potential in breeding programs and germplasm screening and could be used in fundamental studies as well.
Innate nonhost immunity in barley to different heterologous rust fungi is controlled by sets of resistance genes with different and overlapping specificities
Jafary, H. ; Szabo, L.J. ; Niks, R.E. - \ 2006
Molecular Plant-Microbe Interactions 19 (2006)11. - ISSN 0894-0282 - p. 1270 - 1279.
puccinia-hordei - linkage map - leaf rust - plant defense - arabidopsis - identification - prehaustorial - perception - morphology - pathogens
We developed an evolutionary relevant model system, barley-Puccini rust fungi, to study the inheritance and specificity of plant factors that determine to what extent innate nonhost immunity can be suppressed. A mapping population was developed from a cross between an experimental barley line (Suspired) with exceptional susceptibility to several heterogonous (nonhost) rust fungi and regular, immune, cv. Veda. Seedlings were inoculated with five heterogonous and two homologous (host) species of rust fungi. Resistance segregated quantitatively for each of the rust fungi. In total, 18 chromosomal regions were implicated. For each rust species, a different set of genes was effective. Of the 18 chromosomal regions, 11 were significantly effective to only one rust species and 7 were effective to more than one rust species, implying genetic linkage or pleiotropy. One resistance (R) gene for hypersensitive resistance to Puccinia hordei-secalini was mapped, suggesting occasional contribution of R genes to nonhost resistance in barley. Quantitative trait loci (QTLs) with effects to multiple rust fungi did not tend to be particularly effective to rust species that were phylogenetically related, as determined from their internal transcribed spacer sequence. We suggest that the QTLs described here play a role as specific and quantitative recognition factors that are specifically negated by the rust to successfully suppress innate immunity.
A novel major gene on chromosome 6H for resistance of barley against the barley yellow dwarf virus
Niks, R.E. ; Habekuss, A. ; Bekele, B. ; Ordon, F. - \ 2004
Theoretical and Applied Genetics 109 (2004)7. - ISSN 0040-5752 - p. 1536 - 1543.
hordeum-vulgare - leaf rust - yd2 gene - cultivar chikurin-ibaraki-1 - puccinia-hordei - bydv-tolerance - wheat - sequence - locus - maps
In a mapping population derived from the Ethiopian barley line L94 x Vada, natural infection by barley yellow dwarf virus (BYDV) occurred. While line L94 hardly showed symptoms, Vada was severely affected. The 103 recombinant inbred lines segregated bimodally. The major gene responsible for this resistance mapped to chromosome 6H. We propose to name the locus Ryd3. A subset of recombinant inbred lines, L94, and Vada were planted in a subsequent field test which confirmed the previous field observations. Double antibody sandwich enzyme-linked immunosorbent assays (DAS-ELISA) indicated that the epidemic was due to a combination of the serotypes BYDV-PAV and BYDV-MAV. In the accessions with the least BYDV symptoms no virus was detected, justifying the consideration of the gene as conferring true resistance rather than tolerance to these viruses. In a laboratory/gauze house trial a near-isogenic line carrying the Vada chromosome 6H fragment in an L94 background was affected as much as Vada. The effect of Ryd3 was quantified, and compared with that of the only other known major gene for resistance to BYDV, Ryd2, which is also of Ethiopian origin and is located on chromosome 3H. Both genes seemed to reduce the chance of the viral isolate used in this study to establish infection. In plants in which it became established, the virus concentration reached a similar level as in susceptible accessions, but with less dramatic symptom development. Inoculated plants in which the virus failed to multiply tended to show an increase in the number of ears per plant, resulting in higher grain yield per plant. Ryd3 co-segregates with several PCR-based molecular markers that may serve for marker assisted selection.