KEY MESSAGE : “To find stable resistance using association mapping tools, QTL with major and minor effects on leaf rust reactions were identified in barley breeding lines by assessing seedlings and ...adult plants.” Three hundred and sixty (360) elite barley (Hordeum vulgare L.) breeding lines from the Northern Region Barley Breeding Program in Australia were genotyped with 3,244 polymorphic diversity arrays technology markers and the results used to map quantitative trait loci (QTL) conferring a reaction to leaf rust (Puccinia hordei Otth). The F₃:₅ (Stage 2) lines were derived or sourced from different geographic origins or hubs of international barley breeding ventures representing two breeding cycles (2009 and 2011 trials) and were evaluated across eight environments for infection type at both seedling and adult plant stages. Association mapping was performed using mean scores for disease reaction, accounting for family effects using the eigenvalues from a matrix of genotype correlations. In this study, 15 QTL were detected; 5 QTL co-located with catalogued leaf rust resistance genes (Rph1, Rph3/19, Rph8/14/15, Rph20, Rph21), 6 QTL aligned with previously reported genomic regions and 4 QTL (3 on chromosome 1H and 1 on 7H) were novel. The adult plant resistance gene Rph20 was identified across the majority of environments and pathotypes. The QTL detected in this study offer opportunities for breeding for more durable resistance to leaf rust through pyramiding multiple genomic regions via marker-assisted selection.
Crown rust, caused by
Puccinia coronata
f. sp.
avenae
(
Pca
), is a significant impediment to global oat production. Some 98 alleles at 92 loci conferring resistance to
Pca
in
Avena
have been ...designated; however, allelic relationships and chromosomal locations of many of these are unknown. Long-term monitoring of
Pca
in Australia, North America and elsewhere has shown that it is highly variable even in the absence of sexual recombination, likely due to large pathogen populations that cycle between wild oat communities and oat crops. Efforts to develop cultivars with genetic resistance to
Pca
began in the 1950s. Based almost solely on all all-stage resistance, this has had temporary benefits but very limited success. The inability to eradicate wild oats, and their common occurrence in many oat growing regions, means that future strategies to control
Pca
must be based on the assumption of a large and variable prevailing pathogen population with high evolutionary potential, even if cultivars with durable resistance are deployed and grown widely. The presence of minor gene, additive APR to
Pca
in hexaploid oat germplasm opens the possibility of pyramiding several such genes to give high levels of resistance. The recent availability of reference genomes for diploid and hexaploid oat will undoubtedly accelerate efforts to discover, characterise and develop high throughput diagnostic markers to introgress and pyramid resistance to
Pca
in high yielding adapted oat germplasm.
Key message
Genome-wide association studies of barley breeding populations identified candidate minor genes for pairing with the adult plant resistance gene
Rph20
to provide stable leaf rust ...resistance across environments.
Stable resistance to barley leaf rust (BLR, caused by
Puccinia hordei
) was evaluated across environments in barley breeding populations (BPs). To identify genomic regions that can be combined with
Rph20
to improve adult plant resistance (APR), two BPs genotyped with the Diversity Arrays Technology genotyping-by-sequencing platform (DArT-seq) were examined for reaction to BLR at both seedling and adult growth stages in Australian environments. An integrated consensus map comprising both first- and second-generation DArT platforms was used to integrate QTL information across two additional BPs, providing a total of four interrelated BPs and 15 phenotypic data sets. This enabled identification of key loci underpinning BLR resistance. The APR gene
Rph20
was the only active resistance region consistently detected across BPs. Of the QTL identified,
RphQ27
on chromosome 6HL was considered the best candidate for pairing with
Rph20
.
RphQ27
did not align or share proximity with known genes and was detected in three of the four BPs. The combination of
RphQ27
and
Rph20
was of low frequency in the breeding material; however, strong resistance responses were observed for the lines carrying this pairing. This suggests that the candidate minor gene
RphQ27
can interact additively with
Rph20
to provide stable resistance to BLR across diverse environments.
We assembled an international barley panel comprising 282 entries from 26 countries with various levels of field resistance to leaf rust caused by
Puccinia hordei
. The panel was screened for leaf ...rust response with an array of pathotypes at the seedling stage, and at the adult plant stage in multiple environments (2013–2015) in Australia and Uruguay, and genotyped using > 13 K polymorphic DArT-Seq markers. Multipathotype testing in the greenhouse postulated the presence of seedling resistance genes
Rph1
,
Rph2
,
Rph3
,
Rph4
,
Rph7
,
Rph9.am
,
Rph12
,
Rph14
,
Rph15, Rph19
, and
Rph25
. Genome-wide association studies (GWAS) based on field data identified 13 QTLs significantly associated with DArT-Seq markers on chromosomes 2H (
Rph_G_Q1
,
Rph_G_Q2
,
Rph_G_Q3
, and
Rph_G_Q4
), 4H (
Rph_G_Q5
), 5H (
Rph_G_Q6
,
Rph_G_Q7
,
Rph_G_Q8
), 6H (
Rph_G_Q9
and
Rph_G_Q10
), and 7H (
Rph_G_Q11
,
Rph_G_Q12
, and
Rph_G_Q13
). Three QTLs (
Rph_G_Q3
,
Rph_G_Q5
, and
Rph_G_Q6
) were detected under all environments, whereas the other ten were variable, being detected in 1–4 environments;
Rph_G_Q1
and
Rph_G_Q13
being detected only in Uruguay. Among the three QTLs detected under all environments,
Rph_G_Q6
on chromosome 5H had the largest effect and corresponded to a region where the cataloged APR gene
Rph20
is located.
Rph_G_Q3
and
Rph_G_Q5
detected on chromosome 2H and 4H aligned with QTLs reported in at least three previous studies. The studies provide useful information towards better understanding of the genetic architecture of seedling and adult plant resistance to leaf rust in diverse global barley germplasm.
Understanding the genetic diversity and mechanisms underlying genetic variation in pathogen populations is crucial to the development of effective control strategies. We investigated the genetic ...diversity and reproductive biology of Colletotrichum graminicola isolates which infect maize by sequencing the genomes of 108 isolates collected from 14 countries using restriction site-associated DNA sequencing (RAD-seq) and whole-genome sequencing (WGS). Clustering analyses based on single-nucleotide polymorphisms revealed three genetic groups delimited by continental origin, compatible with short-dispersal of the pathogen and geographic subdivision. Intra- and intercontinental migration was observed between Europe and South America, likely associated with the movement of contaminated germplasm. Low clonality, evidence of genetic recombination, and high phenotypic diversity were detected. We show evidence that, although it is rare (possibly due to losses of sexual reproduction- and meiosis-associated genes)
can undergo sexual recombination. Our results support the hypotheses that intra- and intercontinental pathogen migration and genetic recombination have great impacts on the
population structure.
Plant pathogens cause significant reductions in yield and crop quality and cause enormous economic losses worldwide. Reducing these losses provides an obvious strategy to increase food production without further degrading natural ecosystems; however, this requires knowledge of the biology and evolution of the pathogens in agroecosystems. We employed a population genomics approach to investigate the genetic diversity and reproductive biology of the maize anthracnose pathogen (
) in 14 countries. We found that the populations are correlated with their geographical origin and that migration between countries is ongoing, possibly caused by the movement of infected plant material. This result has direct implications for disease management because migration can cause the movement of more virulent and/or fungicide-resistant genotypes. We conclude that genetic recombination is frequent (in contrast to the traditional view of
being mainly asexual), which strongly impacts control measures and breeding programs aimed at controlling this disease.
Fungicide use is integral to reduce yield loss from
on dry bean and soybean. Increasing fungicide use against this fungus may lead to resistance to the most common fungicides. Resistance has been ...reported in Brazil (
) and China (
subsp.
), however, few studies have investigated fungicide sensitivity of
in the United States. This work was conducted to determine if there was a difference in fungicide sensitivity of
isolates in the United States from: (i) dry bean versus soybean and (ii) fields with different frequencies of fungicide application. We further hypothesized that isolates with fungicide applications of a single active ingredient from tropical Brazil and subtropical Mexico were less sensitive than temperate U.S. isolates due to different management practices and climates. The EC
fungicide sensitivity of 512
isolates from the United States (443), Brazil (36), and Mexico (33) was determined using a discriminatory concentration (DC) previously identified for tetraconazole (2.0 ppm; EC
range of 0.197 to 2.27 ppm), boscalid (0.2; 0.042 to 0.222), picoxystrobin (0.01; 0.006 to 0.027), and thiophanate-methyl, which had a qualitative DC of 10 ppm. Among the 10 least sensitive isolates to boscalid and picoxystrobin, 2 presented mutations known to confer resistance in the
(qualitative) and
(quantitative) genes; however, no strong resistance was found. This study established novel DCs that can be used for further resistance monitoring and baseline sensitivity of
.
to tetraconazole worldwide plus baseline sensitivity to boscalid in the United States.
As soybean (
) production continues to expand in the United States and Canada, so do pathogens and pests that directly threaten soybean yield potential and economic returns for farmers. One such ...pathogen is the soybean cyst nematode (SCN;
). SCN has traditionally been managed using SCN-resistant cultivars and rotation with nonhost crops, but the interaction of SCN with sudden death syndrome (SDS; caused by
) in the field makes management more difficult. Nematode-protectant seed treatments have become options for SCN and SDS management. The objectives of this study were to evaluate nematode-protectant seed treatments for their effects on (i) early and full season SCN reproduction, (ii) foliar symptoms and root-rot caused by SDS, and (iii) soybean yield across environments accounting for the above factors. Using a standard protocol, field trials were implemented in 13 states and one Canadian province from 2019 to 2021 constituting 51 site-years. Six nematode-protectant seed treatment products were compared with a fungicide + insecticide base treatment and a nontreated check. Initial (at soybean planting) and final (at soybean harvest) SCN egg populations were enumerated, and SCN females were extracted from roots and counted at 30 to 35 days postplanting. Foliar disease index (FDX) and root rot caused by the SDS pathogen were evaluated, and yield data were collected for each plot. No seed treatment offered significant nematode control versus the nontreated check for in-season and full-season nematode response, no matter the initial SCN population or FDX level. Of all treatments, ILEVO (fluopyram) and Saltro (pydiflumetofen) provided more consistent increases in yield over the nontreated check in a broader range of SCN environments, even when FDX level was high.
This paper reports original evidence regarding the potential role of seed transmission of
pv.
in the epidemiology of bacterial leaf streak (BLS) in maize. We evaluated the occurrence of the pathogen ...on seeds from diseased fields and its subsequent transmission to seedlings. In 2016 and 2017,
pv.
was detected by TaqMan PCR from 22 of 41 maize seed lots harvested from naturally infected fields in Colorado, Nebraska, and Iowa. However, many of the PCR-positive samples did not yield culturable
pv.
colonies. The highest levels of seed contamination were detected in dent maize and popcorn from NE and CO. Seed transmission was evaluated in greenhouse grow-outs from eight seed lots, totaling more than 14,000 plants. Putative seed transmission events from naturally contaminated seed lots, estimated from PCR results, occurred at a frequency between 0.1 and 0.5% in 10-seedling pooled samples and at a frequency of 2.7% from individual plant assays. However, no seedling symptoms were observed during these assays and live
pv.
colonies were not recovered from PCR-positive seedlings. In contrast, seed transmission was readily demonstrated from artificially contaminated seed lots, including typical symptoms and recovery of live bacteria. Seed transmission consistently occurred from seeds soaked in bacterial suspensions with concentrations of ≥10
CFU/ml, suggesting that a threshold population of the bacterium is necessary for the development of BLS symptoms and recovery of live bacteria. The low bacterial populations on naturally contaminated seeds apparently were not sufficient to result in diseased seedlings.
Annual decreases in corn yield caused by diseases were estimated by surveying members of the Corn Disease Working Group in 22 corn-producing states in the United States and in Ontario, Canada, from ...2012 through 2015. Estimated loss from each disease varied greatly by state and year. In general, foliar diseases such as northern corn leaf blight, gray leaf spot, and Goss's wilt commonly caused the largest estimated yield loss in the northern United States and Ontario during non-drought years. Fusarium stalk rot and plant-parasitic nematodes caused the most estimated loss in the southern-most United States. The estimated mean economic loss due to yield loss by corn diseases in the United States and Ontario from 2012 to 2015 was $76.51 USD per acre. The cost of disease-mitigating strategies is another potential source of profit loss. Results from this survey will provide scientists, breeders, government, and educators with data to help inform and prioritize research, policy, and educational efforts in corn pathology and disease management.
Accepted for publication 26 August 2016.
The goal of this survey was to determine the relative importance of the various corn diseases regionally and over time, equipping researchers, breeders, government, and Extension specialists with data to help prioritize educational opportunities, research investigations, and funding requests. Thus, the objective of this survey was to determine the annual estimated disease losses in field corn for each of the top corn-producing states in the United States and Ontario, Canada.
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