Discovery of three loci increasing resistance to charcoal rot caused by Macrophomina phaseolina in octoploid strawberry

Abstract Charcoal rot caused by Macrophomina phaseolinais an increasing economic problem in annualized strawberry production systems around the world. Currently there are no effective postfumigation chemical controls for managing charcoal rot, and no information is available on the genetic architecture of resistance to M. phaseolina in strawberry (Fragaria ×ananassa). In this study, three multiparental discovery populations and two validation populations were inoculated at planting and evaluated for mortality in three consecutive growing seasons. Genome-wide SNP genotyping and pedigree-based analysis with FlexQTL™ software were performed. Two large-effect quantitative trait loci (QTL) increasing charcoal rot resistance were discovered and validated in cultivated germplasm. FaRMp1 was located on linkage group 2A in the interval 20.4to 24.9 cM, while FaRMp2 was located on linkage group 4B in the interval 41.1to 61.2 cM. Together these QTLs explained 27% and 17% of the phenotypic variance in two discovery populations consisting of elite breeding germplasm. For both QTLs, the resistant allele showed some evidence of partial dominance, but no significant interaction was detected between the two loci. As the dosage of resistant alleles increased from 0 to 4 across the two QTLs, mortality decreased regardless of the combination of alleles.A third locus, FaRMp3 on 4D, was discovered in FVC 11–58, a reconstituted F.×ananassa originating from diverse F. virginiana and F. chiloensis accessions. This locus accounted for 44% of phenotypic variation in four segregating crosses. These findings will form the basis for DNA-informed breeding for resistance to charcoal rot in cultivated strawberry.

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Genome-wide association study reveals the genetic architecture of 27 yield-related traits in tomato

10.21203/rs.3.rs-86537/v1 ◽

2020 ◽

Author(s):

Jie Ye ◽

Xin Wang ◽

Wenqian Wang ◽

Huiyang Yu ◽

Guo Ai ◽

...

Keyword(s):

Association Study ◽

Genetic Architecture ◽

Genome Wide Association Study ◽

Genetic Research ◽

Reproductive Development ◽

Genome Wide Association ◽

Phenotypic Variance ◽

Vegetable Crop ◽

Genome Wide ◽

Malate Transporter

Abstract Tomato (Solanum lycopersicum) is a highly valuable vegetable crop and yield is one of the most important traits. Uncovering the genetic architecture of yield-related traits in tomato is critical for the management of vegetative and reproductive development, thereby enhancing yield. Here we perform a comprehensive genome-wide association study for 27 yield-related traits in tomato. A total of 239 significant associations corresponding to 129 loci, harboring many reported and novel genes related to vegetative and reproductive development, were identified, and these loci explained an average of ~8.8% of the phenotypic variance. A total of 51 loci associated with 25 traits have been under selection, especially during tomato improvement. Furthermore, a candidate gene, SlALMT15 that encodes an aluminum-activated malate transporter, was functionally characterized and shown to act as a pivotal regulator of leaf stomata formation through increasing photosynthesis and drought resistance. This study provides valuable information for tomato genetic research and breeding.

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Identification and Validation of Genomic Regions Associated With Charcoal Rot Resistance in Tropical Maize by Genome-Wide Association and Linkage Mapping

Frontiers in Plant Science ◽

10.3389/fpls.2021.726767 ◽

2021 ◽

Vol 12 ◽

Author(s):

Zerka Rashid ◽

Harleen Kaur ◽

Veerendra Babu ◽

Pradeep Kumar Singh ◽

Sharanappa I. Harlapur ◽

...

Keyword(s):

Genome Wide Association Study ◽

Macrophomina Phaseolina ◽

Genome Wide Association ◽

Common Disease ◽

Chromosome 6 ◽

Charcoal Rot ◽

Stalk Rot ◽

Genome Wide ◽

A Genome ◽

Mapping Populations

Charcoal rot is a post-flowering stalk rot (PFSR) disease of maize caused by the fungal pathogen, Macrophomina phaseolina. It is a serious concern for smallholder maize cultivation, due to significant yield loss and plant lodging at harvest, and this disease is expected to surge with climate change effects like drought and high soil temperature. For identification and validation of genomic variants associated with charcoal rot resistance, a genome-wide association study (GWAS) was conducted on CIMMYT Asia association mapping panel comprising 396 tropical-adapted lines, especially to Asian environments. The panel was phenotyped for disease severity across two locations with high disease prevalence in India. A subset of 296,497 high-quality SNPs filtered from genotyping by sequencing was correcting for population structure and kinship matrices for single locus mixed linear model (MLM) of GWAS analysis. A total of 19 SNPs were identified to be associated with charcoal rot resistance with P-value ranging from 5.88 × 10−06 to 4.80 × 10−05. Haplotype regression analysis identified 21 significant haplotypes for the trait with Bonferroni corrected P ≤ 0.05. For validating the associated variants and identifying novel QTLs, QTL mapping was conducted using two F2:3 populations. Two QTLs with overlapping physical intervals, qMSR6 and qFMSR6 on chromosome 6, identified from two different mapping populations and contributed by two different resistant parents, were co-located with the SNPs and haplotypes identified at 103.51 Mb on chromosome 6. Similarly, several SNPs/haplotypes identified on chromosomes 3, 6 and 8 were also found to be physically co-located within QTL intervals detected in one of the two mapping populations. The study also noted that several SNPs/haplotypes for resistance to charcoal rot were located within physical intervals of previously reported QTLs for Gibberella stalk rot resistance, which opens up a new possibility for common disease resistance mechanisms for multiple stalk rots.

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Effect of Formulations of Allyl Isothiocyanate on Survival of Macrophomina phaseolina from Strawberry

Plant Disease ◽

10.1094/pdis-01-18-0172-re ◽

2018 ◽

Vol 102 (11) ◽

pp. 2212-2219 ◽

Cited By ~ 7

Author(s):

Juliana S. Baggio ◽

Manuel Chamorro ◽

Leandro G. Cordova ◽

Joseph W. Noling ◽

Gary E. Vallad ◽

...

Keyword(s):

Production Systems ◽

Allyl Isothiocyanate ◽

Macrophomina Phaseolina ◽

The United States ◽

Organic Production ◽

Soilborne Pathogens ◽

Corn Cob ◽

Charcoal Rot ◽

Phase Out ◽

Research Facilities

Management of Macrophomina phaseolina, causal agent of charcoal rot in many crops worldwide, including strawberry, has become more challenging since the phase out of methyl bromide (MeBr). The search for a fumigant equally effective as MeBr to control soilborne pathogens has been extensive. Allyl isothiocyanate (AITC), a biofumigant recently registered in the United States, was evaluated at different rates, formulations, fumigant combinations, and application methods in the fall of 2014 and 2015 at two research facilities in Balm and Dover, FL. The efficacy of treatments was determined by evaluating the survival of M. phaseolina inoculum on infested corn-cob litter buried in bags 7.6 and 20.3 cm deep in the center, and 7.6 cm deep in the side, of plastic mulched raised beds. The biofumigant was shown to be more or as effective in reducing populations of M. phaseolina in the soil compared with standard fumigants, such as chloropicrin and 1,3-dichloropropene with chloropicrin. Thus, AITC is a promising biofumigant alternative for managing charcoal rot of strawberry, particularly in organic production systems, and should be evaluated for the management of other soilborne pathogens.

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Genome-wide association study reveals the genetic architecture of 27 yield-related traits in tomato

10.1101/2020.10.01.322214 ◽

2020 ◽

Author(s):

Jie Ye ◽

Xin Wang ◽

Wenqian Wang ◽

Huiyang Yu ◽

Guo Ai ◽

...

Keyword(s):

Association Study ◽

Genetic Architecture ◽

Genome Wide Association Study ◽

Genetic Research ◽

Reproductive Development ◽

Genome Wide Association ◽

Phenotypic Variance ◽

Vegetable Crop ◽

Genome Wide ◽

Malate Transporter

ABSTRACTTomato (Solanum lycopersicum) is a highly valuable vegetable crop and yield is one of the most important traits. Uncovering the genetic architecture of yield-related traits in tomato is critical for the management of vegetative and reproductive development, thereby enhancing yield. Here we perform a comprehensive genome-wide association study for 27 yield-related traits in tomato. A total of 239 significant associations corresponding to 129 loci, harboring many reported and novel genes related to vegetative and reproductive development, were identified, and these loci explained an average of ∼8.8% of the phenotypic variance. A total of 51 loci associated with 25 traits have been under selection, especially during tomato improvement. Furthermore, a candidate gene, SlALMT15 that encodes an aluminum-activated malate transporter, was functionally characterized and shown to act as a pivotal regulator of leaf stomata formation through increasing photosynthesis and drought resistance. This study provides valuable information for tomato genetic research and breeding.

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Abstract 048: Association Analyses of up to ∼263,000 Individuals Provide New Insights into the Biology and Genetic Architecture of the Extremes of Anthropometric Traits

Circulation ◽

10.1161/circ.125.suppl_10.a048 ◽

2012 ◽

Vol 125 (suppl_10) ◽

Author(s):

Erik Ingelsson ◽

Reedik Mägi ◽

Stefan Gustafsson ◽

Andrea Ganna ◽

Eleanor Wheeler ◽

...

Keyword(s):

General Population ◽

Genetic Architecture ◽

Class Ii ◽

Overweight And Obesity ◽

European Ancestry ◽

Continuous Measure ◽

Phenotypic Variance ◽

Obesity Class ◽

Genome Wide ◽

Meta Analyses

Anthropometric traits have a strong genetic component with heritability estimates between 40–70% for body mass index (BMI) and ∼80% for height; however, established loci only account for a small fraction (1–10%) of the phenotypic variance of these complex traits. It has been hypothesized that the extremes of the distributions of these traits are enriched for genetic loci and may have a distinct genetic architecture compared to the general population. To explore the genetic contribution of the extremes (defined as the upper and lower 5th percentile) of BMI, height, and waist-hip ratio [WHR] adjusted for BMI and clinical classes of obesity (including overweight and obesity classes I, II, and III), we conducted meta-analyses of ∼2.8 million SNPs from 49 genome-wide association studies of European ancestry totaling from 4,774 cases and 5,481 controls (extreme WHR) to 93,015 cases and 65,840 controls (overweight) for these traits. The most promising loci from each meta-analysis (P<5 x 10 −6 ) were taken forward for replication into up to 65,332 cases and 39,294 controls. In meta-analyses of the combined stages, we observed genome-wide significant associations (P<5 x 10 −8 ) for 191 loci (extreme BMI, height and WHR: 10, 96 and 2 loci, respectively; overweight and obesity classes I, II, and III: 25, 33, 24 and 1 loci, respectively). Out of these 191 loci, we identified 9 novel loci that have not been previously associated with anthropometric traits when studying the whole distributions (P<5 x 10 −8 ), including three loci for extreme height ( ZNF36, H6PD , RSRC1 ), three for obesity class II ( OLFM4 , HS6ST3 , AK5/ZZZ3 ), two for obesity class I ( GNAI3/MIR197/GNAT2, HNF4G ), and two for overweight ( RPTOR, HNF4G ). Several loci for obesity were located near genes expressed primarily in the brain (e.g. CACNA1D, AK5 ), suggesting a neuronal influence, whereas the loci for overweight were near genes involved in other processes, such as mTOR signaling (e.g. RPTOR ). All of the novel loci discovered for the extremes and obesity classes were nominally associated with the trait as a continuous measure in the general population (N = 123,865) but at a lesser significance level (P range: 0.003 – 1.4x10 −5 ). A polygenetic risk score including all independent SNPs associated with BMI (at different P-value thresholds) revealed that significantly more of the variance was explained for the extremes of BMI and obesity class II, than for BMI as a continuous measure in the population (variance explained, 20%, 10% and 5%, respectively), suggesting a greater genetic influence on the extremes. Investigations are underway to evaluate haplotypes and additional signals at known BMI and height loci in the extreme samples to explore allelic heterogeneity. In conclusion, this study identifies additional loci and provides novel insights into the genetic architecture of the extremes of anthropometric traits.

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Tillage Effects on Macrophomina phaseolina Population Density and Soybean Yield

Plant Disease ◽

10.1094/pdis.1998.82.2.247 ◽

1998 ◽

Vol 82 (2) ◽

pp. 247-250 ◽

Cited By ~ 24

Author(s):

J. A. Wrather ◽

S. R. Kendig ◽

D. D. Tyler

Keyword(s):

Population Density ◽

Production Systems ◽

Macrophomina Phaseolina ◽

The United States ◽

Reduced Tillage ◽

No Tillage ◽

Charcoal Rot ◽

Soybean Yield ◽

University Of Tennessee ◽

Soil Population

Reduced-tillage production systems have become popular with soybean farmers in the United States. During 1992 to 1994, soil and soybean root samples were collected from disk-tillage, no-tillage, and moldboard plow treatments in an experiment conducted since 1979 at the University of Tennessee in Jackson. The objective was to determine if reduced-tillage production systems affected charcoal rot incidence and severity. There were no differences at planting in soil population density of Macrophomina phaseolina in the 0- to 15-cm layer of soil among treatments. However, the soil population density of M. phaseolina in disk-tillage and no-tillage plots was significantly greater in the 0- to 7.5-cm layer of soil than in the 7.5- to 15-cm layer. Similarly, soil population densities were significantly greater in the 0- to 7.5-cm layer of soil in no-tillage than in either disk-tillage or moldboard plowed plots. Tillage did not affect the number of M. phaseolina infection sites in 6-week-old plant roots or the percentage of root segments of physiologically mature plants colonized by M. phaseolina. There was no significant correlation between soybean yield and M. phaseolina soil population density. These data suggest that long-term tillage did not affect charcoal rot incidence and severity.

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A genomic region containing REC8 and RNF212B is associated with individual recombination rate variation in a wild population of red deer (Cervus elaphus)

10.1101/248468 ◽

2018 ◽

Cited By ~ 1

Author(s):

Susan E. Johnston ◽

Jisca Huisman ◽

Josephine M. Pemberton

Keyword(s):

Linkage Group ◽

Cervus Elaphus ◽

Recombination Rate ◽

Genetic Architecture ◽

Red Deer ◽

Wild Population ◽

Genomic Region ◽

Rate Variation ◽

Phenotypic Variance ◽

Recombination Rate Variation

AbstractRecombination is a fundamental feature of sexual reproduction, ensuring proper disjunction, preventing mutation accumulation and generating new allelic combinations upon which selection can act. However it is also mutagenic, and breaks up favourable allelic combinations previously built up by selection. Identifying the genetic drivers of recombination rate variation is a key step in understanding the causes and consequences of this variation, how lociassociated with recombination are evolving and how they affect the potential of a population to respond to selection. However, to date, few studies have examined the genetic architecture of recombination rate variation in natural populations. Here, we use pedigree data from ‐2,600 individuals genotyped at ‐38,000 SNPs to investigate the genetic architecture of individual autosomal recombination rate in a wild population of red deer (Cervus elaphus). Female red deer exhibited a higher mean and phenotypic variance in autosomal crossover counts (ACC). Animal models fitting genomic relatedness matrices showed that ACC was heritable in females (h2 = 0.12) but not in males. A regional heritability mapping approach showed that almost all heritable variation in female ACC was explained by a genomic region on deer linkage group 12 containing the candidate loci REC8 and RNF212B, with an additional region on linkage group 32 containing TOP2B approaching genome-wide significance. The REC8/RNF212B region and its paralogue RNF212 have been associated with recombination in cattle, mice, humans and sheep. Our findings suggest that mammalian recombination rates have a relatively conserved genetic architecture in both domesticated and wild systems, and provide a foundation for understanding the association between recombination lociand individual fitness within this population.

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Seasonal Progress of Charcoal Rot and Its Impact on Soybean Productivity

Plant Disease ◽

10.1094/pdis-02-11-0100 ◽

2011 ◽

Vol 95 (9) ◽

pp. 1159-1166 ◽

Cited By ~ 37

Author(s):

Alemu Mengistu ◽

J. R. Smith ◽

J. D. Ray ◽

N. Bellaloui

Keyword(s):

Yield Loss ◽

Macrophomina Phaseolina ◽

Growth Stages ◽

Breeding Programs ◽

Charcoal Rot ◽

Growing Seasons ◽

Progress Curve ◽

Colony Forming Units ◽

Soybean Genotypes ◽

Root Tissues

The seasonal progress of charcoal rot (caused by Macrophomina phaseolina) was measured over two growing seasons in four separate experiments: irrigated infested, irrigated non-infested, non-irrigated infested, and non-irrigated noninfested. Disease was assessed at V5, R1, R3, R5, R6, and R7 growth stages based on colony forming units (CFU) of M. phaseolina recovered from the lower stem and root tissues and the area under the disease progress curve (AUDPC). The population density of M. phaseolina increased slowly from the V5 to R6 growth stages and then rapidly from the R6 to R7 growth stages for all genotypes in all four experiments. Yield loss due to charcoal rot ranged from 6 to 33% in irrigated environments. The extent of yield loss was affected by severity of charcoal rot, which in turn was affected by year. Yield loss due to charcoal rot was consistently measured in all paired comparisons in irrigated environments, suggesting that charcoal rot can be an important disease in irrigated environments. Disease severity based on CFU accounted for more yield loss variation (42%) than did the AUDPC (36%) when used to assess disease. Growth stage R7 was found to be the optimum stage for assessing disease using CFU. In addition, screening soybean genotypes under irrigation environment may have utility in breeding programs where there is a need for evaluating soybean genotypes for both disease resistance and yield.

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Diseases of Amaranthus spp. caused by Pythium aphanidermatum and Macrophomina phaseolina

Canadian Journal of Botany ◽

10.1139/b93-143 ◽

1993 ◽

Vol 71 (9) ◽

pp. 1219-1223 ◽

Cited By ~ 2

Author(s):

J. D. Mihail ◽

E. R. Champaco

Keyword(s):

Stem Canker ◽

Macrophomina Phaseolina ◽

Pythium Aphanidermatum ◽

Commercial Production ◽

Charcoal Rot ◽

Amaranthus Cruentus ◽

Grain Amaranth ◽

Amaranthus Hypochondriacus ◽

Growing Seasons ◽

Amaranthus Spp

Experimental plantings of several species and crosses of Amaranthus were monitored during the 1990–1992 growing seasons to identify diseases that might limit commercial production of grain amaranth in Missouri. Two diseases, previously unreported on the Amaranthus spp. being evaluated in Missouri, are described. Pythium stem canker, caused by Pythium aphanidermatum, was observed when high temperatures coincided with prolonged periods of soil saturation. Tan cankers with black borders developed at the soil line on nearly mature (flowering) plants and lodging was associated with 2.7% of plants examined. Of the species and crosses examined, A. cruentus (cultivar K436) and A. hypochondriacus × A. hybridus (cultivars K432, K433, and K593) were affected most severely by the disease. Differences in susceptibility among the 11 cultivars suggest the potential for the development of disease-resistant cultivars. Charcoal rot, caused by Macrophomina phaseolina, affected A. hypochondriacus × A. hybridus (cultivars K432 and K433) growing in two mid-Missouri locations in 1990. Key words: Amaranthus cruentus, Amaranthus hypochondriacus, Amaranthus hypochondriacus × Amaranthus hybridis, charcoal rot, grain amaranth, stem canker.

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