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Schematic of putative deletion within the 27 kb of chalcone synthase (CHS) Cluster A and B from BAC104J7 (Clough et al., 2004; Tuteja et al., 2004). An X indicates the fragment was not amplified in the polymerase chain reaction verification of 27 kb CHS Cluster A and B for the 15 fragments in PI 567301B (top) and Wyandot (bottom).
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Fusarium graminearum Schwabe [teleomorph: Gibberella zeae (Schweintiz) Petch] has been identified as a pathogen of soybean [Glycine max (L.) Merr.] causing seed, seedling damping‐off and root rot in North America. A major quantitative disease resistance locus (QDRL) that contributed 38.5% of the phenotypic variance toward F. graminearum in soybean...
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Citations
... The possible explanations for this result are as follows: (i) the small size of the mapping population may lead to a relatively biased recombination frequency in this region [53], (ii) chromosomal rearrangement or structurally variable regions by genotype may exist between the representative U.S. variety (i.e., Williams82) and non-U.S. variety [54], or (iii) unequal crossing over, a driving force of R-gene evolution, may increase the variability of this region [55]. These factors can result in an overestimated recombinant frequency, leading to prolonged marker intervals. ...
Phytophthora root and stem rot (PRSR) disease results in substantial losses in soybean production worldwide. The occurrence of PRSR caused by Phytophthora sojae Kaufmann & Gerdemann has become increasingly important for soybean production in the Republic of Korea, but domestic soybean–P. sojae interaction has been less studied. The disease has been managed by developing varieties harboring resistance to the Phytophthora sojae (Rps) gene. The present study aimed to identify a major gene locus conferring resistance to new P. sojae isolate 2858 in the recombinant inbred line population derived from a cross between parental lines ‘Daepung’ (susceptible) and ‘Saedanbaek’ (resistant). Seventy-three recombination inbred lines (RILs) were evaluated for resistance to P. sojae isolate 2858. A resistance locus was identified in the approximate 3.3–4.3 megabase pair region on chromosome 3 using both single-marker and linkage analyses. The Rps of Saedanbaek (RpsSDB) was located on the well-known Rps gene/allele cluster region, which also partially overlapped with a locus previously identified in the Korean soybean variety, ‘Daewon’, resistant to another P. sojae isolate 2457 (RpsDW). Approximately 402 kilobase pairs of the interval region overlapped, including six nucleotide-binding site-leucine-rich repeat (NBS-LRR)-coding genes. Additional phenotypic assays revealed that Saedanbaek was susceptible to isolate 2457 and that Daewon was susceptible to isolate 2858, indicating that RpsSDB and RpsDW are different genes or alleles that confer race-specific resistance to the two P. sojae isolates. These results provide information that will be helpful for breeders developing P. sojae-resistant cultivars.
... Acharya et al. identified two QTL from PI 567301 B accounting for 38.5 and 8.1% of the phenotypic variation under the conditions of their experiments [23]. A follow-up study fine-mapped the major QTL and predicted candidate genes related to seed coat properties [24]. When the seed coat of PI 567301 B was mechanically removed, the resistant phenotype was lost, suggesting a potential role of seed coat properties in soybean resistance to F. graminearum. ...
... Seed coat properties, such as permeability and pigments indicating high flavonoid concentrations, have previously been linked to resistance against seed rot pathogens, particularly in soybean [24]. The eight significantly resistant accessions included a mixture of four yellow, one brown, one greenish brown, one light green, and one black seed coat accessions. ...
Soybean ranks second by total production of all crops grown in the United States. From surveys of soybean production regions in the US and Canada, seedling diseases have been consistently identified as one of the top five biotic limitations on yield for over two decades. The role of Fusarium graminearum as an aggressive member of this complex was unknown until relatively recently and, consequently, publicly and commercially available varieties with resistance to this pathogen are unavailable. To address the need for resistant germplasm and to improve our understanding of the genetic basis underlying the resistance, we screened a set of 208 accessions of soybean from the United States Department of Agriculture Soybean Germplasm Collection (USDA-SGC) under controlled greenhouse conditions. A ratio of the root weight of inoculated plants compared to mock-inoculated controls was used to evaluate the degree of resistance. A linear mixed model identified eight resistant accessions (PI 548311, PI 438500, PI 561318 A, PI 547690, PI 391577, PI 157484, PI 632418, and PI 70466 -3) with significantly higher resistance than the population mean. Previous genotyping publicly available through the SoyBase database was used in a genome-wide association study (GWAS) to determine single nucleotide polymorphism (SNP) markers associated with resistant and susceptible phenotypes. A total of five significant marker-trait associations (MTAs) were discovered on chromosomes Gm02, Gm03, Gm06, Gm07, and Gm13, each accounting for 4.8, 4.3, 3.8, 4.1, and 3.0% of the phenotypic variance, respectively. This study, thus, lays a foundation for the better dissection of germplasm resistant to F. graminearum.
... In addition, performing a hybrid assembly guarantee to take advantage, from one side, of the depth coverage and basecalling quality given by the Illumina reads and, on the other side, to increase the genome contiguity with the ONT reads (Chen et al., 2020). In fact, this method proved to be very successful in fungal genome assembly, either within the Fusarium world (Million et al., 2019;Degradi et al., 2021;Dvorianinova et al., 2021;Fan et al., 2021) or to extended species (Faino et al., 2015;Saud et al., 2021). ...
In summer 2019, during a survey on the health status of a hazelnut orchard located in the Tuscia area (the province of Viterbo, Latium, Italy), nuts showing symptoms, such as brown-grayish spots at the bottom of the nuts progressing upward to the apex, and necrotic patches on the bracts and, sometimes, on the petioles, were found and collected for further studies. This syndrome is associated with the nut gray necrosis (NGN), whose main causal agent is Fusarium lateritium. Aiming to increase knowledge about this fungal pathogen, the whole-genome sequencing of a strain isolated from symptomatic hazelnut was performed using long Nanopore reads technology in combination with the higher precision of the Illumina reads, generating a high-quality genome assembly. The following phylogenetic and comparative genomics analysis suggested that this isolate is caused by the F. tricinctum species complex rather than F. lateritium one, as initially hypothesized. Thus, this study demonstrates that different Fusarium species can infect Corylus avellana producing the same symptomatology. In addition, it sheds light onto the genetic features of the pathogen in subject, clarifying facets about its biology, epidemiology, infection mechanisms, and host spectrum, with the future objective to develop specific and efficient control strategies.
... The lack of whole genome sequencing decreases the confidence that one has when using molecular assays and genes encoding hypothetical proteins used for differentiation must be confirmed to have direct involvement in the infection process. Resistance to various Fusarium species is identified as quantitative in multiple hosts [43][44][45][46]. Thus, amplification of a single gene or region is unlikely to fully capture the pathogenicity of the isolate. ...
Watermelon is an important commercial crop in the Southeastern United States and around the world. However, production is significantly limited by biotic factors including fusarium wilt caused by the hemibiotrophic fungus Fusarium oxysporum forma specialis niveum (Fon). Unfortunately, this disease has increased significantly in its presence over the last several decades as races have emerged which can overcome the available commercial resistance. Management strategies include rotation, improved crop resistance, and chemical control, but early and accurate diagnostics are required for appropriate management. Accurate diagnostics require molecular and genomic strategies due to the near identical genomic sequences of the various races. Bioassays exist for evaluating both the pathogenicity and virulence of an isolate but are limited by the time and resources required. Molecular strategies are still imperfect but greatly reduce the time to complete the diagnosis. This article presents the current state of the research surrounding races, both how races have been detected and diagnosed in the past and future prospects for improving the system of differentiation. Additionally, the available Fon genomes were analyzed using a strategy previously described in separate formae speciales avirulence gene association studies in Fusarium oxysporum races.
... A subsequent study identified four differentially expressed genes that mapped to this QTL located on chromosome 8. These genes included an actin-related protein 2/3 complex subunit, an unknown protein, a hypothetical protein, and a chalcone synthase 3 [324]. This study demonstrated that removal of the seed coat of highly resistant soybean lines makes them susceptible to F. graminareum, indicating that proteins or secondary compounds in the seed coat may be involved in resistance [324]. ...
... These genes included an actin-related protein 2/3 complex subunit, an unknown protein, a hypothetical protein, and a chalcone synthase 3 [324]. This study demonstrated that removal of the seed coat of highly resistant soybean lines makes them susceptible to F. graminareum, indicating that proteins or secondary compounds in the seed coat may be involved in resistance [324]. ...
Root rot diseases remain a major global threat to the productivity of agricultural crops. They are usually caused by more than one type of pathogen and are thus often referred to as a root rot complex. Fungal and oomycete species are the predominant participants in the complex, while bacteria and viruses are also known to cause root rot. Incorporating genetic resistance in cultivated crops is considered the most efficient and sustainable solution to counter root rot, however, resistance is often quantitative in nature. Several genetics studies in various crops have identified the quantitative trait loci associated with resistance. With access to whole genome sequences, the identity of the genes within the reported loci is becoming available. Several of the identified genes have been implicated in pathogen responses. However, it is becoming apparent that at the molecular level, each pathogen engages a unique set of proteins to either infest the host successfully or be defeated or contained in attempting so. In this review, a comprehensive summary of the genes and the potential mechanisms underlying resistance or susceptibility against the most investigated root rots of important agricultural crops is presented.
... A subsequent study identified four differentially expressed genes that mapped to this QTL located on chromosome 8. These genes included an actin-related protein 2/3 complex subunit, an unknown protein, a hypothetical protein, and a chalcone synthase 3 [324]. This study demonstrated that removal of the seed coat of highly resistant soybean lines makes them susceptible to F. graminareum, indicating that proteins or secondary compounds in the seed coat may be involved in resistance [324]. ...
... These genes included an actin-related protein 2/3 complex subunit, an unknown protein, a hypothetical protein, and a chalcone synthase 3 [324]. This study demonstrated that removal of the seed coat of highly resistant soybean lines makes them susceptible to F. graminareum, indicating that proteins or secondary compounds in the seed coat may be involved in resistance [324]. ...
Root rot diseases remain a major global threat to the productivity of agricultural crops. They are usually caused by more than one type of pathogen and are thus often referred to as a root rot complex. Fungal and oomycete species are the predominant participants in the complex, while bacteria and viruses are also known to cause root rot. Incorporating genetic resistance in cultivated crops is considered as the most efficient and sustainable solution to counter root rot; however, resistance is often quantitative in nature. Several genetics studies in various crops have identified quantitative trait loci associated with resistance. With access to whole genome sequences, the identity of the genes within the reported loci is becoming available. Several of the identified genes have been implicated in pathogen response. However, it is becoming apparent that at the molecular level, each pathogen engages a unique set of proteins to either infest the host successfully or be defeated or contained in doing so. In this review, a comprehensive summary of the genes and potential mechanisms underlying resistance or susceptibility against the most investigated root rots of important agricultural crops is presented.
... The BARCSoySNP6K assay has been applied in various genetic research, e.g., it has been used to construct linkage maps (Lee et al., 2015), identify QTL/genes controlling a number of traits such as sudden death syndrome resistance Lightfoot et al., 2018), aphid resistance (Bhusal et al., 2017;Zhang et al., 2017), charcoal rot resistance (Vinholes et al., 2019), Phytophthora sojae, Pythium irregulare and Fusarium graminearum resistance (Stasko et al., 2016;Million et al., 2019), salt tolerance (Do et al., 2018), waterlogging (Ye et al., 2018), iron deficiency chlorosis (Merry et al., 2019), nitrogen fixation (Huo et al., 2019), growth period , seed isoflavone content (Li et al., 2018), oil and fatty acids (Priolli et al., 2019), protein content (Nascimento et al., 2018) and yield (Ye et al., 2018). These studied not only confirmed previously identified QTL but also resulted in the discovery of new QTL, candidate genes or pathways controlling these traits. ...
... irregulare and F. graminearum colocalized on chromosome 19. Million et al. (2019) identified a major quantitative disease resistance locus on chromosome 8 that contributed 38.5% of the phenotypic variance toward F. graminearum from a cross, together with other markers, they mapped this QTL to a 305 kb region harboring 36 genes. Ye et al. (2018) mapped a waterlogging tolerance QTL, qWT_Gm03, into a genomic region of <380 kbp in a RIL population. ...
The limited number of recombinant events in recombinant inbred lines suggests that for a biparental population with a limited number of recombinant inbred lines, it is unnecessary to genotype the lines with many markers. For genomic prediction and selection, previous studies have demonstrated that only 1,000~2,000 genome‐wide common markers across all lines/accessions are needed to reach maximum efficiency of genomic prediction in populations. Evaluation of too many markers will not only increase the cost but also generate redundant information. We developed a soybean (Glycine max) assay –BARCSoySNP6K containing 6,000 markers which were carefully chosen from the SoySNP50K assay based on their position in soybean genome and haplotype block, polymorphism among accessions and genotyping quality. The assay includes 5,000 SNPs from euchromatic and 1,000 from heterochromatic regions. The percentage of SNPs with minor allele frequency >0.10 was 95% and 91% in the euchromatic and heterochromatic regions, respectively. Analysis of progeny from two large families genotyped with SoySNP50K vs. BARCSoySNP6K showed that the position of the common markers and number of unique bins along linkage maps were consistent based on the SNPs genotyped with the two assays, however, the rate of redundant markers was dramatically reduced with the BARCSoySNP6K. The BARCSoySNP6K assay is proven an excellent tool for detecting quantitative trait loci, genomic selection and assessing genetic relationship. The assay is commercialized by Illumina Inc and being used by soybean breeders and geneticists and the list of SNPs in the assay is an ideal resource for SNP genotyping by targeted amplicon sequencing.
... Some protocols require up to 200 ng or more of genomic DNA, especially for detection of low allele frequency mutations (Wang et al. 2018). A study about hybrid genome assembly of a major QTL in soybean used 200 ng of input DNA to amplify the targeted region (Million et al. 2019). Chung et al. (2016) conducted a study to identify the relationship between coverage depth and input DNA amount. ...
Fine mapping quantitative trait loci (QTL) and understanding the molecular mechanism and underlying functions of genes are vital to the advancement of plant research and plant breeding. Target region sequencing (TRS) provides an efficient way to assist in accomplishing these goals. Once a genomic region is found to be responsible for a phenotype, TRS can be deployed to characterize that region. Understanding the available methodologies to perform TRS will be advantageous when determining how to proceed with specific projects. In this article, we reviewed and summarized four main methods that are being used for TRS in plants, including hybrid capture, PCR-based enrichment, DNA fragment circularization, and RNA capture. We also discussed the potential uses of these technologies in plant research, especially the marker discovery for breeding selection. The TRS techniques outlined in this review have the potential to become commonplace in plant research, thereby having a large impact.
Key message
This review provides a comprehensive atlas of QTLs, genes, and alleles conferring resistance to 28 important diseases in all major soybean production regions in the world.
Abstract
Breeding disease-resistant soybean [Glycine max (L.) Merr.] varieties is a common goal for soybean breeding programs to ensure the sustainability and growth of soybean production worldwide. However, due to global climate change, soybean breeders are facing strong challenges to defeat diseases. Marker-assisted selection and genomic selection have been demonstrated to be successful methods in quickly integrating vertical resistance or horizontal resistance into improved soybean varieties, where vertical resistance refers to R genes and major effect QTLs, and horizontal resistance is a combination of major and minor effect genes or QTLs. This review summarized more than 800 resistant loci/alleles and their tightly linked markers for 28 soybean diseases worldwide, caused by nematodes, oomycetes, fungi, bacteria, and viruses. The major breakthroughs in the discovery of disease resistance gene atlas of soybean were also emphasized which include: (1) identification and characterization of vertical resistance genes reside rhg1 and Rhg4 for soybean cyst nematode, and exploration of the underlying regulation mechanisms through copy number variation and (2) map-based cloning and characterization of Rps11 conferring resistance to 80% isolates of Phytophthora sojae across the USA. In this review, we also highlight the validated QTLs in overlapping genomic regions from at least two studies and applied a consistent naming nomenclature for these QTLs. Our review provides a comprehensive summary of important resistant genes/QTLs and can be used as a toolbox for soybean improvement. Finally, the summarized genetic knowledge sheds light on future directions of accelerated soybean breeding and translational genomics studies.
