Integrated QTL mapping, gene expression and nucleotide variation analyses to investigate complex quantitative traits: a case study with the soybean-Phytophthora sojae interaction.
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SUBMITTER: de Ronne M
PROVIDER: S-EPMC7292538 | biostudies-literature | 2020 Jul
REPOSITORIES: biostudies-literature
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Integrated QTL mapping, gene expression and nucleotide variation analyses to investigate complex quantitative traits: a case study with the soybean-Phytophthora sojae interaction.
de Ronne Maxime M Labbé Caroline C Lebreton Amandine A Sonah Humira H Deshmukh Rupesh R Jean Martine M Belzile François F O'Donoughue Louise L Bélanger Richard R
Plant biotechnology journal 20191206 7
Similar Datasets
Project description:To identify soybean genes and QTLs associated with quantitative resistance to infection by the oomycete pathogen Phytophthora sojae, we conducted a very large-scale microarray experiment using 2522 Affymetrix GeneChips. The experiment involved assaying a total of 298 soybean recombinant inbred lines together with internal checks.
2008-05-30 | GSE11611 | GEO
Project description:BackgroundPhytophthora sojae is the primary pathogen of soybeans that are grown on poorly drained soils. Race-specific resistance to P. sojae in soybean is gene-for-gene, although in many areas of the US and worldwide there are populations that have adapted to the most commonly deployed resistance to P. sojae ( Rps) genes. Hence, this system has received increased attention towards identifying mechanisms and molecular markers associated with partial resistance to this pathogen. Several quantitative trait loci (QTL) have been identified in the soybean cultivar 'Conrad' that contributes to the expression of partial resistance to multiple P. sojae isolates.ResultsIn this study, two of the Conrad QTL on chromosome 19 were dissected through sequence and expression analysis of genes in both resistant (Conrad) and susceptible ('Sloan') genotypes. There were 1025 single nucleotide polymorphisms (SNPs) in 87 of 153 genes sequenced from Conrad and Sloan. There were 304 SNPs in 54 genes sequenced from Conrad compared to those from both Sloan and Williams 82, of which 11 genes had SNPs unique to Conrad. Eleven of 19 genes in these regions analyzed with qRT-PCR had significant differences in fold change of transcript abundance in response to infection with P. sojae in lines with QTL haplotype from the resistant parent compared to those with the susceptible parent haplotype. From these, 8 of the 11 genes had SNPs in the upstream, untranslated region, exon, intron, and/or downstream region. These 11 candidate genes encode proteins potentially involved in signal transduction, hormone-mediated pathways, plant cell structural modification, ubiquitination, and basal resistance.ConclusionsThese findings may indicate a complex defense network with multiple mechanisms underlying these two soybean QTL conferring resistance to P. sojae. SNP markers derived from these candidate genes can contribute to fine mapping of QTL and marker assisted breeding for resistance to P. sojae.
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Project description:Isoflavone, protein, and oil are the most important quality traits in soybean. Since these phenotypes are typically quantitative traits, quantitative trait locus (QTL) mapping has been an efficient way to clarify their complex and unclear genetic background. However, the low-density genetic map and the absence of QTL integration limited the accurate and efficient QTL mapping in previous researches. This paper adopted a recombinant inbred lines (RIL) population derived from 'Zhongdou27'and 'Hefeng25' and a high-density linkage map based on whole-genome resequencing to map novel QTL and used meta-analysis methods to integrate the stable and consentaneous QTL. The candidate genes were obtained from gene functional annotation and expression analysis based on the public database. A total of 41 QTL with a high logarithm of odd (LOD) scores were identified through composite interval mapping (CIM), including 38 novel QTL and 2 Stable QTL. A total of 660 candidate genes were predicted according to the results of the gene annotation and public transcriptome data. A total of 212 meta-QTL containing 122 stable and consentaneous QTL were mapped based on 1,034 QTL collected from previous studies. For the first time, 70 meta-QTL associated with isoflavones were mapped in this study. Meanwhile, 69 and 73 meta-QTL, respectively, related to oil and protein were obtained as well. The results promote the understanding of the biosynthesis and regulation of isoflavones, protein, and oil at molecular levels, and facilitate the construction of molecular modular for great quality traits in soybean.
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Project description:Phytophthora root rot (PRR) causes serious annual soybean yield losses worldwide. The most effective method to prevent PRR involves growing cultivars that possess genes conferring resistance to Phytophthora sojae (Rps). In this study, QTL-sequencing combined with genetic mapping was used to identify RpsX in soybean cultivar Xiu94-11 resistance to all P. sojae isolates tested, exhibiting broad-spectrum PRR resistance. Subsequent analysis revealed RpsX was located in the 242-kb genomic region spanning the RpsQ locus. However, a phylogenetic investigation indicated Xiu94-11 carrying RpsX is distantly related to the cultivars containing RpsQ, implying RpsX and RpsQ have different origins. An examination of candidate genes revealed RpsX and RpsQ share common nonsynonymous SNP and a 144-bp insertion in the Glyma.03g027200 sequence encoding a leucine-rich repeat (LRR) region. Glyma.03g027200 was considered to be the likely candidate gene of RpsQ and RpsX. Sequence analyses confirmed that the 144-bp insertion caused by an unequal exchange resulted in two additional LRR-encoding fragments in the candidate gene. A marker developed based on the 144-bp insertion was used to analyze the genetic population and germplasm, and proved to be useful for identifying the RpsX and RpsQ alleles. This study implies that the number of LRR units in the LRR domain may be important for PRR resistance in soybean.
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Project description:Isoflavone reductase (IFR) is an enzyme involved in the biosynthetic pathway of isoflavonoid phytoalexin in plants. IFRs are unique to the plant kingdom and are considered to have crucial roles in plant response to various biotic and abiotic environmental stresses. Here, we report the characterization of a novel member of the soybean isoflavone reductase gene family GmIFR. Overexpression of GmIFR transgenic soybean exhibited enhanced resistance to Phytophthora sojae. Following stress treatments, GmIFR was significantly induced by P. sojae, ethephon (ET), abscisic acid (placeCityABA), salicylic acid (SA). It is located in the cytoplasm when transiently expressed in soybean protoplasts. The daidzein levels reduced greatly for the seeds of transgenic plants, while the relative content of glyceollins in transgenic plants was significantly higher than that of non-transgenic plants. Furthermore, we found that the relative expression levels of reactive oxygen species (ROS) of transgenic soybean plants were significantly lower than those of non-transgenic plants after incubation with P. sojae, suggesting an important role of GmIFR might function as an antioxidant to reduce ROS in soybean. The enzyme activity assay suggested that GmIFR has isoflavone reductase activity.
| S-EPMC4655237 | biostudies-literature
Project description:Examination of soybean hypocotyls, G. max cv. Harosoy (Rps7), at 3, 6, 12, 24 and 48 hours after inoculation with P. sojae, race 2, isolate P6497 Patterns of Gene Expression Upon Infection of Soybean Plants by Phytophthora sojae. P. Moy, D. Qutob, B. P. Chapman, I. Atkinson, and M. Gijzen. Pages 1051-1062. Publication no. M-2004-0728-01R. Molecular Plant-Microbe Interactions, October 2004, Volume 17, Number 10. Keywords: time-course
2004-09-14 | GSE1352 | GEO
Project description:Phytophthora sojae and soybean cyst nematode (SCN) are important pathogens of soybean. Although these pathogens infect soybean roots, there is limited evidence of any interaction between them. The objective of this study was to examine the interaction between SCN and P. sojae on soybean in the greenhouse. Seeds of four soybean cultivars (Jack, Surge, Williams 82, Williams) were pre-germinated and placed in cone-tainers (Stuewe and Sons Inc., Tangent, OR, USA), containing a steam pasteurized sand-clay mixture. The experiment was set up in a completely randomized design with five replications and performed twice. Two P. sojae isolates were used in this study that represented two different virulence pathotypes (simple and complex pathotypes). For each isolate, soybean plants were not inoculated, inoculated with one of the treatments-SCN, P. sojae, and combination of P. sojae and SCN. After 35 DOI, stem length, root length, plant weight, root weight, lesion length, and SCN population were recorded. On all soybean cultivars with different types of incomplete resistance, the complex pathotype (PS-15-TF3) influenced the lesion length (mm) in the presence of SCN. However, the SCN population was reduced by both complex and simple pathotypes of P. sojae. This suggests that use both SCN and P. sojae resistance cultivars, can manage the disease complex and reduce soybean yield loss.
| S-EPMC8880169 | biostudies-literature
Project description:Phytophthora root and stem rot of soybean (Glycine max), caused by the oomycete Phytophthora sojae, is an extremely destructive disease worldwide. In this study, we identified GmEIL1, which encodes an ethylene-insensitive3 (EIN3) transcription factor. GmEIL1 was significantly induced following P. sojae infection of soybean plants. Compared to wild-type soybean plants, transgenic soybean plants overexpressing GmEIL1 showed enhanced resistance to P. sojae and GmEIL1-silenced RNA-interference lines showed more severe symptoms when infected with P. sojae. We screened for target genes of GmEIL1 and confirmed that GmEIL1 bound directly to the GmERF113 promoter and regulated GmERF113 expression. Moreover, GmEIL1 positively regulated the expression of the pathogenesis-related gene GmPR1. The GmEIL1-regulated defence response to P. sojae involved both ethylene biosynthesis and the ethylene signalling pathway. These findings suggest that the GmEIL1-GmERF113 module plays an important role in P. sojae resistance via the ethylene signalling pathway.
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Project description: Not available
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Project description:Phytophthora sojae is a soil-borne oomycete and the causal agent of Phytophthora root and stem rot (PRR) in soybean (Glycine max [L.] Merrill). Yield losses attributed to P. sojae are devastating in disease-conducive environments, with global estimates surpassing 1.1 million tonnes annually. Historically, management of PRR has entailed host genetic resistance (both vertical and horizontal) complemented by disease-suppressive cultural practices (e.g., oomicide application). However, the vast expansion of complex and/or diverse P. sojae pathotypes necessitates developing novel technologies to attenuate PRR in field environments. Therefore, the objective of the present study was to couple high-throughput sequencing data and deep learning to elucidate molecular features in soybean following infection by P. sojae. In doing so, we generated transcriptomes to identify differentially expressed genes (DEGs) during compatible and incompatible interactions with P. sojae and a mock inoculation. The expression data were then used to select two defense-related transcription factors (TFs) belonging to WRKY and RAV families. DNA Affinity Purification and sequencing (DAP-seq) data were obtained for each TF, providing putative DNA binding sites in the soybean genome. These bound sites were used to train Deep Neural Networks with convolutional and recurrent layers to predict new target sites of WRKY and RAV family members in the DEG set. Moreover, we leveraged publicly available Arabidopsis (Arabidopsis thaliana) DAP-seq data for five TF families enriched in our transcriptome analysis to train similar models. These Arabidopsis data-based models were used for cross-species TF binding site prediction on soybean. Finally, we created a gene regulatory network depicting TF-target gene interactions that orchestrate an immune response against P. sojae. Information herein provides novel insight into molecular plant-pathogen interaction and may prove useful in developing soybean cultivars with more durable resistance to P. sojae.
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