Identification of root rot resistance QTLs in pea using Fusarium solani f. sp. pisi-responsive differentially expressed genes

AbstractPisum sativum (pea) yields have declined significantly over the last decades, predominantly due to susceptibility to root rot diseases. One of the main causal agents of root rot is the fungus Fusarium solani f. sp. pisi (Fsp), leading to yield losses ranging from 15 to 60%. Determining and subsequently incorporating the genetic basis for resistance in new cultivars offers one of the best solutions to control this pathogen; however, no green-seeded pea cultivars with complete resistance to Fsp have been identified. To date, only partial levels of resistance to Fsp has been identified among pea genotypes. SNPs mined from Fsp-responsive differentially expressed genes (DEGs) identified in a preceding study were utilized to identify QTLs associated with Fsp resistance using composite interval mapping in two recombinant inbred line (RIL) populations segregating for partial root rot resistance. A total of 769 DEGs with single nucleotide polymorphisms (SNPs) were identified, and the putative SNPs were evaluated for being polymorphic across four partially resistant and four susceptible P. sativum genotypes. The SNPs with validated polymorphisms were used to screen two RIL populations using two phenotypic criteria: root disease severity and plant height. One QTL, WB.Fsp-Ps 5.1 that mapped to chromosome V explained 14.76 % of the variance with a confidence interval of 10.36 cM. The other four QTLs located on chromosomes II, III, and V, explained 5.26–8.05 % of the variance. The use of SNPs derived from Fsp-responsive DEGs for QTL mapping proved to be an efficient way to identify molecular markers associated with Fsp resistance in pea. These QTLs are potential candidates for marker-assisted selection and gene pyramiding to obtain high levels of partial resistance in pea cultivars to combat root rot caused by Fsp.

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Identification of Root Rot Resistance QTLs in Pea Using Fusarium solani f. sp. pisi-Responsive Differentially Expressed Genes

Frontiers in Genetics ◽

10.3389/fgene.2021.629267 ◽

2021 ◽

Vol 12 ◽

Author(s):

Bruce A. Williamson-Benavides ◽

Richard M. Sharpe ◽

Grant Nelson ◽

Eliane T. Bodah ◽

Lyndon D. Porter ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Fusarium Solani ◽

Root Rot ◽

Gene Pyramiding ◽

The United States ◽

Interval Mapping ◽

Differentially Expressed ◽

Nucleotide Polymorphisms ◽

Resistance Qtls ◽

Single Nucleotide

Pisum sativum (pea) yields in the United States have declined significantly over the last decades, predominantly due to susceptibility to root rot diseases. One of the main causal agents of root rot is the fungus Fusarium solani f. sp. pisi (Fsp), leading to yield losses ranging from 15 to 60%. Determining and subsequently incorporating the genetic basis for resistance in new cultivars offers one of the best solutions to control this pathogen; however, no green-seeded pea cultivars with complete resistance to Fsp have been identified. To date, only partial levels of resistance to Fsp has been identified among pea genotypes. SNPs mined from Fsp-responsive differentially expressed genes (DEGs) identified in a preceding study were utilized to identify QTLs associated with Fsp resistance using composite interval mapping in two recombinant inbred line (RIL) populations segregating for partial root rot resistance. A total of 769 DEGs with single nucleotide polymorphisms (SNPs) were identified, and the putative SNPs were evaluated for being polymorphic across four partially resistant and four susceptible P. sativum genotypes. The SNPs with validated polymorphisms were used to screen two RIL populations using two phenotypic criteria: root disease severity and plant height. One QTL, WB.Fsp-Ps 5.1 that mapped to chromosome 5 explained 14.8% of the variance with a confidence interval of 10.4 cM. The other four QTLs located on chromosomes 2, 3, and 5, explained 5.3–8.1% of the variance. The use of SNPs derived from Fsp-responsive DEGs for QTL mapping proved to be an efficient way to identify molecular markers associated with Fsp resistance in pea. These QTLs are potential candidates for marker-assisted selection and gene pyramiding to obtain high levels of partial resistance in pea cultivars to combat root rot caused by Fsp.

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Lipidomic, Transcriptomic, and BSA-660K Single Nucleotide Polymorphisms Profiling Reveal Characteristics of the Cuticular Wax in Wheat

Frontiers in Plant Science ◽

10.3389/fpls.2021.794878 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jun Zheng ◽

Chenkang Yang ◽

Xingwei Zheng ◽

Suxian Yan ◽

Fei Qu ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Differentially Expressed Genes ◽

Cuticular Wax ◽

Differentially Expressed ◽

Wax Ester ◽

Nucleotide Polymorphisms ◽

Wheat Varieties ◽

Single Nucleotide ◽

Genetic Characteristics ◽

Chip Analysis

Plant epidermal wax helps protect plants from adverse environmental conditions, maintains the function of tissues and organs, and ensures normal plant development. However, the constituents of epidermal wax and the regulatory mechanism of their biosynthesis in wheat have not been fully understood. Wheat varieties with different wax content, Jinmai47 and Jinmai84, were selected to comparatively analyze their waxy components and genetic characteristics, using a combination of lipidomic, transcriptomic, and BSA-Wheat 660K chip analysis. Through lipidomic analysis, 1287 lipid molecules were identified representing 31 lipid subclasses. Among these, Diacylglycerols (DG), (O-acyl)-ω-hydroxy fatty acids (OAHFA), wax ester (WE), Triacylglycerols (TG), and Monoradylglycerols (MG) accounted for 96.4% of the total lipids in Jinmai84 and 94.5% in Jinmai47. DG, OAHFA, and WE were higher in Jinmai84 than in Jinmai47 with the content of OAHFA 2.88-fold greater and DG 1.66-fold greater. Transcriptome sequence and bioinformatics analysis revealed 63 differentially expressed genes related to wax biosynthesis. Differentially expressed genes (DEGs) were found to be involved with the OAHFA, DG, and MG of synthesis pathways, which enriched the wax metabolism pathway. Non-glaucous and glaucous bulks from a mapping population were used to identify single nucleotide polymorphisms (SNP) via 660K chip analysis. Two loci centered on chromosomes 2D and 4B were detected and the locus on 4B is likely novel. These data improve understanding of complex lipid metabolism for cuticular wax biosynthesis in wheat and lay the foundation for future detailed investigation of mechanisms regulating wax metabolism.

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Application of structural equation models to construct genetic networks using differentially expressed genes and single-nucleotide polymorphisms

BMC Proceedings ◽

10.1186/1753-6561-1-s1-s76 ◽

2007 ◽

Vol 1 (Suppl 1) ◽

pp. S76 ◽

Cited By ~ 2

Author(s):

Seungmook Lee ◽

Mina Jhun ◽

Eun-Kyung Lee ◽

Taesung Park

Keyword(s):

Single Nucleotide Polymorphisms ◽

Differentially Expressed Genes ◽

Structural Equation ◽

Structural Equation Models ◽

Genetic Networks ◽

Differentially Expressed ◽

Nucleotide Polymorphisms ◽

Single Nucleotide

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Genetics of Lactose Intolerance: An Updated Review and Online Interactive World Maps of Phenotype and Genotype Frequencies

Nutrients ◽

10.3390/nu12092689 ◽

2020 ◽

Vol 12 (9) ◽

pp. 2689

Author(s):

Augusto Anguita-Ruiz ◽

Concepción M. Aguilera ◽

Ángel Gil

Keyword(s):

Genetic Basis ◽

Human Populations ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Genotype Frequencies ◽

Genetic Mechanisms ◽

Visualization Tools ◽

Available Information ◽

Static World ◽

Interactive Resources

In humans the ability to digest milk lactose is conferred by a β-galactosidase enzyme called lactase-phlorizin hydrolase (LPH). While in some humans (approximately two-thirds of humankind) the levels of this enzyme decline drastically after the weaning phase (a trait known as lactase non-persistence (LNP)), some other individuals are capable of maintaining high levels of LPH lifelong (lactase persistence (LP)), thus being able to digest milk during adulthood. Both lactase phenotypes in humans present a complex genetic basis and have been widely investigated during the last decades. The distribution of lactase phenotypes and their associated single nucleotide polymorphisms (SNPs) across human populations has also been extensively studied, though not recently reviewed. All available information has always been presented in the form of static world maps or large dimension tables, so that it would benefit from the newly available visualization tools, such as interactive world maps. Taking all this into consideration, the aims of the present review were: (1) to gather and summarize all available information on LNP and LP genetic mechanisms and evolutionary adaptation theories, and (2) to create online interactive world maps, including all LP phenotype and genotype frequency data reported to date. As a result, we have created two online interactive resources, which constitute an upgrade over previously published static world maps, and allow users a personalized data exploration, while at the same time accessing complete reports by population or ethnicity.

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Narrowing a region on rat chromosome 13 that protects against hypertension in Dahl SS-13BN congenic strains

AJP Heart and Circulatory Physiology ◽

10.1152/ajpheart.01026.2010 ◽

2011 ◽

Vol 300 (4) ◽

pp. H1530-H1535 ◽

Cited By ~ 21

Author(s):

Carol Moreno ◽

Jan M. Williams ◽

Limin Lu ◽

Mingyu Liang ◽

Jozef Lazar ◽

...

Keyword(s):

Congenic Strain ◽

Region Of Interest ◽

Differentially Expressed ◽

Brown Norway ◽

Nucleotide Polymorphisms ◽

Coding Region ◽

Single Nucleotide ◽

Chromosome 13 ◽

Protein Excretion ◽

Sequencing Studies

Transfer of chromosome 13 from the Brown Norway (BN) rat onto the Dahl salt-sensitive (SS) genetic background attenuates the development of hypertension, but the genes involved remain to be identified. The purpose of the present study was to confirm by telemetry that a congenic strain [SS.BN-(D13Hmgc37-D13Got22)/Mcwi, line 5], carrying a 13.4-Mb segment of BN chromosome 13 from position 32.4 to 45.8 Mb, is protected from the development of hypertension and then to narrow the region of interest by creating and phenotyping 11 additional subcongenic strains. Mean arterial pressure (MAP) rose from 118 ± 1 to 186 ± 5 mmHg in SS rats fed a high-salt diet (8.0% NaCl) for 3 wk. Protein excretion increased from 56 ± 11 to 365 ± 37 mg/day. In contrast, MAP only increased to 152 ± 9 mmHg in the line 5 congenic strain. Six subcongenic strains carrying segments of BN chromosome 13 from 32.4 and 38.2 Mb and from 39.9 to 45.8 Mb were not protected from the development of hypertension. In contrast, MAP was reduced by ∼30 mmHg in five strains, carrying a 1.9-Mb common segment of BN chromosome 13 from 38.5 to 40.4 Mb. Proteinuria was reduced by ∼50% in these strains. Sequencing studies did not identify any nonsynonymous single nucleotide polymorphisms in the coding region of the genes in this region. RT-PCR studies indicated that 4 of the 13 genes in this region were differentially expressed in the kidney of two subcongenic strains that were partially protected from hypertension vs. those that were not. These results narrow the region of interest on chromosome 13 from 13.4 Mb (159 genes) to a 1.9-Mb segment containing only 13 genes, of which 4 are differentially expressed in strains partially protected from the development of hypertension.

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Reverse transcriptase-related enzymes are associated with horizontal chromosome transfer in an asexual pathogen

10.7287/peerj.preprints.1324v1 ◽

2015 ◽

Author(s):

Xiaoqiu Huang ◽

Anindya Das ◽

Binod B Sahu ◽

Subodh K Srivastava ◽

Leonor F Leandro ◽

...

Keyword(s):

Reverse Transcriptase ◽

Root Rot ◽

Supernumerary Chromosome ◽

Open Reading Frames ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Chromosome Transfer ◽

Supernumerary Chromosomes ◽

The Mean ◽

Reading Frames

Supernumerary chromosomes have been shown to transfer horizontally from one isolate to another. However, the mechanism by which horizontal chromosome transfer (HCT) occurs is unknown. In this study, we compared the genomes of 11 isolates comprising six Fusarium species that cause soybean sudden death syndrome (SDS) or bean root rot (BRR), and detected numerous instances of HCT in supernumerary chromosomes. We also identified a statistically significant number (21 standard deviations above the mean) of single nucleotide polymorphisms (SNPs) in the supernumerary chromosomes between isolates of the asexual pathogen F. virguliforme. Supernumerary chromosomes carried reverse transcriptase-related genes (RVT); the presence of long RVT open reading frames (ORFs) in the supernumerary chromosome was correlated with the presence of two or more chromosome copies with a significant number of SNPs between them. Our results suggest that supernumerary chromosomes transfer horizontally via an RNA intermediate. Understanding the mechanism by which HCT occurs will have a profound impact on understanding evolution and applying biotechnology as well as accepting HCT as a natural source of genetic variation.

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Identification of differentially expressed genes from Trichoderma harzianum during growth on cell wall of Fusarium solani as a tool for biotechnological application

BMC Genomics ◽

10.1186/1471-2164-14-177 ◽

2013 ◽

Vol 14 (1) ◽

pp. 177 ◽

Cited By ~ 44

Author(s):

Pabline Marinho Vieira ◽

Alexandre Siqueira Guedes Coelho ◽

Andrei Stecca Steindorff ◽

Saulo José Linhares de Siqueira ◽

Roberto do Nascimento Silva ◽

...

Keyword(s):

Cell Wall ◽

Differentially Expressed Genes ◽

Trichoderma Harzianum ◽

Fusarium Solani ◽

Differentially Expressed ◽

Biotechnological Application

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Genomic Determinants of Hypertension With a Focus on Metabolomics and the Gut Microbiome

American Journal of Hypertension ◽

10.1093/ajh/hpaa022 ◽

2020 ◽

Vol 33 (6) ◽

pp. 473-481

Author(s):

Panayiotis Louca ◽

Cristina Menni ◽

Sandosh Padmanabhan

Keyword(s):

Blood Pressure ◽

Genetic Basis ◽

Salt Water ◽

Nucleotide Polymorphisms ◽

Pressure Regulation ◽

Single Nucleotide ◽

Multiple Factors ◽

Single Marker ◽

Genomic Studies ◽

Diet And Lifestyle

Abstract Epidemiologic and genomic studies have progressively improved our understanding of the causation of hypertension and the complex relationship with diet and environment. The majority of Mendelian forms of syndromic hypotension and hypertension (HTN) have all been linked to mutations in genes whose encoded proteins regulate salt–water balance in the kidney, supporting the primacy of the kidneys in blood pressure regulation. There are more than 1,477 single nucleotide polymorphisms associated with blood pressure and hypertension and the challenge is establishing a causal role for these variants. Hypertension is a complex multifactorial phenotype and it is likely to be influenced by multiple factors including interactions between diet and lifestyle factors, microbiome, and epigenetics. Given the finite genetic variability that is possible in humans, it is likely that incremental gains from single marker analyses have now plateaued and a greater leap in our understanding of the genetic basis of disease will come from integration of other omics and the interacting environmental factors. In this review, we focus on emerging results from the microbiome and metabolomics and discuss how leveraging these findings may facilitate a deeper understanding of the interrelationships between genomics, diet, and microbial ecology in humans in the causation of essential hypertension.

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