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

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.

Download Full-text

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

Download Full-text

Analysis of 4 Single-Nucleotide Polymorphisms in Relation to Cervical Dysplasia and Cancer Development Using a High-Throughput Ligation-Detection Reaction Procedure

International Journal of Gynecological Cancer ◽

10.1097/igc.0b013e31822b6299 ◽

2011 ◽

Vol 21 (9) ◽

pp. 1664-1671 ◽

Cited By ~ 12

Author(s):

Helmut von Keyserling ◽

Thomas Bergmann ◽

Miriam Schuetz ◽

Ursula Schiller ◽

Jonas Stanke ◽

...

Keyword(s):

Cervical Cancer ◽

Single Nucleotide Polymorphisms ◽

Genetic Markers ◽

Cervical Dysplasia ◽

Semantic Integration ◽

Cancer Development ◽

Large Sample Size ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Genetic Characteristics

BackgroundHost genetic characteristics and environmental factors may correlate with risk for cervical cancer development. Here we describe a retrospective screening study for single nucleotide polymorphisms (SNPs) in genetic markersTP53, MTHFR, CYP1A1,andCYP2E1in 749 patients.MethodsA multiplex ligation-dependent polymerase chain reaction approach was applied. We used archived material from human papillomavirus tests and correlated SNP genotypes to the corresponding clinical data. Semantic integration was used to identify and evaluate the clinical status from electronic health records.ResultsAn association with cervical cancer and high-grade dysplasia was found for the rare homozygous CC genotype (rs4646903) inCYP1A1(odds ratio [OR], 8.862). Odds ratios were also significantly elevated for heterozygousMTHFRCT genotype (rs1801133; OR, 1.457). No significant association was found inTP53(rs1042522) andCYP2E1(rs3813867). In addition, we found smokers at higher risk (OR, 2.688) and identified pregnancies as a significant risk factor (OR, 1.54).ConclusionsOur protocol enables a feasible way for further retrospective large sample size evaluation of potential genetic markers. This study revealed genetic associations of a rare SNP genotype with cervical dysplasia in one of the largest patient sample to date that warrants further investigation.

Download Full-text

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

10.1101/2020.11.13.382077 ◽

2020 ◽

Author(s):

Bruce A. Williamson-Benavides ◽

Richard Sharpe ◽

Grant Nelson ◽

Eliane T. Bodah ◽

Lyndon D. Porter ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Fusarium Solani ◽

Root Rot ◽

Genetic Basis ◽

Gene Pyramiding ◽

Interval Mapping ◽

Differentially Expressed ◽

Nucleotide Polymorphisms ◽

Resistance Qtls ◽

Single Nucleotide

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.

Download Full-text

Characterization of a mini core collection of Japanese wheat varieties using single-nucleotide polymorphisms generated by genotyping-by-sequencing

Breeding Science ◽

10.1270/jsbbs.66.213 ◽

2016 ◽

Vol 66 (2) ◽

pp. 213-225 ◽

Cited By ~ 13

Author(s):

Fuminori Kobayashi ◽

Tsuyoshi Tanaka ◽

Hiroyuki Kanamori ◽

Jianzhong Wu ◽

Yuichi Katayose ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Core Collection ◽

Genotyping By Sequencing ◽

Nucleotide Polymorphisms ◽

Wheat Varieties ◽

Single Nucleotide ◽

Mini Core Collection

Download Full-text

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.

Download Full-text