Exploring the phenotypic expression of a regulatory proteome-altering gene by spectroscopy and chemometrics

Munck, L.; Nielsen, Jesper Pram; Møller, Birger Lindberg; Jacobsen, Susanne; Søndergaard, Ib; Engelsen, Søren B.; Nørgaard, Lars; Bro, Rasmus

doi:10.1016/s0003-2670(01)01056-x

Cited by 92 publications

(60 citation statements)

References 14 publications

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“…There is a base line shift from field to greenhouse environment [51] demonstrated in four spectra 1660-1860 nm in two parallel lines of the lys3a mutant in Figure 1B with starling reproducibility in each environment. Figure 1C displays specific spectral patterns 2280-2360 nm of four mutants grown in the field-the P mutant lys3a (bglucan 3.1%) and the C mutants lys5g (8.9%), lys5f (16.5%) and mutant 16 (12.0%).…”

Section: Description Of Data Set and Methodsmentioning

confidence: 90%

“…to explain the pleiotropic regulation of the glucose from the a-glucan to the b-glucan pathway through molecular biology. The lys3a gene is, however, regulatory and involves suppression and stimulation of many different protein genes in several chromomes [51,67]. The basic function of the gene is that it inhibits demetylation [67] Omholt [70] has recently published a theoretical study on classical genetic dominance by causal hard modelling mathematics as a candidate for a more precise modelling of gene expression than classical statistics.…”

Section: From Fingerprints By Near Infrared Technology To Improved Thmentioning

confidence: 99%

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A new holistic exploratory approach to Systems Biology by Near Infrared Spectroscopy evaluated by chemometrics and data inspection

Munck

2007

Journal of Chemometrics

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There is a need for an improved biological and theoretical interpretation of Near Infra‐Red Spectral (NIRS) fingerprints from tissues that could contribute with holistic overview to fine‐grained detail modelled in Systems Biology. The concept of gene expression in self‐organised networks was experimentally tested in a barley endosperm model with molecularly defined and undefined mutants. Surprisingly reproducible gene‐specific NIRS fingerprints were observed directly in log1/R MSC pre‐treated spectra that could not be accurately represented by destructive mathematical models. A mutant spectrum in an isogenic background represents the physiochemical expression of the gene in the whole network (tissue). The necessary holistic overview that is needed experimentally to introduce Ilya Prigogine's theory on self‐organisation in Systems Biology was supplied by defining the spectral phenome. Interval spectral information on genotypes and environment was classified by interval Extended Canonical Variates Analysis (iECVA). Genetic changes in spectra were interpreted by interval Partial Least Squares Regression (iPLSR) correlations to chemical variables. A new pathway regulation was detected. The finely grained ‘bottom up’ modelling of molecular and chemical data from pathways requires a coarsely grained exploratory ‘top down’ overview by NIRS to account for the outcome of self‐organisation. The amplification of expression from a gene to the phenome (pleiotropy) can now for the first time be quantified as a whole reproducible phenomenological pattern by NIRS and compared to other gene spectra. It explains published findings that transformed respectively mutated genes in genetically modified organisms (GMOs) and cancer patients can be detected unsupervised from tissues by spectroscopy, chemometrics and data inspection. Copyright © 2007 John Wiley & Sons, Ltd.

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Section: Description Of Data Set and Methodsmentioning

confidence: 90%

Section: From Fingerprints By Near Infrared Technology To Improved Thmentioning

confidence: 99%

A new holistic exploratory approach to Systems Biology by Near Infrared Spectroscopy evaluated by chemometrics and data inspection

Munck

2007

Journal of Chemometrics

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“…Theoretical 31,32 and experimental 33,34 evidence have indicated that wavelength selection can significantly improve the performance of full-spectrum calibration techniques, such as PLS, and various wavelength or wavenumber selection methods have been proposed and used. [35][36][37][38][39][40][41] We developed several new chemometrics algorithms for wavelength interval selection and sample selection in multicomponent spectral analysis. 29,30,42,43 In this section, recently proposed new wavelength selection methods, moving window partial least squares regression (MWPLSR) (Fig.…”

Section: ·2 Chemometricsmentioning

confidence: 99%

Near-Infrared Spectroscopy—Its Versatility in Analytical Chemistry

2012

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“…The average protein level of the 17 587 cultivars of unmilled (brown) rice in the International Rice Research Institute (IRRI) germplasm collection was 9.5%, and ranged from 4.3 to 18.2%. This phenotypic variation in protein content provides a useful genetic basis for breeding.Protein content and AAC in crop seed have been confirmed to be inherited as quantitative traits with a complex genetic basis that was controlled by multiple genes (Munck et al 2001). Identification of the genes controlling AAC is important to facilitate breeding for improved amino acid composition.…”

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confidence: 99%

Quantitative trait loci controlling the amino acid content in rice (Oryza sativa L.)

Yoo

2017

J Plant Biotechnol

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The amino acid composition of rice is a major concern of rice breeders because amino acids are among the most important nutrient components in rice. In this study, a genetic map was constructed with a population of 134 recombinant inbred lines (RILs) from a cross between Dasanbyeo (Tongil-type indica) and TR22183 (temperate japonica), as a means to detect the main and epistatic effect quantitative trait loci (QTLs) for the amino acid content (AAC). Using a linkage map which covered a total of 1458 cM based on 239 molecular marker loci, a total of six main-effect QTLs (M-QTLs) was identified for the content of six amino acids that were mapped onto chromosome 3. For all the M-QTLs, the TR22183 allele increased the trait values. The QTL cluster (flanked by id3015453 and id3016090) on chromosome 3 was associated with the content of five amino acids. The phenotypic variation, explained by the individual QTLs located in this cluster, ranged from 10.2 to 12.4%. In addition, 26 epistatic QTLs (Ep-QTLs) were detected and the 25 loci involved in this interaction were distributed on all nine chromosomes. Both the M-QTLs and Ep-QTLs detected in this study will be useful in breeding programs which target the development of rice with improved amino acid composition.Keywords Quantitative trait loci, Amino acid content, rice, QTL mapping Introduction Rice (Oryza sativa L.) is one of the most important staple cereal crops for more than 50% of the world's population (Mather et al. 2007). A total of 85% of rice production is consumed by humans, and rice provides 21% of the global human per capita energy and 15% of the per capita protein.Amino acids are the principal building blocks of enzymes and other proteins (Panthee et al. 2006), and protein content and amino acid content (AAC) are key factors in the nutritional quality of rice. Thus, improvement of these factors is a major breeding objective in the effort to meet the food demands of an increasing global population. The 20 amino acids have been classified into two groups, essential and non-essential. Essential amino acids, which cannot be synthesized by animals, need to be taken up from plants or other organisms (D'Mello 2003). Non-essential amino acids are also important because they are required for the synthesis of essential amino acids and other biochemical compounds (Wen et al. 2009). Therefore, genetic knowledge regarding non-essential amino acids will also be beneficial to balancing amino acid composition and improving protein quality. Because rice protein content differs greatly among varieties (Maclean et al. 2002), it is important to utilize rice varieties containing high levels of essential amino acids as genetic resources to breed for improved protein content. The average protein level of the 17 587 cultivars of unmilled (brown) rice in the International Rice Research Institute (IRRI) germplasm collection was 9.5%, and ranged from 4.3 to 18.2%. This phenotypic variation in protein content provides a useful genetic basis for breeding.Protein content and AAC...

show abstract

Exploring the phenotypic expression of a regulatory proteome-altering gene by spectroscopy and chemometrics

Cited by 92 publications

References 14 publications

A new holistic exploratory approach to Systems Biology by Near Infrared Spectroscopy evaluated by chemometrics and data inspection

A new holistic exploratory approach to Systems Biology by Near Infrared Spectroscopy evaluated by chemometrics and data inspection

Near-Infrared Spectroscopy—Its Versatility in Analytical Chemistry

Quantitative trait loci controlling the amino acid content in rice (Oryza sativa L.)

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