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Score: 6.00 |
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| Title: Identification of QTL and association of a phytoene synthase gene with endosperm colour in durum wheat .
| | Author: Pozniak CJ Knox RE Clarke FR Clarke JM .
| | Journal: Theor . Appl . Genet . Citation: V : 114 ( 3 ) P : 525-37 Year: 2007 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub17131106 Accession (PMID): 17131106 | | Abstract: The yellow colour of durum wheat ( Triticum turgidum L var durum ) semolina is due in part to the presence of carotenoid pigments found in the endosperm and is an important end-use quality trait .
We hypothesized that variation in the genes coding for phytoene synthase ( Psy ) , a critical enzyme in carotenoid biosynthesis , may partially explain the phenotypic variation in endosperm colour observed among durum cultivars .
Using rice sequence information , primers were designed to PCR clone and sequence the Psy genes from Kofa ( high colour ) and W9262-260D3 ( medium colour ) durum cultivars .
Sequencing confirmed the presence of four Psy genes in each parent , corresponding to a two member gene family designated as Psy1-1 , Psy1-2 and Psy2-1 and Psy2-2 .
A genetic map was constructed using 155 F1-derived doubled haploid lines from the cross W9262-260D3/Kofa with 194 simple sequence repeat and DArT markers .
Using Psy1-1 and Psy2-1 allele-specific markers and chromosome mapping , the Psy1 and Psy2 genes were located to the group 7 and 5 chromosomes , respectively .
Four quantitative trait loci ( QTL ) underlying phenotypic variation in endosperm colour were identified on chromosomes 2A , 4B , 6B , and 7B .
The Psy1-1 locus co-segregated with the 7B QTL , demonstrating an association of this gene with phenotypic variation for endosperm colour .
This work is the first report of mapping Psy genes and supports the role of Psy1-1 in elevated levels of endosperm colour in durum wheat .
This gene is a target for the further development of a molecular marker to enhance selection for endosperm colour in durum wheat breeding programs .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 3.00 |
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| Title: Gene duplication in the carotenoid biosynthetic pathway preceded evolution of the grasses .
| | Author: Gallagher CE Matthews PD Li F Wurtzel ET .
| | Journal: Plant Physiol .
Citation: V : 135 ( 3 ) P : 1776-83 Year: 2004 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub15247400 Accession (PMID): 15247400 | | Abstract: Despite ongoing research on carotenoid biosynthesis in model organisms , there is a paucity of information on pathway regulation operating in the grasses ( Poaceae ) , which include plants of world-wide agronomic importance .
As a result , efforts to either breed for or metabolically engineer improvements in carotenoid content or composition in cereal crops have led to unexpected results .
In comparison to maize ( Zea mays ) , rice ( Oryza sativa ) accumulates no endosperm carotenoids , despite having a functional pathway in chloroplasts .
To better understand why these two related grasses differ in endosperm carotenoid content , we began to characterize genes encoding phytoene synthase ( PSY ) , since this nuclear-encoded enzyme appeared to catalyze a rate-controlling step in the plastid-localized biosynthetic pathway .
The enzyme had been previously associated with the maize Y1 locus thought to be the only functional gene controlling PSY accumulation , though function of the Y1 gene product had never been demonstrated .
We show that both maize and rice possess and express products from duplicate PSY genes , PSY1 ( Y1 ) and PSY2 ; PSY1 transcript accumulation correlates with carotenoid-containing endosperm .
Using a heterologous bacterial system , we demonstrate enzyme function of PSY1 and PSY2 that are largely conserved in sequence except for N and C-terminal domains .
By database mining and use of ortholog-specific universal PCR primers , we found that the PSY duplication is prevalent in at least eight subfamilies of the Poaceae , suggesting that this duplication event preceded evolution of the Poaceae .
These findings will impact study of grass phylogeny and breeding of enhanced carotenoid content in an entire taxonomic group of plant crops critical for global food security . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 3.00 |
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| Title: Nucleotide diversity and molecular evolution of the PSY1 gene in Zea mays compared to some other grass species .
| | Author: Fu Z Yan J Zheng Y Warburton ML Crouch JH Li JS | | Journal: Theor Appl Genet Citation: V : 120 P : 709-20 Year: 2010 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub19885651 Accession (PMID): 19885651 | | Abstract: Phytoene synthase ( PSY ) , which is encoded by the phytoene synthase 1 ( PSY1 ) gene , is the first rate-limiting enzyme in the plant carotenoid biosynthetic pathway .
In order to examine the genetic diversity and evolution pattern of PSY1 within the Andropogoneae , sequences of 76 accessions from 5 species ( maize , teosinte , tripsacum , coix , and sorghum ) of the Andropogoneae were tested , along with 4 accessions of rice ( Oryza sativa L ) included as outliers .
Both the number and the order of exons and introns were relatively conserved across the species tested .
Three domains were identified in the coding sequence , including signal peptide ( SP ) , PSY , and highly conserved squalene synthase ( SQS ) domain .
Although no positive selection signal was detected at an overall coding level among all species tested , the SP domain and the region upstream of the SQS-PSY domain appear to have undergone rapid evolution , as evidenced by a high d ( N ) /d ( S ) ratio ( >1 . 0 ) .
At the nucleotide level , positive selection and balancing selection were detected only among the yellow maize germplasm and the white maize germplasm , respectively .
The phylogenetic tree based on full-length sequences of PSY1-like regions supported the monophyletic theory of the Andropogoneae and the closest relationship between Zea and Tripsacum among the Andropogoneae .
Coix , which was theorized to have a closer relationship with maize due to similarities in morphology and chromosome number , has been shown in this study to have diverged relatively early from the other Andropogoneae , including maize .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 2.00 |
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| Title: Deciphering the genomic structure , function and evolution of carotenogenesis related phytoene synthases in grasses .
| | Author: Dibari B Murat F Chosson A Gautier V Poncet C Lecomte P Mercier I Berges H Pont C Blanco A Salse J | | Journal: BMC Genomics Citation: V : 13 P : 221 Year: 2012 Type: In-Data-Review | | Literature: oryza Field: abstract Doc ID: pub22672222 Accession (PMID): 22672222 | | Abstract: ABSTRACT : BACKGROUND : Carotenoids are isoprenoid pigments , essential for photosynthesis and photoprotection in plants .
The enzyme phytoene synthase ( PSY ) plays an essential role in mediating condensation of two geranylgeranyl diphosphate molecules , the first committed step in carotenogenesis .
PSY are nuclear enzymes encoded by a small gene family consisting of three paralogous genes ( PSY1-3 ) that have been widely characterized in rice , maize and sorghum .
RESULTS : In wheat , for which yellow pigment content is extremely important for flour colour , only PSY1 has been extensively studied because of its association with QTLs reported for yellow pigment whereas PSY2 has been partially characterized .
Here , we report the isolation of bread wheat PSY3 genes from a Renan BAC library using Brachypodium as a model genome for the Triticeae to develop Conserved Orthologous Set markers prior to gene cloning and sequencing .
Wheat PSY3 homoeologous genes were sequenced and annotated , unravelling their novel structure associated with intron-loss events and consequent exonic fusions .
A wheat PSY3 promoter region was also investigated for the presence of cis-acting elements involved in the response to abscisic acid ( ABA ) , since carotenoids also play an important role as precursors of signalling molecules devoted to plant development and biotic/abiotic stress responses .
Expression of wheat PSYs in leaves and roots was investigated during ABA treatment to confirm the up-regulation of PSY3 during abiotic stress .
CONCLUSIONS : We investigated the structural and functional determinisms of PSY genes in wheat .
More generally , among eudicots and monocots , the PSY gene family was found to be associated with differences in gene copy numbers , allowing us to propose an evolutionary model for the entire PSY gene family in Grasses .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 2.00 |
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| Title: Isolation and functional characterisation of banana phytoene synthase genes as potential cisgenes .
| | Author: Mlalazi B Welsch R Namanya P Khanna H Geijskes RJ Harrison MD Harding R Dale JL Bateson M | | Journal: Planta Citation: V : P : Year: 2012 Type: Publisher | | Literature: oryza Field: abstract Doc ID: pub22843244 Accession (PMID): 22843244 | | Abstract: Carotenoids occur in all photosynthetic organisms where they protect photosystems from auto-oxidation , participate in photosynthetic energy transfer and are secondary metabolites .
Of the more than 600 known plant carotenoids , few can be converted into vitamin A by humans and so these pro-vitamin A carotenoids ( pVAC ) are important in human nutrition .
Phytoene synthase ( PSY ) is a key enzyme in the biosynthetic pathway of pVACs and plays a central role in regulating pVAC accumulation in the edible portion of crop plants .
Banana is a major commercial crop and serves as a staple crop for more than 30 million people .
There is natural variation in fruit pVAC content across different banana cultivars , but this is not well understood .
Therefore , we isolated PSY genes from banana cultivars with relatively high ( cv .
Asupina ) and low ( cv .
Cavendish ) pVAC content .
We provide evidence that PSY in banana is encoded by two paralogs ( PSY1 and PSY2 ) , each with a similar gene structure to homologous genes in other monocots .
Further , we demonstrate that PSY2 is more highly expressed in fruit pulp compared to leaf .
Functional analysis of PSY1 and PSY2 in rice callus and E coli demonstrates that both genes encode functional enzymes , and that Asupina PSYs have approximately twice the enzymatic activity of the corresponding Cavendish PSYs .
These results suggest that differences in PSY enzyme activity contribute significantly to the differences in Asupina and Cavendish fruit pVAC content .
Importantly , Asupina PSY genes could potentially be used to generate new cisgenic or intragenic banana cultivars with enhanced pVAC content .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
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| Title: Timing and biosynthetic potential for carotenoid accumulation in genetically diverse germplasm of maize .
| | Author: Vallabhaneni R Wurtzel ET | | Journal: Plant Physiol Citation: V : P : Year: 2009 Type: Publisher | | Literature: oryza Field: abstract Doc ID: pub19346441 Accession (PMID): 19346441 | | Abstract: Enhancement of the carotenoid biosynthetic pathway in food crops benefits human health and adds commercial value of natural food colorants .
However , predictable metabolic engineering or breeding is limited by the incomplete understanding of endogenous pathway regulation , including rate-controlling steps and timing of expression in carotenogenic it issues .
The Grass family ( Poaceae ) contains the major crop staples , including maize , wheat , rice , sorghum , and millets .
Maize carotenogenesis was investigated using a novel approach to discover genes encoding limiting biosynthetic steps in the nutritionally targeted seed endosperm .
A combination of bioinformatics and cloning were first used to identify and map gene families encoding enzymes in maize and other grasses .
These enzymes represented upstream pathways for IPP and GGPP synthesis and the downstream carotenoid biosynthetic pathway , including conversion to ABA .
A maize germplasm collection was used for statistical testing of correlation between carotenoid content and candidate gene transcript levels .
Multiple pathway bottlenecks for isoprenoid biosynthesis and carotenoid biosynthesis were discovered in specific temporal windows of endosperm development .
Transcript levels of paralogs encoding isoprenoid IPP and GGPP-producing enzymes , DXS3 , DXR , HDR , and GGPPS1 , were found to positively correlate with endosperm carotenoid content .
For carotenoid pathway enzymes , transcript levels for CrtISO inversely correlated with seed carotenoid content , as compared to positive correlation of PSY1 transcripts .
Since ZEP depletes the carotenoid pool in subsequent conversion to ABA , ZEP transcripts were examined .
Carotenoid accumulation was found to be inversely associated with ZEP1 and ZEP2 transcript levels .
Extension of the maize results using phylogenetic analysis identified orthologs in other Grass species that may serve as potential metabolic engineering targets .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
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| Title: Production of porphyrin intermediates in Escherichia coli carrying soil metagenomic genes .
| | Author: Kim JS Lim HK Lee MH Park JH Hwang EC Moon BJ Lee SW | | Journal: FEMS Microbiol Lett Citation: V : 295 P : 42-9 Year: 2009 Type: In-Process | | Literature: oryza Field: abstract Doc ID: pub19473249 Accession (PMID): 19473249 | | Abstract: Tetrapyrrole pigments are important components of many biological processes , and many of them are produced primarily by microorganisms .
We constructed a soil metagenomic library using rice paddy soil consisting of 107 000 fosmid clones with an average DNA insert size of 35 kb .
We isolated a clone carrying genes in the porphyrin biosynthetic pathway based on function-driven screening of the library .
Through subcloning and mutagenesis analysis , we showed that two genes from soil metagenome , gtrA and hemC , were responsible for pigmentation in Escherichia coli .
HPLC and LC-MS analysis of the purified pigments from E coli carrying pSY143 identified coproporphyrin III without metal as a major compound as well as some other minor porphyrin intermediates .
As gtrA and hemC encode glutamyl-tRNA reductase and porphobilinogen deaminase , respectively , which are enzymes involved in the C5 biosynthetic pathway for porphyrin intermediates , our results suggest that hemL , hemB , hemD , and hemE should be provided by the E coli chromosome to generate a hybrid biosynthetic pathway for production of porphyrin intermediates using E coli and metagenomic genes .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
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| Title: Nucleotide diversity and molecular evolution of the PSY1 gene in Zea mays compared to some other grass species .
| | Author: Fu Z Yan J Zheng Y Warburton ML Crouch JH Li JS | | Journal: Theor Appl Genet Citation: V : 120 P : 709-20 Year: 2010 Type: MEDLINE | | Literature: oryza Field: title Doc ID: pub19885651 Accession (PMID): 19885651 | | Abstract: Phytoene synthase ( PSY ) , which is encoded by the phytoene synthase 1 ( PSY1 ) gene , is the first rate-limiting enzyme in the plant carotenoid biosynthetic pathway .
In order to examine the genetic diversity and evolution pattern of PSY1 within the Andropogoneae , sequences of 76 accessions from 5 species ( maize , teosinte , tripsacum , coix , and sorghum ) of the Andropogoneae were tested , along with 4 accessions of rice ( Oryza sativa L ) included as outliers .
Both the number and the order of exons and introns were relatively conserved across the species tested .
Three domains were identified in the coding sequence , including signal peptide ( SP ) , PSY , and highly conserved squalene synthase ( SQS ) domain .
Although no positive selection signal was detected at an overall coding level among all species tested , the SP domain and the region upstream of the SQS-PSY domain appear to have undergone rapid evolution , as evidenced by a high d ( N ) /d ( S ) ratio ( >1 . 0 ) .
At the nucleotide level , positive selection and balancing selection were detected only among the yellow maize germplasm and the white maize germplasm , respectively .
The phylogenetic tree based on full-length sequences of PSY1-like regions supported the monophyletic theory of the Andropogoneae and the closest relationship between Zea and Tripsacum among the Andropogoneae .
Coix , which was theorized to have a closer relationship with maize due to similarities in morphology and chromosome number , has been shown in this study to have diverged relatively early from the other Andropogoneae , including maize .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
