Comparative analysis of a Brassica BAC clone containing several major aliphatic glucosinolate genes with its corresponding Arabidopsis sequence

Genome ◽  
2004 ◽  
Vol 47 (4) ◽  
pp. 666-679 ◽  
Author(s):  
Muqiang Gao ◽  
Genyi Li ◽  
Bo Yang ◽  
W Richard McCombie ◽  
Carlos F Quiros
Keyword(s):  
Gene Family ◽  
Brassica Oleracea ◽  
Copy Number ◽  
Artificial Chromosome ◽  
Homologous Region ◽  
Bac Clone ◽  
The Third ◽  
Aliphatic Glucosinolates ◽  
High Conservation ◽  
Equivalent Region

We compared the sequence of a 101-kb-long bacterial artificial chromosome (BAC) clone (B21H13) from Brassica oleracea with its homologous region in Arabidopsis thaliana. This clone contains a gene family involved in the synthesis of aliphatic glucosinolates. The A. thaliana homologs for this gene family are located on chromosome IV and correspond to three 2-oxoglutarate-dependent dioxygenase (AOP) genes. We found that B21H13 harbors 23 genes, whereas the equivalent region in Arabidopsis contains 37 genes. All 23 common genes have the same order and orientation in both Brassica and Arabidopsis. The 16 missing genes in the broccoli BAC clone were arranged in two major blocks of 5 and 7 contiguous genes, two singletons, and a twosome. The 118 exons comprising these 23 genes have high conservation between the two species. The arrangement of the AOP gene family in A. thaliana is as follows: AOP3 (GS-OHP) – AOP2 (GS-ALK) – pseudogene – AOP1. In contrast, in B. oleracea (broccoli and collard), two of the genes are duplicated and the third, AOP3, is missing. The remaining genes are arranged as follows: Bo-AOP2.1 (BoGSL-ALKa) – pseudogene – AOP2.2 (BoGSL-ALKb) – AOP1.1 – AOP1.2. When the survey was expanded to other Brassica accessions, we found variation in copy number and sequence for the Brassica AOP2 homologs. This study confirms that extensive rearrangements have taken place during the evolution of the Brassicacea at both gene and chromosomal levels.Key words: Brassica oleracea, B. rapa, comparative genomics, glucosinolates.

scholarly journals Inheritance of Three Major Genes Involved in the Synthesis of Aliphatic Glucosinolates in Brassica oleracea

2001 ◽  
Vol 126 (4) ◽  
pp. 427-431 ◽  
Author(s):  
G. Li ◽  
A. Riaz ◽  
S. Goyal ◽  
S. Abel ◽  
C.F. Quiros
Keyword(s):  
Arabidopsis Thaliana ◽  
Brassica Oleracea ◽  
Major Genes ◽  
Breeding Lines ◽  
The Third ◽  
Aliphatic Glucosinolates ◽  
Crop Enhancement

Inheritance of three major genes involved in synthesis of aliphatic glucosinolates (GSL) was followed in segregating populations of Brassica oleracea L. generated from three crosses: broccoli × cauliflower, collard × broccoli, and collard × cauliflower. Two of these genes, GSL-PRO and GSL-ELONG, regulate sidechain length. The action of the former results in three-carbon GSL, whereas action of the latter produces four-carbon GSL. We determined that these two genes act and segregate independently from each other in B. oleracea. The double recessive genotype produces only trace amounts of aliphatic GSL. The third gene, GSL-ALK controls sidechain desaturation and, as it has been observed in Arabidopsis thaliana (L.) Heynh., we found that this gene cosegregates with a fourth gene, GSL-OH, that is responsible for sidechain hydroxylation. Elucidation of the inheritance of major genes controlling biosynthesis of GSL will allow for manipulation of these genes and facilitate development of lines with specific GSL profiles. This capability will be important for improvement of Brassica breeding lines with high content of desirable GSL, like glucoraphanin, a demonstrated precursor of anticarcinogenic compounds. Additionally, this work is the first step towards cloning the major genes of the aliphatic GSL pathway, and to use these clones in transformation strategies for further crop enhancement.

scholarly journals Genome-wide identification and expression analysis of the Brassica oleracea L. chitin-binding genes and response to pathogens infections

Planta ◽  
2021 ◽  
Vol 253 (4) ◽  
Author(s):  
Mingzhao Zhu ◽  
Shujin Lu ◽  
Mu Zhuang ◽  
Yangyong Zhang ◽  
Honghao Lv ◽  
...  
Keyword(s):  
Powdery Mildew ◽  
Gene Family ◽  
Brassica Oleracea ◽  
Downy Mildew ◽  
Fusarium Wilt ◽  
Black Spot ◽  
Housekeeping Genes ◽  
Chitinase Gene ◽  
Genome Wide ◽  
A Genome

Abstract Main conclusion Chitinase family genes were involved in the response of Brassica oleracea to Fusarium wilt, powdery mildew, black spot and downy mildew. Abstract Abstract Chitinase, a category of pathogenesis-related proteins, is believed to play an important role in defending against external stress in plants. However, a comprehensive analysis of the chitin-binding gene family has not been reported to date in cabbage (Brassica oleracea L.), especially regarding the roles that chitinases play in response to various diseases. In this study, a total of 20 chitinase genes were identified using a genome-wide search method. Phylogenetic analysis was employed to classify these genes into two groups. The genes were distributed unevenly across six chromosomes in cabbage, and all of them contained few introns (≤ 2). The results of collinear analysis showed that the cabbage genome contained 1–5 copies of each chitinase gene (excluding Bol035470) identified in Arabidopsis. The heatmap of the chitinase gene family showed that these genes were expressed in various tissues and organs. Two genes (Bol023322 and Bol041024) were relatively highly expressed in all of the investigated tissues under normal conditions, exhibiting the expression characteristics of housekeeping genes. In addition, under four different stresses, namely, Fusarium wilt, powdery mildew, black spot and downy mildew, we detected 9, 5, 8 and 8 genes with different expression levels in different treatments, respectively. Our results may help to elucidate the roles played by chitinases in the responses of host plants to various diseases.

Extraordinary Heterosis Found In A Forage Grass Hybrid, Festuca apennina × F. pratensis

2020 ◽  
Author(s):  
Beat Boller ◽  
David Kopecký
Keyword(s):  
Chromosome Doubling ◽  
Artificial Chromosome ◽  
Dry Mass ◽  
Hybrid Vigor ◽  
Hybrid Breeding ◽  
Forage Grass ◽  
Breeding Programs ◽  
The Third ◽  
Specific Trait ◽  
Second Year

Abstract Background: Heterosis (or hybrid vigor) is the over-performance of a hybrid over its parents in a specific trait or a set of traits. As such, hybrid breeding serves as a tool to efficiently trigger gains in breeding programs. Moreover, hybrids of genetically distant landraces, varieties or even species may become evolutionary successful. In Swiss alpine swards, we observed frequent prevalence of triploid hybrids of Festuca pratensis × F. apennina with outstanding competitiveness relative to their parental species in the sites of sympatric occurrence. Results: Observations of these highly vigorous hybrids prompted the study on their heterosis across various environmental conditions. Phenotypic observations during three years at four locations at different altitudes (from 200 m a.s.l. to 1850 m a.s.l.) have shown significant heterosis for dry biomass production at all sites during the first and second year, and at the mid- and high altitude sites also in the third year. At mid-altitude (1000 m a.s.l.), heterosis increased steadily and reached a maximum of +508 % for annual yield (+626% for a single cut) in the third year. This is by far the highest value of heterosis ever reported for annual dry mass yield of a forage grass. Conclusions: Further utilization of triploid hybrids in forage grass breeding is hampered by their sterility hence a need for vegetative propagation. However, artificial chromosome doubling of triploids to create fertile hexaploids, or seeking ways to propagate them vegetatively at an industrial scale might overcome this limitation.

scholarly journals Genomic amplification of chromosome 20q13.33 is the early biomarker for the development of sporadic colorectal carcinoma

2020 ◽  
Vol 13 (S10) ◽  
Author(s):  
Vo-Minh-Hoang Bui ◽  
Clément Mettling ◽  
Jonathan Jou ◽  
H. Sunny Sun
Keyword(s):  
Colorectal Carcinoma ◽  
Microsatellite Instability ◽  
Copy Number ◽  
Chromosomal Abnormalities ◽  
Quantitative Polymerase Chain Reaction ◽  
Copy Number Gain ◽  
Comparative Genomic ◽  
Colon Polyps ◽  
Genomic Amplification ◽  
The Third

Abstract Background Colorectal carcinoma (CRC) is the third most common cancer in the world and also the third leading cause of cancer-related mortality in Taiwan. CRC tumorigenesis is a multistep process, starting from mutations causing loss of function of tumor suppressor genes, canonically demonstrated in adenomatous polyposis coli pathogenesis. Although many genes or chromosomal alterations have been shown to be involved in this process, there are still unrecognized molecular events within CRC tumorigenesis. Elucidating these mechanisms may help improve the management and treatment. Methods In this study, we aimed to identify copy number alteration of the smallest chromosomal regions that is significantly associated with sporadic CRC tumorigenesis using high-resolution array-based Comparative Genomic Hybridization (aCGH) and quantitative Polymerase chain reaction (qPCR). In addition, microsatellite instability assay and sequencing-based mutation assay were performed to illustrate the initiation event of CRC tumorigenesis. Results A total of 571 CRC patients were recruited and 377 paired CRC tissues from sporadic CRC cases were used to define the smallest regions with chromosome copy number changes. In addition, 198 colorectal polyps from 160 patients were also used to study the role of 20q13.33 gain in CRC tumorigenesis. We found that gain in 20q13.33 is the main chromosomal abnormalities in this patient population and counts 50.9 and 62.8% in CRC and colon polyps, respectively. Furthermore, APC and KRAS gene mutations were profiled simultaneously and co-analyzed with microsatellite instability and 20q13.33 gain in CRC patients. Our study showed that the frequency of 20q13.33 copy number gain was highest among all reported CRC mutations. Conclusion As APC or KRAS mutations are currently identified as the most important targets for CRC therapy, this study proposes that 20q13.33 copy number gain and the associated chromosomal genes function as promising biomarkers for both early stage detection and targeted therapy of sporadic CRCs in the future.

scholarly journals Use of Recombination-Mediated Genetic Engineering for Construction of Rescue Human Cytomegalovirus Bacterial Artificial Chromosome Clones

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Kalpana Dulal ◽  
Benjamin Silver ◽  
Hua Zhu
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Homologous Recombination ◽  
Human Cytomegalovirus ◽  
Artificial Chromosome ◽  
Bac Clone ◽  
Dna Viruses ◽  
E Coli ◽  
Recombination System ◽  
Capture Method

Bacterial artificial chromosome (BAC) technology has contributed immensely to manipulation of larger genomes in many organisms including large DNA viruses like human cytomegalovirus (HCMV). The HCMV BAC clone propagated and maintained insideE. coliallows for accurate recombinant virus generation. Using this system, we have generated a panel of HCMV deletion mutants and their rescue clones. In this paper, we describe the construction of HCMV BAC mutants using a homologous recombination system. A gene capture method, or gap repair cloning, to seize large fragments of DNA from the virus BAC in order to generate rescue viruses, is described in detail. Construction of rescue clones using gap repair cloning is highly efficient and provides a novel use of the homologous recombination-based method inE. colifor molecular cloning, known colloquially as recombineering, when rescuing large BAC deletions. This method of excising large fragments of DNA provides important prospects forin vitrohomologous recombination for genetic cloning.

A yeast artificial chromosome covering the tyrosinase gene confers copy number-dependent expression in transgenic mice

Nature ◽  
1993 ◽  
Vol 362 (6417) ◽  
pp. 258-261 ◽  
Author(s):  
Andreas Schedl ◽  
Lluís Montoliu ◽  
Gavin Kelsey ◽  
Günther Schütz
Keyword(s):  
Transgenic Mice ◽  
Copy Number ◽  
Yeast Artificial Chromosome ◽  
Artificial Chromosome ◽  
Tyrosinase Gene

scholarly journals The Avr1b Locus of Phytophthora sojae Encodes an Elicitor and a Regulator Required for Avirulence on Soybean Plants Carrying Resistance Gene Rps1b

2004 ◽  
Vol 17 (4) ◽  
pp. 394-403 ◽  
Author(s):  
Weixing Shan ◽  
Minh Cao ◽  
Dan Leung ◽  
Brett M. Tyler
Keyword(s):  
Resistance Gene ◽  
Artificial Chromosome ◽  
Phytophthora Sojae ◽  
Secreted Protein ◽  
Bac Clone ◽  
Bac Contig ◽  
Soybean Plants ◽  
Substitution Mutations ◽  
Race 2 ◽  
Soybean Leaves

We have used map-based approaches to clone a locus containing two genes, Avr1b-1 and Avr1b-2, required for avirulence of the oomycete pathogen Phytophthora sojae (Kaufmann & Gerdemann) on soybean plants carrying resistance gene Rps1b. Avr1b-1 was localized to a single 60-kb bacterial artificial chromosome (BAC) clone by fine-structure genetic mapping. Avr1b-1 was localized within the 60-kb region by identification of an mRNA that is expressed in a race-specific and infection-specific manner and that encodes a small secreted protein. When the Avr1b-1 protein was synthesized in the yeast Pichia pastoris and the secreted protein infiltrated into soybean leaves, it triggered a hypersensitive response specifically in host plants carrying the Rps1b resistance gene. This response eventually spread to the entire inoculated plant. In some isolates of P. sojae virulent on Rps1b-containing cultivars, such as P7081 (race 25) and P7076 (race 19), the Avr1b-1 gene had numerous substitution mutations indicative of strong divergent selection. In other isolates, such as P6497 (race 2) and P9073 (race 25), there were no substitutions in Avr1b-1, but Avr1b-1 mRNA did not accumulate. Genetic complementation experiments with P6497 revealed the presence of a second gene, Avr1b-2, required for the accumulation of Avr1b-1 mRNA. Avr1b-2 was genetically mapped to the same BAC contig as Avr1b-1, using a cross between P7064 (race 7) and P6497. The Avr1k gene, required for avirulence on soybean cultivars containing Rps1k, was mapped to the same interval as Avr1b-1.

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