Comparative bioinformatic analysis of genes expressed in common bean (Phaseolus vulgaris L.) seedlings

Genome ◽  
2005 ◽  
Vol 48 (3) ◽  
pp. 562-570 ◽  
Author(s):  
Maeli Melotto ◽  
Claudia B Monteiro-Vitorello ◽  
Adriano G Bruschi ◽  
Luis E.A Camargo
Keyword(s):  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Expressed Sequence Tag ◽  
Gene Families ◽  
Bioinformatic Analysis ◽  
Colletotrichum Lindemuthianum ◽  
Cdna Libraries ◽  
Nucleotide Polymorphisms ◽  
Phaseolus Vulgaris L ◽  
Single Nucleotide

To rapidly and cost-effectively generate gene expression data, we developed an annotated unigene database of common bean (Phaseolus vulgaris L.). In this study, 3 cDNA libraries were constructed from the bean breeding line SEL1308, 1 from young leaf and 2 from seedlings inoculated or not inoculated with the fungal pathogen Colletotrichum lindemuthianum (Sacc. & Magnus) Briosi & Cavara, which causes anthracnose in common bean. To this date, 5255 single-pass sequences have been included in the database after selection based on sequence quality. These ESTs were trimmed and clustered using the computer programs Phred and CAP3 to form a unigene collection of 3126 unique sequences. Within clusters, 318 single nucleotide polymorphisms (SNPs) and 68 insertions–deletions (indels) were found, indicating the presence of paralogous gene families in our database. Each unigene sequence was analyzed for possible function using their similarity to known genes represented in the GenBank database and classified into 14 categories. Only 314 unigenes showed significant similarities to Phaseolus genomic sequences and P. vulgaris ESTs, which indicates that 90% (2818 unigenes) of our database represent newly discovered common bean genes. In addition, 12% (387 unigenes) were shown to be specific to common bean. This study represents a first step towards the discovery of novel genes in beans and a valuable source of molecular markers for expressed gene tagging and mapping.Key words: expressed sequence tag (EST), Colletotrichum lindemuthianum, Phaseolus vulgaris, simple sequence repeat (SSR), single nucleotide polymorphism (SNP).

Arikara Yellow common bean

2004 ◽  
Vol 84 (3) ◽  
pp. 807-809 ◽  
Author(s):  
Hans-Henning Mündel, David Gehl ◽  
Henry C. Huang ◽  
Robert L. Conner
Keyword(s):  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Colletotrichum Lindemuthianum ◽  
Phaseolus Vulgaris L ◽  
Canadian Prairies ◽  
Yellow Seed ◽  
White Mould ◽  
Early Maturing ◽  
Wide Adaptation ◽  
Cultivar Description

Arikara Yellow is an early-maturing heritage bean (Phaseolus vulgaris L.) cultivar with a tan-yellow seed belonging to the Canario mexicano (syn. Mantequilla) market class. It has a determinate bush type growth habit, with wide adaptation on the Canadian prairies. Arikara Yellow is resistant to white mould caused by Sclerotinia sclerotiorum (Lib.) de Bary and to three of four common races of anthracnose, caused by Colletotrichum lindemuthianum (Sacc. & Magnus) Lams.-Scrib. Key words: Common bean, Phaseolus vulgaris, heritage bean, cultivar description

scholarly journals Characterization of Colletotrichum lindemuthianum isolates using differential cultivars of common bean in Santa Catarina State, Brazil

2008 ◽  
Vol 51 (5) ◽  
pp. 883-888 ◽  
Author(s):  
Maria Celeste Gonçalves-Vidigal ◽  
Claudia Thomazella ◽  
Pedro Soares Vidigal Filho ◽  
Marcus Vinícius Kvitschal ◽  
Haroldo Tavares Elias
Keyword(s):  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Colletotrichum Lindemuthianum ◽  
Phaseolus Vulgaris L ◽  
Santa Catarina ◽  
First Report ◽  
Differential Cultivars ◽  
Differential Cultivar ◽  
Santa Catarina State

In 2003 and 2004, 32 isolates of Colletotrichum lindemuthianum obtained from the infected plants of field-grown common bean (Phaseolus vulgaris L.) in Santa Catarina state, Brazil were analyzed based on the virulence to 12 differential cultivars of Phaseolus vulgaris L.. Thirteen distinct races were identified, six of which had not been reported previously in Santa Catarina. This is the first report of the occurrence of 67, 83,101,103,105, and 581 races of C. lindemuthianum. Race 65 was most common (34%). All the isolates were compatible to the cultivars Michelite and Mexico 222. Some isolates infected not only differential cultivar of Mesoamerican origin, but also the ones of Andean origin.

Bolt common bean

2016 ◽  
Vol 96 (2) ◽  
pp. 218-221 ◽  
Author(s):  
Raja Khanal ◽  
Terry Rupert ◽  
Alireza Navabi ◽  
Thomas H. Smith ◽  
Thomas E. Michaels ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Plant Architecture ◽  
Colletotrichum Lindemuthianum ◽  
Yield Potential ◽  
High Yield ◽  
Breeding Line ◽  
Phaseolus Vulgaris L ◽  
Dry Bean ◽  
High Yield Potential

The breeding line ACUG10-1 named as Bolt (CFIA registration no. 7366) of common bean (Phaseolus vulgaris L.) is resistant to anthracnose [caused by Colletotrichum lindemuthianum (Sacc. & Magnus)] with an upright plant architecture, suitable for direct harvest and high yield potential. Bolt is recommended for the dry bean growing areas in southwestern Ontario.

scholarly journals Confirming Single Nucleotide Polymorphisms from Expressed Sequence Tag Datasets Derived from Three Cattle cDNA Libraries

BMB Reports ◽  
2006 ◽  
Vol 39 (2) ◽  
pp. 183-188 ◽  
Author(s):  
Seung-Hwan Lee ◽  
Eung-Woo Park ◽  
Yong-Min Cho ◽  
Ji-Woong Lee ◽  
Hyoung-Yong Kim ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Expressed Sequence Tag ◽  
Cdna Libraries ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Expressed Sequence

scholarly journals Genetic resistance to Colletotrichum lindemuthianum in the Andean cultivar Jalo Pintado 2 of common bean

2016 ◽  
Vol 2 (1) ◽  
pp. 21
Author(s):  
Angêlica Albuquerque Tomilhero Frias ◽  
Maria Celeste Gonçalves-Vidigal ◽  
Danielle Sayuri Yoshida Nanami ◽  
Sandra Aparecida de Lima Castro ◽  
Pedro Soares Vidigal Filho ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Dominant Gene ◽  
Genetic Resistance ◽  
Colletotrichum Lindemuthianum ◽  
Phaseolus Vulgaris L ◽  
Bean Cultivar ◽  
F2 Population ◽  
Allelism Tests ◽  
Common Bean Cultivar

The anthracnose caused by fungus Colletotrichum lindemuthianum (Sacc. & Magnus) Briosi & Cavara is the most widespread disease and economically important fungal disease of common bean (Phaseolus vulgaris L.). The use of resistant cultivars is considered as one of the most effective methods in controlling this disease. The present study had as aim to characterize the genetic resistance of the Andean common bean cultivar Jalo Pintado 2 to the C. lindemuthianum through inheritance and allelism tests. The experiment was conducted under greenhouse conditions at Laboratório de Melhoramento do Feijão Comum e de Biologia Molecular do Núcleo de Pesquisa Aplicada a Agricultura (Nupagri) at Universidade Estadual de Maringá, Paraná, Brazil. The results of the F2 population from the crossing 'Jalo Pintado 2' (R) × Cornell 49-242 (S), inoculated with race 73 of C. lindemuthianum, adjusted to the ratio of 3R: 1S, demonstrating the action of a dominant gene in the cultivar Jalo Pintado 2. The allelism tests evidenced that the gene in the 'Jalo Pintado 2' is independent from those previously characterized: Co-1, Co-2,Co-3, Co-34, Co-4, Co-42, Co-43, Co-5, Co-6, Co-11, Co-12, Co-13, Co-14, Co-15 and Co-16. This gene is also independent from those genes not yet named present in Paloma, Perla and Amendoim Cavalo cultivars. The authors propose the Co-

scholarly journals Mining SNPs From EST Databases

1999 ◽  
Vol 9 (2) ◽  
pp. 167-174 ◽  
Author(s):  
Leslie Picoult-Newberg ◽  
Trey E. Ideker ◽  
Mark G. Pohl ◽  
Scott L. Taylor ◽  
Miriam A. Donaldson ◽  
...  
Keyword(s):  
Expressed Sequence Tag ◽  
De Novo ◽  
Cdna Libraries ◽  
Human Populations ◽  
Data Sets ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Using Data

There is considerable interest in the discovery and characterization of single nucleotide polymorphisms (SNPs) to enable the analysis of the potential relationships between human genotype and phenotype. Here we present a strategy that permits the rapid discovery of SNPs from publicly available expressed sequence tag (EST) databases. From a set of ESTs derived from 19 different cDNA libraries, we assembled 300,000 distinct sequences and identified 850 mismatches from contiguous EST data sets (candidate SNP sites), without de novo sequencing. Through a polymerase-mediated, single-base, primer extension technique, Genetic Bit Analysis (GBA), we confirmed the presence of a subset of these candidate SNP sites and have estimated the allele frequencies in three human populations with different ethnic origins. Altogether, our approach provides a basis for rapid and efficient regional and genome-wide SNP discovery using data assembled from sequences from different libraries of cDNAs.[The SNPs identified in this study can be found in the National Center of Biotechnology (NCBI) SNP database under submitter handles ORCHID (SNPS-981210-A) and debnick (SNPS-981209-A and SNPS-981209-B).]

AAC Scotty cranberry common bean

2018 ◽  
Vol 98 (6) ◽  
pp. 1416-1420
Author(s):  
Anfu Hou ◽  
Robert L. Conner ◽  
Parthiba M. Balasubramanian
Keyword(s):  
Phaseolus Vulgaris ◽  
Research And Development ◽  
Common Bean ◽  
Seed Size ◽  
River Valley ◽  
Colletotrichum Lindemuthianum ◽  
Red River ◽  
Phaseolus Vulgaris L ◽  
Dry Bean ◽  
Red River Valley

AAC Scotty (CFIA registration No. 8374) is a high-yielding cranberry bean (Phaseolus vulgaris L.) cultivar with a large seed size and resistance to races 73 and 105 of Colletotrichum lindemuthianum developed at the Agriculture and Agri-Food Canada Morden Research and Development Centre in Morden, MB. AAC Scotty is adapted to the dry bean producing regions of the Red River Valley with an average maturity of 97 d. AAC Scotty has acceptable cooking and canning quality.

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