scholarly journals Genetic mapping reveals complex architecture and candidate genes involved in common bean response to Meloidogyne incognita infection

2021 ◽  
Author(s):  
Willian Giordani ◽  
Henrique Castro Gama ◽  
Alisson Fernando Chiorato ◽  
João Paulo Rodrigues Marques ◽  
Heqiang Huo ◽  
...  
Keyword(s):  
Genetic Mapping ◽  
Common Bean ◽  
Candidate Genes ◽  
Meloidogyne Incognita ◽  
Complex Architecture

scholarly journals Genetic Mapping Reveals Complex Architecture and Candidate Genes Involved in Common Bean Response to Meloidogyne Incognita Infection

2021 ◽  
Author(s):  
Willian Giordani ◽  
Henrique Castro Gama ◽  
Alisson Fernando Chiorato ◽  
João Paulo Rodrigues Marques ◽  
Luis Eduardo Aranha Camargo ◽  
...  
Keyword(s):  
Common Bean ◽  
Candidate Genes ◽  
Resistance Genes ◽  
Meloidogyne Incognita ◽  
Genetic Architecture ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Crop Species ◽  
Egg Masses ◽  
Genomic Regions

Abstract Root-knot nematodes (RKN), particularly Meloidogyne incognita, are among the most damaging and prevalent agricultural pathogens due to their ability to infect roots of almost all crop species, including common bean. The best strategy for their control is through the use of resistant cultivars. However, laborious phenotyping procedures make it difficult to assess nematode resistance in breeding programs. For common bean, this task is especially challenging since little has been done to discover resistance genes or find markers to assist selection. In this study, we performed genome-wide association studies and QTL mapping to explore the genetic architecture and genomic regions underlying the resistance to M. incognita and to identify candidate resistance genes. Phenotypic data were collected by a high-throughput assay, and the number of egg masses and root-galling index were evaluated 30 days after inoculation. Complex genetic architecture and independent genomic regions were associated with each trait according to the Fixed and random model Circulating Probability Unification. SNPs located on chromosomes Pv06, Pv07, Pv08 and Pv11 were associated with the number of egg masses, and on Pv01, Pv02, Pv05 and Pv10 with root-galling. A total of 215 candidate genes were identified, including 14 resistance gene analogs and five differentially expressed in a previous RNA-seq analysis. The histochemical analysis indicated that the reactive oxygen species might play a role in the resistance response. Our findings open new perspectives to improve selection efficiency for RKN resistance in common bean, and the candidate genes are valuable targets for functional investigation and gene editing approaches.

scholarly journals Fine mapping and identification of candidate genes for a QTL affecting Meloidogyne incognita reproduction in Upland cotton

BMC Genomics ◽  
2016 ◽  
Vol 17 (1) ◽  
Author(s):  
Pawan Kumar ◽  
Yajun He ◽  
Rippy Singh ◽  
Richard F. Davis ◽  
Hui Guo ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Fine Mapping ◽  
Meloidogyne Incognita ◽  
Upland Cotton

scholarly journals Natural Variation in Portuguese Common Bean Germplasm Reveals New Sources of Resistance Against Fusarium oxysporum f. sp. phaseoli and Resistance-Associated Candidate Genes

2020 ◽  
Vol 110 (3) ◽  
pp. 633-647 ◽  
Author(s):  
Susana T. Leitão ◽  
Marcos Malosetti ◽  
Qijan Song ◽  
Fred van Eeuwijk ◽  
Diego Rubiales ◽  
...  
Keyword(s):  
Common Bean ◽  
Fusarium Oxysporum ◽  
Candidate Genes ◽  
Fusarium Wilt ◽  
Functional Markers ◽  
Gene Pools ◽  
Primary Metabolism ◽  
Sources Of Resistance ◽  
Wilt Resistance ◽  
Fusarium Wilt Resistance

Common bean (Phaseolus vulgaris) is one of the most consumed legume crops in the world, and Fusarium wilt, caused by the fungus Fusarium oxysporum f. sp. phaseoli, is one of the major diseases affecting its production. Portugal holds a very promising common bean germplasm with an admixed genetic background that may reveal novel genetic resistance combinations between the original Andean and Mesoamerican gene pools. To identify new sources of Fusarium wilt resistance and detect resistance-associated single-nucleotide polymorphisms (SNPs), we explored, for the first time, a diverse collection of the underused Portuguese common bean germplasm by using genome-wide association analyses. The collection was evaluated for Fusarium wilt resistance under growth chamber conditions, with the highly virulent F. oxysporum f. sp. phaseoli strain FOP-SP1 race 6. Fourteen of the 162 Portuguese accessions evaluated were highly resistant and 71 intermediate. The same collection was genotyped with DNA sequencing arrays, and SNP–resistance associations were tested via a mixed linear model accounting for the genetic relatedness between accessions. The results from the association mapping revealed nine SNPs associated with resistance on chromosomes Pv04, Pv05, Pv07, and Pv08, indicating that Fusarium wilt resistance is under oligogenic control. Putative candidate genes related to phytoalexin biosynthesis, hypersensitive response, and plant primary metabolism were identified. The results reported here highlight the importance of exploring underused germplasm for new sources of resistance and provide new genomic targets for the development of functional markers to support selection in future disease resistance breeding programs.

Integration of expression profiles and genetic mapping data to identify candidate genes in intracranial aneurysm

2007 ◽  
Vol 32 (1) ◽  
pp. 45-57 ◽  
Author(s):  
Shantel Weinsheimer ◽  
Guy M. Lenk ◽  
Monique van der Voet ◽  
Susan Land ◽  
Antti Ronkainen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Intracranial Aneurysm ◽  
Genetic Mapping ◽  
Candidate Genes ◽  
Expression Profiles ◽  
Adherens Junction ◽  
Gene Expression Profiles ◽  
Mapping Data ◽  
Positional Candidate ◽  
Genetic Mapping Data

Intracranial aneurysm (IA) is a complex genetic disease for which, to date, 10 loci have been identified by linkage. Identification of the risk-conferring genes in the loci has proven difficult, since the regions often contain several hundreds of genes. An approach to prioritize positional candidate genes for further studies is to use gene expression data from diseased and nondiseased tissue. Genes that are not expressed, either in diseased or nondiseased tissue, are ranked as unlikely to contribute to the disease. We demonstrate an approach for integrating expression and genetic mapping data to identify likely pathways involved in the pathogenesis of a disease. We used expression profiles for IAs and nonaneurysmal intracranial arteries (IVs) together with the 10 reported linkage intervals for IA. Expressed genes were analyzed for membership in Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathways. The 10 IA loci harbor 1,858 candidate genes, of which 1,561 (84%) were represented on the microarrays. We identified 810 positional candidate genes for IA that were expressed in IVs or IAs. Pathway information was available for 294 of these genes and involved 32 KEGG biological function pathways represented on at least 2 loci. A likelihood-based score was calculated to rank pathways for involvement in the pathogenesis of IA. Adherens junction, MAPK, and Notch signaling pathways ranked high. Integration of gene expression profiles with genetic mapping data for IA provides an approach to identify candidate genes that are more likely to function in the pathology of IA.

Identification of candidate genes associated with CBB resistance in common bean HR45 (Phaseolus vulgaris L.) using cDNA-AFLP

2010 ◽  
Vol 38 (1) ◽  
pp. 75-81 ◽  
Author(s):  
Chun Shi ◽  
Sarita Chaudhary ◽  
Kangfu Yu ◽  
Soon J. Park ◽  
Alireza Navabi ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Candidate Genes ◽  
Phaseolus Vulgaris L

Identification of common bean (Phaseolus vulgaris) genotypes having resistance against root knot nematode Meloidogyne incognita

2015 ◽  
Vol 38 (5) ◽  
Author(s):  
Refik Bozbuga ◽  
H. Yildiz Dasgan ◽  
Yelderem Akhoundnejad ◽  
Mustafa Imren ◽  
Halil Toktay ◽  
...  
Keyword(s):  
Common Bean ◽  
Meloidogyne Incognita ◽  
Resistance Index ◽  
Egg Mass ◽  
Yield Losses ◽  
Fresh Weight ◽  
Root Knot Nematode ◽  
Resistance Response ◽  
Parental Material ◽  
Moderately Resistant

Root knot nematodes (<italic>Meloidogyne</italic> spp.) cause immense yield losses in crops throughout the world. Use of resistant germplasms of plants limits the root knot nematode damages. In this study, 87 common bean (<italic>Phaseoulus vulgaris</italic> L.) genotypes were screened against the root knot nematode, <italic>Meloidogyne incognita</italic> to determine the resistance response under growth chamber conditions in Turkey. <italic>P. vulgaris</italic> genotypes were evaluated based on resistance index (RI); root galling severity and nematode egg mass production on a 1-9 scale. The nematode negatively influenced the growth (fresh weight) of bean genotypes. At the completion of the study, 13 bean genotypes were found as immune (Sehirali), highly resistant (TR42164, Seleksiyon 5, Seker Fasulye, Fas-Agadir-Suk-1) and moderately resistant (Acik Badem, TR68587, TR43477, TR53827, TR28018, Gülnar-3, Siyah Fasulye, Kibris Amerikan) against <italic>M. incognita</italic> thus suggesting the use of such genotypes in breeding studies as a parental material to develop the root knot nematode resistant cultivars.

Inheritance of seed phytate and phosphorus levels in common bean (Phaseolus vulgaris L.) and association with newly-mapped candidate genes

2012 ◽  
Vol 30 (3) ◽  
pp. 1265-1277 ◽  
Author(s):  
Matthew W. Blair ◽  
Andrea Lorena Herrera ◽  
Tito Alejandro Sandoval ◽  
Gina Viviana Caldas ◽  
Marizia Filleppi ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Candidate Genes ◽  
Phaseolus Vulgaris L ◽  
Phosphorus Levels
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