scholarly journals Fine Mapping for Identification of Citrus Alternaria Brown Spot Candidate Resistance Genes and Development of New SNP Markers for Marker-Assisted Selection

2016 ◽  
Vol 7 ◽  
Author(s):  
Jose Cuenca ◽  
Pablo Aleza ◽  
Andres Garcia-Lor ◽  
Patrick Ollitrault ◽  
Luis Navarro
Keyword(s):  
Resistance Genes ◽  
Fine Mapping ◽  
Marker Assisted Selection ◽  
Snp Markers ◽  
Brown Spot ◽  
Alternaria Brown Spot

scholarly journals Genetically Based Location from Triploid Populations and Gene Ontology of a 3.3-Mb Genome Region Linked to Alternaria Brown Spot Resistance in Citrus Reveal Clusters of Resistance Genes

PLoS ONE ◽  
2013 ◽  
Vol 8 (10) ◽  
pp. e76755 ◽  
Author(s):  
José Cuenca ◽  
Pablo Aleza ◽  
Antonio Vicent ◽  
Dominique Brunel ◽  
Patrick Ollitrault ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Resistance Genes ◽  
Brown Spot ◽  
Genome Region ◽  
Alternaria Brown Spot

scholarly journals Fine mapping of Ur-3, a historically important rust resistance locus in common bean

2016 ◽  
Author(s):  
O.P. Hurtado-Gonzales ◽  
G. Valentini ◽  
T.A.S Gilio ◽  
A.M. Martins ◽  
Q. Song ◽  
...  
Keyword(s):  
Common Bean ◽  
Resistance Genes ◽  
Fine Mapping ◽  
Rust Resistance ◽  
Bulked Segregant Analysis ◽  
Snp Markers ◽  
Resistance Locus ◽  
Bean Rust ◽  
Rust Pathogen ◽  
Rust Resistance Genes

AbstractBean rust is a devastating disease of common bean in the Americas and Africa. The historically important Ur-3 gene confers resistance to many races of the highly variable bean rust pathogen that overcome all known rust resistance genes. Existing molecular markers tagging Ur-3 for use in marker assisted selection produce false results. We described here the fine mapping of Ur-3 for the development of highly accurate markers linked to this gene. An F2 population from Pinto 114 × Aurora was evaluated for its reaction to four different races of the bean rust pathogen. A bulked segregant analysis using the SNP chip BARCBEAN6K_3 positioned the approximate location of the Ur-3 locus to the lower arm of chromosome Pv11. Specific SSR and SNP markers and haplotype analysis of 18 sequenced bean lines led to position the Ur-3 locus to a 46.5 Kb genomic region. We discovered a KASP marker, SS68 that was tightly linked to the Ur-3 locus. Validation of SS68 on a panel of 130 diverse common bean lines and varieties containing all known rust resistance genes revealed that it was highly accurate producing no false results. The SS68 marker will be of great value to pyramid Ur-3 with other rust resistance genes. It will also reduce significantly time and labor associated with the current phenotypic detection of Ur-3. This is the first utilization of fine mapping to discover markers linked to a rust resistance in common bean.

scholarly journals Fine mapping of the male-sterile genes (MS1, MS2, MS3, and MS4) and development of SNP markers for marker-assisted selection in Japanese cedar (Cryptomeria japonica D. Don)

PLoS ONE ◽  
2018 ◽  
Vol 13 (11) ◽  
pp. e0206695 ◽  
Author(s):  
Yoichi Hasegawa ◽  
Saneyoshi Ueno ◽  
Asako Matsumoto ◽  
Tokuko Ujino-Ihara ◽  
Kentaro Uchiyama ◽  
...  
Keyword(s):  
Fine Mapping ◽  
Marker Assisted Selection ◽  
Cryptomeria Japonica ◽  
Japanese Cedar ◽  
Snp Markers ◽  
Male Sterile

scholarly journals Disease Resistant Citrus Breeding Using Newly Developed High Resolution Melting and CAPS Protocols for Alternaria Brown Spot Marker Assisted Selection

Agronomy ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1368
Author(s):  
Carmen Arlotta ◽  
Angelo Ciacciulli ◽  
Maria Concetta Strano ◽  
Valeria Cafaro ◽  
Fabrizio Salonia ◽  
...  
Keyword(s):  
High Resolution ◽  
Nested Pcr ◽  
Marker Assisted Selection ◽  
High Resolution Melting ◽  
Brown Spot ◽  
Restriction Enzyme Digestion ◽  
Resistance Locus ◽  
Citrus Breeding ◽  
Alternaria Brown Spot ◽  
Young Leaves

Alternaria alternata is a fungus that causes a serious disease in susceptible genotypes of citrus, particularly in mandarins. The Alternaria citri toxin (ACT) produced by the pathogen induces necrotic lesions on young leaves and fruits, defoliation and fruit drop. Here, we describe two methods of marker-assisted selection (MAS) that could be used for the early identification of Alternaria brown spot (ABS)-resistant mandarin hybrids. The first method is based on a nested PCR coupled to high resolution melting (HRM) analysis at the SNP08 locus, which is located at 0.4 cM from the ABS resistance locus, and was previously indicated as the most suitable for the selection of ABS-resistant hybrids. The method was validated on 41 mandarin hybrids of the CREA germplasm collection, and on 862 progenies generated from five crosses involving different susceptible parents. Four out of five populations showed Mendelian segregation at the analyzed locus, while a population involving Murcott tangor as male parent showed distorted segregation toward the susceptible hybrids. The second method is based on a cleaved amplified polymorphic sequences (CAPS) marker that was developed using the same primers as the nested PCR at the SNP08 locus, coupled with BccI restriction enzyme digestion. To verify the reliability of the two genotyping methods, in vitro leaf phenotyping was carried out by inoculating A. alternata spores onto young leaves of 101 hybrids, randomly chosen among the susceptible and resistant progenies. The phenotyping confirmed the SNP08 genotyping results, so the proposed method of selection based on HRM or CAPS genotyping could be routinely used as an alternative to KBioscience competitive allele specific polymerase chain reaction (KASPar) single nucleotide polymorphism (SNP) genotyping system to improve citrus breeding programs. While the study confirmed that the SNP08 marker is a reliable tool for MAS of new citrus hybrids with different genetic backgrounds, it also identified a small group of genotypes where the resistance mechanism requires further investigation.

Fine Mapping of Resistance Genes to SMV Strains SC6 and SC17 in Soybean

2013 ◽  
Vol 39 (2) ◽  
pp. 216 ◽  
Author(s):  
Xiao-Feng YANG ◽  
Yong-Qing YANG ◽  
Gui-Jie ZHENG ◽  
Hai-Jian ZHI ◽  
Xiao-Hong LI
Keyword(s):  
Resistance Genes ◽  
Fine Mapping

Comparative Mapping of Three Bacterial, Three Fungal, and One Virus Disease-resistance Genes in Common Bean

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 547a-547
Author(s):  
Geunhwa Jung ◽  
James Nienhuis ◽  
Dermot P. Coyne ◽  
H.M. Ariyarathne
Keyword(s):  
Disease Resistance ◽  
Common Bean ◽  
Pseudomonas Syringae ◽  
Resistance Genes ◽  
Fungal Pathogens ◽  
Xanthomonas Campestris ◽  
Virus Disease ◽  
Disease Resistance Genes ◽  
Brown Spot ◽  
Viral Pathogen

Common bacterial blight (CBB), bacterial brown spot (BBS), and halo blight (HB), incited by the bacterial pathogens Xanthomonas campestris pv. phaseoli (Smith) Dye, Pseodomonas syringae pv. syringa, and Pseudomonas syringae pv. phaseolicola, respectively are important diseases of common bean. In addition three fungal pathogens, web blight (WB) Thanatephorus cucumeris, rust Uromyces appendiculatus, and white mold (WM) Sclerotinia sclerotiorum, are also destructive diseases attacking common bean. Bean common mosaic virus is also one of most major virus disease. Resistance genes (QTLs and major genes) to three bacterial (CBB, BBS, and HB), three fungal (WB, rust, and WM), and one viral pathogen (BCMV) were previously mapped in two common bean populations (BAC 6 × HT 7719 and Belneb RR-1 × A55). The objective of this research was to use an integrated RAPD map of the two populations to compare the positions and effect of resistance QTL in common bean. Results indicate that two chromosomal regions associated with QTL for CBB resistance mapped in both populations. The same chromosomal regions associated with QTL for disease resistance to different pathogens or same pathogens were detected in the integrated population.

scholarly journals Development of genic KASP SNP markers from RNA-Seq data for map-based cloning and marker-assisted selection in maize

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhengjie Chen ◽  
Dengguo Tang ◽  
Jixing Ni ◽  
Peng Li ◽  
Le Wang ◽  
...  
Keyword(s):  
Marker Assisted Selection ◽  
Inbred Lines ◽  
Average Density ◽  
Snp Markers ◽  
Data Sets ◽  
Rna Seq ◽  
Specific Pcr ◽  
Maize Inbred Lines ◽  
Allele Specific ◽  
Allele Specific Pcr

Abstract Background Maize is one of the most important field crops in the world. Most of the key agronomic traits, including yield traits and plant architecture traits, are quantitative. Fine mapping of genes/ quantitative trait loci (QTL) influencing a key trait is essential for marker-assisted selection (MAS) in maize breeding. However, the SNP markers with high density and high polymorphism are lacking, especially kompetitive allele specific PCR (KASP) SNP markers that can be used for automatic genotyping. To date, a large volume of sequencing data has been produced by the next generation sequencing technology, which provides a good pool of SNP loci for development of SNP markers. In this study, we carried out a multi-step screening method to identify kompetitive allele specific PCR (KASP) SNP markers based on the RNA-Seq data sets of 368 maize inbred lines. Results A total of 2,948,985 SNPs were identified in the high-throughput RNA-Seq data sets with the average density of 1.4 SNP/kb. Of these, 71,311 KASP SNP markers (the average density of 34 KASP SNP/Mb) were developed based on the strict criteria: unique genomic region, bi-allelic, polymorphism information content (PIC) value ≥0.4, and conserved primer sequences, and were mapped on 16,161 genes. These 16,161 genes were annotated to 52 gene ontology (GO) terms, including most of primary and secondary metabolic pathways. Subsequently, the 50 KASP SNP markers with the PIC values ranging from 0.14 to 0.5 in 368 RNA-Seq data sets and with polymorphism between the maize inbred lines 1212 and B73 in in silico analysis were selected to experimentally validate the accuracy and polymorphism of SNPs, resulted in 46 SNPs (92.00%) showed polymorphism between the maize inbred lines 1212 and B73. Moreover, these 46 polymorphic SNPs were utilized to genotype the other 20 maize inbred lines, with all 46 SNPs showing polymorphism in the 20 maize inbred lines, and the PIC value of each SNP was 0.11 to 0.50 with an average of 0.35. The results suggested that the KASP SNP markers developed in this study were accurate and polymorphic. Conclusions These high-density polymorphic KASP SNP markers will be a valuable resource for map-based cloning of QTL/genes and marker-assisted selection in maize. Furthermore, the method used to develop SNP markers in maize can also be applied in other species.

scholarly journals Mapping of quantitative trait loci influencing daily body weight gain (DBWG) on chromosome 6 in German Holstein population

2006 ◽  
Vol 22 (1-2) ◽  
pp. 35-46 ◽  
Author(s):  
M. Reißmann ◽  
P. Reinecke ◽  
U. Müller ◽  
S. Abdel-Rahman
Keyword(s):  
Body Weight ◽  
Weight Gain ◽  
Fine Mapping ◽  
Marker Assisted Selection ◽  
Growth Traits ◽  
Body Weight Gain ◽  
Chromosome 6 ◽  
Production Traits ◽  
Daily Body Weight ◽  
Holstein Population

Twelve microsatellite markers on chromosome 6 were analyzed in German Holstein population to detect and locate QTL affecting daily body weight gain (DBWG). The results indicate promising location for QTL controlling daily body weight gain trait on chromosome 6. Where, three markers BMS2508 BM3026 and TGLA37 at three different positions in a distance 15.2 cM on BTA6 were associated with significant effects for daily body weight gain trait (DBWG). Comparison between this finding and previously identified QTL support the location of a QTL for growth traits on chromosome 6, where a significant QTL for birth and yearling weight was previously identified on chromosome 6 tightly close to marker BM3026. Finding from this study could be used in subsequent fine-mapping work and applied to marker-assisted selection (MAS) of production traits.

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