Mapping of STS markers obtained from oat resistance gene analog sequences

Genome ◽  
2009 ◽  
Vol 52 (7) ◽  
pp. 608-619 ◽  
Author(s):  
Yolanda Loarce ◽  
María Jesús Sanz ◽  
María Luisa Irigoyen ◽  
Araceli Fominaya ◽  
Esther Ferrer
Keyword(s):  
Linkage Group ◽  
Resistance Gene ◽  
Scar Marker ◽  
Crown Rust ◽  
Nucleotide Polymorphisms ◽  
Sequence Characterized Amplified Region ◽  
Sts Markers ◽  
Ril Population ◽  
Reference Map ◽  
Complex Locus

Two previously isolated resistance gene analogs (RGAs) of oat have been located as RFLPs in the reference map of Avena byzantina ‘Kanota’ × Avena sativa ‘Ogle’ in regions either homologous or homoeologous to loci for resistance to Puccinia coronata , the causal agent of crown rust. In this study, the RGAs were mapped in two recombinant inbred line (RIL) populations that segregate for crown rust resistance: the diploid Avena strigosa × Avena wiestii RIL population (Asw), which has been used for mapping the complex locus PcA, and the hexaploid MN841801-1 × Noble-2 RIL population (MN), in which QTLs have been located. To obtain single-locus markers, RGAs were converted to sequence tagged site (STS) markers using a procedure involving extension of the original RGA sequence lengths by PCR genome walking, amplification and cloning of the parental fragments, and identification of single nucleotide polymorphisms. The procedure successfully obtained STSs from different members of the L7M2 family of sequences, the initial NBS of which have nucleotide similarities of >83%. However, for RGA III2.18, the parental lines were not polymorphic for the STSs assayed. A sequence characterized amplified region (SCAR) marker with features of an RGA had been previously identified for gene Pc94. This marker was also mapped in the above RIL populations. Markers based on RGA L7M2 co-localized with markers defining the QTL Prq1a in linkage group MN3, and were located 15.2 cM from PcA in linkage group AswAC. The SCAR marker for Pc94 was also located in the QTL Prq1a but at 39.5 cM from PcA in AswAC, indicating that the NBS-LRR sequence represented by this marker is not related to PcA. L7M2 was also excluded as a member of the PcA cluster, although it could be an appropriate marker for the Prq1a cluster if chromosome rearrangements are postulated.

scholarly journals Identification of a sequence characterized amplified region (SCAR) marker linked to the Puccinia psidii resistance gene 1 (Ppr1) in Eucalyptus grandis

2015 ◽  
Vol 10 (18) ◽  
pp. 1957-1964 ◽  
Author(s):  
Luiz Laia Marcelo ◽  
Couto Alfenas Acelino ◽  
Herminio Brommonschenkel Sergio ◽  
Oda Shinitiro ◽  
Jose de Mello Eduardo ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Scar Marker ◽  
Eucalyptus Grandis ◽  
Puccinia Psidii ◽  
Sequence Characterized Amplified Region

scholarly journals A Molecular Marker Correlated with Selected Virulence Against the Tomato Resistance Gene Mi in Meloidogyne incognita, M. javanica, and M. arenaria

2001 ◽  
Vol 91 (4) ◽  
pp. 377-382 ◽  
Author(s):  
Jianhua Xu ◽  
Takashi Narabu ◽  
Takayuki Mizukubo ◽  
Tadaaki Hibi
Keyword(s):  
Resistance Gene ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Nucleotide Polymorphisms ◽  
Sequence Characterization ◽  
Sequence Characterized Amplified Region ◽  
Major Species ◽  
Wide Range ◽  
Meloidogyne Spp

Root-knot nematodes of the genus Meloidogyne are economically important pathogens of a wide range of crops. The tomato resistance gene Mi typically confers resistance to the three major species, M. incognita, M. javanica, and M. arenaria. However, virulent populations completely overcoming the Mi resistance still occur. In an attempt to develop molecular markers for virulence against Mi and gain insights into the genetic relationships among virulent populations of different species and origins, random amplified polymorphic DNA (RAPD) analyses of laboratory-selected virulent, field virulent, and avirulent populations of M. incognita, M. javanica, and M. arenaria were carried out. A RAPD marker, specific for selected virulent populations, was identified, and subsequently, converted to a sequence characterized amplified region (SCAR). Sequence characterization of the SCAR locus showed that alleles from laboratory- and field-selected virulent populations were highly similar to each other and clearly different from alleles from natural virulent and avirulent populations. This result suggests that the genetic mechanism for virulence against Mi may be similar among selected virulent populations of the three Meloidogyne spp., but different between selected and natural virulent populations. Based on the nucleotide polymorphisms at the SCAR locus, codominant and dominant polymerase chain reaction-based markers were developed enabling rapid diagnosis of selected virulent genotypes in M. incognita, M. javanica, and M. arenaria.

scholarly journals Localization of the Stem Rust Resistance Gene Pg2 to Linkage Group Mrg20 in Cultivated Oat (Avena sativa)

2020 ◽  
Vol 110 (10) ◽  
pp. 1721-1726
Author(s):  
Aida Z. Kebede ◽  
Wubishet A. Bekele ◽  
Jennifer W. Mitchell Fetch ◽  
Aaron D. Beattie ◽  
Shiaoman Chao ◽  
...  
Keyword(s):  
Linkage Group ◽  
Resistance Gene ◽  
Stem Rust ◽  
Avena Sativa ◽  
Rust Resistance ◽  
Stem Rust Resistance ◽  
Rust Resistance Gene ◽  
Stem Rust Resistance Gene ◽  
Ril Population ◽  
Oat Breeding

Stem rust is an important disease of cultivated oat (Avena sativa) caused by Puccinia graminis f. sp. avenae. In North America, host resistance is the primary strategy to control this disease and is conferred by a relatively small number of resistance genes. Pg2 is a widely deployed stem rust resistance gene that originates from cultivated oat. Oat breeders wish to develop cultivars with multiple Pg genes to slow the breakdown of single gene resistance, and often require DNA markers suited for marker-assisted selection. Our objectives were to (i) construct high density linkage maps for a major oat stem rust resistance gene using three biparental mapping populations, (ii) develop Kompetitive allele-specific PCR (KASP) assays for Pg2-linked single-nucleotide polymorphisms (SNPs), and (iii) test the prediction accuracy of those markers with a diverse panel of spring oat lines and cultivars. Genotyping-by-sequencing SNP markers linked to Pg2 were identified in an AC Morgan/CDC Morrison recombinant inbred line (RIL) population. Pg2-linked SNPs were then analyzed in an AC Morgan/RL815 F2 population and an AC Morgan/CDC Dancer RIL population. Linkage analysis identified a common location for Pg2 in all three populations on linkage group Mrg20 of the oat consensus genetic map. The most predictive markers were identified and converted to KASP assays for use in oat breeding programs. When used in combination, the KASP assays for the SNP loci avgbs2_126549.1.46 and avgbs_cluster_23819.1.27 were highly predictive of Pg2 status in panel of 54 oat breeding lines and cultivars.

Integration of a molecular linkage group containing the broomrape resistance gene Or5 into an RFLP map in sunflower

Genome ◽  
1999 ◽  
Vol 42 (3) ◽  
pp. 453-456 ◽  
Author(s):  
Yun Hai Lu ◽  
Geneviève Gagne ◽  
Bruno Grezes-Besset ◽  
Philippe Blanchard
Keyword(s):  
Linkage Group ◽  
Linkage Map ◽  
Resistance Gene ◽  
Scar Marker ◽  
Rapd Marker ◽  
Rflp Marker ◽  
Rflp Markers ◽  
Scar Markers ◽  
Molecular Linkage Group ◽  
Rflp Map

A linkage group containing the Or5 gene conferring resistance to Orobanche cumana race E, as well as 5 SCAR markers and 1 RAPD marker has been recently identified in sunflower. A SCAR marker RTS05, mapped 5.6 cM proximal to the Or5 locus, was analysed in an F2 population for which the segregation data of 80 RFLP markers (GIE cartisol - Phase II, France) were available. An association was found between the SCAR marker RTS05 and an RFLP marker S009 (32.1 cM, LOD = 4.7) that had been mapped to the linkage group 17 of the GIE Cartisol RFLP map. Another RFLP marker S010, tightly linked to S009 (0.0 cM) in the same linkage group, was screened in the F2 population that had been previously used for the Or5 linkage map identification. S010 was found to be significantly linked to all 5 SCAR markers as well as to the single RAPD marker with a LOD > 3.0 in each case. This RFLP marker was mapped between two SCAR markers and was situated at 35.1 cM from the resistance gene with a LOD = 2.7. These results showed that the Or5 linkage group could be integrated with the linkage group 17 of the GIE Cartisol RFLP map.Key words: Helianthus, Orobanche, RFLP, SCAR, linkage map.

scholarly journals Mapping of the Oat Crown Rust Resistance Gene Pc39 Relative to Single Nucleotide Polymorphism Markers

Plant Disease ◽  
2020 ◽  
Vol 104 (5) ◽  
pp. 1507-1513
Author(s):  
Jun Zhao ◽  
Aida Z. Kebede ◽  
Wubishet A. Bekele ◽  
Jim G. Menzies ◽  
James Chong ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Linkage Group ◽  
Rust Resistance ◽  
Genetic Distances ◽  
Snp Markers ◽  
Crown Rust ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Ril Population ◽  
Oat Breeding

Crown rust, caused by Puccinia coronata f. sp. avenae Eriks. (Pca), is among the most important oat diseases resulting in significant yield losses in many growing regions. A gene-for-gene interaction is well established in this pathosystem and has been exploited by oat breeders to control crown rust. Pc39 is a seedling crown rust resistance gene that has been widely deployed in North American oat breeding. DNA markers are desired to accurately predict the specific Pc genes present in breeding germplasm. The objectives of the study were as follows: (i) to map Pc39 in two recombinant inbred line (RIL) populations (AC Assiniboia/MN841801 and AC Medallion/MN841801) and (ii) to identify single nucleotide polymorphism (SNP) markers for postulation of Pc39 in oat germplasm. Pc39 was mapped to a linkage group consisting of 16 SNP markers, which placed the gene on linkage group Mrg11 (chromosome 1C) of the oat consensus map. Pc39 cosegregated with SNP marker GMI_ES01_c12570_390 in the AC Assiniboia/MN841801 RIL population and was flanked by the SNP markers avgbs_126086.1.41 and GMI_ES15_c276_702, with genetic distances of 1.7 and 0.3 cM, respectively. In the AC Medallion/MN841801 RIL population, similar results were obtained but the genetic distances of the flanking markers were 0.4 and 0.4 cM, respectively. Kompetitive Allele-Specific PCR assays were successfully designed for Pc39-linked SNP loci. Two SNP loci defined a haplotype that accurately predicted Pc39 status in a diverse panel of oat germplasm and will be useful for marker-assisted selection in oat breeding.

Association of a region of bovine chromosome 1 (BTA1) with age at puberty in Angus bulls

2016 ◽  
Vol 28 (10) ◽  
pp. 1618 ◽  
Author(s):  
María E. Fernández ◽  
Alberto Prando ◽  
Andrés Rogberg-Muñoz ◽  
Pilar Peral-García ◽  
Andrés Baldo ◽  
...  
Keyword(s):  
Integration Site ◽  
Bovine Genome ◽  
Chromosome 1 ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Complex Locus ◽  
Age At Puberty ◽  
Virus Integration ◽  
Ecotropic Virus ◽  
Larger Sample

Age at puberty is an important component of reproductive performance in cattle, so it is important to identify genes that contribute to the regulation of the onset of puberty and polymorphisms that explain differences between bulls. In a previous study, we found putative associations between age at puberty in Angus bulls and single-nucleotide polymorphisms (SNPs) in Chromosomes 1 and X. In the present work we aimed to confirm these findings in a larger sample of Angus bulls (n = 276). Four SNPs located in these regions were genotyped using SEQUENOM technology and the genotypes obtained were tested for association with age at puberty. The results showed that SNPs rs135953349 and rs110604205 on BTA1 were still significantly associated with age of puberty estimated at progressive sperm motility of 10% (P < 0.05). The association previously found on Chromosome X could not be confirmed. Analysis of the bovine genome revealed that the associated region (99.17–99.99 Mb) contained four predicted loci: myelodysplasia syndrome 1 (MDS1) and ecotropic virus integration site 1 (EVI1) complex locus (MECOM), eGF-like and EMI domain-containing 1 pseudogene-like (LOC100337483), microRNA mir-551b (MIR551B) and mCG140927-like (LOC100139843). The results obtained could contribute to the understanding of puberty regulation and could be useful for further identification and annotation of gene function in the context of reproduction.

scholarly journals Genetic linkage map and mapping of the locus of biological nitrogen fixation inefficiency in cowpea

2019 ◽  
Vol 41 ◽  
pp. e42603
Author(s):  
Sirando Lima Seido ◽  
Carlos Antonio Fernandes Santos
Keyword(s):  
Linkage Group ◽  
Average Distance ◽  
Strong Association ◽  
Snp Markers ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
F2 Population ◽  
Reference Map ◽  
Additional Reference ◽  
Biological Nitrogen

The objectives of the present study were to construct a cowpea genetic map using the F2 population resulting from the cross IC-1 x BRS Marataoã, based on single nucleotide polymorphism (SNP) markers, and to map the cpi gene, with additional reference to introgression with the consensus map of species, aiming to identify markers for assisted selection to develop more efficient cultivars for BNF. The parents and 89 F2 plants were genotyped with 51,128 SNP markers, of which 910 polymorphic markers were used to construct the map. The results revealed 11 linkage groups, with an average of 82 markers per chromosome and average distance of 1.26 cM between markers. Recombination analysis of the SNPs indicated that markers 2_12850 and 2_00188, located in linkage group 11, flanked the cpi gene at a distance of 6.7 cM and 5.64 cM, respectively. The introgression of linkage group 11 with the cowpea reference map revealed short distances (from zero to 0.6 cM) for these markers, indicating a strong association with the cpi gene. The constructed map and cpi mapping provide basic information that can assist the genetic breeding of more efficient cowpea plants for BNF by marker-assisted selection.

Rps 8 Maps to a Resistance Gene Rich Region on Soybean Molecular Linkage Group F

Crop Science ◽  
2006 ◽  
Vol 46 (1) ◽  
pp. 168-173 ◽  
Author(s):  
Stuart G. Gordon ◽  
Steven K. St. Martin ◽  
Anne E. Dorrance
Keyword(s):  
Linkage Group ◽  
Resistance Gene ◽  
Rich Region ◽  
Molecular Linkage Group ◽  
Gene Rich Region
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