Genotyping Lupinus angustifolius cultivars with SRAP molecular markers and degenerate primers

Abstract We examined 18 combinations of SRAP primers with resistance gene analog (RGA) and chitinase degenerate primers in order to determine their utility for genotyping L. angustifolius. Primer pairs ResAn51-f/Me8, p-loop/Em5, TM/Me8, Chit3-r/Em5 were the most effective for detection of genetic polymorphism of different narrow-leaved lupine varieties.

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Development of resistance gene analog polymorphism markers for the Yr9 gene resistance to wheat stripe rust

Genome ◽

10.1139/g01-028 ◽

2001 ◽

Vol 44 (4) ◽

pp. 509-516 ◽

Cited By ~ 34

Author(s):

Z X Shi ◽

X M Chen ◽

R F Line ◽

H Leung ◽

C R Wellings

Keyword(s):

Molecular Markers ◽

Resistance Gene ◽

Stripe Rust ◽

Puccinia Striiformis ◽

Resistance Gene Analog ◽

Stripe Rust Resistance ◽

Isogenic Line ◽

Wheat Cultivars ◽

Development Of Resistance ◽

Rye Translocations

The Yr9 gene, which confers resistance to stripe rust caused by Puccinia striiformis f.sp. tritici (P. s. tritici) and originated from rye, is present in many wheat cultivars. To develop molecular markers for Yr9, a Yr9 near-isogenic line, near-isogenic lines with nine other Yr genes, and the recurrent wheat parent 'Avocet Susceptible' were evaluated for resistance in the seedling stage to North American P. s. tritici races under controlled temperature in the greenhouse. The resistance gene analog polymorphism (RGAP) technique was used to identify molecular markers for Yr9. The BC7:F2 and BC7:F3 progeny, which were developed by backcrossing the Yr9 donor wheat cultivar Clement with 'Avocet Susceptible', were evaluated for resistance to stripe rust races. Genomic DNA was extracted from 203 BC7:F2 plants and used for cosegregation analysis. Of 16 RGAP markers confirmed by cosegregation analysis, 4 were coincident with Yr9 and 12 were closely linked to Yr9 with a genetic distance ranging from 1 to 18 cM. Analyses of nulli-tetrasomic 'Chinese Spring' lines with the codominant RGAP marker Xwgp13 confirmed that the markers and Yr9 were located on chromosome 1B. Six wheat cultivars reported to have 1B/1R wheat-rye translocations and, presumably, Yr9, and two rye cultivars were inoculated with four races of P. s. tritici and tested with 9 of the 16 RGAP markers. Results of these tests indicate that 'Clement', 'Aurora', 'Lovrin 10', 'Lovrin 13', and 'Riebesel 47/51' have Yr9 and that 'Weique' does not have Yr9. The genetic information and molecular markers obtained from this study should be useful in cloning Yr9, in identifying germplasm that may have Yr9, and in using marker-assisted selection for combining Yr9 with other stripe rust resistance genes.Key words: molecular markers, Puccinia striiformis f.sp. tritici, resistance gene analog polymorphism, Triticum aestivum.

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Construction of a Linkage Map and Identification of Resistance Gene Analog Markers for Root-knot Nematodes in Wild Peach, Prunus kansuensis

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.136.3.190 ◽

2011 ◽

Vol 136 (3) ◽

pp. 190-197 ◽

Cited By ~ 11

Author(s):

Ke Cao ◽

Lirong Wang ◽

Gengrui Zhu ◽

Weichao Fang ◽

Chenwen Chen ◽

...

Keyword(s):

Linkage Map ◽

Resistance Gene ◽

Dna Sequences ◽

Open Reading Frames ◽

Resistance Gene Analog ◽

Root Knot Nematode ◽

Degenerate Primers ◽

Morphological Marker ◽

Backcross Population ◽

Peach Genome

The root-knot nematode (RKN) Meloidogyne incognita can cause severe crop loss in economically important Prunus species like peach (P. persica), almond (P. communis), plum (P. salicina), and apricot (P. armeniaca). Some peach rootstock, including Nemaguard (P. persica), Nemared (P. persica), and Myrobalan plum (P. cerasifera), display significant resistance to RKN. We present a genetic linkage map constructed by using simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) for a peach backcross population (190 individuals) of RKN-resistant ‘Honggengansutao’ (P. kansuensis) and susceptible ‘Bailey’ (P. persica). Degenerate primers designed from conserved motifs of known plant resistance gene (R) products were used to amplify genomic DNA sequences. Twenty-two resistance gene analog (RGA) sequences were selected from 48 RGAs with open-reading frames to design sequence-tagged site markers. The linkage map of ‘Honggengansutao’ is composed of 138 loci (30 SSRs, 102 SRAPs, five RGAs, and one morphological marker for RKN resistance) assigned to eight linkage groups. The map covers 616 cM of the peach genome with an average marker spacing of 4.9 cM. The five RGAs were mapped to Groups 2, 7, and 8. One gene (designated PkMi) involved in resistance to RKN was mapped to Group 2 (which also includes the known RKN-resistance RMia gene). BLASTN analysis mapped all RGAs to the peach genome sequence. The map constructed in the study will aid future rootstock breeding with marker-assisted selection to identify additional candidate RGA sequences.

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Genetic variation of populations of Pinus oocarpa revealed by resistance gene analog polymorphism (RGAP)

Genome ◽

10.1139/g03-023 ◽

2003 ◽

Vol 46 (3) ◽

pp. 404-410 ◽

Cited By ~ 7

Author(s):

V Díaz ◽

E Ferrer

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Molecular Markers ◽

Resistance Gene ◽

Population Diversity ◽

Resistance Gene Analog ◽

Resistance Gene Analogs ◽

Analysis Of Molecular Variance ◽

Molecular Variance ◽

Pinus Oocarpa

Primers based on conserved motifs of plant resistance genes were used to generate multilocus molecular markers referred to as resistance gene analog polymorphisms (RGAPs) in Pinus oocarpa subsp. oocarpa. Ten populations from three regions of Nicaragua were analyzed with 53 RGAPs. The aim of this study was to determine the levels of within- and between-population diversity with this kind of marker, and to compare estimates with previously obtained results based on RAPD and AFLP. All populations showed high levels of diversity. GST values and the analysis of molecular variance (AMOVA) revealed most variation to be within populations, although significant differences between populations and regions were also detected. This pattern of genetic diversity was similar to that obtained for RAPD and AFLP, which suggests that variation at RGAP loci as detected in this work is mostly influence by non-selective forces.Key words: resistance gene analogs, molecular markers, genetic diversity, population structure, Pinus oocarpa.

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Genetic Diversity Analysis Using Resistance Gene Analog-Based Markers to Support Morphological Characterization of Shallots

Jurnal AgroBiogen ◽

10.21082/jbio.v14n2.2018.p65-74 ◽

2018 ◽

Vol 14 (2) ◽

pp. 65

Author(s):

Lina Herlina ◽

Reflinur Reflinur ◽

Kristianto Nugroho ◽

Rerenstradika T. Terryana ◽

Sobir Sobir ◽

...

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Resistance Gene ◽

Molecular Breeding ◽

Morphological Characterization ◽

Resistance Gene Analog ◽

Phenotypic Variance ◽

Vegetable Crops ◽

Conserved Domain

<p>Shallot (Allium cepa var. aggregatum) is one of the most important vegetable crops grown in Indonesia. The limited knowledge available on the genetic diversity and the threat of plant disease have been major problems to maintain high shallot production in Indonesia. Development of molecular markers linked to disease resistance is required for molecular breeding activity in this crop. This study aimed to assess the genetic diversity at conserved domain of resistance gene analog (RGA) in a set of 36 Indonesian shallot genotypes to complement morphological characterization. Twelve morphological and fifteen molecular markers traits were investigated in an attempt to characterize and to discriminate the Indonesian shallots genotypes. Characterization at orphological level indicated that phenotypic variance was highest for total bulb weight (TWB, cv = 99.39%) and the least for the plant height (PH, cv = 28.16%). The correlation analysis between traits showed that TWB and number of bulb (NB), TWB and bulb weight per plant (WB), NB and WB, and WB and PH were positively correlated. Molecular analysis revealed a total of 1,512 alleles with an average of 1.946 alleles per locus. The Polymorphism Information Content (PIC) values ranged from 0.253 to 0.676 and six out of 15 RGA markers were highly informative with PIC values ≥0.50. Based on cluster analysis, the 36 Indonesian shallot genotypes were clearly discriminated into six major groups. These results revealed that the RGA-based markers could support the morphological characterization in evaluating the genetic diversity of shallots. </p>

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