Marker-assisted selection for low phytic acid (lpa1-1) with single nucleotide polymorphism marker and amplified fragment length polymorphisms for background selection in a maize backcross breeding programme

The analysis of F2 progeny and derived F3 families of Lactuca sativa segregating for resistance to corky root rot caused by Rhizomonas suberifaciens permitted the identification of restriction fragment length polymorphism (RFLP) and single nucleotide polymorphism (SNP) markers linked to the recessive resistance gene cor. PCR-based markers were identified by bulked segregant analysis (BSA). Allele-specific primers were generally designed with the 3´ terminal base coinciding with an SNP, matching one of the alleles and mismatching the other, and with an additional subterminal 3´ base mismatching both alleles. Codominant, robust, and inexpensive molecular markers were obtained that used standardized PCR conditions. Some of the markers could be analyzed in multiple Lactuca mapping populations that did not segregate for disease resistance allowing the cor locus to be located on several maps. The consistent low density of markers around cor in these maps suggests that cor may be in an area with an elevated rate of recombination. Evaluation of these markers in a large sample of cultivars and landraces identified pairs of flanking polymorphic markers that can be used for marker-assisted selection of corky root resistance.Key words: single nucleotide polymorphism (SNP), sequence characterized amplified region (SCAR), marker-assisted selection (MAS), genetic map, resistance gene.

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Generation of SNP markers for short straw in oat (Avena sativa L.)

Genome ◽

10.1139/g05-100 ◽

2006 ◽

Vol 49 (3) ◽

pp. 282-287 ◽

Cited By ~ 19

Author(s):

Pirjo Tanhuanpää ◽

Ruslan Kalendar ◽

Jaana Laurila ◽

Alan H Schulman ◽

Outi Manninen ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Avena Sativa ◽

Marker Assisted Selection ◽

Rapd Markers ◽

Bulked Segregant Analysis ◽

Random Amplified Polymorphic Dna ◽

Snp Markers ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Dwarfing Gene

Short straw is a desired trait in oat germplasm (Avena sativa L.). Marker-assisted selection, a key tool for achieving this objective, is limited by the presence and number of available markers. Here, we have attempted to develop markers sufficiently linked to a gene specifying short straw so that marker-assisted selection could be applied. Bulked-segregant analysis was used to identify anonymous PCR-based markers associated with the dwarfing gene Dw6 in an F2 population from the cross between A. sativa 'Aslak' and A. sativa 'Kontant'. One random amplified polymorphic DNA (RAPD) and 1 retrotransposon-microsatellite amplified polymorphism (REMAP) marker were found to be associated with height. These were converted into codominant single-nucleotide polymorphism (SNP) markers. The SNP–REMAP and the SNP–RAPD markers were located 5.2 and 12.6 cM from Dw6, respectively. They can be used in future efforts both to enhance oat germplasm by application of molecular markers and to determine the nature of the gene through positional cloning.Key words: Avena sativa, short straw, marker-assisted selection, RAPD, REMAP, SNP.

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