A consensus map of chromosome 6R in rye (Secale cereale L.)

Abstract

Abbreviations used: AFLP -amplified fragment length polymorphism; cMcentimorgan; ISSR -inter-simple sequence repeat; LOD -logarithm of odds; QTLquantitative trait locus; RAPD -random amplified polymorphic DNA; RFLP -restriction fragment length polymorphism; SCAR -sequence-characterized amplified region; SSRsimple sequence repeat; STS -sequence-tagged site Abstract: Four F 2 mapping populations derived from crosses between rye inbred lines DS2×RXL10, 541×Ot1-3, S120×S76 and 544×Ot0-20 were used to develop a consensus map of chromosome 6R. Thirteen marker loci that were polymorphic in more than one mapping population constituted the basis for the alignment of the four maps using the JoinMap v. 3.0 software package. The consensus map consists of 104 molecular marker loci including RFLPs, RAPDs, AFLPs, SSRs, ISSRs, SCARs, STSs and isozymes. The average distance between the marker loci is 1.3 cM, and the total map length is 135.5 cM. This consensus map may be used as a source of molecular markers for the rapid development of new maps of chromosome 6R in any mapping population.

The application of high-density genetic maps of rye for the detection of QTLs controlling morphological traits

“…Recently, two types of research activities have had a strong impact on the mapping progress in rye. The first was the application of new software allowing joint exploration of data from different mapping populations and the construction of integrated/consensus maps of chromosomes (Gustafson et al 2009 ; Stojałowski et al 2009 ). The second was the development of a new molecular marker system for rye based on a very efficient method of polymorphism detection, i.e.…”

Genetic mapping of the ScHd1 gene in rye and an assessment of its relationship with earliness per se and plant morphology

“…TaHd1 was located on the long arm of chromosomes belonging to group 6 in hexaploid wheat (Nemoto et al 2003 ). A rye gene was also mapped to the pericentromeric region of chromosome 6, with a genetic distance of 5cM, above the RAPD – APR6.41 marker localised to the short arm on the integrated 6R map (Stojałowski et al 2009 ). In the light of new data concerning rearrangements of the rye genome in comparison to wheat (Li et al 2013 ), the short arm 6R corresponds not only to the short arm of wheat chromosome 6, which was previously postulated (Devos et al 1993 ), but also includes fragment of the long arm in the centromeric region.…”

The application of GBS markers for extending the dense genetic map of rye (Secale cereale L.) and the localization of the Rfc1 gene restoring male fertility in plants with the C source of sterility-inducing cytoplasm

“…The first genetic map of all seven rye chromosomes was established more than 20 years ago, mainly based on restriction fragment length polymorphism (RFLP) markers (Devos et al 1993 ). Subsequently, different marker systems have been utilized for mapping rye chromosomes, for example, RAPD (Masojć et al 2001 ; Milczarski et al 2007 ; Stojałowski et al 2009 ), AFLP (Bednarek et al 2003 ), and SSR (Hackauf and Wehling 2003 ; Khlestkina et al 2004 ; Stojałowski et al 2009 ; Myśków et al 2010 ) markers, but only the application of DArT—the first available high-throughput method of genotyping S. cereale —created the possibility to construct high-density genetic maps of this species (Bolibok-Brągoszewska et al 2009 ; Milczarski et al 2011 ). Sequence analyses of RNA generated by Haseneyer et al ( 2011 ) provided the opportunity for the development of the next high-throughput marker technology: the SNP arrays successfully used for the study of the structure of the rye genome as well as for genetic mapping (Martis et al 2013 ).…”

“…Within both studied mapping populations, three methods were applied for the generation of molecular markers: Polymerase chain reaction (PCR): two types of sequence-specific markers were used: sequence characterized amplified regions (SCARs) and simple sequence repeats (SSRs). Analyses of these markers within the RIL-S population had previously been used for the construction of a consensus genetic map, so all important methodological information can be found in Milczarski et al ( 2011 ) and Stojałowski et al ( 2009 ). DArT: the microarray-based analyses were performed as a commercial service offered by Diversity Arrays Technology Pty Ltd. (Canberra, Australia), and the methodological procedure for the development of DArT markers in rye is described by Bolibok-Brągoszewska et al ( 2009 ).…”

“…Polymerase chain reaction (PCR): two types of sequence-specific markers were used: sequence characterized amplified regions (SCARs) and simple sequence repeats (SSRs). Analyses of these markers within the RIL-S population had previously been used for the construction of a consensus genetic map, so all important methodological information can be found in Milczarski et al ( 2011 ) and Stojałowski et al ( 2009 ).…”