Comparative mapping of DNA sequences in rye (Secale cereale L.) in relation to the rice genome

Abstract

The rice genome has proven a valuable resource for comparative approaches to address individual genomic regions in Triticeae species at the molecular level. To exploit this resource for rye genetics and breeding, an inventory was made of EST-derived markers with known genomic positions in rye, which were related with those in rice. As a first inventory set, 92 EST-SSR markers were mapped which had been drawn from a non-redundant rye EST collection representing 5,423 unigenes and 2.2 Mb of DNA. Using a BC1 mapping population which involved an exotic rye accession as donor parent, these EST-SSR markers were arranged in a linkage map together with 25 genomic SSR markers as well as 131 AFLP and four STS markers. This map comprises seven linkage groups corresponding to the seven rye chromosomes and covers 724 cM of the rye genome. For comparative studies, additional inventory sets of EST-based markers were included which originated from the rye-mapping data published by other authors. Altogether, 502 EST-based markers with known chromosomal localizations in rye were used for BlastN search and 334 of them could be in silico mapped in the rice genome. Additionally, 14 markers were included which lacked sequence information but had been genetically mapped in rice. Based on the 348 markers, each of the seven rye chromosomes could be aligned with distinct portions of the rice genome, providing improved insight into the status of the rye-rice genome relationships. Furthermore, the aligned markers provide genomic anchor points between rye and rice, enabling the identification of conserved ortholog set markers for rye. Perspectives of rice as a model for genome analysis in rye are discussed.

Reticulate Evolution of the Rye Genome

“…Furthermore, 1385 gene-based SSRs were datamined and evaluated for their use as SSR markers from previously published rye EST resources (Haseneyer et al, 2011) by applying the software tool Misa (Thiel et al, 2003). In addition, 45 more markers (SSR and STS) previously mapped in different rye populations (Hackauf et al, 2009(Hackauf et al, , 2012 provided anchoring information to other published genetic maps of rye and to assign the obtained L2039-NxDH-linkage groups to the seven rye chromosomes and for orienting chromosome maps. The marker TC427 (ALDH2b) was derived from a rye mitochondrial aldehyde dehydrogenase mRNA sequence (GenBank accession number AB084896.1) and assayed using the primer pair 59-TGTCCCTGGTTGAAAAACAG-39 and 59-TGATGTATGGCTGGAAAGTTG-39 as previously described (Hackauf and Wehling, 2005).…”

“…For rye, existing genetic maps comprised limited numbers of gene-based markers (Gustafson et al, 2009;Hackauf et al, 2009) or were composed of anonymous genomic Diversity Arrays Technology markers (Milczarski et al, 2011). Recently, a large data set of gene-based single nucleotide polymorphisms (SNPs) could be data-mined from RNA sequencing data of rye, providing the basis for developing a high-throughput SNP genotyping assay comprising 5234 markers (Haseneyer et al, 2011).…”

The Perennial Ryegrass GenomeZipper: Targeted Use of Genome Resources for Comparative Grass Genomics

“…An excellent example of this is the rice genome, which has proven to be a valuable resource for comparative studies in many grass species at both the gene and genome levels (Sorrells et al, 2003;Stein et al, 2007;Hackauf et al, 2009;Tamura et al, 2009). More recently, the genome sequence of Brachypodium, a member of the Pooideae subfamily, has become available and provides great promise to become a powerful model system to study the genomes of economically more important pooid grasses, including wheat, barley, oat (Avena sativa), rye (Secale cereale), as well as forage and turf grass species (International Brachypodium Initiative, 2010).…”

Hybrid breeding boosted molecular genetics in rye

“…Первые генетические карты включали ограниченное число генных маркеров (Gustafson et al, 2009;Hackauf et al, 2009). С помощью Gustafson et al, 2009;Hackauf et al, 2009Hackauf et al, ). С помощью et al, 2009Hackauf et al, 2009).…”

“…С помощью Gustafson et al, 2009;Hackauf et al, 2009Hackauf et al, ). С помощью et al, 2009Hackauf et al, 2009). С помощью RNAseq-анализа удалось выявить большой набор свя-занных с генами SNP-маркеров, которые стали основой для развития высокопроизводительного генотипирования ржи с использованием 5 234 маркеров (Haseneyer et al, 2011;Milczarski et al, 2011).…”