DArT markers tightly linked with the Rfc1 gene controlling restoration of male fertility in the CMS-C system in cultivated rye (Secale cereale L.)

Stojałowski, Stefan; Milczarski, Paweł; Hanek, Monika; Bolibok-Brągoszewska, Hanna; Myśków, Beata; Kilian, Andrzej; Rakoczy-Trojanowska, Monika

doi:10.1007/s13353-011-0049-x

Cited by 26 publications

(28 citation statements)

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“…The first high-throughput genotyping technology was established for rye in 2009 with the development of a 1520-clone DArT genotyping panel (Bolibok-Bragoszewska et al, 2009). Since then, it was successfully applied for high density genetic map construction, both in rye and triticale (Bolibok-Bragoszewska et al, 2009; Milczarski et al, 2011; Tyrka et al, 2011, 2015), genome-wide germplasm characterization (Bolibok-Bragoszewska et al, 2014), QTL/gene mapping (Stojałowski et al, 2011; Miedaner et al, 2012; Myśków et al, 2012; Milczarski et al, 2016), and genomic selection (Wang et al, 2014, 2015; Schulthess et al, 2015). Following transcriptome sequencing a Rye5K SNP genotyping panel was developed and used for construction of high density transcript map (Haseneyer et al, 2011; Martis et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

DArT Markers Effectively Target Gene Space in the Rye Genome

et al. 2016

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Large genome size and complexity hamper considerably the genomics research in relevant species. Rye (Secale cereale L.) has one of the largest genomes among cereal crops and repetitive sequences account for over 90% of its length. Diversity Arrays Technology is a high-throughput genotyping method, in which a preferential sampling of gene-rich regions is achieved through the use of methylation sensitive restriction enzymes. We obtained sequences of 6,177 rye DArT markers and following a redundancy analysis assembled them into 3,737 non-redundant sequences, which were then used in homology searches against five Pooideae sequence sets. In total 515 DArT sequences could be incorporated into publicly available rye genome zippers providing a starting point for the integration of DArT- and transcript-based genomics resources in rye. Using Blast2Go pipeline we attributed putative gene functions to 1101 (29.4%) of the non-redundant DArT marker sequences, including 132 sequences with putative disease resistance-related functions, which were found to be preferentially located in the 4RL and 6RL chromosomes. Comparative analysis based on the DArT sequences revealed obvious inconsistencies between two recently published high density consensus maps of rye. Furthermore we demonstrated that DArT marker sequences can be a source of SSR polymorphisms. Obtained data demonstrate that DArT markers effectively target gene space in the large, complex, and repetitive rye genome. Through the annotation of putative gene functions and the alignment of DArT sequences relative to reference genomes we obtained information, that will complement the results of the studies, where DArT genotyping was deployed, by simplifying the gene ontology and microcolinearity based identification of candidate genes.

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Section: Introductionmentioning

confidence: 99%

DArT Markers Effectively Target Gene Space in the Rye Genome

et al. 2016

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“…In successful hybrid breeding, one of the most important factors is the careful choice of parental components displaying a high combining ability strictly associated with their genetic distance (GD). It was demonstrated that molecular markers can also be useful for identification of rye cytoplasmic male sterility forms and Rfc genes (Stojałowski et al, 2011). The relationship between the heterosis effect of particular traits and the GD of parental forms has been studied in wheat (Dreisigacker et al, 2005;Krystkowiak et al, 2009;Zhao et al, 2013), barley (Hordeum vulgare L.; Zhong et al, 2009), maize (Zea mays L.; Riedelsheimer et al, 2012;Windhausen et al, 2012), and rice (Oryza sativa L.; Xu et al, 2014).…”

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DArTseq Genotyping Reveals High Genetic Diversity of Polish Rye Inbred Lines

2017

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The assessment of genetic diversity in available germplasm is crucial for improvement. In rye (Secale cereale L.) breeding programs, the knowledge of genetic variation on molecular level could be helpful in selection of appropriate components for crossing. The aim of this study was to assess genetic diversity of 150 Polish rye inbred lines with the use of diversity arrays technology sequencing (DArTseq) genotyping and the following bioinformatic tools: Bayesian clustering, principal coordinates analysis, and neighbor‐joining clustering. Altogether, 14,892 silicoDArT and 5031 single‐nucleotide polymorphism (SNP) markers were analyzed. The average polymorphic information content values calculated for both marker types were 0.22 and 0.37 for silicoDArTs and SNPs, respectively. The presented results point to a relatively high degree of genetic diversity within Polish rye breeding material, with a mean genetic similarity of 0.15 and heterozygosity from 0.01 to 0.39. These results can be applied in rye breeding, especially for selecting parental components for cross hybridization, as well as exploiting the natural genetic variation in existing resources.

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“…, Stojałowski et al. ). This could point to a single origin of the Rf mutation in Southwest Asia, the region where rye evolved.…”

Section: Discussionmentioning

confidence: 99%

“…, Stojałowski et al. ) was linked to the same marker loci as the three Rfp genes mentioned. The Rfp gene from IRAN IX has been extensively used in practical breeding with the cultivar ‘Pollino’ (listed in 2005) being the first of a series of hybrids with superior male‐fertility restoration.…”

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Correlated effects of exotic pollen‐fertility restorer genes on agronomic and quality traits of hybrid rye

et al. 2017

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In CMS (cytoplasmic male sterility)‐based hybrid rye (Secale cereale L.) breeding, effective pollen‐fertility restoration is an essential prerequisite for achieving maximum grain yield on the one hand and for minimizing ergot (Claviceps purpurea) infestation on the other. Restorer genes for the CMS‐inducing ‘Pampa’ cytoplasm derived from landraces collected in Iran and Argentina are used by breeders for achieving this goal. Here, restorer genes from four germplasm sources (‘Altevogt 14160’, ‘IRAN III’, ‘Trenelense’ and ‘Pico Gentario’) were analysed by producing three‐way cross hybrids between an elite CMS single cross and pollinators with and without a given restorer gene. Materials were evaluated on large drilled plots for restorer index (RI), grain yield, plant height and other traits in six environments. In experiment 1, a restorer gene from ‘Altevogt 14160’ was used. Seven pairs of marker‐selected carrier and non‐carrier backcross lines served as pollinators. In experiment 2, the pollinators were 17 backcross line pairs from the other three germplasm sources. These lines were grouped as high (RI > 67%) and low restorers (RI < 30%), respectively, using testcrosses with a highly diagnostic CMS tester. Hybrids carrying an exotic restorer gene suffered from a significant grain yield reduction by 4.4% and 9.4% and were 9.3 and 4.8 cm taller in experiments 1 and 2, respectively. Thousand‐kernel weight was reduced, whereas quality traits were only slightly affected. For all traits, significant genetic variance existed among the testcrosses to the presence vs. absence of a given exotic restorer gene. This offers a chance for the breeder to reduce or ultimately overcome the presently observed performance reductions brought about by exotic restorer genes.

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DArT markers tightly linked with the Rfc1 gene controlling restoration of male fertility in the CMS-C system in cultivated rye (Secale cereale L.)

Cited by 26 publications

References 11 publications

DArT Markers Effectively Target Gene Space in the Rye Genome

DArT Markers Effectively Target Gene Space in the Rye Genome

DArTseq Genotyping Reveals High Genetic Diversity of Polish Rye Inbred Lines

Correlated effects of exotic pollen‐fertility restorer genes on agronomic and quality traits of hybrid rye

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