First insights into the genotype–phenotype map of phenotypic stability in rye

Wang, Yu; Mette, Michael Florian; Miedaner, Thomas; Wilde, Peer; Reif, Jochen C.; Zhao, Yusheng

doi:10.1093/jxb/erv145

Cited by 24 publications

(21 citation statements)

References 53 publications

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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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“…Recent studies concluded that genomic prediction for yield stability in rye 9 and wheat 10 could be effective. However, to fully exploit plasticity it is important to understand its genetic architecture.…”

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confidence: 99%

“…Third, the structural (or regulatory) gene model states that plastic responses are caused by the regulation of mean phenotype genes by genes that integrate environmental stimuli 14,15 . Numerous studies involving modest numbers of genotypes have found evidence for both the allelic sensitivity and structural gene models to varying degrees in various organisms and phenotypes 9,16–20 .…”

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confidence: 99%

Distinct genetic architectures for phenotype means and plasticities in Zea mays

et al. 2017

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Phenotypic plasticity describes the phenotypic variation of a trait when a genotype is exposed to different environments. Understanding the genetic control of phenotypic plasticity in crops such as maize is of paramount importance for maintaining and increasing yields in a world experiencing climate change. Here, we report the results of genome-wide association analyses of multiple phenotypes and two measures of phenotypic plasticity in the maize nested association mapping (US-NAM) population grown in multiple environments and genotyped with ~2.5 million single nucleotide polymorphisms (SNPs). We show that across all traits the candidate genes for mean phenotype values and plasticity measures form structurally and functionally distinct groups. Such independent genetic control suggests that breeders will be able to select semi-independently for mean phenotype values and plasticity, thereby generating varieties with both high mean phenotype values and levels of plasticity that are appropriate for the target performance environments.

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“…Hybrid rye breeding started in Germany as early as in the 1970s, and the first hybrid cultivar was released in 1984 (Geiger and Miedaner, 1999). Recently, hybrid breeding programs have been started in Russia, Poland, Belarus, and Sweden (Tomerius et al, 2008;Wang et al, 2015). In multilocal testing trials, rye hybrids yielded ~10% higher than standard population cultivars; they are also shorter, have better resistance to preharvest sprouting, and demonstrate unchanged lodging resistance (Schlegel, 2006).…”

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confidence: 99%

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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First insights into the genotype–phenotype map of phenotypic stability in rye

Abstract: HighlightYield stability in rye is controlled by many QTLs with small effects. This is in contrast to phenotypic stability of several quality traits, which are influenced by some large-effect QTLs.

Cited by 24 publications

References 53 publications

DArT Markers Effectively Target Gene Space in the Rye Genome

DArT Markers Effectively Target Gene Space in the Rye Genome

Distinct genetic architectures for phenotype means and plasticities in Zea mays

DArTseq Genotyping Reveals High Genetic Diversity of Polish Rye Inbred Lines

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