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Historical phenotypic data from seven decades of seed regeneration in a wheat ex situ collection.

ABSTRACT: Genebanks are valuable sources of genetic diversity, which can help to cope with future problems of global food security caused by a continuously growing population, stagnating yields and climate change. However, the scarcity of phenotypic and genotypic characterization of genebank accessions severely restricts their use in plant breeding. To warrant the seed integrity of individual accessions during periodical regeneration cycles in the field phenotypic characterizations are performed. This study provides non-orthogonal historical data of 12,754 spring and winter wheat accessions characterized for flowering time, plant height, and thousand grain weight during 70 years of seed regeneration at the German genebank. Supported by historical weather observations outliers were removed following a previously described quality assessment pipeline. In this way, ready-to-use processed phenotypic data across regeneration years were generated and further validated. We encourage international and national genebanks to increase their efforts to transform into bio-digital resource centers. A first important step could consist in unlocking their historical data treasures that allows an educated choice of accessions by scientists and breeders.

SUBMITTER: Philipp N

PROVIDER: S-EPMC6662709 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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Historical phenotypic data from seven decades of seed regeneration in a wheat ex situ collection.

Philipp Norman N Weise Stephan S Oppermann Markus M Börner Andreas A Keilwagen Jens J Kilian Benjamin B Arend Daniel D Zhao Yusheng Y Graner Andreas A Reif Jochen C JC Schulthess Albert W AW

Scientific data 20190729 1

Genebanks are valuable sources of genetic diversity, which can help to cope with future problems of global food security caused by a continuously growing population, stagnating yields and climate change. However, the scarcity of phenotypic and genotypic characterization of genebank accessions severely restricts their use in plant breeding. To warrant the seed integrity of individual accessions during periodical regeneration cycles in the field phenotypic characterizations are performed. This stu ...[more]

PMID: 31358775

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Project description:Genebanks are a rich source of genetic variation. Most of this variation is absent in breeding programs but may be useful for further crop plant improvement. However, the lack of phenotypic information forms a major obstacle for the educated choice of genebank accessions for research and breeding. A promising approach to fill this information gap is to exploit historical information gathered routinely during seed regeneration cycles. Still, this data is characterized by a high non-orthogonality hampering their analysis. By examining historical data records for flowering time, plant height, and thousand grain weight collected during 70 years of regeneration of 6,207 winter wheat (Triticum aestivum L.) accessions at the German Federal ex situ Genebank, we aimed to elaborate a strategy to analyze and validate non-orthogonal historical data in order to charge genebank information platforms with high quality ready-to-use phenotypic information. First, a three-step quality control assessment considering the plausibility of trait values and a standard as well as a weather parameter index based outlier detection was implemented, resulting in heritability estimates above 0.90 for all three traits. Then, the data was analyzed by estimating best linear unbiased estimations (BLUEs) applying a linear mixed-model approach. An in silico resampling study mimicking different missing data patterns revealed that accessions should be regenerated in a random fashion and not blocked by origin or acquisition date in order to minimize estimation biases in historical data sets. Validation data was obtained from multi-environmental orthogonal field trials considering a random subsample of 3,083 accessions. Correlations above 0.84 between BLUEs estimated for historical data and validation trials outperformed previous approaches and confirmed the robustness of our strategy as well as the high quality of the historical data. The results indicate that the IPK winter wheat collection reveals an extraordinary high phenotypic diversity compared to other collections. The quality checked ready-to-use phenotypic information resulting from this study is the first brick to extend traditional, conservation driven genebanks into bio-digital resource centers.

Project description:BACKGROUND AND AIMS:The germination test currently represents the most used method to assess seed viability in germplasm banks, despite the difficulties caused by the occurrence of seed dormancy. Furthermore, seed longevity can vary considerably across species and populations from different environments, and studies related to the eco-physiological processes underlying such variations are still limited in their depth. The aim of the present work was the identification of reliable molecular markers that might help in monitoring seed deterioration. METHODS:Dry seeds were subjected to artificial ageing and collected at different time points for molecular/biochemical analyses. DNA damage was measured using the RAPD (random amplified polymorphic DNA) approach while the seed antioxidant profile was obtained using both the DPPH (1,1-diphenyl, 2-picrylhydrazyl) assay and the Folin-Ciocalteu reagent method. Electron paramagnetic resonance (EPR) provided profiles of free radicals. Quantitative real-time polymerase chain reaction (QRT-PCR) was used to assess the expression profiles of the antioxidant genes MT2 (type 2 metallothionein) and SOD (superoxide dismutase). A modified QRT-PCR protocol was used to determine telomere length. KEY RESULTS:The RAPD profiles highlighted different capacities of the two Silene species to overcome DNA damage induced by artificial ageing. The antioxidant profiles of dry and rehydrated seeds revealed that the high-altitude taxon Silene acaulis was characterized by a lower antioxidant specific activity. Significant upregulation of the MT2 and SOD genes was observed only in the rehydrated seeds of the low-altitude species. Rehydration resulted in telomere lengthening in both Silene species. CONCLUSIONS:Different seed viability markers have been selected for plant species showing inherent variation of seed longevity. RAPD analysis, quantification of redox activity of non-enzymatic antioxidant compounds and gene expression profiling provide deeper insights to study seed viability during storage. Telomere lengthening is a promising tool to discriminate between short- and long-lived species.

Dataset Information

Historical phenotypic data from seven decades of seed regeneration in a wheat ex situ collection.

Publications

Historical phenotypic data from seven decades of seed regeneration in a wheat ex situ collection.

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