BRAVO target sequence capture V3

Steuernagel, Burkhard; Woodhouse, Shannon; He, Zhesi; Hepworth, Jo; Tidy, Alison C; Siles-Suarez, Laura; Havlikova, Lenka; Calderwood, Alex; Woolfenden, Hugh; Chinoy, Catherine; Bilham, Lorelei; Corke, Fiona; Graham, Neil; Doonan, John; Teakle, Graham R.; Eastmond, Peter J.; Morris, Richard; Wilson, Zoë L.; Kurup, Smita; Penfield, Steven; Bancroft, Ian; Irwin, Judith A.; Wells, Rachel; Østergaard, Lars

doi:10.5281/zenodo.4473283

Cited by 1 publication

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“…Thus, few population scale studies have attempted to measure variation in these traits. This generates an important gap in our knowledge given their importance to yield (Kirkegaard et al, 2018;Siles et al, 2021). The yield of winter OSR in the UK is reduced by warmth in early winter (Brown et al, 2019;O'Neill et al, 2019) and this can only partly be explained by a delayed floral transition (Lu et al, 2022).…”

Section: Discussionmentioning

confidence: 99%

“…However, the greater duration of flowering in response to 10°C vernalization in spring OSR and swedes is such that total flowering over this period (F07; Figure 4D) is very similar between treatments, while semiwinters flower more after 10°C. As flowering was not completely finished at the termination of the experiment, trait F07 (total flower area to peak) is the most likely trait of those investigated here to correspond to yield for the OSR varieties (Kirkegaard et al, 2018;Siles et al, 2021). While 5°C vernalization generally promotes flower production in winter crops as expected, it does not much affect the total flower area for springs, while the 'facultative responding' semiwinters show a marked improvement in response to warmer vernalization temperaturesand the highest flower area of all on average.…”

Section: Figure 1 Workflow For Segmentation Of Images For Data Analysismentioning

confidence: 95%

“…In order to identify specific DNA variants that could be causing phenotypic effects, we generated high-quality sequence information for a subset of a priori candidate genes by exome capture, and interrogated existing sequences produced by others (Chalhoub et al, 2014;Schiessl et al, 2017;Sun et al, 2017;Lee et al, 2020;Song et al, 2020;Steuernagel et al, 2021; Table 2). These candidates included two genes underneath GWAS peaks; BnaAGL24.A01 (BnaA01g13920D, G03 at 10v5) and BnaAGL15.A03 (BnaA03g04490D, R11 at 10°C).…”

Section: Gwas Identifies Candidate Chromosomal Regionsmentioning

confidence: 99%

“…We used a bait library targeting a priori flowering time genes for sequence enrichment. The bait library is available at https://doi.org/10.5281/zenodo.4473283 (Steuernagel et al, 2021). Bait synthesis and target enrichment was performed by Arbor Biosciences (https://arborbiosci.com/).…”

Section: Targeted Sequence Capturementioning

confidence: 99%

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Integrated Phenomics and Genomics reveals genetic loci associated with inflorescence growth inBrassica napus

Williams

Hepworth

Nichols

et al. 2023

Preprint

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A fundamental challenge to the production of climate-resilient crops is how to measure dynamic yield-relevant responses to the environment, such as growth rate, at a scale which informs mechanistic understanding and accelerates breeding. The timing, duration and architectural characteristics of inflorescence growth are crucial for optimising crop productivity and have been targets of selection during domestication. We report a robust and versatile procedure for computationally assessing environmentally-responsive flowering dynamics. In the oilseed crop, Brassica napus, there is wide variation in flowering response to winter cold (vernalization). We subjected a diverse set of B. napus accessions to different vernalization temperatures and monitored shoot responses using automated image acquisition. We developed methods to computationally infer multiple aspects of flowering from this dynamic data, enabling characterisation of speed, duration and peaks of inflorescence development across different crop types. We input these multiple traits to genome- and transcriptome-wide association studies, and identified potentially causative variation in a priori phenology genes (FLOWERING LOCUS C, EARLY FLOWERING3) for known traits and in uncharacterised genes for computed traits. These results could be used in marker assisted breeding to design new ideotypes for improved yield and better adaptation to changing climatic conditions.

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Section: Discussionmentioning

confidence: 99%

Section: Figure 1 Workflow For Segmentation Of Images For Data Analysismentioning

confidence: 95%