Integrating genomic resources to present full gene and promoter capture probe sets for bread wheat

Gardiner, Laura-Jayne; Brabbs, Thomas; Akhunova, Alina; Jordan, Katherine W.; Budak, Hikmet; Richmond, Todd; Singh, Sukhwinder; Catchpole, Leah; Akhunov, Eduard; Hall, Anthony

doi:10.1101/363663

Cited by 3 publications

(13 citation statements)

References 22 publications

(13 reference statements)

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“…Many current capture arrays were designed based on the gene models from the 2014 genome, and as such are missing or mis‐representing various genes (Brinton et al ., ). Efforts are underway to develop new capture arrays based on the improved annotations (Gardiner et al ., 2018a).…”

Section: New Strategies Accelerate Gene Discovery In Wheatmentioning

confidence: 99%

Applying the latest advances in genomics and phenomics for trait discovery in polyploid wheat

Borrill

Harrington

Uauy

2018

Plant J

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Summary Improving traits in wheat has historically been challenging due to its large and polyploid genome, limited genetic diversity and in‐field phenotyping constraints. However, within recent years many of these barriers have been lowered. The availability of a chromosome‐level assembly of the wheat genome now facilitates a step‐change in wheat genetics and provides a common platform for resources, including variation data, gene expression data and genetic markers. The development of sequenced mutant populations and gene‐editing techniques now enables the rapid assessment of gene function in wheat directly. The ability to alter gene function in a targeted manner will unmask the effects of homoeolog redundancy and allow the hidden potential of this polyploid genome to be discovered. New techniques to identify and exploit the genetic diversity within wheat wild relatives now enable wheat breeders to take advantage of these additional sources of variation to address challenges facing food production. Finally, advances in phenomics have unlocked rapid screening of populations for many traits of interest both in greenhouses and in the field. Looking forwards, integrating diverse data types, including genomic, epigenetic and phenomics data, will take advantage of big data approaches including machine learning to understand trait biology in wheat in unprecedented detail.

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Section: New Strategies Accelerate Gene Discovery In Wheatmentioning

confidence: 99%

Applying the latest advances in genomics and phenomics for trait discovery in polyploid wheat

Borrill

Harrington

Uauy

2018

Plant J

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“…Researchers adopting these methods are clear on the importance and utility of the data generated (e.g., Johnson et al, 2019), but often face a difficult decision during the early stages of project design. They must typically choose between the use of a universal probe set (e.g., Buddenhagen et al, 2016;Johnson et al, 2019) developed to work across larger taxonomic scales (e.g., the angiosperms), or a narrower lineage-specific probe set designed for the group of interest (e.g., Mandel et al, 2014;Weitemier et al, 2014;Vatanparast et al, 2018;Gardiner et al, 2019;Koenen et al, 2020). When considering target enrichment options, the core exons of universal probe sets are perhaps viewed as best suited for higher-level phylogenetic problems, where their conserved nature tends to have greatest utility (but see Mitchell et al, 2017;Wanke et al, 2017).…”

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confidence: 99%

The best of both worlds: Combining lineage‐specific and universal bait sets in target‐enrichment hybridization reactions

et al. 2021

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Researchers adopting target-enrichment approaches often struggle with the decision of whether to use universal or lineage-specific probe sets. To circumvent this quandary, we investigate the efficacy of a simultaneous enrichment by combining universal probes and lineage-specific probes in a single hybridization reaction, to benefit from the qualities of both probe sets with little added cost or effort. METHODS AND RESULTS:Using 26 Brassicaceae libraries and standard enrichment protocols, we compare results from three independent data sets. A large average fraction of reads mapping to the Angiosperms353 (24-31%) and Brassicaceae (35-59%) targets resulted in a sizable reconstruction of loci for each target set (x̄ ≥ 70%).CONCLUSIONS: High levels of enrichment and locus reconstruction for the two target sets demonstrate that the sampling of genomic regions can be easily extended through the combination of probe sets in single enrichment reactions. We hope that these findings will facilitate the production of expanded data sets that answer individual research questions and simultaneously allow wider applications by the research community as a whole.

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“…The NimbleGen order numbers for the probe sets are as follows: Gene Capture 4 000 026 820; Promoter Capture v1, 4 000 030 160; and Promoter Capture v2, 4 000 032 530. All data are also available from the GigaScience GigaDB repository [40].…”

Section: Availability Of Supporting Data and Materialsmentioning

confidence: 99%

Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat

et al. 2019

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Background Whole-genome shotgun resequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome, making it difficult to unambiguously assign variation. Resequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits. Previous studies have implemented complementary DNA/exon or gene-based probe sets in which the promoter and intron sequence is largely missing alongside newly characterized genes from the recent improved reference sequences. Results We present and validate 2 gold standard capture probe sets for hexaploid bread wheat, a gene and a putative promoter capture, which are designed using recently developed genome sequence and annotation resources. The captures can be combined or used independently. We demonstrate that the capture probe sets effectively enrich the high-confidence genes and putative promoter regions that were identified in the genome alongside a large proportion of the low-confidence genes and associated promoters. Finally, we demonstrate successful sample multiplexing that allows generation of adequate sequence coverage for single-nucleotide polymorphism calling while significantly reducing cost per sample for gene and putative promoter capture. Conclusions We show that a capture design employing an “island strategy” can enable analysis of the large gene/putative promoter space of wheat with only 2 × 160 Mbp probe sets. Furthermore, these assays extend the regions of the wheat genome that are amenable to analyses beyond its exome, providing tools for detailed characterization of these regulatory regions in large populations.

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Integrating genomic resources to present full gene and promoter capture probe sets for bread wheat

Abstract: Background

Cited by 3 publications

References 22 publications

Applying the latest advances in genomics and phenomics for trait discovery in polyploid wheat

Applying the latest advances in genomics and phenomics for trait discovery in polyploid wheat

The best of both worlds: Combining lineage‐specific and universal bait sets in target‐enrichment hybridization reactions

Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat

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