Whole-genome resequencing facilitates the development of a 50K single nucleotide polymorphism genotyping array for Scots pine (Pinus sylvestris L.) and its transferability to other pine species. Estravis Barcala, M., van der Valk, T., Chen, Z., Funda, T., Chaudhary, R., Klingberg, A., Fundova, I., Suontama, M., Hallingbäck, H., Bernhardsson, C., Nystedt, B., Ingvarsson, P. K., Sherwood, E., Street, N., Gyllensten, U., Nilsson, O., & Wu, H. X. The Plant Journal, 117(3):944–955, 2024. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.16535![Whole-genome resequencing facilitates the development of a 50K single nucleotide polymorphism genotyping array for Scots pine (Pinus sylvestris L.) and its transferability to other pine species [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex Scots pine (Pinus sylvestris L.) is one of the most widespread and economically important conifer species in the world. Applications like genomic selection and association studies, which could help accelerate breeding cycles, are challenging in Scots pine because of its large and repetitive genome. For this reason, genotyping tools for conifer species, and in particular for Scots pine, are commonly based on transcribed regions of the genome. In this article, we present the Axiom Psyl50K array, the first single nucleotide polymorphism (SNP) genotyping array for Scots pine based on whole-genome resequencing, that represents both genic and intergenic regions. This array was designed following a two-step procedure: first, 192 trees were sequenced, and a 430K SNP screening array was constructed. Then, 480 samples, including haploid megagametophytes, full-sib family trios, breeding population, and range-wide individuals from across Eurasia were genotyped with the screening array. The best 50K SNPs were selected based on quality, replicability, distribution across the draft genome assembly, balance between genic and intergenic regions, and genotype–environment and genotype–phenotype associations. Of the final 49 877 probes tiled in the array, 20 372 (40.84%) occur inside gene models, while the rest lie in intergenic regions. We also show that the Psyl50K array can yield enough high-confidence SNPs for genetic studies in pine species from North America and Eurasia. This new genotyping tool will be a valuable resource for high-throughput fundamental and applied research of Scots pine and other pine species.
@article{estravis_barcala_whole-genome_2024,
title = {Whole-genome resequencing facilitates the development of a {50K} single nucleotide polymorphism genotyping array for {Scots} pine ({Pinus} sylvestris {L}.) and its transferability to other pine species},
volume = {117},
copyright = {© 2023 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley \& Sons Ltd.},
issn = {1365-313X},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.16535},
doi = {10.1111/tpj.16535},
abstract = {Scots pine (Pinus sylvestris L.) is one of the most widespread and economically important conifer species in the world. Applications like genomic selection and association studies, which could help accelerate breeding cycles, are challenging in Scots pine because of its large and repetitive genome. For this reason, genotyping tools for conifer species, and in particular for Scots pine, are commonly based on transcribed regions of the genome. In this article, we present the Axiom Psyl50K array, the first single nucleotide polymorphism (SNP) genotyping array for Scots pine based on whole-genome resequencing, that represents both genic and intergenic regions. This array was designed following a two-step procedure: first, 192 trees were sequenced, and a 430K SNP screening array was constructed. Then, 480 samples, including haploid megagametophytes, full-sib family trios, breeding population, and range-wide individuals from across Eurasia were genotyped with the screening array. The best 50K SNPs were selected based on quality, replicability, distribution across the draft genome assembly, balance between genic and intergenic regions, and genotype–environment and genotype–phenotype associations. Of the final 49 877 probes tiled in the array, 20 372 (40.84\%) occur inside gene models, while the rest lie in intergenic regions. We also show that the Psyl50K array can yield enough high-confidence SNPs for genetic studies in pine species from North America and Eurasia. This new genotyping tool will be a valuable resource for high-throughput fundamental and applied research of Scots pine and other pine species.},
language = {en},
number = {3},
urldate = {2024-02-02},
journal = {The Plant Journal},
author = {Estravis Barcala, Maximiliano and van der Valk, Tom and Chen, Zhiqiang and Funda, Tomas and Chaudhary, Rajiv and Klingberg, Adam and Fundova, Irena and Suontama, Mari and Hallingbäck, Henrik and Bernhardsson, Carolina and Nystedt, Björn and Ingvarsson, Pär K. and Sherwood, Ellen and Street, Nathaniel and Gyllensten, Ulf and Nilsson, Ove and Wu, Harry X.},
year = {2024},
note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.16535},
keywords = {Pinus sylvestris, SNP array, genome resequencing, genome-wide association studies, genomic selection, pines},
pages = {944--955},
}
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The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.","issn":"1365-313X","url":"https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.16535","doi":"10.1111/tpj.16535","abstract":"Scots pine (Pinus sylvestris L.) is one of the most widespread and economically important conifer species in the world. Applications like genomic selection and association studies, which could help accelerate breeding cycles, are challenging in Scots pine because of its large and repetitive genome. For this reason, genotyping tools for conifer species, and in particular for Scots pine, are commonly based on transcribed regions of the genome. In this article, we present the Axiom Psyl50K array, the first single nucleotide polymorphism (SNP) genotyping array for Scots pine based on whole-genome resequencing, that represents both genic and intergenic regions. 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The Plant Journal published by Society for Experimental Biology and John Wiley \\& Sons Ltd.},\n\tissn = {1365-313X},\n\turl = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.16535},\n\tdoi = {10.1111/tpj.16535},\n\tabstract = {Scots pine (Pinus sylvestris L.) is one of the most widespread and economically important conifer species in the world. Applications like genomic selection and association studies, which could help accelerate breeding cycles, are challenging in Scots pine because of its large and repetitive genome. For this reason, genotyping tools for conifer species, and in particular for Scots pine, are commonly based on transcribed regions of the genome. In this article, we present the Axiom Psyl50K array, the first single nucleotide polymorphism (SNP) genotyping array for Scots pine based on whole-genome resequencing, that represents both genic and intergenic regions. 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