Application of genotyping by sequencing technology to a variety of crop breeding programs
- PMID:26566821
- DOI: 10.1016/j.plantsci.2015.04.016
Application of genotyping by sequencing technology to a variety of crop breeding programs
Abstract
Since the Arabidopsis genome was completed, draft sequences or pseudomolecules have been published for more than 100 plant genomes including green algae, in large part due to advances in sequencing technologies. Advanced DNA sequencing technologies have also conferred new opportunities for high-throughput low-cost crop genotyping, based on single-nucleotide polymorphisms (SNPs). However, a recurring complication in crop genotyping that differs from other taxa is a higher level of DNA sequence duplication, noting that all angiosperms are thought to have polyploidy in their evolutionary history. In the current article, we briefly review current genotyping methods using next-generation sequencing (NGS) technologies. We also explore case studies of genotyping-by-sequencing (GBS) applications to several crops differing in genome size, organization and breeding system (paleopolyploids, neo-allopolyploids, neo-autopolyploids). GBS typically shows good results when it is applied to an inbred diploid species with a well-established reference genome. However, we have also made some progress toward GBS of outcrossing species lacking reference genomes and of polyploid populations, which still need much improvement. Regardless of some limitations, low-cost and multiplexed genotyping offered by GBS will be beneficial to breed superior cultivars in many crop species.
Keywords: Genetic study; Genomics; Genotype-by-sequencing; Marker-assisted selection.
Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.
Similar articles
- Role of NGS and SNP genotyping methods in sugarcane improvement programs.Manimekalai R, Suresh G, Govinda Kurup H, Athiappan S, Kandalam M.Manimekalai R, et al.Crit Rev Biotechnol. 2020 Sep;40(6):865-880. doi: 10.1080/07388551.2020.1765730. Epub 2020 Jun 7.Crit Rev Biotechnol. 2020.PMID:32508157Review.
- Next generation breeding.Barabaschi D, Tondelli A, Desiderio F, Volante A, Vaccino P, Valè G, Cattivelli L.Barabaschi D, et al.Plant Sci. 2016 Jan;242:3-13. doi: 10.1016/j.plantsci.2015.07.010. Epub 2015 Jul 19.Plant Sci. 2016.PMID:26566820Review.
- A comparison of genotyping-by-sequencing analysis methods on low-coverage crop datasets shows advantages of a new workflow, GB-eaSy.Wickland DP, Battu G, Hudson KA, Diers BW, Hudson ME.Wickland DP, et al.BMC Bioinformatics. 2017 Dec 28;18(1):586. doi: 10.1186/s12859-017-2000-6.BMC Bioinformatics. 2017.PMID:29281959Free PMC article.
- Skim sequencing: an advanced NGS technology for crop improvement.Kumar P, Choudhary M, Jat BS, Kumar B, Singh V, Kumar V, Singla D, Rakshit S.Kumar P, et al.J Genet. 2021;100:38.J Genet. 2021.PMID:34238778Review.
- Revolution in Genotyping Platforms for Crop Improvement.Scheben A, Batley J, Edwards D.Scheben A, et al.Adv Biochem Eng Biotechnol. 2018;164:37-52. doi: 10.1007/10_2017_47.Adv Biochem Eng Biotechnol. 2018.PMID:29356847
Cited by
- Identification of a novel major QTL from Chinese wheat cultivar Ji5265 for Fusarium head blight resistance in greenhouse.Li H, Zhang F, Zhao J, Bai G, Amand PS, Bernardo A, Ni Z, Sun Q, Su Z.Li H, et al.Theor Appl Genet. 2022 Jun;135(6):1867-1877. doi: 10.1007/s00122-022-04080-5. Epub 2022 Mar 31.Theor Appl Genet. 2022.PMID:35357527
- Genotyping by Sequencing of 393Sorghum bicolor BTx623 × IS3620C Recombinant Inbred Lines Improves Sensitivity and Resolution of QTL Detection.Kong W, Kim C, Zhang D, Guo H, Tan X, Jin H, Zhou C, Shuang LS, Goff V, Sezen U, Pierce G, Compton R, Lemke C, Robertson J, Rainville L, Auckland S, Paterson AH.Kong W, et al.G3 (Bethesda). 2018 Jul 31;8(8):2563-2572. doi: 10.1534/g3.118.200173.G3 (Bethesda). 2018.PMID:29853656Free PMC article.
- Benchmarking small-variant genotyping in polyploids.Cooke DP, Wedge DC, Lunter G.Cooke DP, et al.Genome Res. 2022 Feb;32(2):403-408. doi: 10.1101/gr.275579.121. Epub 2021 Dec 29.Genome Res. 2022.PMID:34965940Free PMC article.
- Tools for Genetic Studies in Experimental Populations of Polyploids.Bourke PM, Voorrips RE, Visser RGF, Maliepaard C.Bourke PM, et al.Front Plant Sci. 2018 Apr 18;9:513. doi: 10.3389/fpls.2018.00513. eCollection 2018.Front Plant Sci. 2018.PMID:29720992Free PMC article.Review.
- Genetic Diversity, Pedigree Relationships, and A Haplotype-Based DNA Fingerprinting System of Red Bayberry Cultivars.Wu B, Zhong Y, Wu Q, Chen F, Zhong G, Cui Y.Wu B, et al.Front Plant Sci. 2020 Sep 9;11:563452. doi: 10.3389/fpls.2020.563452. eCollection 2020.Front Plant Sci. 2020.PMID:33013982Free PMC article.
Publication types
MeSH terms
Related information
LinkOut - more resources
Full Text Sources
Other Literature Sources