Genotyping-by-Sequencing in Plants

Overview

Journal Biology (Basel)

Publisher MDPI

Specialty Biology

Date 2014 May 17

PMID 24832503

Citations 120

Authors

Stephane Deschamps

Victor Llaca

Gregory D May

Affiliations

Soon will be listed here.

Abstract

The advent of next-generation DNA sequencing (NGS) technologies has led to the development of rapid genome-wide Single Nucleotide Polymorphism (SNP) detection applications in various plant species. Recent improvements in sequencing throughput combined with an overall decrease in costs per gigabase of sequence is allowing NGS to be applied to not only the evaluation of small subsets of parental inbred lines, but also the mapping and characterization of traits of interest in much larger populations. Such an approach, where sequences are used simultaneously to detect and score SNPs, therefore bypassing the entire marker assay development stage, is known as genotyping-by-sequencing (GBS). This review will summarize the current state of GBS in plants and the promises it holds as a genome-wide genotyping application.

Citing Articles

Study on the Genetic Diversity Characteristics of the Endemic Plant in Guizhou, China Based on SNP Molecular Markers.

Luo J, Yuan C, Wang H, Zhang J, Chen J, He S Ecol Evol. 2025; 15(2):e70966.

PMID: 39926301 PMC: 11806379. DOI: 10.1002/ece3.70966.

Genetic diversity and population structure studies of West African sweetpotato [Ipomoea batatas (L.) Lam] collection using DArTseq.

Mahaman Mourtala I, Gouda A, Baina D, Maxwell N, Adje C, Barage M PLoS One. 2025; 20(1):e0312384.

PMID: 39752435 PMC: 11698414. DOI: 10.1371/journal.pone.0312384.

SNP loci identification and KASP marker development system for genetic diversity, population structure, and fingerprinting in sweetpotato (Ipomoea batatas L.).

Yang F, Lang T, Wu J, Zhang C, Qu H, Pu Z BMC Genomics. 2024; 25(1):1245.

PMID: 39719557 PMC: 11668102. DOI: 10.1186/s12864-024-11139-8.

Genomic exploration of Iranian almond (Prunus dulcis) germplasm: decoding diversity, population structure, and linkage disequilibrium through genotyping-by-sequencing analysis.

Khojand S, Zeinalabedini M, Azizinezhad R, Imani A, Ghaffari M BMC Genomics. 2024; 25(1):1101.

PMID: 39558316 PMC: 11575021. DOI: 10.1186/s12864-024-11044-0.

Genome-Wide Association Studies and QTL Mapping Reveal a New Locus Associated with Resistance to Bacterial Pustule Caused by pv. in Soybean.

Cardoso-Sichieri R, Oliveira L, Lopes-Caitar V, Silva D, Lopes I, Oliveira M Plants (Basel). 2024; 13(17).

PMID: 39273969 PMC: 11397087. DOI: 10.3390/plants13172484.

References

Yu J, Hu S, Wang J, Wong G, Li S, Liu B . A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science. 2002; 296(5565):79-92. DOI: 10.1126/science.1068037. View

Johnson D, Mortazavi A, Myers R, Wold B . Genome-wide mapping of in vivo protein-DNA interactions. Science. 2007; 316(5830):1497-502. DOI: 10.1126/science.1141319. View

Prince J, Feuk L, Howell W, Jobs M, Emahazion T, Blennow K . Robust and accurate single nucleotide polymorphism genotyping by dynamic allele-specific hybridization (DASH): design criteria and assay validation. Genome Res. 2001; 11(1):152-62. PMC: 311016. DOI: 10.1101/gr.150201. View

Jaillon O, Aury J, Noel B, Policriti A, Clepet C, Casagrande A . The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature. 2007; 449(7161):463-7. DOI: 10.1038/nature06148. View

Rabinowicz P, Citek R, Budiman M, Nunberg A, Bedell J, Lakey N . Differential methylation of genes and repeats in land plants. Genome Res. 2005; 15(10):1431-40. PMC: 1240086. DOI: 10.1101/gr.4100405. View

Fahlgren N, Howell M, Kasschau K, Chapman E, Sullivan C, Cumbie J . High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS One. 2007; 2(2):e219. PMC: 1790633. DOI: 10.1371/journal.pone.0000219. View

Novaes E, Drost D, Farmerie W, Pappas Jr G, Grattapaglia D, Sederoff R . High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics. 2008; 9:312. PMC: 2483731. DOI: 10.1186/1471-2164-9-312. View

Holloway B, Luck S, Beatty M, Rafalski J, Li B . Genome-wide expression quantitative trait loci (eQTL) analysis in maize. BMC Genomics. 2011; 12:336. PMC: 3141675. DOI: 10.1186/1471-2164-12-336. View

Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M . AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 1995; 23(21):4407-14. PMC: 307397. DOI: 10.1093/nar/23.21.4407. View

10.

Belo A, Zheng P, Luck S, Shen B, Meyer D, Li B . Whole genome scan detects an allelic variant of fad2 associated with increased oleic acid levels in maize. Mol Genet Genomics. 2007; 279(1):1-10. DOI: 10.1007/s00438-007-0289-y. View

11.

Young N, Debelle F, Oldroyd G, Geurts R, Cannon S, Udvardi M . The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature. 2011; 480(7378):520-4. PMC: 3272368. DOI: 10.1038/nature10625. View

12.

Morgante M, De Paoli E, Radovic S . Transposable elements and the plant pan-genomes. Curr Opin Plant Biol. 2007; 10(2):149-55. DOI: 10.1016/j.pbi.2007.02.001. View

13.

Hansen M, Kraft T, Ganestam S, Sall T, Nilsson N . Linkage disequilibrium mapping of the bolting gene in sea beet using AFLP markers. Genet Res. 2001; 77(1):61-6. DOI: 10.1017/s0016672300004857. View

14.

Trick M, Adamski N, Mugford S, Jiang C, Febrer M, Uauy C . Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map genes in polyploid wheat. BMC Plant Biol. 2012; 12:14. PMC: 3296661. DOI: 10.1186/1471-2229-12-14. View

15.

Hodges E, Xuan Z, Balija V, Kramer M, Molla M, Smith S . Genome-wide in situ exon capture for selective resequencing. Nat Genet. 2007; 39(12):1522-7. DOI: 10.1038/ng.2007.42. View

16.

Ragoussis J . Genotyping technologies for all. Drug Discov Today Technol. 2014; 3(2):115-22. DOI: 10.1016/j.ddtec.2006.06.013. View

17.

Wang D, Fan J, Siao C, Berno A, Young P, Sapolsky R . Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science. 1998; 280(5366):1077-82. DOI: 10.1126/science.280.5366.1077. View

18.

Wheeler D, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A . The complete genome of an individual by massively parallel DNA sequencing. Nature. 2008; 452(7189):872-6. DOI: 10.1038/nature06884. View

19.

Sunkar R, Zhou X, Zheng Y, Zhang W, Zhu J . Identification of novel and candidate miRNAs in rice by high throughput sequencing. BMC Plant Biol. 2008; 8:25. PMC: 2292181. DOI: 10.1186/1471-2229-8-25. View

20.

Flavell A, Pearce S, Kumar A . Plant transposable elements and the genome. Curr Opin Genet Dev. 1994; 4(6):838-44. DOI: 10.1016/0959-437x(94)90068-x. View