Czech J. Genet. Plant Breed., 2017, 53(3):89-96 | DOI: 10.17221/192/2016-CJGPB
Application of next-generation sequencing in plant breedingReview
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
In the past decade, next-generation sequencing (NGS) platforms have changed the impact of sequencing on our knowledge of crop genomes and gene regulation. These techniques are today acquiring a great potential in metagenomic and agrigenomic research while showing prospects for their utilization in plant breeding. We can now obtain new and beneficial information about gene regulation on the cellular as well as whole-plant level through RNA-sequencing and subsequent expression analyses of genes participating in plant defence reactions to pathogens and in abiotic stress tolerance. NGS has facilitated the development of methods to genotype very large numbers of single-nucleotide polymorphisms. Genotyping- by-sequencing and whole-genome resequencing can lead to the development of molecular markers suited to studies of genetic relationships among breeding materials, creation of detailed genetic mapping of targeted genes and genome-wide association studies. Plant genotyping can benefit plant breeding through selection of individuals resistant to climatic stress and to pathogens causing substantial losses in agriculture.
Keywords: gene expression; marker-assisted selection; molecular marker; RNA-sequencing; SNP
Published: September 30, 2017 Show citation
References
- Ainley W.M., Sastry-Dent L., Welter M.E., Murray M.G., Zeitler B., Amora R., Corbin D.R., Miles R.R., Arnold N.L., Strange T.L., Simpson M.A., Cao Z., Carroll C., Pawelczak K.S., Blue R., West K., Rowland L.M., Perkins D., Samuel P., Dewes C.M., Shen L., Sriram S., Evans S.L., Rebar E.J., Zhang L., Gregory P.D., Urnov D., Webb S.R., Petolino J.F. (2013): Trait stacking via targeted genome editing. Plant Biotechnology Journal, 11: 1126-1134. Go to original source... Go to PubMed...
- Alagna F., Agostino N.D., Torchia L., Servili M., Rao R., Pietrella M., Giuliano G., Chiusano M.L., Baldoni L., Perrotta G. (2008): Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development. BMC Genomics, 10: 399. Go to original source... Go to PubMed...
- Ando K., Carr K.M., Grumet R. (2012): Transcriptome analyses of early cucumber fruit growth identifies distinct gene modules associated with phases of development. BMC Genomics, 13: 518. Go to original source... Go to PubMed...
- Azam S., Thakur V., Ruperao P., Shah T., Balaji J., Amindala B., Farmer A.D., Studholme D.J., May G.D., Edwards D., Jones J.D.G., Varshney R.K. (2012): Coverage-based consensus calling (CbCC) of short sequence reads and comparison of CbCC results to identify SNPs in chickpea (Cicer arietinum; Fabaceae), a crop species without a reference genome. American Journal of Botany, 99: 186-192. Go to original source... Go to PubMed...
- Barabaschi D., Tondelli A., Desiderio F., Volante A., Vaccino P., Valè G., Cattivelli L. (2016): Next generation breeding. Plant Science, 242: 3-13. Go to original source... Go to PubMed...
- Bonnet E., Wuyts J., Rouzé P., Van de Peer Y. (2004): Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proceedings of the National Academy of Sciences of the United States of America, 101: 11511-11516. Go to original source... Go to PubMed...
- Brenner S., Johnson M., Bridgham J., Golda G., Lloyd D. H., Johnson D., Luo S., McCurdy S., Foy M., Ewan M., Roth R., George D., Eletr S., Albrecht G., Vermaas E., Williams S.R., Moon K., Burcham T., Pallas M., DuBridge R.B., Kirchner J., Fearon K., Mao J., Corcoran K. (2000): Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nature Biotechnology, 18: 630-634. Go to original source... Go to PubMed...
- Buck M.J., Lieb J.D. (2004): ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics, 84: 349-360. Go to original source... Go to PubMed...
- Celton J.M., Gaillard S., Bruneau M., Pelletier S., Aubourg S., Martin-Magniette M.L., Navarro L., Laurens F., Renou J.P. (2014): Widespread anti-sense transcription in apple is correlated with siRNA production and indicates a large potential for transcriptional and/or posttranscriptional control. The New Phytologist, 203: 287-299. Go to original source... Go to PubMed...
- Chandrasekaran J., Brumin M., Wolf D., Leibman D., Klap C., Pearlsman M., Sherman A., Arazi T., Gal-On A. (2016): Development of broad virus resistance in nontransgenic cucumber using CRISPR/Cas9 technology. Molecular Plant Pathology, 17: 1140-1153. Go to original source... Go to PubMed...
- Chen W., Gao Y., Xie W., Gong L., Lu K., Wang W., Li Y., Liu X., Zhang H., Dong H., Zhang W., Zhang L., Yu S., Wang G., Lian X., Luo J. (2014): Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Nature Genetics, 46: 714-721. Go to original source... Go to PubMed...
- Chu Y., Wu C.L., Holbrook C.C., Tillman B.L., Person G., Ozias-Akins P. (2011): Marker-assisted selection to pyramid Nematode resistance and the high oleic trait in peanut. Plant Genome, 4: 110-117. Go to original source...
- Cortés A.J., Chavarro M.C., Blair M.W. (2011): SNP marker diversity in common bean (Phaseolus vulgaris L.). Theoretical and Applied Genetics, 123: 827-845. Go to original source... Go to PubMed...
- Dassanayake M., Haas J.S., Bohnert H.J., Cheeseman J.M. (2009): Shedding light on an extremophile lifestyle through transcriptomics. The New Phytologist, 183: 764-775. Go to original source... Go to PubMed...
- Davey J.W., Hohenlohe P.A., Etter P.D., Boone J.Q., Catchen J.M., Blaxter M.L. (2011): Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature, 12: 499-510. Go to original source... Go to PubMed...
- Elshire R.J., Glaubitz J.C., Sun Q., Poland J.A., Kawamoto K., Buckler E.S., Mitchell S.E. (2011): A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE, 6: e19379. Go to original source... Go to PubMed...
- Fan X.D., Wang J.Q., Yang N., Dong Y.Y., Liu L., Wang F.W., Wang N., Chen H., Liu W.C., Sun Y.P., Wu J.Y., Li H.Y. (2012): Gene expression profiling of soybean leaves and roots under salt, saline-alkali and drought stress by highthroughput Illumina sequencing. Gene, 512: 392-402. Go to original source... Go to PubMed...
- Flachowsky H., Le Roux P.M., Peil A., Patocchi A., Richter K., Hanke M.V. (2011): Application of a high-speed breeding technology to apple (Malus × domestica) based on transgenic early flowering plants and marker-assisted selection. New Phytologist, 192: 364-377. Go to original source... Go to PubMed...
- Gaines T.A., Lorentz L., Figge A., Herrmann J., Maiwald F., Ott M.C., Han H., Busi R., Yu Q., Powles S.B., Beffa R. (2014): RNA-Seq transcriptome analysis to identify genes involved in metabolism-based diclofop resistance in Lolium rigidum. Plant Journal, 78: 865-876. Go to original source... Go to PubMed...
- Garnica D.P., Upadhyaya N.M., Dodds P.N., Rathjen J.P. (2013): Strategies for wheat stripe rust pathogenicity identified by transcriptome sequencing. PLoS ONE, 8: e67150. Go to original source... Go to PubMed...
- He J., Zhao X., Laroche A., Lu Z.X., Liu H., Li Z. (2014): Genotyping-by-sequencing (GBS), an ultimate markerassisted selection (MAS) tool to accelerate plant breeding. Frontiers in Plant Science, 5: 484. Go to original source... Go to PubMed...
- Heffner E.L., Sorrells M.E., Jannink J.-L. (2009): Genomic selection for crop improvement. Crop Science, 49: 1-12. Go to original source...
- Ištvánek J., Jaroš M., Křenek A., Řepková J. (2014): Genome assembly and annotation for red clover (Trifolium pratense; Fabaceae). American Journal of Botany, 101: 327-337. Go to original source... Go to PubMed...
- Ištvánek J., Dluhošová J., Dluhoš P., Pátková L., Nedělník J., Řepková J. (2017): Gene classification and mining of molecular markers useful in red clover (Trifolium pratense) breeding. Frontiers in Plant Science, 8: 367. Go to original source... Go to PubMed...
- Juntawong P., Sirikhachornkit A., Pimjan R., Sonthirod C., Sangsrakru D., Yoocha T., Tangphatsornruang S., Srinives P. (2014): Elucidation of the molecular responses to waterlogging in Jatropha roots by transcriptome profiling. Frontiers in Plant Science, 5: 658. Go to original source... Go to PubMed...
- Kamei C.L.A., Severing E.I., Dechesne A., Furrer H., Dolstra O., Trindade L.M. (2016): Orphan Crops Browser: a bridge between model and orphan crops. Molecular Breeding, 36: 9. Go to original source... Go to PubMed...
- Kumar J., Mir R.R., Kumar N., Kumar A., Mohan A., Prabhu K.V., Balyan H.S., Gupta P.K. (2010): Marker-assisted selection for pre-harvest sprouting tolerance and leaf rust resistance in bread wheat. Plant Breeding, 129: 617-621. Go to original source...
- Kumar S., Banks T.W., Cloutier S. (2012): SNP discovery through next-generation sequencing and its applications. International Journal of Plant Genomics: e831460. Go to original source... Go to PubMed...
- Lado B., Matus I., Rodríguez A., Inostroza L., Poland J., Belzile F., del Pozo A., Quincke M., Castro M., von Zitzewitz J. (2013): Increased genomic prediction accuracy in wheat breeding through spatial adjustment of field trial data. G3-Genes Genomes Genetics, 3: 2105-2114. Go to original source... Go to PubMed...
- Le D.T., Nishiyama R., Watanabe Y., Mochida K., YamaguchiShinozaki K., Shinozaki K., Tran L.S. (2011): Genome-wide survey and expression analysis of the plant-specific NAC transcription factor family in soybean during development and dehydration stress. DNA Research, 18: 263-276. Go to original source... Go to PubMed...
- Lehmensiek A., Bovill W., Wenzl P., Langridge P., Appels R. (2009): Genetic mapping in the triticeae. In: Feuillet C., Muehlbauer G.J. (eds): Genetics and Genomics of the Triticeae. Heidelberg, Springer: 201-236. Go to original source...
- Lor V.S., Starker C.G., Voytas D.F., Weiss D., Olszewski N.E. (2014): Targeted mutagenesis of the tomato PROCERA gene using transcription activator-like effector nucleases. Plant Physiology, 166: 1288-1291. Go to original source... Go to PubMed...
- Lu T., Cui L., Zhou Y., Zhu Q., Fan D., Gong H., Zhao Q., Zhou C., Zhao Y., Lu D., Luo J., Wang Y., Tian Q., Feng Q., Huang T., Han B. (2015): Transcriptome-wide investigation of circular RNAs in rice. RNA, 21: 2076-2087. Go to original source... Go to PubMed...
- Miller M.R., Dunham J.P., Amores A., Cresko W.A., Johnson E.A. (2007): Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Research, 17: 240-248. Go to original source... Go to PubMed...
- Myles S., Chia J., Hurwitz B., Simon C., Zhong G.Y., Buckler E., Ware D. (2010): Rapid genomic characterization of the genus Vitis. PLoS ONE, 5: e8219. Go to original source... Go to PubMed...
- Nigam D., Kavita P., Tripathi R.K., Ranjan A., Goel R., Asif M., Shukla A., Singh G., Rana D., Sawant S.V. (2014): Transcriptome dynamics during fibre development in contrasting genotypes of Gossypium hirsutum L. Plant Biotechnology Journal, 12: 204-18. Go to original source... Go to PubMed...
- Novaes E., Drost D.R., Farmerie W.G., Appas G.J.P., Grattapaglia D., Sederoff R.R., Kirst M. (2008): High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics, 9: 312. Go to original source... Go to PubMed...
- Petrozza A., Santaniello A., Summerer S., Di Tommaso G., Di Tommaso D., Paparelli E., Piaggesi E., Perata P., Cellini F. (2014): Physiological responses to Megafol treatments in tomato plants under drought stress: a phenomic and molecular approach. Scientia Horticulturae, 174: 185-192. Go to original source...
- Poland J.A., Rife T.W. (2012): Genotyping-by-sequencing for plant breeding and genetics. Plant Genome, 5: 92-102. Go to original source...
- Rahman H., Jagadeeshselvam N., Valarmathi R., Sachin B., Sasikala R., Senthil N., Sudhakar D., Robin S., Muthurajan R. (2014): Transcriptome analysis of salinity responsiveness in contrasting genotypes of finger millet (Eleusine coracana L.) through RNA-sequencing. Plant Molecular Biology, 85: 485-503. Go to original source... Go to PubMed...
- Ray S., Satya P. (2014): Next generation sequencing technologies for next generation plant breeding. Frontiers in Plant Science, 5: 367. Go to original source... Go to PubMed...
- Shan Q., Wang Y., Li J., Zhang Y., Chen K., Liang Z., Zhang K., Liu J., Xi J.J., Qiu J.L., Gao C. (2013): Targeted genome modification of crop plants using a CRISPR-Cas system. Nature Biotechnology, 7: 686-688. Go to original source... Go to PubMed...
- Shuai P., Liang D., Tang S., Zhang Z., Ye C.Y., Su Y., Xia X., Yin W. (2014): Genome-wide identification and functional prediction of novel and drought-responsive lincRNAs in Populus trichocarpa. Journal of Experimental Botany, 65: 4975-4983. Go to original source... Go to PubMed...
- Swarbreck S.M., Lindquist E.A., Ackerly D.D., Andersen G.L. (2011): Analysis of leaf and root transcriptomes of soil-grown Avena barbata plants. Plant & Cell Physiology, 52: 317-332. Go to original source... Go to PubMed...
- Tang S., Liang H., Yan D., Zhao Y., Han X., Carlson J.E., Xia X., Yin W. (2013): Populus euphratica: the transcriptomic response to drought stress. Plant Molecular Biology, 83: 539-557. Go to original source... Go to PubMed...
- Tisné S., Serrand Y., Bach L., Gilbault E., Ben Ameur R., Balasse H., Voisin R., Bouchez D., Durand-Tardif M., Guerche P., Chareyron G., Da Rugna J., Camilleri C., Loudet O. (2013): Phenoscope: an automated large-scale phenotyping platform offering high spatial homogeneity. Plant Journal, 74: 534-544. Go to original source... Go to PubMed...
- Townsend J.A., Wright D.A., Winfrey R.J., Fu F., Maeder M.L., Joung J.K., Voytas D.F. (2009): High-frequency modification of plant genes using engineered zinc-finger nucleases. Nature, 459: 442-445. Go to original source... Go to PubMed...
- Trebbi D., Maccaferri M., de Heer P., Sorensen A., Giuliani S., Salvi S., Sanguineti M.C., Massi A., van der Vossen E.A.G., Tuberosa R. (2011): High-throughput SNP discovery and genotyping in durum wheat (Triticum durum Desf.). Theoretical and Applied Genetics, 123: 555-569. Go to original source... Go to PubMed...
- Trick M., Long Y., Meng J., Bancroft I. (2009): Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing. Plant Biotechnology Journal, 7: 334-346. Go to original source... Go to PubMed...
- Van Bel M., Proost S., Van Neste C., Deforce D., Van de Peer Y., Vandepoele K. (2013): TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNASeq transcriptomes. Genome Biology, 14: R134. Go to original source... Go to PubMed...
- Wang H., Chung P.J., Liu J., Jang I.C., Kean M.J., Xu J., Chua N.H. (2014): Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis. Genome Research, 24: 444-453. Go to original source... Go to PubMed...
- Wang X., Elling A.A., Li X., Li N., Peng Z., He G., Sun H., Qi Y., Liu X.S., Deng X.W. (2009a): Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. Plant Cell, 21: 1053-1069. Go to original source...
- Wang Y., Dong C., Xue Z., Jin Q., Xu Y. (2015): De novo transcriptome sequencing and discovery of genes related to copper tolerance in Paeonia ostii. Gene, 576: 126-135. Go to original source... Go to PubMed...
- Wang Z., Gerstein M., Snyder M. (2009b): RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics, 10: 57-63. Go to original source... Go to PubMed...
- Wilkins K.E., Booher N.J., Wang L., Bogdanove A.J. (2015): TAL effectors and activation of predicted host targets distinguish Asian from African strains of the rice pathogen Xanthomonas oryzae pv. oryzicola while strict conservation suggests universal importance of five TAL effectors. Frontiers in Plant Science, 6: 536. Go to original source... Go to PubMed...
- Windhausen V.S., Atlin C.N., Hickey J.M., Crossa J., Jannink J.L., Sorrells M.E., Raman B., Cairns J.E., Tarekegne A., Semagn K., Beyene Y., Grudloyma P., Technow F., Riedelsheimer C., Melchinger A.E. (2012): Effectiveness of genomic predictions of maize hybrid performance in different breeding populations and environments. G3Genes Genomes Genetics, 2: 1427-1436. Go to original source... Go to PubMed...
- Würschum T., Reif J.C., Kraft T., Janssen G., Zhao Y. (2013): Genomic selection in sugar beet breeding populations. BMC Genetics, 14: 85. Go to original source... Go to PubMed...
- Xin M., Wang Y., Yao Y., Song N., Hu Z., Qin D., Xie C., Peng H., Ni Z., Sun Q. (2011): Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing. BMC Plant Biology, 11: 61. Go to original source... Go to PubMed...
- Xu Y. (2003): Developing marker-assisted selection strategies for breeding hybrid rice. Plant Breeding Reviews, 23: 73-174. Go to original source...
- Xu Y., Crouch J.H. (2008): Marker-assisted selection in plant breeding: from publications to practice. Crop Science, 48: 391-407. Go to original source...
- Xu P., Liu Z., Fan X., Gao J., Zhang X., Zhang X., Shen X. (2013a): De novo transcriptome sequencing and comparative analysis of differentially expressed genes in Gossypium aridum under salt stress. Gene, 525: 26-34. Go to original source... Go to PubMed...
- Xu L., Wang Y., Zhai L., Xu Y., Wang L., Zhu X., Gong Y., Yu R., Limera C., Liu L. (2013b): Genome-wide identification and characterization of cadmium-responsive microRNAs and their target genes in radish (Raphanus sativus L.) roots. Journal of Experimental Botany, 64: 4271-4287. Go to original source... Go to PubMed...
- Yamamoto N., Takano T., Tanaka K., Ishige T., Terashima S., Endo C., Kurusu T., Yajima S., Yano K., Tada Y. (2015): Comprehensive analysis of transcriptome response to salinity stress in the halophytic turf grass Sporobolus virginicus. Frontiers in Plant Science, 6: 241. Go to original source... Go to PubMed...
- Yates S.A., Swain M.T., Hegarty M.J., Chernukin I., Lowe M., Allison G.G., Ruttink T., Abberton M. T., Jenkins G., Skøt L. (2014): De novo assembly of red clover transcriptome based on RNA-Seq data provides insight into drought response, gene discovery and marker identification. BMC Genomics, 15: 453. Go to original source... Go to PubMed...
- Yu X., Yang J., Li X., Liu X., Sun C., Wu F., He Y. (2013): Global analysis of cis-natural antisense transcripts and their heat responsive nat-siRNAs in Brassica rapa. BMC Plant Biology, 13: 208. Go to original source... Go to PubMed...
- Zhang N., Wang S., Zhang X., Dong Z., Chen F., Cui D. (2016): Transcriptome analysis of the Chinese bread wheat cultivar Yunong 201 and its ethyl methanesulfonate mutant line. Gene, 575: 285-293. Go to original source... Go to PubMed...
- Zhang W., Han Z., Guo Q., Liu Y., Zheng Y., Wu F., Jin W. (2014): Identification of maize long non-coding RNAs responsive to drought stress. PLoS ONE 9: e98958. Go to original source... Go to PubMed...
- Zhong S., Fei Z., Chen Y.R., Vrebalov J., Mcquinn R., Gapper N., Giovannoni J. (2013): Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nature Biotechnology, 31: 154-159. Go to original source... Go to PubMed...
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