The omics sciences used for crop improvement programs
DOI:
https://doi.org/10.22267/rcia.183502.92Keywords:
Phylogenetics, genomics, MAS, TranscriptomicsAbstract
Population growth, climate change and the loss of ecosystem services are some of the challenges facing agriculture in recent decades to ensure long-term food security. Plant breeding programs can contribute to the development of genotypes adapted to new environmental conditions. The development and implementation of high-throughput sequencing technologies have accelerated breeding programs for crops that feed the world's population. This article reviews the main technological developments in “omics” used for genetic crop improvement. Here, we briefly discuss four technologies and their applications in the field of agriculture: phylogenomics, comparative genomics, comparative transcriptomics and marker assisted selection. These approaches allow to understand the evolutionary history of crops and their wild relatives, as well as identify the structure and function of genes of interest in agriculture. In addition, these help to reveal the expression of important genes in the domestication process and characterize individuals of agricultural species using molecular approaches that allow streamlining selection processes. It is necessary to implement genetic improvement programs that include the use of some or all of these technologies with the purpose of accelerating processes that can contribute to current agricultural challenges.
Downloads
Download data is not yet available.
Metrics
Metrics Loading ...
References
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology. 215(3): 403-410.
Atwell, S., Huang, Y. S., Vilhjálmsson, B. J., Willems, G., Horton, M., Li, Y., Meng. D., Platt, A., Tarone, A. M., Hu, T. T., Jiang, R., Muliyati, N. W., Zhang, X., Amer, M. A., Baxter, I., Brachi, B., Chory, J., Dean, C., Debieu, M., de Meaux, J., Ecker, J. R., Faure, N., Kniskern, J. M., Jones, J. D., Michael, T., Nemri, A., Roux, F., Salt, D. E., Tang, C., Todesco, M., Traw, M.B., Weigel, D., Marjoram, P., Borevitz, J.O., Bergelson, J. & Nordborg, M. (2010). Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature. 465(7298): 627-631. doi: https://10.1038/nature08800
Bakker, E., Borm, T., Prins, P., van der Vossen, E., Uenk, G., Arens, M., Boer, J., Eck, H., Muskens, M., Vossen, J., Linden, G., Ham, R., Klein-Lankhorst, R., Visser, R., Smant, G, Bakker, J. & Goverse, A. (2011). A genome-wide genetic map of NB-LRR disease resistance loci in potato. Theoretical and Applied Genetics. 123(3): 493-508. doi: 10.1007/s00122-011-1602-z
Bolger, M. E., Weisshaar, B., Scholz, U., Stein, N., Usadel, B. & Mayer, K. F. (2014). Plant genome sequencing - applications for crop improvement. Current Opinion in Biotechnology. 26: 31-37. doi: 10.1016/j.copbio.2013.08.019
Bonham-Carter, O., Steele, J. & Bastola, D. (2013). Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis. Briefings in Bioinformatics. 15(6): 890-905. doi: https:// 10.1093/bib/bbt052
Borozan, I., Watt, S. & Ferretti, V. (2015). Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification. Bioinformatics. 31(9): 1396–1404. doi: https:// 10.1093/bioinformatics/btv006
Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. (2016). Near-optimal probabilistic RNA-seq quantification. Nature Biotechnology. 34(5): 525-527. doi: https://10.1038/nbt.3519
Brozynska, M., Furtado, A. & Henry, R. J. (2015). Genomics of crop wild relatives: expanding the gene pool for crop improvement. Plant Biotechnology Journal. 14(4): 1070-1085. doi: https:// 10.1111/pbi.12454
Buermans, H. P. J. & den Dunnen, J. T. (2014). Next generation sequencing technology: Advances and applications. Biochimica et Biophysica Acta (BBA)-Molecular Basis of Disease. 1842(10): 1932-1941. doi: https://10.1016/J.BBADIS.2014.06.015
Catchen, J. M., Amores, A., Hohenlohe, P., Cresko, W. & Postlethwait, J. H. (2011). Stacks: building and genotyping Loci de novo from short-read sequences. G3: Genes, genomes, genetics. 1(3): 171-182. doi: https:// 10.1534/g3.111.000240
Chan, C. X. & Ragan, M. A. (2013). Next-generation phylogenomics. Biology Direct. 8(3). doi: 10.1186/1745-6150-8-3
Clark, R. M., Wagler, T. N., Quijada, P. & Doebley, J. (2006). A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture. Nature Genetics. 38(5): 594-597. doi: 10.1038/ng1784
Conesa, A., Madrigal, P., Tarazona, S., Gomez-Cabrero, D., Cervera, A., McPherson, A., Wojciech, M., Gaffney, D., Elo, L., Zhang, X. & Mortazavi, A. (2016). A survey of best practices for RNA-seq data analysis. Genome Biology. 17(1): 13. doi: 10.1186/s13059-016-0881-8
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 Reviews Genetics. 12: 499-510. doi: https://doi.org/10.1038/nrg3012
Dempewolf, H., Baute, G., Anderson, J., Kilian, B., Smith, C. & Guarino, L. (2017). Past and Future Use of Wild Relatives in Crop Breeding. Crop Science. 57(3): 1070-1082. doi:10.2135/cropsci2016.10.0885
Doebley, J. (2004).The genetics of maize evolution. Annual review of genitcs. 38:37-59. doi: 10.1146/annurev.genet.38.072902.092425
Drummond, A. & Rambaut, A. (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology. 7(1):214. doi: 10.1186/1471-2148-7-214
Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research. 32(5): 1792-1797. doi: 10.1093/nar/gkh340
Ekblom, R. & Wolf, J. B. W. (2014). A field guide to whole-genome sequencing, assembly and annotation. Evolutionary Applications. 7(9): 1026-1042. doi: 10.1111/eva.12178
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(5): e19379. doi: 10.1371/journal.pone.0019379
Gao, J., Zhang, Y., Zhang, C., Qi, F., Li, X., Mu, S. & Peng, Z. (2014). Characterization of the Floral Transcriptome of Moso Bamboo (Phyllostachys edulis) at Different Flowering Developmental Stages by Transcriptome Sequencing and RNA-Seq Analysis. PLoS ONE. 9(6): e98910. doi: 10.1371/journal.pone.0098910
Glaubitz, J. C., Casstevens, T. M., Lu, F., Harriman, J., Elshire, R. J., Sun, Q. & Buckler, E. S. (2014). TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline. PLoS ONE. 9(2): e90346. doi: 10.1371/journal.pone.0090346
Gore, M. A., Fang, D. D., Poland, J. A., Zhang, J., Percy, R. G., Cantrell, R. G., Thyssen, G. & Lipka, A. E. (2014). Linkage Map Construction and Quantitative Trait Locus Analysis of Agronomic and Fiber Quality Traits in Cotton. The Plant Genome. 7(1): 0. doi: 10.3835/plantgenome2013.07.0023
Haas, B. J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P. D., Bowden. J., Couger, MB., Eccles, D., Li B., Lieber, M., MacManes, M. D., Ott, M., Orvis J., Pochet, N., Strozzi, F., Weeks, N., Westerman, R., William, T., Dewey, C. N., Henschel, R., LeDuc, R., Friedman, N. & Regev A. (2013). De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature Protocols. 8(8): 1494-1512. doi: 10.1038/nprot.2013.084
Hajjar, R. & Hodgkin, T. (2007). The use of wild relatives in crop improvement: a survey of developments over the last 20 years. Euphytica. 156(1–2): 1-13. doi: 10.1007/s10681-007-9363-0
Han, X.-J., Wang, Y.-D., Chen, Y.-C., Lin, L.-Y., & Wu, Q.-K. (2013). Transcriptome Sequencing and Expression Analysis of Terpenoid Biosynthesis Genes in Litsea cubeba. PLoS ONE. 8(10): e76890. doi: 10.1371/journal.pone.0076890
He, J., Zhao, X., Laroche, A., Lu, Z.-X., Liu, H. & Li, Z. (2014). Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. Frontiers in Plant Science. 30(5): 484. doi: 10.3389/fpls.2014.00484
He, Z., Zhai, W., Wen, H., Tang, T., Wang, Y., Lu, X., Greenberg, A. J., Hudson, R. R., Wu, CI. & Shi, S. (2011). Two Evolutionary Histories in the Genome of Rice: the Roles of Domestication Genes. PLoS Genetics. 7(6): e1002100. doi: 10.1371/journal.pgen.1002100
Heffner, E. L., Lorenz, A. J., Jannink, J. L., & Sorrells, M. E. (2010). Plant breeding with Genomic selection: Gain per unit time and cost. Crop Science. 50(5): 1681-1690. doi: 10.2135/cropsci2009.11.0662
Hoisington, D., Khairallah, M., Reeves, T., Ribaut, J. M., Skovmand, B., Taba, S., & Warburton, M. (1999). Plant genetic resources: what can they contribute toward increased crop productivity? Proceedings of the National Academy of Sciences of the United States of America. 96(11): 5937-5943. doi: 10.1073/PNAS.96.11.5937
Huang, X., Zhao, Y., Wei, X., Li, C., Wang, A., Zhao, Q., Li W, Guo, Y., Deng. L., Zhu, C., Fan, D., Lu, Y., Weng, Q., Liu, K., Zhou, T., Jing, Y., Si, L., Dong, G., Huang, T., Lu, T., Feng, Q., Qian, Q., Li, J. & Han, B. (2011). Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nature Genetics. 44(1): 32-39. doi: 10.1038/ng.1018
Huelsenbeck, J. P., & Ronquist, F. (2001). MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics. 17(8): 754-755. doi: https:// 10.1093/bioinformatics/17.8.754
Hufford, M. B., Xu, X., van Heerwaarden, J., Pyhäjärvi, T., Chia, J.-M., Cartwright, R. A., Elshire, R. J., Glaubitz J. C., Guill, K. E., Kaeppler, S. M., Lai, J., Morrell, P. L., Shannon, L. M., Song, C., Springer, N. M., Swanson-Wagner, R. A., Tiffin, P., Wang, J., Zhang, G., Doebley, J., McMullen, M. D., Ware, D., Buckler, E.S., Yang, S. & Jeffrey Ross-Ibarra (2012). Comparative population genomics of maize domestication and improvement. Nature Genetics. 44(7): 808-811. doi: 10.1038/ng.2309
Jackson, S. A., Iwata, A., Lee, S.-H., Schmutz, J., & Shoemaker, R. (2011). Sequencing crop genomes: approaches and applications. New Phytologist. 191(4): 915-925. doi: 10.1111/j.1469-8137.2011.03804.x
Katoh, K., Misawa, K., Kuma, K. & Miyata, T. (2002a). MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research. 30(14): 3059-3066.
Katoh, K., Misawa, K., Kuma, K. & Miyata, T. (2002b). MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research. 30(14): 3059-3066.
Koenig, D., Jimenez-Gomez, J. M., Kimura, S., Fulop, D., Chitwood, D. H., Headland, L. R., Kumar, R., Covington, M. F., Devisetty, U.K., Tat, A.V., Tohge, T., Bolger, A., Schneeberger, K., Ossowski, S., Lanz, C., Xiong, G., Taylor-Teeples, M., Brady, S. M., Pauly, M., Weigel, D., Usadel, B., Fernie, A. R., Peng, J., Sinha, N.R. & Maloof, J. N. (2013). Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato. Proceedings of the National Academy of Sciences. 110(28): E2655-E2662. doi: 10.1073/pnas.1309606110
Kubatko, L. S., Carstens, B. C., & Knowles, L. L. (2009). STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics. 25(7): 971-973. doi: https://doi.org/10.1093/bioinformatics/btp079
Kudapa, H., Ramalingam, A., Nayakoti, S., Chen, X., Zhuang, W.-J., Liang, X., Kahl, G., Edwards, D. & Varshney, R. K. (2013). Functional genomics to study stress responses in crop legumes: progress and prospects. Functional Plant Biology. 40(12):1221. doi: https://10.1071/FP13191
Larget, B. R., Kotha, S. K., Dewey, C. N. & Ané, C. (2010). BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis. Phylogenetics. 26(22): 2910-2911.
Liu, L. (2008). BEST: Bayesian estimation of species trees under the coalescent model. Bioinformatics. 24(21): 2542-2543. doi: 10.1093/bioinformatics/btn484
Lomsadze, A., Ter-hovhannisyan, V., Chernoff, Y. O. & Borodovsky, M. (2005). Gene identification in novel eukaryotic genomes by self-training algorithm. Nucleic Acids Research. 33(20): 6494-6506. doi: 10.1093/nar/gki937
Love, M. I., Huber, W. & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology. 15(12): 550. doi: 10.1186/s13059-014-0550-8
Majoros, W. ., Pertea, M., & Salzberg, S. (2004). TigrScan and GlimmerHMM : two open-source ab initio eukaryotic gene-finders. Bioinformatics. 20(16): 2878-2879.
Martinez-Castillo, J., Camacho-Perez, L., Villanueva-Viramontes, S., Andueza-Noh, R. H., & Chacon-Sanchez, M. I. (2014). Genetic structure within the Mesoamerican gene pool of wild Phaseolus lunatus (Fabaceae) from Mexico as revealed by microsatellite markers: Implications for conservation and the domestication of the species. American Journal of Botany. 101(5): 851-864. doi: 10.3732/ajb.1300412
Mooney, H. A. (2010). The ecosystem-service chain and the biological diversity crisis. Philosophical Transactions of the Royal Society B: Biological Sciences. 365(1537): 31–39. doi: 10.1098/rstb.2009.0223
Mutz, K.-O., Heilkenbrinker, A., Lönne, M., Walter, J.G. & Stahl, F. (2013). Transcriptome analysis using next-generation sequencing. Current Opinion in Biotechnology. 24(1): 22-30. doi: 10.1016/j.copbio.2012.09.004
Nookaew, I., Papini, M., Pornputtapong, N., Scalcinati, G., Fagerberg, L., Uhlén, M. & Nielsen, J. (2012). A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae. Nucleic Acids Researc. 40(20): 10084-10097. doi: 10.1093/nar/gks804
Notredame, C., Higgins, D. G. & Heringa, J. (2000). T-coffee: a novel method for fast and accurate multiple sequence alignment 1 1Edited by J. Thornton. Journal of Molecular Biology. 302(1): 205-217. doi: 10.1006/jmbi.2000.4042
Olsen, K. M. & Wendel, J. F. (2013). A Bountiful Harvest: Genomic Insights into Crop Domestication Phenotypes. Annual Review of Plant Biology. 64(1): 47–70. doi: 10.1146/annurev-arplant-050312-120048
Parker, J. (2011). The 9 billion-people question. Recuperada de: http://www.economist.com/node/18200618
Patro, R., Mount, S. M. & Kingsford, C. (2014). Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms. Nature Biotechnology. 32(5): 462-464. doi: 10.1038/nbt.2862
Pearson, T. A. & Manolio, T. A. (2008). How to Interpret a Genome-wide Association Study. JAMA. 2299(11):1335-1344. doi: 10.1001/jama.299.11.1335
Poland, J. A. & Rife, T. W. (2012). Genotyping-by-Sequencing for Plant Breeding and Genetics. The Plant Genome. 58(5): 425-431. doi: 10.3835/plantgenome2012.05.0005
Posada, D. (2008). jModelTest : Phylogenetic Model Averaging. Molecular Biology and Evolution. 25(7): 1253-1256. doi: 10.1093/molbev/msn083
Ramos-Madrigal, J., Smith, B.D., Moreno-Mayar, J.V., Gopalakrishnan, S, Ross-Ibarra. J., Gilbert, M.T.P. & Wales N. (2016). Genome Sequence of a 5,310-Year-Old Maize Cob Provides Insights into the Early Stages of Maize Domestication. Current Biology. 26(23):3195-3201. doi: 10.1016/j.cub.2016.09.036
Ranc, N., Muños, S., Xu, J., Le Paslier, M.-C., Chauveau, A., Bounon, R., Rolland, S., Bouchet, J. P., Brunel, D. & Causse, M. (2012). Genome-wide association mapping in tomato (Solanum lycopersicum) is possible using genome admixture of Solanum lycopersicum var. cerasiforme. G3: Genes, Genomes, Genetics. 2(8): 853-864. doi: 10.1534/g3.112.002667
Rosenzweig, C., Iglesius, A., Yang, X. B., Epstein, P. R. & Chivian, E. (2001). Climate change and extreme weather events - Implications for food production, plant diseases, and pests. Global change & human health, nasa publications. 2(2): 90-104.
Schmutz, J., McClean, P. E., Mamidi, S., Wu, G. A., Cannon, S. B., Grimwood, J., Jenkins, J., Shu, S., Song, Q., Chavarro, C., Torres-Torres, M., Geffroy, V., Moghaddam, S. M., Gao, D., Abernathy, B., Barry, K., Blair, M., Brick, M,A., Chovatia, M., Gepts, P., Goodstein, D, M., Gonzales, M., Hellsten, U., Hyten, D, L., Jia, G., Kelly, J. D., Kudrna, D., Lee, R., Richard, M, M., Miklas, P. N., Osorno, J, M., Rodrigues, J., Thareau, V., Urrea, C. A., Wang, M., Yu, Y., Zhang, M., Wing, R. A., Cregan, P. B., Rokhsar, D. S. & Jackson, S. A. (2014). A reference genome for common bean and genome-wide analysis of dual domestications. Nature Genetics. 46(7): 707–713. doi: 10.1038/ng.3008
Schurch, N. J., Schofield, P., Gierliński, M., Cole, C., Sherstnev, A., Singh, V., Wrobel, N., Gharbi, K., Simpson, G. G., Owen-Hughes, T., Blaxter, M. & Barton, G. J. (2016). How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? RNA Society. 22(6): 839–851. doi: 10.1261/rna.053959.115
Simpson, J. T. & Pop, M. (2015). The Theory and Practice of Genome Sequence Assembly. Annual Review of Genomics and Human Genetics. 16(1): 153–172. doi: 10.1146/annurev-genom-090314-050032
Sims, D., Sudbery, I., Ilott, N. E., Heger, A. & Ponting, C. P. (2014). Sequencing depth and coverage: key considerations in genomic analyses. Nature Reviews Genetics. 15(2): 121-132. doi: 10.1038/nrg3642
Smýkal, P., Coyne, C. J., Ambrose, M. J., Maxted, N., Schaefer, H., Blair, M. W., Berger, J., Greene, S. L., Nelson, M. N,. Besharat, N. Vymyslický, T., Toker, C., Saxena, R. K., Roorkiwal, M., Pandey, M. K., Hu, J., Li, Y. H., Wang, L. X., Guo, Y., Qiu, L. J., Redden R.J. & Varshney, R. K. (2015). Legume Crops Phylogeny and Genetic Diversity for Science and Breeding. Critical Reviews in Plant Sciences. 34(1–3): 43-104. doi: https://doi.org/10.1080/07352689.2014.897904
Soto, J. C., Ortiz, J. F., Perlaza-Jiménez, L., Vásquez, A. X., Lopez-Lavalle, L. A. B., Mathew, B., Léon, J., Bernal, A. J., Ballvora, A. & López, C. E. (2015). A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes. BMC Genomics. 16(1): 190. doi: 10.1186/s12864-015-1397-4
Spindel, J., Wright, M., Chen, C., Cobb, J., Gage, J., Harrington, S., Lorieux, M., Ahmadi, N. & McCouch, S. (2013). Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations. Theoretical and Applied Genetics. 126(11): 2699–2716. doi: 10.1007/s00122-013-2166-x
Stamatakis, A. (2006). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 22(21): 2688–2690. doi: 10.1093/bioinformatics/btl446
Stanke, M., Steinkamp, R., Waack, S. & Morgenstern, B. (2004). AUGUSTUS : a web server for gene finding in eukaryotes. Nucleic Acids Research. 32(2): W309–W312. doi: https://doi.org/10.1093/nar/gkh379
Stormo, G. D. (2009). An introduction to sequence similarity (“homology”) searching. Current protocols in bioinformatics, 27(1): 3.1.1–3.1.7 doi: https://doi.org/10.1002/0471250953.bi0301s27
Straub, S. C. K., Parks, M., Weitemier, K., Fishbein, M., Cronn, R. C., & Liston, A. (2012). Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics. American Journal of Botany. 99(2): 349-364. doi: https://doi.org/10.3732/ajb.1100335
Swamy, B. M., Vikram, P., Dixit, S., Ahmed, H., & Kumar, A. (2011). Meta-analysis of grain yield QTL identified during agricultural drought in grasses showed consensus. BMC Genomics. 12(1): 319. doi: https://doi.org/10.1186/1471-2164-12-319
Swofford, D. L. (2003). Phylogenetic analysis using parsimony. Recuperada de https://paup.phylosolutions.com/
Tang, H., Bomhoff, M. D., Briones, E., Zhang, L., Schnable, J. C., & Lyons, E. (2015). SynFind: Compiling Syntenic Regions across Any Set of Genomes on Demand. Genome Biology and Evolution. 7(12): 3286–3298. doi: https://doi.org/10.1093/gbe/evv219
Tester, M., & Langridge, P. (2010). Breeding Technologies to Increase Crop Production in a Changing World. Science. 327(5967): 818–822. doi: https://doi.org/10.1126/science.1183700
The Potato Genome Sequencing Consortium. (2011). Genome sequence and analysis of the tuber crop potato. Nature. 475(7355): 189-195. doi: https://doi.org/10.1038/nature10158
Torkamaneh, D., Laroche, J., & Belzile, F. (2016). Genome-Wide SNP Calling from Genotyping by Sequencing (GBS) Data: A Comparison of Seven Pipelines and Two Sequencing Technologies. PLOS ONE. 11(8): e0161333. doi: https://doi.org/10.1371/journal.pone.0161333
Trapnell, C., Pachter, L., & Salzberg, S. L. (2009). TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 25(9): 1105-1111. doi: https://doi.org/10.1093/bioinformatics/btp120
Valliyodan, B., & Nguyen, H. T. (2006). Understanding regulatory networks and engineering for enhanced drought tolerance in plants. Current Opinion in Plant Biology. 9(2): 189-195. doi: https://doi.org/10.1016/j.pbi.2006.01.019
Varshney, R.K., Nayak, S.N., May, G.D. & Jackson, S.A. (2009). Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnology. 27(9):522-530. doi: 10.1016/j.tibtech.2009.05.006
Van de Mortel, J. E., Almar Villanueva, L., Schat, H., Kwekkeboom, J., Coughlan, S., Moerland, P. D., Van Themaat, E. V. L., Koornneef, M. & Aarts, M. G. M. (2006). Large expression differences in genes for iron and zinc homeostasis, stress response, and lignin biosynthesis distinguish roots of Arabidopsis thaliana and the related metal hyperaccumulator Thlaspi caerulescens. Plant Physiology. 142(3): 1127-1147. doi: https://doi.org/10.1104/pp.106.082073
Venditti, C., Meade, A. & Pagel, M. (2008). Phylogenetic mixture models can reduce node-density artifacts. Systematic Biology. 57(2): 286–293. doi: https://doi.org/10.1080/10635150802044045
Wang, M., Jiang, N., Jia, T., Leach, L., Cockram, J., Comadran, J., Shaw, .P, Waugh, R. & Luo, Z. (2012). Genome-wide association mapping of agronomic and morphologic traits in highly structured populations of barley cultivars. Theoretical and Applied Genetics. 124(2): 233-246. doi: https://doi.org/10.1007/s00122-011-1697-2
Wang, X., Wang, H., Wang, J., Sun, R., Wu, J., Liu, S., Bai, Y., Mun, J. H., Bancroft, I., Cheng, F., Huang, S., Li, X., Hua, W., Wang, J., Wang, X., Freeling, M., Pires, J. C., Paterson, A.H., Chalhoub, B., Wang, B., Hayward, A., Sharpe, A.G., Park, B.S., Weisshaar, B., Liu, B., Li, B., Liu, B., Tong, C., Song, C., Duran, C., Peng, C., Geng, C., Koh, C., Lin, C., Edwards, D., Mu, D., Shen, D., Soumpourou, E., Li, F., Fraser, F., Conant, G., Lassalle, G., King, G. J., Bonnema, G., Tang, H., Wang, H., Belcram, H., Zhou, H., Hirakawa, H., Abe, H., Guo, H., Wang, H., Jin, H., Parkin, I. A., Batley, J., Kim, J. S., Just, J., Li, J., Xu, J., Deng, J., Kim, J. A., Li, J., Yu, J., Meng, J., Wang, J., Min, J., Poulain, J., Wang, J., Hatakeyama, K., Wu, K., Wang, L., Fang, L., Trick, M., Links, M. G., Zhao, M., Jin, M., Ramchiary, N., Drou, N., Berkman, P. J., Cai, Q., Huang, Q., Li, R., Tabata, S., Cheng, S., Zhang, S., Zhang, S., Huang, S., Sato, S., Sun, S., Kwon, S. J., Choi, S. R., Lee, T. H., Fan, W., Zhao, X., Tan, X., Xu, X., Wang, Y., Qiu, Y., Yin, Y., Li, Y., Du, Y., Liao, Y., Lim, Y., Narusaka, Y., Wang, Y., Wang, Z., Li, Z., Wang, Z., Xiong, Z. & Zhang Z. (2011). The genome of the mesopolyploid crop species Brassica rapa. Nature Genetics. 43(10): 1035-1039. doi: http://dx.doi.org/10.1038/ng.919
Wang, Z., Gerstein, M. & Snyder, M. (2009). RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics. 10(1): 57–63. https://doi.org/10.1038/nrg2484
Ward, J. A., Bhangoo, J., Fernández-Fernández, F., Moore, P., Swanson, J., Viola, R., Velasco, R., Bassil, N., Weber, C. A. & Sargent, D. J. (2013). Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation. BMC Genomics. 14(1): 1-14. doi: https://doi.org/10.1186/1471-2164-14-2
Whankaew, S., Poopear, S., Kanjanawattanawong, S., Tangphatsornruang, S., Boonseng, O., Lightfoot, D. A., & Triwitayakorn, K. (2011). A genome scan for quantitative trait loci affecting cyanogenic potential of cassava root in an outbred population. BMC Genomics, 12(1):266. doi: https://doi.org/10.1186/1471-2164-12-266
Wicke, S., & Schneeweiss, G. M. (2015). Next-generation organellar genomics: Potentials and pitfalls of high-throughput technologies for molecular evolutionary studies and plant systematics. In: E. Hörandl & M. S. Appelhans (Eds.), Next-Generation Sequencing in Plant Systematics. pp.1 - 42. Königstein, Germany : Koeltz Scientific Books. 298p.
Xie, Y., Wu, G., Tang, J., Luo, R., Patterson, J., Liu, S., Huang, W., He, G., Gu, S., Li, S., Zhou, X., Lam, T. W., Li, Y., Xu, X., Wong, G. K. & Wang, J. (2014). SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads. Bioinformatics. 30(12): 1660–1666. doi: https://doi.org/10.1093/bioinformatics/btu077
Xu, J., Li, Y., Ma, X., Ding, J., Wang, K., Wang, S., Tian, Y., Zhang, H. & Zhu, X. G. (2013). Whole transcriptome analysis using next-generation sequencing of model species Setaria viridis to support C4 photosynthesis research. Plant Molecular Biology. 83(1–2): 77–87. doi: https://doi.org/10.1007/s11103-013-0025-4
Xu, X., Liu, X., Ge, S., Jensen, J. D., Hu, F., Li, X., Dong, Y., Gutenkunst, R. N., Fang, L., Huang, L., Li, J., He, W., Zhang, G., Zheng, X., Zhang, F., Li, Y., Yu, C., Kristiansen, K., Zhang, X., Wang, J., Wright, M., McCouch, S., Nielsen, R., Wang, J. & Wang, W. (2011). Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nature Biotechnology. 30(1): 105–111. doi: https://doi.org/10.1038/nbt.2050
Yang, I. S., & Kim, S. (2015). Analysis of Whole Transcriptome Sequencing Data: Workflow and Software. Genomics & Informatics. 13(4): 119–125. doi: https://doi.org/10.5808/GI.2015.13.4.119
Zhou, X., Lindsay, H., & Robinson, M. D. (2014). Robustly detecting differential expression in RNA sequencing data using observation weights. Nucleic Acids Research. 42(11): e91–e91. doi: https://doi.org/10.1093/nar/gku310
Zhu, H., Choi, H.-K., Cook, D. R. & Shoemaker, R. C. (2005). Bridging model and crop legumes through comparative genomics. Plant Physiology. 137(4): 1189-1196.
Atwell, S., Huang, Y. S., Vilhjálmsson, B. J., Willems, G., Horton, M., Li, Y., Meng. D., Platt, A., Tarone, A. M., Hu, T. T., Jiang, R., Muliyati, N. W., Zhang, X., Amer, M. A., Baxter, I., Brachi, B., Chory, J., Dean, C., Debieu, M., de Meaux, J., Ecker, J. R., Faure, N., Kniskern, J. M., Jones, J. D., Michael, T., Nemri, A., Roux, F., Salt, D. E., Tang, C., Todesco, M., Traw, M.B., Weigel, D., Marjoram, P., Borevitz, J.O., Bergelson, J. & Nordborg, M. (2010). Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature. 465(7298): 627-631. doi: https://10.1038/nature08800
Bakker, E., Borm, T., Prins, P., van der Vossen, E., Uenk, G., Arens, M., Boer, J., Eck, H., Muskens, M., Vossen, J., Linden, G., Ham, R., Klein-Lankhorst, R., Visser, R., Smant, G, Bakker, J. & Goverse, A. (2011). A genome-wide genetic map of NB-LRR disease resistance loci in potato. Theoretical and Applied Genetics. 123(3): 493-508. doi: 10.1007/s00122-011-1602-z
Bolger, M. E., Weisshaar, B., Scholz, U., Stein, N., Usadel, B. & Mayer, K. F. (2014). Plant genome sequencing - applications for crop improvement. Current Opinion in Biotechnology. 26: 31-37. doi: 10.1016/j.copbio.2013.08.019
Bonham-Carter, O., Steele, J. & Bastola, D. (2013). Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis. Briefings in Bioinformatics. 15(6): 890-905. doi: https:// 10.1093/bib/bbt052
Borozan, I., Watt, S. & Ferretti, V. (2015). Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification. Bioinformatics. 31(9): 1396–1404. doi: https:// 10.1093/bioinformatics/btv006
Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. (2016). Near-optimal probabilistic RNA-seq quantification. Nature Biotechnology. 34(5): 525-527. doi: https://10.1038/nbt.3519
Brozynska, M., Furtado, A. & Henry, R. J. (2015). Genomics of crop wild relatives: expanding the gene pool for crop improvement. Plant Biotechnology Journal. 14(4): 1070-1085. doi: https:// 10.1111/pbi.12454
Buermans, H. P. J. & den Dunnen, J. T. (2014). Next generation sequencing technology: Advances and applications. Biochimica et Biophysica Acta (BBA)-Molecular Basis of Disease. 1842(10): 1932-1941. doi: https://10.1016/J.BBADIS.2014.06.015
Catchen, J. M., Amores, A., Hohenlohe, P., Cresko, W. & Postlethwait, J. H. (2011). Stacks: building and genotyping Loci de novo from short-read sequences. G3: Genes, genomes, genetics. 1(3): 171-182. doi: https:// 10.1534/g3.111.000240
Chan, C. X. & Ragan, M. A. (2013). Next-generation phylogenomics. Biology Direct. 8(3). doi: 10.1186/1745-6150-8-3
Clark, R. M., Wagler, T. N., Quijada, P. & Doebley, J. (2006). A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture. Nature Genetics. 38(5): 594-597. doi: 10.1038/ng1784
Conesa, A., Madrigal, P., Tarazona, S., Gomez-Cabrero, D., Cervera, A., McPherson, A., Wojciech, M., Gaffney, D., Elo, L., Zhang, X. & Mortazavi, A. (2016). A survey of best practices for RNA-seq data analysis. Genome Biology. 17(1): 13. doi: 10.1186/s13059-016-0881-8
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 Reviews Genetics. 12: 499-510. doi: https://doi.org/10.1038/nrg3012
Dempewolf, H., Baute, G., Anderson, J., Kilian, B., Smith, C. & Guarino, L. (2017). Past and Future Use of Wild Relatives in Crop Breeding. Crop Science. 57(3): 1070-1082. doi:10.2135/cropsci2016.10.0885
Doebley, J. (2004).The genetics of maize evolution. Annual review of genitcs. 38:37-59. doi: 10.1146/annurev.genet.38.072902.092425
Drummond, A. & Rambaut, A. (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology. 7(1):214. doi: 10.1186/1471-2148-7-214
Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research. 32(5): 1792-1797. doi: 10.1093/nar/gkh340
Ekblom, R. & Wolf, J. B. W. (2014). A field guide to whole-genome sequencing, assembly and annotation. Evolutionary Applications. 7(9): 1026-1042. doi: 10.1111/eva.12178
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(5): e19379. doi: 10.1371/journal.pone.0019379
Gao, J., Zhang, Y., Zhang, C., Qi, F., Li, X., Mu, S. & Peng, Z. (2014). Characterization of the Floral Transcriptome of Moso Bamboo (Phyllostachys edulis) at Different Flowering Developmental Stages by Transcriptome Sequencing and RNA-Seq Analysis. PLoS ONE. 9(6): e98910. doi: 10.1371/journal.pone.0098910
Glaubitz, J. C., Casstevens, T. M., Lu, F., Harriman, J., Elshire, R. J., Sun, Q. & Buckler, E. S. (2014). TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline. PLoS ONE. 9(2): e90346. doi: 10.1371/journal.pone.0090346
Gore, M. A., Fang, D. D., Poland, J. A., Zhang, J., Percy, R. G., Cantrell, R. G., Thyssen, G. & Lipka, A. E. (2014). Linkage Map Construction and Quantitative Trait Locus Analysis of Agronomic and Fiber Quality Traits in Cotton. The Plant Genome. 7(1): 0. doi: 10.3835/plantgenome2013.07.0023
Haas, B. J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P. D., Bowden. J., Couger, MB., Eccles, D., Li B., Lieber, M., MacManes, M. D., Ott, M., Orvis J., Pochet, N., Strozzi, F., Weeks, N., Westerman, R., William, T., Dewey, C. N., Henschel, R., LeDuc, R., Friedman, N. & Regev A. (2013). De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature Protocols. 8(8): 1494-1512. doi: 10.1038/nprot.2013.084
Hajjar, R. & Hodgkin, T. (2007). The use of wild relatives in crop improvement: a survey of developments over the last 20 years. Euphytica. 156(1–2): 1-13. doi: 10.1007/s10681-007-9363-0
Han, X.-J., Wang, Y.-D., Chen, Y.-C., Lin, L.-Y., & Wu, Q.-K. (2013). Transcriptome Sequencing and Expression Analysis of Terpenoid Biosynthesis Genes in Litsea cubeba. PLoS ONE. 8(10): e76890. doi: 10.1371/journal.pone.0076890
He, J., Zhao, X., Laroche, A., Lu, Z.-X., Liu, H. & Li, Z. (2014). Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. Frontiers in Plant Science. 30(5): 484. doi: 10.3389/fpls.2014.00484
He, Z., Zhai, W., Wen, H., Tang, T., Wang, Y., Lu, X., Greenberg, A. J., Hudson, R. R., Wu, CI. & Shi, S. (2011). Two Evolutionary Histories in the Genome of Rice: the Roles of Domestication Genes. PLoS Genetics. 7(6): e1002100. doi: 10.1371/journal.pgen.1002100
Heffner, E. L., Lorenz, A. J., Jannink, J. L., & Sorrells, M. E. (2010). Plant breeding with Genomic selection: Gain per unit time and cost. Crop Science. 50(5): 1681-1690. doi: 10.2135/cropsci2009.11.0662
Hoisington, D., Khairallah, M., Reeves, T., Ribaut, J. M., Skovmand, B., Taba, S., & Warburton, M. (1999). Plant genetic resources: what can they contribute toward increased crop productivity? Proceedings of the National Academy of Sciences of the United States of America. 96(11): 5937-5943. doi: 10.1073/PNAS.96.11.5937
Huang, X., Zhao, Y., Wei, X., Li, C., Wang, A., Zhao, Q., Li W, Guo, Y., Deng. L., Zhu, C., Fan, D., Lu, Y., Weng, Q., Liu, K., Zhou, T., Jing, Y., Si, L., Dong, G., Huang, T., Lu, T., Feng, Q., Qian, Q., Li, J. & Han, B. (2011). Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nature Genetics. 44(1): 32-39. doi: 10.1038/ng.1018
Huelsenbeck, J. P., & Ronquist, F. (2001). MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics. 17(8): 754-755. doi: https:// 10.1093/bioinformatics/17.8.754
Hufford, M. B., Xu, X., van Heerwaarden, J., Pyhäjärvi, T., Chia, J.-M., Cartwright, R. A., Elshire, R. J., Glaubitz J. C., Guill, K. E., Kaeppler, S. M., Lai, J., Morrell, P. L., Shannon, L. M., Song, C., Springer, N. M., Swanson-Wagner, R. A., Tiffin, P., Wang, J., Zhang, G., Doebley, J., McMullen, M. D., Ware, D., Buckler, E.S., Yang, S. & Jeffrey Ross-Ibarra (2012). Comparative population genomics of maize domestication and improvement. Nature Genetics. 44(7): 808-811. doi: 10.1038/ng.2309
Jackson, S. A., Iwata, A., Lee, S.-H., Schmutz, J., & Shoemaker, R. (2011). Sequencing crop genomes: approaches and applications. New Phytologist. 191(4): 915-925. doi: 10.1111/j.1469-8137.2011.03804.x
Katoh, K., Misawa, K., Kuma, K. & Miyata, T. (2002a). MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research. 30(14): 3059-3066.
Katoh, K., Misawa, K., Kuma, K. & Miyata, T. (2002b). MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research. 30(14): 3059-3066.
Koenig, D., Jimenez-Gomez, J. M., Kimura, S., Fulop, D., Chitwood, D. H., Headland, L. R., Kumar, R., Covington, M. F., Devisetty, U.K., Tat, A.V., Tohge, T., Bolger, A., Schneeberger, K., Ossowski, S., Lanz, C., Xiong, G., Taylor-Teeples, M., Brady, S. M., Pauly, M., Weigel, D., Usadel, B., Fernie, A. R., Peng, J., Sinha, N.R. & Maloof, J. N. (2013). Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato. Proceedings of the National Academy of Sciences. 110(28): E2655-E2662. doi: 10.1073/pnas.1309606110
Kubatko, L. S., Carstens, B. C., & Knowles, L. L. (2009). STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics. 25(7): 971-973. doi: https://doi.org/10.1093/bioinformatics/btp079
Kudapa, H., Ramalingam, A., Nayakoti, S., Chen, X., Zhuang, W.-J., Liang, X., Kahl, G., Edwards, D. & Varshney, R. K. (2013). Functional genomics to study stress responses in crop legumes: progress and prospects. Functional Plant Biology. 40(12):1221. doi: https://10.1071/FP13191
Larget, B. R., Kotha, S. K., Dewey, C. N. & Ané, C. (2010). BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis. Phylogenetics. 26(22): 2910-2911.
Liu, L. (2008). BEST: Bayesian estimation of species trees under the coalescent model. Bioinformatics. 24(21): 2542-2543. doi: 10.1093/bioinformatics/btn484
Lomsadze, A., Ter-hovhannisyan, V., Chernoff, Y. O. & Borodovsky, M. (2005). Gene identification in novel eukaryotic genomes by self-training algorithm. Nucleic Acids Research. 33(20): 6494-6506. doi: 10.1093/nar/gki937
Love, M. I., Huber, W. & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology. 15(12): 550. doi: 10.1186/s13059-014-0550-8
Majoros, W. ., Pertea, M., & Salzberg, S. (2004). TigrScan and GlimmerHMM : two open-source ab initio eukaryotic gene-finders. Bioinformatics. 20(16): 2878-2879.
Martinez-Castillo, J., Camacho-Perez, L., Villanueva-Viramontes, S., Andueza-Noh, R. H., & Chacon-Sanchez, M. I. (2014). Genetic structure within the Mesoamerican gene pool of wild Phaseolus lunatus (Fabaceae) from Mexico as revealed by microsatellite markers: Implications for conservation and the domestication of the species. American Journal of Botany. 101(5): 851-864. doi: 10.3732/ajb.1300412
Mooney, H. A. (2010). The ecosystem-service chain and the biological diversity crisis. Philosophical Transactions of the Royal Society B: Biological Sciences. 365(1537): 31–39. doi: 10.1098/rstb.2009.0223
Mutz, K.-O., Heilkenbrinker, A., Lönne, M., Walter, J.G. & Stahl, F. (2013). Transcriptome analysis using next-generation sequencing. Current Opinion in Biotechnology. 24(1): 22-30. doi: 10.1016/j.copbio.2012.09.004
Nookaew, I., Papini, M., Pornputtapong, N., Scalcinati, G., Fagerberg, L., Uhlén, M. & Nielsen, J. (2012). A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae. Nucleic Acids Researc. 40(20): 10084-10097. doi: 10.1093/nar/gks804
Notredame, C., Higgins, D. G. & Heringa, J. (2000). T-coffee: a novel method for fast and accurate multiple sequence alignment 1 1Edited by J. Thornton. Journal of Molecular Biology. 302(1): 205-217. doi: 10.1006/jmbi.2000.4042
Olsen, K. M. & Wendel, J. F. (2013). A Bountiful Harvest: Genomic Insights into Crop Domestication Phenotypes. Annual Review of Plant Biology. 64(1): 47–70. doi: 10.1146/annurev-arplant-050312-120048
Parker, J. (2011). The 9 billion-people question. Recuperada de: http://www.economist.com/node/18200618
Patro, R., Mount, S. M. & Kingsford, C. (2014). Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms. Nature Biotechnology. 32(5): 462-464. doi: 10.1038/nbt.2862
Pearson, T. A. & Manolio, T. A. (2008). How to Interpret a Genome-wide Association Study. JAMA. 2299(11):1335-1344. doi: 10.1001/jama.299.11.1335
Poland, J. A. & Rife, T. W. (2012). Genotyping-by-Sequencing for Plant Breeding and Genetics. The Plant Genome. 58(5): 425-431. doi: 10.3835/plantgenome2012.05.0005
Posada, D. (2008). jModelTest : Phylogenetic Model Averaging. Molecular Biology and Evolution. 25(7): 1253-1256. doi: 10.1093/molbev/msn083
Ramos-Madrigal, J., Smith, B.D., Moreno-Mayar, J.V., Gopalakrishnan, S, Ross-Ibarra. J., Gilbert, M.T.P. & Wales N. (2016). Genome Sequence of a 5,310-Year-Old Maize Cob Provides Insights into the Early Stages of Maize Domestication. Current Biology. 26(23):3195-3201. doi: 10.1016/j.cub.2016.09.036
Ranc, N., Muños, S., Xu, J., Le Paslier, M.-C., Chauveau, A., Bounon, R., Rolland, S., Bouchet, J. P., Brunel, D. & Causse, M. (2012). Genome-wide association mapping in tomato (Solanum lycopersicum) is possible using genome admixture of Solanum lycopersicum var. cerasiforme. G3: Genes, Genomes, Genetics. 2(8): 853-864. doi: 10.1534/g3.112.002667
Rosenzweig, C., Iglesius, A., Yang, X. B., Epstein, P. R. & Chivian, E. (2001). Climate change and extreme weather events - Implications for food production, plant diseases, and pests. Global change & human health, nasa publications. 2(2): 90-104.
Schmutz, J., McClean, P. E., Mamidi, S., Wu, G. A., Cannon, S. B., Grimwood, J., Jenkins, J., Shu, S., Song, Q., Chavarro, C., Torres-Torres, M., Geffroy, V., Moghaddam, S. M., Gao, D., Abernathy, B., Barry, K., Blair, M., Brick, M,A., Chovatia, M., Gepts, P., Goodstein, D, M., Gonzales, M., Hellsten, U., Hyten, D, L., Jia, G., Kelly, J. D., Kudrna, D., Lee, R., Richard, M, M., Miklas, P. N., Osorno, J, M., Rodrigues, J., Thareau, V., Urrea, C. A., Wang, M., Yu, Y., Zhang, M., Wing, R. A., Cregan, P. B., Rokhsar, D. S. & Jackson, S. A. (2014). A reference genome for common bean and genome-wide analysis of dual domestications. Nature Genetics. 46(7): 707–713. doi: 10.1038/ng.3008
Schurch, N. J., Schofield, P., Gierliński, M., Cole, C., Sherstnev, A., Singh, V., Wrobel, N., Gharbi, K., Simpson, G. G., Owen-Hughes, T., Blaxter, M. & Barton, G. J. (2016). How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? RNA Society. 22(6): 839–851. doi: 10.1261/rna.053959.115
Simpson, J. T. & Pop, M. (2015). The Theory and Practice of Genome Sequence Assembly. Annual Review of Genomics and Human Genetics. 16(1): 153–172. doi: 10.1146/annurev-genom-090314-050032
Sims, D., Sudbery, I., Ilott, N. E., Heger, A. & Ponting, C. P. (2014). Sequencing depth and coverage: key considerations in genomic analyses. Nature Reviews Genetics. 15(2): 121-132. doi: 10.1038/nrg3642
Smýkal, P., Coyne, C. J., Ambrose, M. J., Maxted, N., Schaefer, H., Blair, M. W., Berger, J., Greene, S. L., Nelson, M. N,. Besharat, N. Vymyslický, T., Toker, C., Saxena, R. K., Roorkiwal, M., Pandey, M. K., Hu, J., Li, Y. H., Wang, L. X., Guo, Y., Qiu, L. J., Redden R.J. & Varshney, R. K. (2015). Legume Crops Phylogeny and Genetic Diversity for Science and Breeding. Critical Reviews in Plant Sciences. 34(1–3): 43-104. doi: https://doi.org/10.1080/07352689.2014.897904
Soto, J. C., Ortiz, J. F., Perlaza-Jiménez, L., Vásquez, A. X., Lopez-Lavalle, L. A. B., Mathew, B., Léon, J., Bernal, A. J., Ballvora, A. & López, C. E. (2015). A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes. BMC Genomics. 16(1): 190. doi: 10.1186/s12864-015-1397-4
Spindel, J., Wright, M., Chen, C., Cobb, J., Gage, J., Harrington, S., Lorieux, M., Ahmadi, N. & McCouch, S. (2013). Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations. Theoretical and Applied Genetics. 126(11): 2699–2716. doi: 10.1007/s00122-013-2166-x
Stamatakis, A. (2006). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 22(21): 2688–2690. doi: 10.1093/bioinformatics/btl446
Stanke, M., Steinkamp, R., Waack, S. & Morgenstern, B. (2004). AUGUSTUS : a web server for gene finding in eukaryotes. Nucleic Acids Research. 32(2): W309–W312. doi: https://doi.org/10.1093/nar/gkh379
Stormo, G. D. (2009). An introduction to sequence similarity (“homology”) searching. Current protocols in bioinformatics, 27(1): 3.1.1–3.1.7 doi: https://doi.org/10.1002/0471250953.bi0301s27
Straub, S. C. K., Parks, M., Weitemier, K., Fishbein, M., Cronn, R. C., & Liston, A. (2012). Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics. American Journal of Botany. 99(2): 349-364. doi: https://doi.org/10.3732/ajb.1100335
Swamy, B. M., Vikram, P., Dixit, S., Ahmed, H., & Kumar, A. (2011). Meta-analysis of grain yield QTL identified during agricultural drought in grasses showed consensus. BMC Genomics. 12(1): 319. doi: https://doi.org/10.1186/1471-2164-12-319
Swofford, D. L. (2003). Phylogenetic analysis using parsimony. Recuperada de https://paup.phylosolutions.com/
Tang, H., Bomhoff, M. D., Briones, E., Zhang, L., Schnable, J. C., & Lyons, E. (2015). SynFind: Compiling Syntenic Regions across Any Set of Genomes on Demand. Genome Biology and Evolution. 7(12): 3286–3298. doi: https://doi.org/10.1093/gbe/evv219
Tester, M., & Langridge, P. (2010). Breeding Technologies to Increase Crop Production in a Changing World. Science. 327(5967): 818–822. doi: https://doi.org/10.1126/science.1183700
The Potato Genome Sequencing Consortium. (2011). Genome sequence and analysis of the tuber crop potato. Nature. 475(7355): 189-195. doi: https://doi.org/10.1038/nature10158
Torkamaneh, D., Laroche, J., & Belzile, F. (2016). Genome-Wide SNP Calling from Genotyping by Sequencing (GBS) Data: A Comparison of Seven Pipelines and Two Sequencing Technologies. PLOS ONE. 11(8): e0161333. doi: https://doi.org/10.1371/journal.pone.0161333
Trapnell, C., Pachter, L., & Salzberg, S. L. (2009). TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 25(9): 1105-1111. doi: https://doi.org/10.1093/bioinformatics/btp120
Valliyodan, B., & Nguyen, H. T. (2006). Understanding regulatory networks and engineering for enhanced drought tolerance in plants. Current Opinion in Plant Biology. 9(2): 189-195. doi: https://doi.org/10.1016/j.pbi.2006.01.019
Varshney, R.K., Nayak, S.N., May, G.D. & Jackson, S.A. (2009). Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnology. 27(9):522-530. doi: 10.1016/j.tibtech.2009.05.006
Van de Mortel, J. E., Almar Villanueva, L., Schat, H., Kwekkeboom, J., Coughlan, S., Moerland, P. D., Van Themaat, E. V. L., Koornneef, M. & Aarts, M. G. M. (2006). Large expression differences in genes for iron and zinc homeostasis, stress response, and lignin biosynthesis distinguish roots of Arabidopsis thaliana and the related metal hyperaccumulator Thlaspi caerulescens. Plant Physiology. 142(3): 1127-1147. doi: https://doi.org/10.1104/pp.106.082073
Venditti, C., Meade, A. & Pagel, M. (2008). Phylogenetic mixture models can reduce node-density artifacts. Systematic Biology. 57(2): 286–293. doi: https://doi.org/10.1080/10635150802044045
Wang, M., Jiang, N., Jia, T., Leach, L., Cockram, J., Comadran, J., Shaw, .P, Waugh, R. & Luo, Z. (2012). Genome-wide association mapping of agronomic and morphologic traits in highly structured populations of barley cultivars. Theoretical and Applied Genetics. 124(2): 233-246. doi: https://doi.org/10.1007/s00122-011-1697-2
Wang, X., Wang, H., Wang, J., Sun, R., Wu, J., Liu, S., Bai, Y., Mun, J. H., Bancroft, I., Cheng, F., Huang, S., Li, X., Hua, W., Wang, J., Wang, X., Freeling, M., Pires, J. C., Paterson, A.H., Chalhoub, B., Wang, B., Hayward, A., Sharpe, A.G., Park, B.S., Weisshaar, B., Liu, B., Li, B., Liu, B., Tong, C., Song, C., Duran, C., Peng, C., Geng, C., Koh, C., Lin, C., Edwards, D., Mu, D., Shen, D., Soumpourou, E., Li, F., Fraser, F., Conant, G., Lassalle, G., King, G. J., Bonnema, G., Tang, H., Wang, H., Belcram, H., Zhou, H., Hirakawa, H., Abe, H., Guo, H., Wang, H., Jin, H., Parkin, I. A., Batley, J., Kim, J. S., Just, J., Li, J., Xu, J., Deng, J., Kim, J. A., Li, J., Yu, J., Meng, J., Wang, J., Min, J., Poulain, J., Wang, J., Hatakeyama, K., Wu, K., Wang, L., Fang, L., Trick, M., Links, M. G., Zhao, M., Jin, M., Ramchiary, N., Drou, N., Berkman, P. J., Cai, Q., Huang, Q., Li, R., Tabata, S., Cheng, S., Zhang, S., Zhang, S., Huang, S., Sato, S., Sun, S., Kwon, S. J., Choi, S. R., Lee, T. H., Fan, W., Zhao, X., Tan, X., Xu, X., Wang, Y., Qiu, Y., Yin, Y., Li, Y., Du, Y., Liao, Y., Lim, Y., Narusaka, Y., Wang, Y., Wang, Z., Li, Z., Wang, Z., Xiong, Z. & Zhang Z. (2011). The genome of the mesopolyploid crop species Brassica rapa. Nature Genetics. 43(10): 1035-1039. doi: http://dx.doi.org/10.1038/ng.919
Wang, Z., Gerstein, M. & Snyder, M. (2009). RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics. 10(1): 57–63. https://doi.org/10.1038/nrg2484
Ward, J. A., Bhangoo, J., Fernández-Fernández, F., Moore, P., Swanson, J., Viola, R., Velasco, R., Bassil, N., Weber, C. A. & Sargent, D. J. (2013). Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation. BMC Genomics. 14(1): 1-14. doi: https://doi.org/10.1186/1471-2164-14-2
Whankaew, S., Poopear, S., Kanjanawattanawong, S., Tangphatsornruang, S., Boonseng, O., Lightfoot, D. A., & Triwitayakorn, K. (2011). A genome scan for quantitative trait loci affecting cyanogenic potential of cassava root in an outbred population. BMC Genomics, 12(1):266. doi: https://doi.org/10.1186/1471-2164-12-266
Wicke, S., & Schneeweiss, G. M. (2015). Next-generation organellar genomics: Potentials and pitfalls of high-throughput technologies for molecular evolutionary studies and plant systematics. In: E. Hörandl & M. S. Appelhans (Eds.), Next-Generation Sequencing in Plant Systematics. pp.1 - 42. Königstein, Germany : Koeltz Scientific Books. 298p.
Xie, Y., Wu, G., Tang, J., Luo, R., Patterson, J., Liu, S., Huang, W., He, G., Gu, S., Li, S., Zhou, X., Lam, T. W., Li, Y., Xu, X., Wong, G. K. & Wang, J. (2014). SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads. Bioinformatics. 30(12): 1660–1666. doi: https://doi.org/10.1093/bioinformatics/btu077
Xu, J., Li, Y., Ma, X., Ding, J., Wang, K., Wang, S., Tian, Y., Zhang, H. & Zhu, X. G. (2013). Whole transcriptome analysis using next-generation sequencing of model species Setaria viridis to support C4 photosynthesis research. Plant Molecular Biology. 83(1–2): 77–87. doi: https://doi.org/10.1007/s11103-013-0025-4
Xu, X., Liu, X., Ge, S., Jensen, J. D., Hu, F., Li, X., Dong, Y., Gutenkunst, R. N., Fang, L., Huang, L., Li, J., He, W., Zhang, G., Zheng, X., Zhang, F., Li, Y., Yu, C., Kristiansen, K., Zhang, X., Wang, J., Wright, M., McCouch, S., Nielsen, R., Wang, J. & Wang, W. (2011). Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nature Biotechnology. 30(1): 105–111. doi: https://doi.org/10.1038/nbt.2050
Yang, I. S., & Kim, S. (2015). Analysis of Whole Transcriptome Sequencing Data: Workflow and Software. Genomics & Informatics. 13(4): 119–125. doi: https://doi.org/10.5808/GI.2015.13.4.119
Zhou, X., Lindsay, H., & Robinson, M. D. (2014). Robustly detecting differential expression in RNA sequencing data using observation weights. Nucleic Acids Research. 42(11): e91–e91. doi: https://doi.org/10.1093/nar/gku310
Zhu, H., Choi, H.-K., Cook, D. R. & Shoemaker, R. C. (2005). Bridging model and crop legumes through comparative genomics. Plant Physiology. 137(4): 1189-1196.
