Elucidating the process of SNPs identification in non-reference genome crops

References

• Abmus, J., Schmitt, A. O., Bortfeldt, R. H., & Brockmann, G. A. (2011). NovelSNPer: A fast tool for the identification and characterization of novel SNPs and InDels. Advances in Bioinformatics, 41, 73–84.
   Google Scholar
• Altshuler, D., Pollara, V. J., Cowles, C. R., Etten, W. J. V., Baldwin, J., Linton, L., & Lander, E. S. (2000). An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature, 407(6803), 513–516.
   PubMed Web of Science ®Google Scholar
• Baird, N. A., Ette, P. D., Atwood, T. S., Currey, M. C., Shiver, A. L., Lewis, Z. A., Selker, E. U., Cresko, W. A., & Johnson, E. A. (2008). Rapid SNP discovery and genetic mapping using sequenced RAD markers. PloS One, 3(10), e3376.
   PubMed Web of Science ®Google Scholar
• Berthouly-Salazar, C., Mariac, C., Couderc, M., Pouzadoux, J., Floc’h, J. B., & Vigouroux, Y. (2016). Genotyping-by-sequencing SNP identification for crops without a reference genome: Using transcriptome based mapping as an alternative strategy. Frontiers in Plant Science, 157, 777.
   Google Scholar
• Boutet, G., Carvalho, S. A., Falque, M., Peterlongo, P., Lhuillier, E., Bouchez, O., Lavaud, C., Pilet-Nayel, M.L., Rivière, N., & Baranger, A. (2016). SNP discovery and genetic mapping using genotyping by sequencing of whole genome genomic DNA from a pea RIL population. BMC Genomics, 17, 121.
   PubMed Web of Science ®Google Scholar
• Clarke, W. E., Higgins, E. E., Plieske, J., Wieseke, R., Sidebottom, C., Khedikar, Y., Batley, J., Edwards, D., Meng, J., Li, R., Lawley, C. T., Pauquet, J., Laga, B., Cheung, W., Iniguez-Luy, F., Dyrszka, E., Rae, S., Stich, B., Snowdon, R. J., … Parkin, I. A. P. (2016). A high‑density SNP genotyping array for Brassica napus and its ancestral diploid species based on optimised selection of single‑locus markers in the allotetraploid genome. TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik, 129(10), 1887–1899. https://doi.org/10.1007/s00122-016-2746-7
   PubMed Web of Science ®Google Scholar
• Clevenger, J., Chavarro, C., Pearl, S. A., Akins, P. O., & Jackson, S. A. (2015). Single nucleotide polymorphism identification in polyploids: A review, example and recommendations. Molecular Plant, 8, 831–846.
   PubMed Web of Science ®Google Scholar
• Coetzee, S. G., Rhie, S. K., Berman, B. P., Coetzee, G. A., & Noushmehr, H. (2012). FunciSNP: An R/bio-conductor tool integrating functional non-coding data sets with genetic association studies to identify candidate regulatory SNPs. Nucleic Acids Research, 40, e139.
   PubMed Web of Science ®Google Scholar
• Dereeper, A., & Nicolas, S. (2011). SNiPlay: A web-based tool for detection, management and analysis of SNPs. BMC Bioinformatics, 12, 134–145.
   PubMed Web of Science ®Google Scholar
• Doran, A. G., & Creevey, C. J. (2013). Snpdat: Easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms. BMC Bioinformatics, 14, 45–52. https://doi.org/10.1186/1471-2105-14-45
   PubMed Web of Science ®Google Scholar
• Eernisse, D. J. (2000). DNA Stacks software package for molecular systematics. http://biology.fullerton.edu/deernisse/dnastacks.
   Google Scholar
• Elshire, R. J., Glaubitz, J. C., & Sun, Q. (2011). A robust, simple genotyping by- sequencing (GBS) approach for high diversity species. PLoS One, 6, e19379.
   PubMed Web of Science ®Google Scholar
• Eltaher, S., Sallam, A., Emara, H. A., Nower, A. A., Salem, K. F., Börner, A., Baenziger, P. S., & Mourad, A. M. (2022). Genome-wide association mapping revealed SNP alleles associated with spike traits in wheat. Agronomy, 12(6), 1469.
   Google Scholar
• Gardner, S. N., Slezak, T., & Hall, B. G. (2015). kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome. Bioinformatics (Oxford, England), 31(17), 2877–2878. https://doi.org/10.1093/bioinformatics/btv271
   PubMed Web of Science ®Google Scholar
• Goya, R., Sun, M. G., Morin, R. D., & Leung, G. (2010). SNVMix: Predicting single nucleotide variants from next-generation sequencing of tumors. Bioinformatics, 26, 730–736.
   PubMed Web of Science ®Google Scholar
• Habib, P. T., Alsamman, A. M., Hassanein, S. E., Shereif, G. A., & Hamwieh, A. (2020). SNPector: SNP inspection tool for diagnosing gene pathogenicity and drug response in a naked sequence. F1000Research, 208(2133), 2133.
   Google Scholar
• Hackett, C. A., Boskamp, B., Vogogias, A., Preedy, K. F., & Milne, I. (2017). TetraploidSNPMap: Software for linkage analysis and QTL mapping in autotetraploid populations using SNP dosage data. Journal of Heredity, 108(4), 438–442.
   Web of Science ®Google Scholar
• Homer, N. S. (2010). Improved variant discovery through local re-alignment of short –read next generation sequencing data using srma. Genome Biology, 11(10), R99.
   PubMed Web of Science ®Google Scholar
• Howie, B. N., Donnelly, P., & Marchini, J. (2009). Impute-A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genetics, 5(6), e1000529. https://doi.org/10.1371/journal.pgen.1000529
   PubMed Web of Science ®Google Scholar
• Huang, S., Deng, L., Li, M., Lu, K., Wang, H., Fu, D., Mason, A. S., Liu, S., & Hua, W. (2013). Identification of genome-wide single nucleotide polymorphisms in allopolyploid crop Brassica napus. BMC Genomics, 14, 717.
   PubMed Web of Science ®Google Scholar
• Koboldt, D. C., Chen, K., Wylie, T., Larson, D. E., McLellan, M. D., Mardis, E. R., Weinstock, G. M., Wilson, R. K., & Ding, L. (2009). VarScan: Variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics (Oxford, England), 25(17), 2283–2285. https://doi.org/10.1093/bioinformatics/btp373
   PubMed Web of Science ®Google Scholar
• Langmead, B., Schatz, M. C., Lin, J., Pop, M., & Salzberg, S. L. (2009). Searching for SNPs with cloud computing- SoapSNP. Genome Biology, 10, 134.
   Web of Science ®Google Scholar
• Larson, D. E., Harns, C. C., Chen, K., Koboldt, D. C., Abbott, T. E., Dooling, D. J., Ley, T. J., Mardis, E. R., Wilson, R. K., & Ding, L. (2011). SomaticSniper: identification of somatic point mutations in whole genome sequencing data. Bioinformatics, 28, 311–317.
   PubMed Web of Science ®Google Scholar
• Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., & Durbin, R. (2009). Genome project data processing subgroup-the sequence alignment/map (SAM) format and SAM tools. Bioinformatics, 25, 2078–2089.
   PubMed Web of Science ®Google Scholar
• Li, Y., Willer, C. J., Ding, J., Scheet, P., & Abecasis, G. R. (2010). MaCH: Using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiology, 34, 816–834.
   PubMed Web of Science ®Google Scholar
• Mckennal, A., Hannal, M., & Banks, E. (2010). The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20, 1297–1303.
   PubMed Web of Science ®Google Scholar
• Meyer, M., Stenzel, U., Myles, S., Prüfer, K., & Hofreiter, M. (2007). Targeted high-throughput sequencing of tagged nucleic acid samples. Nucleic Acids Research, 35, e97.
   PubMed Web of Science ®Google Scholar
• Milne, I., Bayer, M., Cardle, L., & Shaw, P. (2010). Tablet—next generation sequence assembly visualization. Bioinformatics, 26, 401–402.
   PubMed Web of Science ®Google Scholar
• Nickerson, D. A., Tobe, V. O., & Taylor, S. L. (1997). PolyPhred: Automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. Nucleic Acids Research, 25(14), 2745–2751.
   PubMed Web of Science ®Google Scholar
• Nijveen, H., Kaauwen, M. V., Esselink, D. G., Hoegen, B., & Vosman, B. (2013). QualitySNPng: A user-friendly SNP detection and visualization tool. Nucleic Acids Research, 30, 1141–1151.
   Google Scholar
• Ning, Z., Caccamo, M., & Mullikin, J. C. (2005). ssahaSNP - a polymorphism detection tool on a whole genome scale [Paper presentation]. IEEE Computational Systems Bioinformatics Conference Workshops (pp. 251–252).
   Google Scholar
• Ossowski, S., Schneeberger, K., & Clark, R. M. (2008). Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Research, 18, 2014–2033.
   Web of Science ®Google Scholar
• Pers, T. H., Timshel, P., & Hirschhom, J. N. (2015). SNPsnap: a Web-based tool for identification and annotation of matched SNPs. Bioinformatics, 31, 418–430.
   PubMed Web of Science ®Google Scholar
• Peterlongo, P., Schnel, N., Pisanti, N., Sagot, M. F., & Lacroix, V. (2010). Identifying SNPs without a reference genome by comparing raw reads. In String Processing and Information Retrieval: 17th International Symposium, SPIRE. Proceedings (pp. 147–158). Springer.
   Google Scholar
• Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., Daly, M. J., & Sham, P. C. (2007). PLINK: A tool set for whole-genome association and population-based linkage analyses. American Journal of Human Genetics, 81(3), 559–575.
   PubMed Web of Science ®Google Scholar
• Ratan, A., Zhang, Y., Hayes, V. M., Schuster, S. C., & Miller, W. (2010). Calling SNPs without a reference sequence. BMC Bioinformatics, 11(1), 1–3.
   PubMedGoogle Scholar
• Rengasamy, V., & Madduri, K. (2016). SPRITE: A fast parallel SNP detection pipeline. In: J. Kunkel, P. Balaji, & J. Dongarra (Eds.), High performance computing. ISC High Performance 2016. Lecture Notes in Computer Science (p. 967). Springer.
   Google Scholar
• Rimmer, A., Phan, H., & Mathieson, I. (2014). Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications. Nature Genetics, 46, 912–918.
   PubMed Web of Science ®Google Scholar
• Riva, A. (2012). Large-scale computational identification of regulatory SNPs with rSNP-MAPPER. BMC Genomics, 13, S7.
   PubMed Web of Science ®Google Scholar
• Satya, R. V., Zavaljevski, N., & Reifman, J. (2011). SNIT: SNP identification for strain typing. Code for Biology and Medicine, 6, 14–25.
   Google Scholar
• Schirmer, M., D’Amore, R., Ijaz, U. Z., Hall, N., & Quince, C. (2016). Illumina error profiles: Resolving fine-scale variation in metagenomic sequencing data. BMC Bioinformatics, 17(1), 125.
   PubMedGoogle Scholar
• Schmitt, A. O., Assmus, J., Bortfeldt, R. H., & Brockmann, G. A. (2010). CandiSNPer: A web tool for the identification of candidate SNPs for causal variants. Bioinformatics, 26, 969–970.
   PubMed Web of Science ®Google Scholar
• Semalaiyappan, J., Selvanayagam, S., Rathore, A., Gupta, S. K., Chakraborty, A., Gujjula, K. R., Haktan, S., Viswanath, A., Malipatil, R., Shah, P., & Govindaraj, M. (2023). Development of a new AgriSeq 4K mid-density SNP genotyping panel and its utility in pearl millet breeding. Frontiers in Plant Science, 13, 5443.
   Web of Science ®Google Scholar
• Senthilvel, S., Ghosh, A., Shaik, M., Shaw, R. K., & Bagali, P. G. (2019). Development and validation of an SNP genotyping array and construction of a high-density linkage map in castor. Scientific Reports, 9(1), 3003.
   PubMedGoogle Scholar
• Shen, Y., Wan, Z., & Coarfa, C. (2010). A SNP discovery method to assess variant allele probability from next-generation re-sequencing data. Genome Research, 20, 273–280.
   PubMed Web of Science ®Google Scholar
• Singh, R., Bollina, V., Higgins, E. E., Clarke, W. E., Eynck, C., Sidebottom, C., Gugel, R., Snowdon, R., & Parkin, I. A. (2015). Single-nucleotide polymorphism identification and genotyping in Camelina sativa. Molecular Breeding, 35(1), 35.
   PubMed Web of Science ®Google Scholar
• Su, J., Li, L., Zhang, C., Wang, C., Gu, L., Wang, H., Wei, H., Liu, Q., Huang, L., & Yu, S. (2018). Genome-wide association study identified genetic variations and candidate genes for plant architecture component traits in Chinese upland cotton. Theoretical and Applied Genetics, 131(6), 1299–1314.
   PubMed Web of Science ®Google Scholar
• Sun, X., Liu, D., Zhang, X., Li, W., Liu, H., Hong, W., Jiang, C., Guan, N., Ma, C., Zeng, H., & Xu, C. (2013). SLAF-seq: An efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing. PLoS One, 8(3), e58700.
   PubMed Web of Science ®Google Scholar
• Tang, J., Leunissen, J. A. M., & Voorrips, R. (2008). HaploSNPer: A web-based allele and SNP detection tool. BMC Genetics, 9, 23.
   PubMed Web of Science ®Google Scholar
• Tang, J., Vosman, B., & Voorrips, R. E. (2006). QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species. BMC Bioinformatics, 7, 438–447.
   PubMed Web of Science ®Google Scholar
• Terada, A., Ryo, Y., Koji, T., & Jun, S. (2016). LAMPLINK: Detection of statistically significant SNP combinations from GWAS data. Bioinformatics, 32, 3513–3515.
   PubMed Web of Science ®Google Scholar
• Truong, H. T., Ramos, A. M., Yalcin, F., de Ruiter, M., van der Poel, H. J., Huvenaars, K. H., Hogers, R. C., van Enckevort, L. J., Janssen, A., van Orsouw, N. J., & van Eijk, M. J. (2012). Sequence-based genotyping for marker discovery and co-dominant scoring in germplasm and populations. PLoS One, 7(5), e37565.
   PubMed Web of Science ®Google Scholar
• Turner, S. D., Nagraj, V. P., Scholz, M., Jessa, S., Acevedo, C., Ge, J., Woerner, A. E., & Budowle, B. (2022). Skater: An R package for SNP-based kinship analysis, testing, and evaluation. F1000Research. 11.
   Google Scholar
• Van Orsouw, N. J., Hogers, R. C. J., & Janson, A. (2007). Complexity reduction of polymorphic sequences (CRoPS): a novel approach for large-scale polymorphism discovery in complex genomes. PLoS One, 2, e1172.
   PubMed Web of Science ®Google Scholar
• Wang, X., Zheng, Z., Cai, Y., Chen, T., Li, C., Fu, W., & Jiang, Y. (2017). CNVcaller: Highly efficient and widely applicable software for detecting copy number variations in large populations. GigaScience, 6(12), gix115.
   Web of Science ®Google Scholar
• Weckx, S., Favero, J. D., & Rademakers, R. R. (2005). novoSNP, a novel computational tool for sequence variation discovery. Genome Research, 15, 436–442.
   PubMed Web of Science ®Google Scholar
• Wei, Z., Wang, W., Hu, P., Lyon, G. J., & Hakonarson, H. (2011). SNVer: A statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data. Nucleic Acids Research, 39(19), e132. https://doi.org/10.1093/nar/gkr599
   PubMed Web of Science ®Google Scholar
• Wu, X., Islam, A. F., Limpot, N., Mackasmiel, L., Mierzwa, J., Cortés, A. J., & Blair, M. W. (2020). Genome-wide Snp identification and association mapping for seed mineral concentration in mung bean (Vigna radiata L.). Frontiers in Genetics, 11, 656.
   PubMed Web of Science ®Google Scholar
• Zhang, J., Wheeler, D. A., Yakub, I., Wei, S., Sood, R., Rowe, W., Liu, P. P., Gibbs, R. A., & Buetow, K. H. (2005). SNPdetector: A software tool for sensitive and accurate SNP detection. PLoS Computational Biology, 1(5), e53. https://doi.org/10.1371/journal.pcbi.0010053
   PubMed Web of Science ®Google Scholar