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1 Aggarwal, R.K., Brar, D.S., and Khush, G.S. (1997). Two new genomes in the oryza complex identified on the basis of molecular divergence analysis using total genomic hybridization. Molecular & General Genetics 254: 1–12.

2 Akkurt, M., Welter, L., Maul, E. et al. (2007). Development of SCAR markers linked to powdery mildew (Uncinula necator) resistance in grapevine (Vitis vinifera L. and Vitis sp.). Molecular Breeding 19: 103–111.

3 Bachlava, E., Taylor, C.A., Tang, S. et al. (2012). SNP discovery and development of a high‐density genotyping array for sunflower. PLoS One 7 (1): e29814.

4 Batley, J., Barker, G., O’Sullivan, H. et al. (2003). Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data. Plant Physiology 132 (1): 84–91.

5 Bhatia, D. (2020). Advanced quantitative genetics technologies for accelerating plant breeding. In: Accelerated Plant Breeding, vol. I (eds. S.S. Gosal and S.H. Wani). Springer Verlag https://doi.org/10.1007/978‐3‐030‐41866‐3_5.

6 Bhatia, D., Sharma, R., Vikal, Y. et al. (2011). Marker assisted development of bacterial blight resistant, dwarf and high yielding versions of two traditional Basmati rice cultivars. Crop Science 51: 759–770.

7 Bhatia, D., Wing, R.A., and Singh, K. (2013). Genotyping by sequencing, its implications and benefits. Crop Improvement 40: 101–111.

8 Bhatia, D., Wing, R.A., Yu, Y. et al. (2018). Genotyping by sequencing of rice interspecific backcross inbred lines identifies QTLs for grain weight and grain length. Euphytica 214: 41. https://doi.org/10.1007/s10681‐018‐2119‐1.

9 Botstein, D., White, R.L., Skolnick, M., and Davis, R.W. (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics 32 (314): 331.

10 Brar, D.S. and Dhaliwal, H.S. (1997). Molecular markers and their application in crop improvement. In: Proceedings 3rd Agricultural Science Congress (eds. M.S. Bajwa et al.). New Delhi, India: Natl. Acad. Agr. Sci.

11 Brookes, A.J. (1999). The essence of SNPs. Gene 234: 177–186.

12 Chao, W.Z., Tang, C.H., Zhang, J.S. et al. (2018). Development of a stable SCAR marker for rapid identification of Ganoderma lucidum Hunong 5 cultivar using DNA pooling method and inter‐simple sequence repeat markers. Journal of Integrative Agriculture 17 (1): 130–138.

13 Chen, H., Xie, W., He, H. et al. (2013). A high density SNP genotyping array for rice biology and molecular breeding. Molecular Plant 7: 541–553.

14 Ching, A., Caldwell, K.S., Jung, M.T., and Dolan, M. (2002). SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genetics 3 (1): 19. https://doi.org/10.1186/1471‐2156‐3‐19.

15 Cho, Y.G., McCouch, S.R., Kuiper, M. et al. (1997). Integration of AFLP markers into an RFLP and SSLP map of rice (Oryza sativa L.). Rice Genet. Newsletter 14: 106–109.

16 Chung, Y.S., Choi, S.C., Jun, T.‐H., and Kim, C. (2017). Genotyping by sequencing: a promising tool for plant genetics research and breeding. Horticulture, Environment and Biotechnology 58 (5): 425–431.

17 Collard, B.C.Y., Jahufer, M.Z.Z., Brouwer, J.B., and Pang, E.C.K. (2005). An introduction to markers, quantitative trait loci (QTL) mapping and marker‐assisted selection for crop improvement: the basic concepts. Euphytica 142: 169–196.

18 Coryell, V.H., Jessen, H., Schupp, J.M. et al. (1999). Allele‐specific hybridization markers for soybean. Theoretical and Applied Genetics 98: 690–696.

19 Ding, C. and Jin, S. (2009, 2003). High‐throughput methods for SNP genotyping. In: Single Nucleotide Polymorphisms, Methods in Molecular Biology, vol. 578 (ed. A.A. Komar). Humana Press, A Part of Springer Science+Business Media, LLC https://doi.org/10.1007/978‐1‐60327‐411‐1_16.

20 Elkot, A.F.A., Chhuneja, P., Kaur, S. et al. (2015). Marker assisted transfer of two powdery mildew resistance genes PmTb7A.1 and PmTb7A.2 from Triticum boeoticum (Boiss.) to Triticum aestivum (L.). PLoS One 10 (6): e128297.

21 Fang, T., Lei, L., Li, G. et al. (2020). Development and deployment of KASP markers for multiple alleles of Lr34 in wheat. Theoretical and Applied Genetics 133: 2183–2195.

22 Fehr, W. (1984). Genetic Contributions to Yield Gains of Five Major Crop Plants. Madison, Wisconsin: Special publication No. 7 Crop Science Society of America.

23 Fulton, T.M., Nelson, J.C., and Tanksley, S.D. (1997). Introgression and DNA marker analysis of Lycopersicon peruvianum, a wild relative of cultivated tomato into L. esculentum followed through three successive backcross generations. Theoretical and Applied Genetics 95: 895–902.

24 Ganal, M.W., Altmann, T., and Roder, M.S. (2009). SNP identification in crop plants. Current Opinion in Plant Biology 12 (2): 211–217.

25 Ganal, M.W., Durstewitz, G., Polley, A. et al. (2011). A large maize (Zea mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome. PLoS One 6.

26 Gibbs, R.A. et al. (2009). Genome‐wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 324: 528–532.

27 Grewal, S., Othmeni, M., Walker, J. et al. (2020). Development of Wheat‐Aegilops caudata introgression lines and their characterization using genome‐specific KASP markers. Frontiers in Plant Science 11: 606.

28 Grodzicker, T., Williams, J., Sharp, P., and Sambrook, J. (1975). Physical mapping of temperature sensitive mutants of adenovirus. Cold Spring Harbor Symposia on Quantitative Biology 39: 439–446.

29 Gupta, P.K. and Rustgi, S. (2004). Molecular markers from the transcribed/expressed region of the genome in higher plants. Functional & Integrative Genomics 4: 139–162.

30 Haanstra, J.P.W., Wye, C., Odinot, P. et al. (1999). An integrated high density RFLP‐AFLP map of tomato based on two Lycopersicon esculentum x L. pennellii F2 populations. Theoretical and Applied Genetics 99: 254–271.

31 Harushima, Y., Yano, M., Shomura, A. et al. (1998). A high density rice genetic linkage map with 2275 markers using a single F2 population. Genetics 148: 479–494.

32 Helentjaris, T., Slocum, M., Wright, S. et al. (1986). Construction of genetic linkage maps in maize and tomato using restriction fragment length polymorphisms. Theoretical and Applied Genetics 61: 650–658.

33 Huang, N., Angeles, E.R., Domingo, J. et al. (1997). Pyramiding bacterial blight resistance gene in rice: marker assisted selection using RFLP and PCR. Theoretical and Applied Genetics 95: 313–320.

34 Hunt, G.J. (1997). Construction of linkage maps with RAPD markers. In: Fingerprinting Methods Based on Arbitrarily Primed PCR (eds. M.R. Micheli and R. Bova). Berlin, Heidelberg: Springer Lab Manuals. Springer https://doi.org/10.1007/978‐3‐642‐60441‐6_22.

35 Hussain, W., Baenziger, P.S., Belamkar, V. et al. (2017). Genotyping‐by‐Sequencing derived high‐density linkage map and its application to QTL mapping of flag leaf traits in bread wheat. Scientific Reports 7: 16394.

36 IRGSP (2005). The map‐based sequence of the rice genome. Nature 436: 793–800. (Suppl. Table 18).

37 Jaccoud, D., Peng, K., Feinstein, D., and Kilian, A. (2001). Diversity arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Research 29: e25.

38 Jamali, S.H., Cockram, J., and Hickey, L.T. (2019). Insights into deployment of DNA markers in plant variety protection and registration. Theoretical and Applied Genetics 132: 1911–1929.

39 Jena, K.K., Khush, G.S., and Kochert, G. (1992). RFLP analysis of rice introgression lines. Theoretical and Applied Genetics 84: 608–616.

40 Joshi, S.P., Ranjekar, P.K., and Gupta, V.S. (1999). Molecular markers in plant genome analysis. Current Science 77: 230–240.

41 Kagale, S., Koh, C., Clarke, W.E. et al. (2016). Analysis of genotyping by sequencing data. Methods in Molecular Biology 1374: 269–284.

42 Kang, J.‐W., Shin, D., Cho, J.H. et al. (2019). Accelerated development of rice stripe virus‐resistant, near‐isogenic rice lines through marker‐assisted backcrossing. PLoS One 14 (12): e0225974.

43 Kasai, K., Morikawa, Y., Sorri, V.A. et al. (2000). Development of SCAR markers to the PVY resistance gene Ryadg based on a common feature of plant disease resistance genes. Genome 43: 1–8.

44 Kumar, A., Dixit, S., and Henry, A. (2013). Marker‐assisted introgression of major QTLs for grain yield under drought in rice. In: Translational Genomics for Crop Breeding Volume 2: Abiotic Stresses, Yield and Quality (eds. R.K. Varshney and R. Tuberosa). Wiley.

45 Kumar, K., Sarao, P.S., Bhatia, D. et al. (2018). High‐resolution genetic mapping of novel brown planthopper resistance locus, Bph34 in Oryza sativa X Oryza nivara (Sharma & Shastry) derived interspecific F2 population. Theoretical and Applied Genetics 131: 1163–1171.

46 Laucou, V., Haurogne, K., Ellis, N., and Rameau, C. (1998). Genetic mapping in pea. 1. RAPD‐based genetic linkage map of Pisum sativum. Theoretical and Applied Genetics 97: 905–915.

47 Li, H., Vikram, P., Singh, R.P. et al. (2015). A high density GBS map of bread wheat and its application for dissecting complex disease resistance traits. BMC Genomics 16: 216.

48 Litt, M. and Luty, J.M. (1989). A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. American Journal of Human Genetics 44: 397–401.

49 Liu, Z., Sun, Q., Ni, Z., and Yang, T. (1999). Development of SCAR markers linked to the Pm21 gene conferring resistance to powdery mildew in common wheat. Plant Breeding 118: 215–219.

50 Lotti, C., Salvi, S., Pasqualone, A. et al. (2000). Integration of AFLP markers into an RFLP‐based map of durum wheat. Plant Breeding 119 (5): 393–401.

51 Makhoul, M., Rambla, C., Voss‐Fels, K.P. et al. (2020). Overcoming polyploidy pitfalls: a user guide for effective SNP conversion into KASP markers in wheat. Theoretical and Applied Genetics 133 (8): 2413–2430.

52 Mardis, E.R. (2008). Next generation DNA sequencing methods. Annual Review of Genomics and Human Genetics 9: 387–402.

53 Matukumalli, L.K., Lawley, C.T., Schnabel, R.D. et al. (2009). Development and characterization of a high density SNP genotyping assay for cattle. PLoS One 4: e5350.

54 McCouch, S.R., Teytelman, L., Xu, Y. et al. (2002). Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Research 9: 199–207.

55 McCouch, S.R., Zhao, K., Wright, M. et al. (2010). Development of genome‐wide SNP assays for rice. Breeding Science 60: 524–535.

56 McCouch, S.R., Wright, M.H., Tung, C.‐W. et al. (2015). Open access resources for genome‐wide association mapping in rice. Nature Communications 7: 10532.

57 Melchinger, A.E., Messemer, M.M., Lee, M. et al. (1991). Diversity and relationship among US maize inbreds revealed by RFLPs. Crop Science 31: 669–678.

58 Milbourne, D., Meyer, R.C., Collins, A.J. et al. (1998). Isolation, characterization and mapping of simple sequence repeat loci in potato. Molecular & General Genetics 259: 233–245.

59 Mir, R.R., Hiremath, P.J., Lizarazu‐Riera, O., and Varshney, R.K. (2013). Evolving molecular marker technologies in plants: from RFLPs to GBS. In: Diagnostics in Plant Breeding, https://doi.org/10.1007/978‐94‐007‐5687‐8__11 (eds. T. Lübberstedt and R.K. Varshney). Dordrecht: Springer Science Business Media.

60 Mullis, K., Faloona, F., Scharf, S. et al. (1986). Specific enzymatic amplication of DNA in vitro: the polymerase chain reaction. Cold Spring Harbor Symposium on Quantitative Biology. 51: 263–273.

61 Nguyen, K.L., Grondin, A., Courtois, B., and Gantet, P. (2019). Next‐Generation sequencing accelerates crop genome discovery. Trends in Plant Science 24: 263–274.

62 Olsen, M., Hood, L., Cantor, C., and Botstein, D. (1989). A common language for physical mapping of the human genome. Science 245: 1434–1435.

63 Orjuela, J., Garavito, A., Bouniol, M. et al. (2010). A universal core genetic map for rice. Theoretical and Applied Genetics 120: 563–572.

64 Parasnis, A.S., Ramakrishna, W., Chowdari, K.V. et al. (1999). Microsatellite (GATA)n reveals sex‐specific differences in papaya. Theoretical and Applied Genetics 99: 1047–1052.

65 Paterson, A.H., Tanksley, S.D., and Sorrels, M.E. (1991). DNA markers in crop improvement. Advances in Agronomy 46: 39–90.

66 Paull, J.G., Chalmers, K.J., Karakousis, A. et al. (1998). Genetic diversity in Australian wheat varieties and breeding material based on RFLP data. Theoretical and Applied Genetics 96: 435–446.

67 Poland, J. and Rife, T.W. (2012). Genotyping‐by‐sequencing for plant breeding and genetics. Plant Genitics 5: 92–102.

68 Poland, J.A., Brown, P.J., Sorrells, M.E., and Jannink, J.‐L. (2012). Development of high‐density genetic maps for barley and wheat using a novel two‐enzyme genotyping‐by‐sequencing approach. PLoS One 7 (2): e32253.

69 Puritz, J.B., Hollenbeck, C.M., and Gold, J.R. (2014). dDocent: a RADseq, variant‐calling pipeline designed for population genomics of non‐model organisms. Peer Journal 2: e431.

70 Qi, L., Echalier, B., Friebe, B., and Gill, B.S. (2003). Molecular characterization of a set of wheat deletion stocks for use in chromosome bin mapping of ESTs. Functional & Integrative Genomics 3: 39–55. https://doi.org/10.1007/s10142‐002‐0063‐5.

71 Ramos, A.M., Crooijmans, R.P.M.A., Affara, N.A. et al. (2009). Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. PLoS One 4: e6524.

72 Richard, I. and Beckman, J.S. (1995). How neutral are synonymous codon mutations? Nature Genetics 10: 259.

73 Roder, M.S., Korzun, V., Wendehake, K. et al. (1998). A microsatellite map of wheat. Genetics 149: 2007–2023.

74 Rosas, J.E., Bonnecarrère, V., and Pérez de Vida, V.F. (2014). One‐step, codominant detection of imidazolinone resistance mutations in weedy rice (Oryza sativa L.). Electronic Journal of Biotechnology 17: 95–101.

75 Sachidanandam, R., Weissman, D., Schmidt, S.C. et al. (2001). A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409 (6822): 928–933.

76 Sanger, F., Nicklen, S., and Coulson, A.R. (1977). DNA sequencing with chain chain‐terminating inhibitors. Proceedings of the National Academy Sciences of the United States of America 74: 5463–5467.

77 Semagn, K., Bjornstad, A., and Ndjiondjop, M.N. (2006). An overview of molecular marker methods for plants. African Journal of Biotechnology 5 (25): 2540–2568.

78 Semagn, K., Babu, R., Hearne, S., and Olsen, M. (2013). Single nucleotide polymorphism genotyping using Kometitive allele specific PCR (KASP): overview of the technology and its application in crop improvement. Molecular Breeding 33: 1–14.

79 Sharopova, N., McMullen, M.D., Schultz, L. et al. (2002). Development and mapping of SSR markers for maize. Plant Molecular Biology 48: 463–481.

80 Shendure, J.A., Porreca, G.J., Church, G.M. et al. (2011). Overview of DNA sequencing strategies. Current Protocols in Molecular Biology 7 (1): 1–7.1.23. https://doi.org/10.1002/0471142727.mb0701s96.

81 Sidhu, G.K., Rustgi, S., Shafqat, M.N. et al. (2008). Fine structure mapping of a gene‐rich region ofwheat carrying Ph1, a suppressor of crossing over between homoeologous chromosomes. Proceedings of the National Academy Sciences of the United States of America 15: 5815–5820.

82 Sim, S.‐C., Durstewitz, G., Plieske, J. et al. (2012). Development of a large SNP genotyping array and generation of high‐density genetic maps in tomato. PLoS One 7 (7): e40563. https://doi.org/10.1371/journal.pone.0040563.

83 Singh, B.D. and Singh, A.K. (2015). Marker‐Assisted Plant Breeding: Principles and Practices. https://doi.org/10.1007/978‐81‐322‐2316‐0. Springer (India) Pvt. Ltd.

84 Singh, S., Sidhu, J.S., Huang, N. et al. (2001). Pyramiding three bacterial blight resistance genes (xa5, xa13 and Xa21) using marker assisted selection into indica cultivar PR106. Theoretical and Applied Genetics 102: 1011–1015.

85 Smith, J.S.C. and Smith, O.S. (1992). Fingerprinting crop varieties. Advances in Agronomy 47: 85–140.

86 Sobrino, B., Briona, M., and Carracedoa, A. (2005). SNPs in forensic genetics: a review on SNP typing methodologies. Forensic Science International 154: 181–194.

87 Soleimani, V.D., Baum, B.R., and Johnson, D.A. (2003). Efficient validation of single nucleotide polymorphisms in plants by allele‐specific PCR, with an example from barley. Plant Molecular Biology Reporter 21: 281–288.

88 Somers, D.J., Isaac, P., and Edwards, K. (2004). A high‐density microsatellite consensus map for bread wheat (Triticum aestivum L.). Theoretical and Applied Genetics 109: 1105–1114.

89 Song, Q.J., Shi, J.R., Singh, S. et al. (2005). Development and mapping of microsatellite (SSR) markers in wheat. Theoretical and Applied Genetics 110: 550–560.

90 Su, A., Song, W., Xing, J. et al. (2016). Identification of genes potentially associated with the fertility instability of S‐Type cytoplasmic male sterility in maize via bulked segregant RNA‐Seq. PLoS One 11 (9): e0163489.

91 Su, C., Wang, W., Gong, S. et al. (2017). High density linkage map construction and mapping of yield trait QTLs in maize (Zea mays) using the genotyping‐by‐sequencing (GBS) technology. Frontiers in Plant Science 8: 706. https://doi.org/10.3389/fpls.2017.00706.

92 Takagi, H., Tamiru, M., Abe, A. et al. (2015). MutMap accelerates breeding of a salt‐tolerant rice cultivar. Nature Biotechnology 33: 445–449.

93 Tanksley, S.D. and Nelson, J.C. (1996). Advanced backcross QTL analysis: a method for simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theoretical and Applied Genetics 92: 191–203.

94 Tanksley, S.D., Ganal, M.W., Prince, J.P. et al. (1992). High density molecular linkage maps of tomato and potato genomes. Genetics 132: 1141–1160.

95 Tanksley, S.D., Grandillo, S., Fulton, T.M. et al. (1996). Advanced backcross QTL analysis in a cross between an elite processing line of tomato and its wild relative L. pimpinellifolium. Theoretical and Applied Genetics 92: 213–224.

96 Temnykh, S., Park, W.D., Ayres, N. et al. (2000). Mapping and genome organization of mirosatellite sequences in rice (Oryza sativa) Theor. Applied Genetics 100: 697–712.

97 Tung, C.W., Zhao, K., Wright, M.H. et al. (2010). Development of a research platform for dissecting phenotype genotype associations in rice (Oryza spp.). Rice 3: 205–217.

98 Vos, P., Hogers, R., Bleeker, M. et al. (1995). AFLP: a new technique for DNA fingerprinting. Nucleic Acids Research 23: 4407–4414.

99 Wang, D.G., Fan, J.B., Siao, C.J. et al. (1998). Large‐scale identification, mapping, and genotyping of single‐nucleotide polymorphisms in the human genome. Science 280: 1077–1082.

100 Wickland, D.P., Battu, G., Hudson, K.A. et al. (2017). A comparison of genotyping‐by‐sequencing analysis methods on low‐coverage crop datasets shows advantages of a new workflow, GB‐eaSy. BMC Bioinformatics 18: 586.

101 Williams, J.G.K., Kublelik, A.R., Livak, K.J. et al. (1990). DNA polymorphism’s amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research 18: 6531–6535.

102 Xiao, J., Grandillo, S., Ahn, S.N. et al. (1996). Genes from wild rice improved yield. Nature 384: 223–224.

103 Xiao, J., Li, J., Grandillo, S. et al. (1998). Identification of trait improving QTL alleles from a wild rice relative Oryza rufipogon. Genetics 150: 899–909.

104 Yang, G., Chen, S., Chen, L. et al. (2019). Development of a core SNP arrays based on the KASP method for molecular breeding of rice. Rice 12: 21.

105 Yasuda, N., Mitsunaga, T., Hayashi, K. et al. (2015). Effects of pyramiding quantitative resistance genes pi21, Pi34, and Pi35 on rice leaf blast disease. Plant Disease 99: 904–909.

106 Zhang, X., Yang, Q., Rucker, E. et al. (2017). Fine mapping of a quantitative resistance gene for gray leaf spot of maize (Zea mays L.) derived from teosinte (Z. mays ssp. parviglumis). Theoretical and Applied Genetics 130: 1285–1295.

107 Zhou, Z., Zhang, C., Zhou, Y. et al. (2016). Genetic dissection of maize plant architecture with an ultra‐high density bin map based on recombinant inbred lines. BMC Genomics 17: 178. https://doi.org/10.1186/s12864‐016‐2555‐z.

108 Zhu, M., Liu, D., Liu, W. et al. (2017). QTL mapping using an ultra‐high‐density SNP map reveals a major locus for grain yield in an elite rice restorer R998. Scientific Reports 7: 10914. https://doi.org/10.1038/s41598‐017‐10666‐7.

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