Browse > Article
http://dx.doi.org/10.9787/KJBS.2018.50.4.364

Current Status and Prospect of Wheat Functional Genomics using Next Generation Sequencing  

Choi, Changhyun (National Institute of Crop Science)
Yoon, Young-Mi (National Institute of Crop Science)
Son, Jae-Han (National Institute of Crop Science)
Cho, Seong-Woo (Institute of Agricultural Sciences and Technology, Chonbuk National University)
Kang, Chon-Sik (National Institute of Crop Science)
Publication Information
Korean Journal of Breeding Science / v.50, no.4, 2018 , pp. 364-377 More about this Journal
Abstract
Hexaploid wheat (common wheat/bread wheat) is one of the most important cereal crops in the world and a model for research of an allopolyploid plant with a large, highly repetitive genome. In the heritability of agronomic traits, variation in gene presence/absence plays an important role. However, there have been relatively few studies on the variation in gene presence/absence in crop species, including common wheat. Recently, a reference genome sequence of common wheat has been fully annotated and published. In addition, advanced next-generation sequencing (NGS) technology provides high quality genome sequences with continually decreasing NGS prices, thereby dawning full-scale wheat functional genomic studies in other crops as well as common wheat, in spite of their large and complex genomes. In this review, we provide information about the available tools and methodologies for wheat functional genomics research supported by NGS technology. The use of the NGS and functional genomics technology is expected to be a powerful strategy to select elite lines for a number of germplasms.
Keywords
Wheat; Ngs; Functional genomics; MAS; SNP; Genome editing; Marker;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Avni R, Nave M, Barad O, Baruch K, Twardziok SO, Gundlach H et al. 2017. Wild emmer genome architecture and diversity elucidate wheat evolution and domestication. Science 357: 93-97.   DOI
2 Bagge M, Xia XC, Lubberstedt T. 2007. Functional markers in wheat. Curr Opin Plant Biol 10: 211-216.   DOI
3 Berkman PJ, Skarshewski A, Lorenc T, Lai K, Duran C, Ling EY et al. 2011. Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS. Plant Biotechnol J 9: 768-775.   DOI
4 Lai K, Lorenc MT, Lee HC, Berkman PJ, Bayer PE, Visendi P et al. 2015. Identification and characterization of more than 4 million inter-varietal SNPs across the group 7 chromossomes of bread wheat. Plant Biotechnol J 13: 97-104.   DOI
5 Li A, Liu D, Wu J, Zhao X, Hao M, Geng S, Yan J, Jiang X, Zhang L, Wu J, Yin L, Zhang R, Wu L, Zheng Y, Mao L. 2014. mRNA and small RNA transcriptomes reveal insights into dynamic homoeolog regulation of allopolyploid heterosis in nascent hexaploid wheat. Plant Cell 26: 1878-1900.   DOI
6 Liang Z, Chen K, Li T, Zhang Y, Wang Y, Zhao Q, Liu J, Zhang H, Liu C, Ran Y, Gao C. 2017. Efficient DNA-free genome editing of bread wheat using CRISPR/Cas9 ribonucleoprotein complexes. Nat Commun 8: 14261.   DOI
7 Ling HQ, Zhao S, Liu D, Wang J, Sun H, Zhang C, Fan H, Li D, Dong L, Tao Y, Gao C et al. 2013. Draft genome of the wheat A-genome progenitor Triticum urartu. Nature 496: 87-90.   DOI
8 Liu Y, He Z, Apppes R, Xia X. 2012. Functional markers in wheat: current status and future prospects. Theor Appl Genet 125: 1-10.   DOI
9 Liu W, Frick M, Huel R, Nykiforuk CL, Wang X, Gaudet DA, Eudes F, Conner RL, Kuzyk A, Chen Q, Kang Z, Laroche A. 2014. The stripe rust resistance gene Yr10 encodes an evolutionary-conserved and unique CC-NBS-LRR sequence in wheat. Mol Plant 7: 1740-1755.   DOI
10 Liu Y, Wang L, Deng M, Li Z, Lu Y, Wang J, Wei Y, Zheng Y. 2015. Genome-wide association study of phosphorus-deficiency-tolerance traits in Aegilops tauschii. Theor Appl Genet 128: 2203-2212.   DOI
11 Liu Y, Lin Y, Gao S, Li Z, Ma J, Deng M, Chen G, Wei Y, Zheng Y. 2017. A genome-wide association study of 23 agronomic traits in Chinese wheat landraces. Plant J 91: 861-873.   DOI
12 Cavanagh CR, Chao S, Wang S, Huang BE, Stephen S, Kiani S et al. 2013. Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars. Proc Natl Acad Sci USA 110: 8057-8062.   DOI
13 Berkman PJ, Skarshewski A, Manoli S, Lorenc MT, Stiller J, Smits L, Lai K, Campbell E, Kubalakova M, Simkova H, Batley J, Dolezel J, Hernandez P, Edwards D. 2012. Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation. Theor Appl Genet 124: 423-432.   DOI
14 Botticella E, Sestili F, Hernandez-Lopez A, Phillips A, Lafiandra D. 2011. High resolution melting analysis for the detection of EMS induced mutations in wheat SBEIIa genes. BMC Plant Biol 11: 156.   DOI
15 Brinton J, Simmonds J, Minter F, Leverington-Waite M, Snape J, Uauy C. 2017. Increased pericarp cell length underlies a major quantitative trait locus for grain weight in hexaploid wheat. New Phytol 215: 1026-1038.   DOI
16 Chapman JA, Mascher M, Buluc A, Barry K, Georganas E et al. 2015. A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. 2015. Genome Biol 16: 26.   DOI
17 Ni F, Qi J, Hao QQ, Lyu B, Luo MC, Wang Y, Chen FJ, Wang SY, Zhang CZ, Epstein L, Zhao XY, Wang HG, Zhang XS, Chen CX, Sun LZ, Fu DL. 2017. Wheat Ms2 encodes for an orphan protein that confers male sterility in grass species. Nat Commun 8: 15121.   DOI
18 Choulet F, Wicker T, Rustenholz C, Paux E, Salse J, Leroy P et al. 2010. Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces. Plant Cell 22: 1686-1701.   DOI
19 Clavijo BJ, Venturini L, Schudoma C, Accinelli GG, Kaithakottil G, Wright J, Borrill P, Kettleborough G, Heavens D, Chapman H et al. 2017. An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations. Genome Res 27: 885-896.   DOI
20 Luo MC, Deal KR, Akhunov ED, Akhunova AR, Anderson OD, Anderson JA, Blake N, Clegg MT, Coleman-Derr D, Conley EJ et al. 2009. Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae. Proc Natl Acad Sci USA 106: 15780-15785.   DOI
21 Maccaferri M, Zhang J, Bulli P, Abate Z, Chao S, Cantu D, Bossolini E, Chen X, Pumphrey M, Dubcovsky J. 2015. A genome-wide association study of resistance to stripe rust (Puccinia striiformis f. sp. tritici) in a worldwide collection of hexaploid spring wheat (Triticum aestivum L.), G3. Genes Genomes Genet 5: 449-465.
22 Montenegro JD, Golicz AA, Bayer PE, Hurgobin B, Lee H, Chan CKK, Visendi P, Lai K, Dolezel J, Batley J, Edwards D. 2017. The pangenome of hexaploid bread wheat. Plant J 90: 1007-1013.   DOI
23 Ovenden B, Milgate A, Wade LJ, Rebetzke GJ, Holland JB. 2017. Genome-wide associations for water-soluble carbohydrate concentration and relative maturity in wheat using SNP and DArT marker arrays, G3. Genes Genomes Genet 7: 2821-2830.
24 Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H et al. 2009. The Sorghum bicolor genome and the diversification of grasses. Nature 457: 551-556.   DOI
25 Paux E, Roger D, Badaeva E, Gay G, Bernard M, Sourdille P et al. 2006. Characterizing the composition and evoloution of homoleologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B. Plant J 48: 463-474.   DOI
26 Gao L, Wang S, Li XY, Wei XJ, Zhang YJ, Wang HY, Liu DQ. 2015. Expression and functional analysis of a pathogenesis-related protein 1 gene, TcLr19PR1, involved in wheat resistance against leaf rust fungus. Plant Mol Biol Rep 33: 797-805.   DOI
27 Cui F, Zhang N, Fan XL, Zhang W, Zhao CH, Yang LJ, Pan RQ et al. 2017. Utilization of a Wheat660K SNP array-derived high-density genetic map for high-resolution mapping of a major QTL for kernel number. Sci Rep 7: 3788.   DOI
28 Feng N, Song G, Guan J, Chen K, Jia M, Huang D, Wu J, Zhang L, Kong X, Geng S, Liu J, Li A, Mao L. 2017. Transcriptome profiling of wheat inflorescence development from spikelet initiation to floral patterning identified stage-specific regulatory genes. Plant Physiol 174: 1779-1794.   DOI
29 Gao F, Jordan MC, Ayele BT. 2012. Transcriptional programs regulating seed dormancy and its release by after-ripening in common wheat (Triticum aestivum L.). Plant Biotechnol J 10: 465-476.   DOI
30 Grover CE, Salmon A, Wendel JF. 2012. Targeted sequence capture as a powerful tool for evolutionary analysis. Am J Bot 99: 312-319.   DOI
31 Rawat N, Sehgal SK, Joshi A, Rothe N, Wilson DL, McGraw N, Vadlani PV, Li WL, Gill BS. 2012. A diploid wheat TILLING resource for wheat functional genomics. BMC Plant Biol 12: 205.   DOI
32 Long YM, Chao WS, Ma GJ, Xu, Qi LL. 2017. An innovative SNP genotyping method adapting to multiple platforms and throughputs. Theor Appl Genet 130: 597-607.   DOI
33 Gupta PK, Mir RR, Mohan A, Kumar J. 2008. Wheat genomics: present status and future prospects. Intl J Plant Genomics 2008: 896-451.
34 Hao C, Wang Y, Chao S, Li T, Liu H, Wang L, Zhang X. 2017. The iSelect 9 K SNP analysis revealed polyploidization induced revolutionary changes and intense human selection causing strong haplotype blocks in wheat. Sci Rep 7: 41247.   DOI
35 Hazard B, Zhang X, Colasuonno P, Uauy C, Beckles DM, Dubcovsky J. 2012. Induced mutations in the starch branching enzyme II (SBEII) genes increase amylose and resistant starch content in durum wheat. Crop Sci 52: 1754-1766.
36 Pfeifer M, Kugler KG, Sandve SR, Zhan B, Rudi H, Hvidsten TR, International Wheat Genome Sequencing Consortium, Mayer KF, Olsen OA. 2014. Genome interplay in the grain transcriptome of hexaploid bread wheat. Science 345: 1250091.   DOI
37 Pennisi E. 2012. ENCODE project writes eulogy for junk DNA. Science 337: 1159-1161.   DOI
38 Qin Q, Li X, Zhuang J, Weng L, Liu W, Tai P. 2015. Long-distance transport of cadmium from roots to leaves of Solanum melongena. Ecotoxicology 24: 2224-2232.   DOI
39 Safar J, Simkova H, Kubalakova M, Cihalikova J, Suchankova P, Bartos J, Dolezel J. 2010. Development of chromosome-specific bac resources for genomics of bread wheat. Genome Res 129: 211-223.   DOI
40 Saintenac C, Zhang W, Salcedo A, Rouse MN, Trick HN, Akhunov E, Dubcovsky J. 2013. Identification of wheat gene Sr35 that confers resistance to Ug99 stem rust race group. Science 341: 783-786.   DOI
41 Sallam AH, Endelman JB, Jannink JL, Smith KP. 2015. Assessing genomic selection prediction accuracy in a dynamic barley breeding pop-ulation. Plant Genome 8: 1-15.
42 Thind AK, Wicker T, Simkova H, Fossati D, Moullet O, Brabant C, Vrana J, Dolezel J, Krattinger SG. 2017. Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly. Nat Biotechnol 35: 793-796.   DOI
43 He X, Qu B, Li W, Zhao X, Teng W, Ma W, Ren Y, Li B, Li Z, Tong Y. 2015. The nitrate-inducible NAC transcription factor TaNAC2-5A controls nitrate response and increases wheat yield. Plant Physiol 169: 1991-2005.
44 Hufford MB, Xu X, van Heerwaarden J, Pyhajarvi T, Chia JM, Cartwright RA, Elshire RJ, Glaubitz JC, Guill KE, Kaeppler SM, Lai J et al. 2012. Comparative population genomics of maize domestication and improvement. Nat Genet 44: 808-811.   DOI
45 Shan Q, Wang Y, Li J, Gao C. 2014. Genome editing in rice and wheat using the CRISPR/Cas system. Nat Protoc 9: 2395-2410.   DOI
46 Sun C, Zhang F, Yan X, Zhang X, Dong Z, Cui D, Chen F. 2017. Genome-wide association study for 13 agronomic traits reveals distribution of superior alleles in bread wheat from the Yellow and Huai Valley of China. Plant Biotechnol J 15: 953-969.   DOI
47 Tang H, Wang X, Bowers JE, Ming R, Alam M, Paterson AH. 2008. Unraveling ancient hexaploidy through multiply-aligned angiosperms gene maps. Genome Research 18: 1944-1954.   DOI
48 Uauy C, Paraiso F, Colasuonno P, Tran RK, Tsai H, Berardi S, Comai L, Dubcovsky J. 2009. A modified TILLING approach to detect induced mutations in tetraploid and hexaploid wheat. BMC Plant Biol 9: 115.   DOI
49 Vasil V, Castillo AM, Fromm ME, Vasil IK. 1992. Herbicide resistant fertile transgenic wheat plants obtained by microprojectile bombardment of regenerable embryogenic callus. Nat Biotechnol 10: 667-674.   DOI
50 Waltz E. 2016a. Gene-edited CRISPR mushroom escapes US regulation. Nature 532: 293.   DOI
51 Waltz E. 2016b. CRISPR-edited crop free to enter market, skip regulation. Nature Biotech 34: 582.   DOI
52 Wang TL, Uauy C, Robson F, Till B. 2012. TILLING in extremis. Plant Biotechnol J 10: 761-772.   DOI
53 Wang Z, Gerstein M, Snyder M. 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57-63.   DOI
54 Andrews KR, Good JM, Miller MR, Luikart G, Hohenlohe PA. 2016. Harnessing the power of RADseq for ecological and evolutionary genomics. Nat Rev Genet 17: 81-92.   DOI
55 Ahmadian A, Ehn M, Hober S. 2006. Pyrosequencing: History, biochemistry and future. Clin Chim Acta 363: 83-94.   DOI
56 Akhunova AR, Matniyazov RT, Liang HQ, Akhunov ED. 2010. Homoeolog-specific transcriptional bias in allopolyploid wheat. BMC Genomics 11: 505.   DOI
57 Allen AM, Barker GL, Berry ST, Coghill JA, Gwilliam R, Kirby S, Robinson P, Brenchley RC, D'Amore R, McKenzie N, Waite D, Hall A, Bevan M, Hall N, Edwards KJ. 2011. Transcript-specific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum aestivum L.). Plant Biotechnol J 9: 1086-1099.   DOI
58 Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the rice genome. Nature 436: 793-800.
59 Arora S, Singh N, Kaur S, Bains NS, Uauy C, Poland J, Chhuneja P. 2017. Genome-wide association study of grain architecture in wild wheat Aegilops tauschii. Front Plant Sci 8: 886.   DOI
60 International Rice Genome Sequencing Project. 2005. The map-based sequence of the rice genome. Nature 436: 793-800.   DOI
61 International Wheat Genome Sequencing consortium (IWGSC). 2014. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345: 1251788.   DOI
62 International wheat genome sequencing consortium (IWGSC). 2018. Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 361: 661.
63 Jia M, Guan J, Zhai Z, Geng S, Zhang X, Mao L, Li A. 2017. Wheat functional genomics in the era of next generation sequencing: An update. The Crop J 6: 7-14.
64 Jiang FG, Doudna JA. 2017. CRISPR-Cas9 structures and mechanisms. Annu Rev Biophys 46: 505-529.   DOI
65 Jordan KW, Wang S, Lun Y, Gardiner LJ, MacLachlan R, Hucl P et al. 2015. A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes. Genome Biol 16: 48.   DOI
66 Jupe F, Witek K, Verweij W, Sliwka J, Pritchard L, Etherington GJ, Maclean D, Cock PJ, Leggett RM, Bryan GJ, Cardle L, Hein I, Jones JD. 2013. Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations. Plant J 76: 530-544.   DOI
67 Wei XN, Shen FD, Hong YT, Rong W, Du LP, Liu X, Xu HJ, Ma LJ, Zhang ZY. 2016. The wheat calcium-dependent protein kinase TaCPK7-D positively regulates host resistance to sharp eyespot disease. Mol Plant Pathol 17: 1252-1264.   DOI
68 Wang GT, Peng B, Leal SM. 2014. Variant association tools for quality control and analysis of large-scale sequence and genotyping array data. Am J Hum Genet 94: 770-783.   DOI
69 Wang Y, Zong Y, Cao C. 2017. Targeted mutagenesis in hexaploid bread wheat using the TALEN and CRISPR/Cas systems. Methods Mol Biol 1679: 169-185.
70 Wei B, Jing RL, Wang CS, Chen JB, Mao XG, Chang XP, Jia JZ. 2009. Dreb1 genes in wheat (Triticum aestivum L.): development of functional markers and gene mapping based on SNPs. Mol Breed 23: 13-22.   DOI
71 Wen W, He Z, Gao F, Liu J, Jin H, Zhai S, Qu Y, Xia X. 2017. A high-density consensus map of common wheat integrating four mapping populations scanned by the 90K SNP array. Front Plant Sci 8: 1389.   DOI
72 Winfield MO, Allen AM, Burridge AJ et al. 2015. High-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool. Plant Biotechnol J 14: 1195-1206.
73 Wisniewski K, Zagdanska B. 2001. Genotype-dependent proteolytic response of spring wheat to water deficiency. J Exp Bot 52: 1455-1463.   DOI
74 Wulff BBH, Moscou MJ. 2014. Strategies for transferring resistance into wheat: from wide crosses to GM cassettes. Front Plant Sci 5: 1-11.
75 Xia C, Zhang LC, Zou C, Gu YQ, Duan JL, Zhao GY, Wu JJ, Liu, Fang XH, Gao LF, Jiao YN, Sun JQ, Pan YH, Liu X, Jia JZ, Kong XY. 2017. A TRIM insertion in the promoter of Ms2 causes male sterility in wheat. Nat Commun 8: 15407.   DOI
76 Zhang H, Zhu B, Qi B, Gou X, Dong Y, Xu C, Zhang B, Huang W, Liu C, Wang X, Yang C, Zhou H, Kashkush K, Feldman M, Wendel JF, Liu B. 2014. Evolution of the BBAA component of bread wheat during its history at the allohexaploid level. Plant Cell 26: 2761-2776.   DOI
77 Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR. 2016. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533: 420-424.   DOI
78 Ye XG, Shirley S, Xu HJ, Du LP, Clement T. 2002. Regular production of transgenic wheat mediated by Agrobacterium tumefaciens. Agric Sci China 1: 239-244.
79 Yu J, Buckler ES. 2006. Genetic association mapping and genome organization of maize. Curr Opin Biotechnol 17: 155-160.   DOI
80 Zhang Z, Liu X, Wang X, Zhou M, Zhou X, Ye X, Wei X. 2012. An R2R3 MYB transcription factor in wheat, TaPIMP1, mediates host resistance to Bipolaris sorokiniana and drought stresses through regulation of defense- and stress-related genes. New Phytol 196: 1155-1170.   DOI
81 Zong Y, Wang Y, Li C, Zhang R, Chen K, Ran Y, Qiu JL, Wang D, Gao C. 2017. Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion. Nat Biotechnol 35: 438-440.   DOI