Functional markers in wheat: Current status and future prospects

Theoretical and Applied Genetics

Volumn 125, Issue 1, 2012, Pages 1-10

  Liu, Yanan ^a   He, Zhonghu ^a   Appels, Rudi ^b   Xia, Xianchun ^a  

^a INSTITUTE OF PLANT PROTECTION   (China)

^b MURDOCH UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

APPLICATION PROGRAMS; CLONE CELLS; CLONING; DNA SEQUENCES;

ALLELIC VARIANTS; COMPARATIVE GENOMICS; DISEASE RESISTANCE; FUNCTIONAL GENES; FUTURE PROSPECTS; MARKER-ASSISTED SELECTION; PROCESSING QUALITY; UPDATED INFORMATIONS;

GENES;

TRITICUM AESTIVUM;

EID: 84857261971     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-012-1829-3     Document Type: Review

References (103)

1. Andersen JR, Lübberstedt T (2003) Functional markers in plant. Trends Plant Sci 8: 554-560.
2. Bagge M, Lübberstedt T (2008) Functional markers in wheat: technical and economic aspects. Mol Breed 22: 319-328.
3. Bagge M, Xia XC, Lübberstedt T (2007) Functional markers in wheat. Curr Opin Plant Biol 10: 211-216.
4. Beales J, Turner A, Griffiths S, Snape JW, Laurie DA (2007) A pseudo-response regulator is misexpressed in the photoperiod insensitive Ppd-D1a mutant of wheat (Triticum aestivum L.). Theor Appl Genet 115: 721-733.
5. Brevis JC, Dubcovsky J (2008) Effect of the Gpc-B1 region from Triticum turgidum ssp. dicoccoides on grain yield, thousand grain weight and protein yield, pp 1-3. In: Appels R, Eastwood R, Lagudah E, Langridge P, Mackay M, McIntyre L, Sharp P (eds) Proceedings of 11th International Wheat Genetics Symposium, Brisbane Australia, 24-29 August 2008. Sydney University Press http://hdl. handle. net/2123/3179.
6. Chai JF, Zhou RH, Jia JZ, Liu X (2006) Development and application of a new codominant PCR marker for detecting 1BL·1RS wheat-rye chromosome translocations. Plant Breed 125: 302-304.
7. Chen YH, Hunger RM, Carver BF, Zhang HL, Yan LL (2009) Genetic characterization of powdery mildew resistance in U. S. hard winter wheat. Mol Breed 24: 141-152.
8. Chen F, Zhang FY, Xia XC, Dong ZD, Cui DQ (2012) Distribution of puroindoline alleles in bread wheat cultivars of the Yellow and Huai valley of China and discovery of a novel puroindoline a allele without PINA protein. Mol Breed. doi: 10. 1007/s11032-011-9553-2.
9. Chu CG, Tan CT, Yu GT, Zhong S, Xu SS, Yan LL (2011) A novel retrotransposon inserted in the dominant Vrn-B1 allele confers spring growth habit in tetraploid wheat (Triticum turgidum L.). G3 (Genes, Genomes, Genetics) 1: 637-645.
10. D'Ovidio R, Anderson OD (1994) PCR analysis to distinguish between alleles of a member of a multigene family correlated with wheat bread-making quality. Theor Appl Genet 88: 759-763.
11. Devos KM (2005) Updating the 'crop circle'. Curr Opin Plant Biol 8: 155-162.
12. Distelfeld A, Fahima T (2007) Wild emmer wheat as a source for high-grain-protein genes: map-based cloning of Gpc-B1. Israel J Plant Sci 55: 297-306.
13. Distelfeld A, Uauy C, Fahima T, Dubcovsky J (2006) Physical map of the wheat high-grain protein content gene Gpc-B1 and development of a high-throughput molecular marker. New Phytol 169: 753-763.
14. Dong CH, Ma ZY, Xia XC, Zhang LP, He ZH (2012) Allelic variation at the TaZds-A1 locus on wheat chromosome 2A and development of a functional marker in common wheat. Agric Sci China (in press).
15. Ellis MH, Spielmeyer W, Gale KR, Rebetzke GJ, Richards RA (2002) "Perfect" markers for the Rht-B1b and Rht-D1b dwarfing genes in wheat. Theor Appl Genet 105: 1038-1042.
16. Fedorova L, Fedorov A (2003) Introns in gene evolution. Genetica 118: 123-131.
17. Feuillet C, Travella S, Stein N, Albar L, Nublat A, Keller B (2003) Map-based isolation of the leaf rust disease resistance gene Lr10 from the hexaploid wheat (Triticum aestivum L.) genome. Proc Natl Acad Sci USA 100: 15253-15258.
18. Froidmont DD (1998) A co-dominant marker for the 1BL 1RS wheat rye translocation via multiplex PCR. J Cereal Sci 27: 229-232.
19. Fu DL, Szu{double acute}cs P, Yan LL, Helguera M, Skinner JS, Zitzewitz JV, Hayes PM, Dubcovsky J (2005) Large deletions within the first intron in VRN-1 are associated with spring growth habit in barley and wheat. Mol Gen Genomics 273: 54-65.
20. Fu DL, Uauy C, Distelfeld A, Blechl A, Epstein L, Chen XM, Sela H, Fahima T, Dubcovsky J (2009) A kinase-START gene confers temperature-dependent resistance to wheat stripe rust. Science 323: 1357-1360.
21. Gazza L, Nocente F, Ng PKW, Pogna NE (2005) Genetic and biochemical analysis of common wheat cultivars lacking puroindoline a. Theor Appl Genet 110: 470-478.
22. Geng HW, He ZH, Zhang LP, Qu YY, Xia XC (2012) Cloning the lipoxygenase gene on chromosome 4BS and development of functional markers in common wheat. Crop Sci 52. doi: 10. 2135/cropsci2011. 07. 0365.
23. Gennaro A, Koebner RMD, Ceoloni C (2009) A candidate for Lr19, an exotic gene conditioning leaf rust resistance in wheat. Funct Integr Genomics 9: 325-334.
24. Gill RW, Sanseau P (2000) Rapid in silico cloning of genes using expressed sequence tags (ESTs). Biotechnol Annu Rev 5: 25-44.
25. Giroux MJ, Morris CF (1997) A glycine to serine change in puroindoline b is associated with wheat grain hardness and low levels of starch-surface friabilin. Theor Appl Genet 95: 857-864.
26. Gupta PK, Rustgi S (2004) Molecular markers from the transcribed/expressed region of the genome in higher plants. Funct Integr Genomics 4: 139-162.
27. Gupta RB, Singh NK, Shepherd KW (1989) The cumulative effects of allelic variation in LMW and HMW glutenin subunits on physical dough properties in the progeny of two bread wheats. Theor Appl Genet 77: 57-62.
28. Gupta PK, Kumar J, Mir RR, Kumar A (2009) Marker-assisted selection as a component of conventional plant breeding. Plant Breed Rev 33: 145-217.
29. Gupta PK, Langridge P, Mir RR (2010) Marker-assisted wheat breeding: present status and future possibilities. Mol Breed 26: 145-161.
30. He ZH, Liu L, Xia XC, Liu JJ, Peña RJ (2005) Composition of HMW and LMW glutenin subunits and their effects on dough properties, pan bread, and noodle quality of Chinese bread wheats. Cereal Chem 82: 345-350.
31. He XY, He ZH, Zhang LP, Sun DJ, Morris CF, Fuerst EP, Xia XC (2007) Allelic variation of polyphenol oxidase (PPO) genes located on chromosomes 2A and 2D and development of functional markers for the PPO genes in common wheat. Theor Appl Genet 115: 47-58.
32. He XY, Zhang YL, He ZH, Wu YP, Xiao YG, Ma CX, Xia XC (2008) Characterization of phytoene synthase 1 gene (Psy1) located on common wheat chromosome 7A and development of a functional marker. Theor Appl Genet 116: 213-221.
33. He XY, He ZH, Ma W, Appels R, Xia XC (2009a) Allelic variants of phytoene synthase 1 (Psy1) genes in Chinese and CIMMYT wheat cultivars and development of functional markers for flour colour. Mol Breed 23: 553-563.
34. He XY, Wang JW, Ammar K, Peña RJ, Xia XC, He ZH (2009b) Allelic variants at the Psy-A1 and Psy-B1 loci in durum wheat and their associations with grain yellowness. Crop Sci 49: 2058-2064.
35. Helguera M, Khan IA, Dubcovsky J (2000) Development of PCR markers for wheat leaf rust resistance gene Lr47. Theor Appl Genet 101: 625-631.
36. Helguera M, Khan IA, Kolmer J, Lijavetzky D, Liu ZQ, Dubcovsky J (2003) PCR assays for the Lr37-Yr17-Sr38 cluster of rust resistance genes and their use to develop isogenic hard red spring wheat lines. Crop Sci 43: 1839-1847.
37. Helguera M, Vanzetti L, Soria M, Khan IA, Kolmer J, Dubcovsky J (2005) PCR markers for Triticum speltoides leaf rust resistance gene Lr51 and their use to develop isogenic hard red spring wheat lines. Crop Sci 45: 728-734.
38. Howitt CA, Pogson BJ (2006) Carotenoid accumulation and function in seeds and non-green tissues. Plant Cell Environ 29: 435-445.
39. Huang J, Chen J, Yu W, Shyur L, Wang A, Sung H, Lee P, Su JC (1996) Complete structures of three rice sucrose synthase isogenes and differential regulation of their expressions. Biosci Biotechnol Biochem 60: 233-239.
40. Huang L, Brooks SA, Li WL, Fellers JP, Trick HN, Gill BS (2003) Map-based cloning of leaf rust resistance gene Lr21 from the large and polyploid genome of bread wheat. Genetics 164: 655-664.
41. Ishikawa G, Nakamura T (2007) A new co-dominant PCR-based marker to identify the high-molecular-weight glutenin subunit combination "5+10" of common wheat. Wheat Inf Serv 103: 1-4.
42. Jiang QY, Hou J, Hao CY, Wang LF, Ge HG, Dong YS, Zhang XY (2011) The wheat (T. aestivum) sucrose synthase 2 gene (TaSus2) active in endosperm development is associated with yield traits. Funct Integr Genomics 11: 49-61.
43. Jin H, Yan J, Peña RJ, Xia XC, Morgounov A, Han LM, Zhang Y, He ZH (2011) Molecular detection of high- and low-molecular-weight glutenin subunit genes in common wheat cultivars from 20 countries using allele-specific markers. Crop Pasture Sci 62: 746-754.
44. Krattinger SG, Lagudah ES, Spielmeyer W, Singh RP, Huerta-Espino J, McFadden H, Bossolini E, Selter LL, Keller B (2009) A putative ABC transporter confers durable resistance to multiple fungal pathogens in wheat. Science 323: 1360-1363.
45. Kruger JE, Matsuo RR, Preston K (1992) A comparison of methods for the prediction of Cantonese noodle colour. Can J Plant Sci 72: 1021-1029.
46. Lagudah ES, Krattinger SG, Herrera-Foessel S, Singh RP, Huerta-Espino J, Spielmeyer W, Brown-Guedira G, Selter LL, Keller B (2009) Gene-specific markers for the wheat gene Lr34/Yr18/Pm38 which confers resistance to multiple fungal pathogens. Theor Appl Genet 119: 889-898.
47. Laroche A, Frick MM, Huel R, Nykiforuk C, Conner B, Kuzyk A (2000) Molecular identification of the wheat stripe rust resistance gene Yr10, the first full-length leucine zipper-nucleotide binding site-leucine-rich-repeat resistance gene in cereals. http://www. ncbi. nlm. nih. gov/entrez/viewer. fcgi?db=nucleotide&val=11990496.
48. Lei ZS, Gale KR, He ZH, Gianibelli C, Larroque O, Xia XC, Butow BJ, Ma W (2006) Y-type gene specific markers for enhanced discrimination of high-molecular weight glutenin alleles at the Glu-B1 locus in hexaploid wheat. J Cereal Sci 43: 94-101.
49. Liang D, Tang JW, Peña RJ, Singh R, He XY, Shen XY, Yao DN, Xia XC, He ZH (2010) Characterization of CIMMYT bread wheats for high- and low-molecular weight glutenin subunits and other quality-related genes with SDS-PAGE, RP-HPLC and molecular markers. Euphytica 172: 235-250.
50. Lillemo M, Skinnes H, Brown JKM (2010) Race specific resistance to powdery mildew in Scandinavian wheat cultivars, breeding lines and introduced genotypes with partial resistance. Plant Breed 129: 297-303.
51. Liu C, Yang ZJ, Li GR, Zeng ZX, Zhang Y, Zhou JP, Liu ZH, Ren ZL (2008a) Isolation of a new repetitive DNA sequence from Secale africanum enables targeting of Secale chromatin in wheat background. Euphytica 159: 249-258.
52. Liu SX, Chao SM, Anderson JA (2008b) New DNA markers for high molecular weight glutenin subunits in wheat. Theor Appl Genet 118: 177-183.
53. Liu L, Ikeda TM, Branlard G, Peña R, Rogers WJ, Lerner SE, Kolman MA, Xia XC, Wang LH, Ma W, Appels R, Yoshida H, Wang AL, Yan YM, He ZH (2010) Comparison of low molecular weight glutenin subunits identified by SDS-PAGE, 2-DE, MALDI-TOF-MS and PCR in common wheat. BMC Plant Biol 10: 124.
54. Lübberstedt T, Zein I, Andersen JR, Wenzel G, Krützfeldt B, Eder J, Ouzunova M, Chun S (2005) Development and application of functional markers in maize. Euphytica 146: 101-108.
55. Luo C, Griffin WB, Branlard G, McNeil DL (2001) Comparison of low- and high- molecular-weight wheat glutenin allele effects on flour quality. Theor Appl Genet 102: 1088-1098.
56. Ma W, Zhang W, Gale KR (2003) Multiplex-PCR typing of high molecular weight glutenin alleles in wheat. Euphytica 134: 51-60.
57. Ma DY, Yan J, He ZH, Wu L, Xia XC (2012) Characterization of a cell wall invertase gene TaCwi-A1 on common wheat chromosome 2A and development of functional markers. Mol Breed 29: 43-52.
58. Matsumoto T, Wu JZ, Kanamori H, Katayose Y, Fujisawa M et al (2005) The map-based sequence of the rice genome. Nature 436: 793-800.
59. Miskelly DM (1984) Flour components affecting paste and noodle colour. J Sci Food Agric 35: 463-471.
60. Mohler V, Bauer A, Bauer C, Flath K, Schweizer G, Hartl L (2011) Genetic analysis of powdery mildew resistance in German winter wheat cultivar Cortez. Plant Breed 130: 35-40.
61. Nakamura T, Vrinten P, Saito M, Konda M (2002) Rapid classification of partial waxy wheat using PCR-based markers. Genome 45: 1150-1156.
62. Parker GD, Chalmers KJ, Rathgen AJ, Langridge P (1998) Mapping loci associated with flour colour in wheat (Triticum aestivum L.). Theor Appl Genet 97: 238-245.
63. Peusha H, Enno T, Jakobson I, Tsõmbalova J, Ingver A, Järve K (2008) Powdery mildew resistance of Nordic spring wheat cultivars grown in Estonia. Acta Agric Scand Sect B-Soil Plant Sci 58: 289-296.
64. OE) high molecular weight glutenin subunit. Theor Appl Genet 116: 283-296.
65. Ram S, Sharma S, Verma A, Tyagi BS, Peña RJ (2011) Comparative analyses of LMW glutenin alleles in bread wheat using allele-specific PCR and SDS-PAGE. J Cereal Sci 54: 488-493.
66. Ravel C, Praud S, Murigneux A, Canaguier A, Sapet F, Samson D, Balfourier F, Dufour P, Chalhoub B, Brunel D, Beckert M, Charmet G (2006) Single-nucleotide polymorphism frequency in a set of selected lines of bread wheat (Triticum aestivum L.). Genome 49: 1131-1139.
67. Reddy ASN (2007) Alternative splicing of pre-messenger RNAs in plants in the genomic era. Annu Rev Plant Biol 58: 267-294.
68. Saito M, Vrinten P, Ishikawa G, Graybosch R, Nakamura T (2009) A novel codominant marker for selection of the null Wx-B1 allele in wheat breeding programs. Mol Breed 23: 209-217.
69. Schnable PS, Ware D, Fulton RS, Stein JC, Wei FS et al (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326: 1112-1115.
70. Schwarz G, Felsenstein FG, Wenzel G (2004) Development and validation of a PCR-based marker assay for negative selection of the HMW glutenin allele Glu-B1-1d (Bx-6) in wheat. Theor Appl Genet 109: 1064-1069.
71. Singh R, Goutam U, Gupta RK, Pandey GC, Shoran J, Tiwari R (2009) Allelic variations of functional markers for polyphenol oxidase (PPO) genes in Indian bread wheat (Triticum aestivum L.) cultivars. J Genet 88: 325-329.
72. Smith RL, Schweder ME, Barnett RD (1994) Identification of glutenin alleles in wheat and triticale using PCR-generated DNA markers. Crop Sci 34: 1373-1378.
73. Song XJ, Huang W, Shi M, Zhu MZ, Lin HX (2007) A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet 39: 623-630.
74. Su ZQ, Hao CY, Wang LF, Dong YC, Zhang XY (2011) Identification and development of a functional marker of TaGW2 associated with grain weight in bread wheat (Triticum aestivum L.). Theor Appl Genet 122: 211-223.
75. Sun DJ, He ZH, Xia XC, Zhang LP, Morris CF, Appels R, Ma WJ, Wang H (2005) A novel STS marker for polyphenol oxidase activity in bread wheat. Mol Breed 16: 209-218.
76. Sun YW, He ZH, Ma WJ, Xia XC (2011) Alternative splicing in the coding region of Ppo-A1 directly influences the polyphenol oxidase activity in common wheat (Triticum aestivum L.). Funct Integr Genomics 11: 85-93.
77. Talbert LE, Blake NK, Chee PW, Blake TK, Magyar GM (1994) Evaluation of "sequence-tagged-site" PCR products as molecular markers in wheat. Theor Appl Genet 87: 789-794.
78. Tommasini L, Yahiaoui N, Srichumpa P, Keller B (2006) Development of functional markers specific for seven Pm3 resistance alleles and their validation in the bread wheat gene pool. Theor Appl Genet 114: 165-175.
79. Uauy C, Distelfeld A, Fahima T, Blechl A, Dubcovsky J (2006) A NAC gene regulating senescence improves grain protein, zinc, and iron content in wheat. Science 314: 1298-1301.
80. Varshney RK, Graner A, Sorrells ME (2005) Genomics-assisted breeding for crop improvement. Trends Plant Sci 10: 621-630.
81. Varshney RK, Beier U, Khlestkina EK, Kota R, Korzun V, Graner A, Börner A (2007) Single nucleotide polymorphisms in rye (Secale cereale L.): discovery, frequency, and applications for genome mapping and diversity studies. Theor Appl Genet 114: 1105-1116.
82. Vogel JP, Garvin DF, Mockler TC et al (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463: 763-768.
83. Wan YX, Zhang XK, Xia XC, Zhang PZ, He ZH (2008) Development of multiplex PCR and identification of major quality genes in cultivars from Yellow and Huai River Valley Wheat Region. Sci Agric Sin 41: 643-653.
84. Wang BB, Brendel V (2006) Genome wide comparative analysis of alternative splicing in plants. Proc Natl Acad Sci 103: 7175-7180.
85. Wang E, Wang JJ, Zhu XD, Wei H, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH (2008) Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nat Genet 40: 1370-1374.
86. Wang JW, He XY, He ZH, Wang H, Xia XC (2009a) Cloning and phylogenetic analysis of phytoene synthase 1 (Psy1) genes in common wheat and related species. Hereditas 146: 208-256.
87. Wang LH, Zhao XL, He ZH, Ma W, Appels R, Peña RJ, Xia XC (2009b) Characterization of low-molecular-weight glutenin subunit Glu-B3 genes and development of STS markers in common wheat (Triticum aestivum L.). Theor Appl Genet 118: 525-539.
88. Wang LH, Li GY, Peña RJ, Xia XC, He ZH (2010) Development of STS markers and establishment of multiplex PCR for Glu-A3 alleles in common wheat (Triticum aestivum L.). J Cereal Sci 51: 305-312.
89. 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.
90. Wu L, Xia XC, Zhu HZ, Li SZ, Zheng YL, He ZH (2010) Molecular characterization of Lr34/Yr18/Pm38 in 273 CIMMYT wheat cultivars and lines using functional markers. Sci Agric Sin 43: 4553-4561.
91. Xiao YG, He XY, Liu JJ, Sun DJ, Xia XC, He ZH (2008) Molecular identification and distribution of the polyphenol oxidase genes in Chinese winter wheat cultivars. Sci Agric Sin 41: 954-960.
92. Yahiaoui N, Srichumpa P, Dudler R, Keller B (2004) Genome analysis at different ploidy levels allows cloning of the powdery mildew resistance gene Pm3b from hexaploid wheat. Plant J 37: 528-538.
93. Yamamori M, Quynh NT (2000) Differential effects of Wx-A1, -B1 and -D1 protein deficiencies on apparent amylose content and starch pasting properties in common wheat. Theor Appl Genet 100: 32-38.
94. Yan LL, Helguera M, Kato K, Fukuyama S, Sherman J, Dubcovsky J (2004a) Allelic variation at the VRN-1 promoter region in polyploid wheat. Theor Appl Genet 109: 1677-1686.
95. Yan LL, Loukoianov A, Blechl A, Tranquilli G, Ramakrishna W, SanMiguel P, Bennetzen JL, Echenique V, Dubcovsky J (2004b) The wheat VRN2 gene is a flowering repressor down-regulated by vernalization. Science 303: 1640-1643.
96. Yan LL, Fu DL, Li C, Blechl A, Tranquilli G, Bonafede M, Sanchez A, Valarik M, Yasuda S, Dubcovsky J (2006) The wheat and barley vernalization gene VRN3 is an orthologue of FT. Proc Natl Acad Sci USA 103: 19581-19586.
97. Yang FP, He XY, He ZH, Shang XW, Yang WX, Xia XC (2008) Molecular detection and distribution of allelic variations of a gene for yellow pigment content in Chinese winter wheat cultivars. Sci Agric Sin 41: 2923-2930.
98. Yang FP, Zhang XK, Xia XC, Laurie DA, Yang WX, He ZH (2009) Distribution of the photoperiod insensitive Ppd-D1a allele in Chinese wheat cultivars. Euphytica 165: 445-452.
99. Zhang W, Gianibelli MC, Rampling LR, Gale KR (2004) Characterisation and marker development for low molecular weight glutenin genes from Glu-A3 alleles of bread wheat (Triticum aestivum L). Theor Appl Genet 108: 1409-1419.
100. Zhang XK, Yang SJ, Zhou Y, He ZH, Xia XC (2006) Distribution of the Rht-B1b, Rht-D1b and Rht8 reduced height genes in autumn-sown Chinese wheats detected by molecular markers. Euphytica 152: 109-116.
101. Zhang XK, Liu L, He ZH, Sun DJ, He XY, Xu ZH, Zhang PP, Chen F, Xia XC (2008a) Development of two multiplex PCR assays targeting improvement of bread-making and noodle qualities in common wheat. Plant Breed 127: 109-115.
102. Zhang XK, Xiao YG, Zhang Y, Xia XC, Dubcovsky J, He ZH (2008b) Allelic variation at the vernalization genes Vrn-A1, Vrn-B1, Vrn-D1, and Vrn-B3 in Chinese wheat cultivars and their association with growth habit. Crop Sci 48: 458-470.
103. Zhang CY, Dong CH, He XY, Zhang LP, Xia XC, He ZH (2011) Allelic variation at the TaZds-D1 locus on wheat chromosome 2DL and their association with yellow pigment content. Crop Sci 51: 1580-1590.