Quantitative trait loci associated with phenological development, low-temperature tolerance, grain quality, and agronomic characters in wheat (Triticum aestivum L.)

PLoS ONE

Volumn 11, Issue 3, 2016, Pages

  Fowler, D B ^a   N'Diaye, A ^a   Laudenci Chingcuanco, D ^b   Pozniak, C J ^a  

^a UNIVERSITY OF SASKATCHEWAN   (Canada)

^b WESTERN REGIONAL RESEARCH CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CANADA; CHROMOSOME 6; COLD TOLERANCE; CONSENSUS; CULTIVAR; GENE POOL; GENETIC MARKER; GENOTYPE ENVIRONMENT INTERACTION; GRAIN; HERITABILITY; MATURITY; QUANTITATIVE TRAIT LOCUS; SEEDLING; SINGLE NUCLEOTIDE POLYMORPHISM; SPRING; TRITICUM AESTIVUM; WHEAT; WINTER WHEAT; ADAPTATION; AGRICULTURE; ANATOMY AND HISTOLOGY; CHROMOSOMAL MAPPING; COLD; CROSS BREEDING; EPISTASIS; GENETICS; PHENOTYPE; PHYSIOLOGY; PLANT LEAF; PLANT SEED;

ADAPTATION, PHYSIOLOGICAL; AGRICULTURE; CHROMOSOME MAPPING; COLD TEMPERATURE; CROSSES, GENETIC; EPISTASIS, GENETIC; PHENOTYPE; PLANT LEAVES; QUANTITATIVE TRAIT LOCI; SEEDS; TRITICUM;

EID: 84962178583     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0152185     Document Type: Article

References (62)

1. FAO. Statistical Yearbook 2013: World Food and Agriculture. Part 3-Feeding the World: Food and Agriculture Organziation of the United Nations. Rome. 2013. p. 123-99.
2. Mayer KFX, Rogers J, Dolezel J, Pozniak C, Eversole K, Feuillet C, et al. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science. 2014;345(6194). doi: ARTN 1251788 doi: 10.1126/science.1251788 PMID: WOS:000343420300004.
3. Cavanagh CR, Chao SM, Wang SC, Huang BE, Stephen S, Kiani S, et al. Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars. P Natl Acad Sci USA. 2013;110(20):8057-62. doi: 10.1073/pnas.1217133110 PMID: WOS:000319803500027.
4. Poland J, Brown PJ, Sorrells M, Jannink JL. Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. Plos One. 2012;7(2):e32253. doi: 10.1371/journal.pone.0032253 PMID: 22389690
5. Saintenac C, Jiang DY, Akhunov ED. Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome. Genome Biol. 2011;12(9). ARTN R88 doi: 10.1186/gb-2011-12-9-r88 PMID: WOS:000298926900005.
6. Jordan KW, Wang S, Lun Y, Gardiner L-J, MacLachlan R, Hucl P, et al. A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes. Genome Biol. 2015;16. doi: 10.1186/s13059-015-0606-4 PMID: WOS:000352266900001.
7. Wang SC, Wong DB, Forrest K, Allen A, Chao SM, Huang BE, et al. Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array. Plant Biotechnol J. 2014;12(6):787-96. doi: 10.1111/pbi.12183 PMID: WOS:000339488200015.
8. Maccaferri M, Ricci A, Salvi S, Milner SG, Noli E, Martelli PL, et al. A high-density, SNP-based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding. Plant Biotechnol J. 2014. Epub 26 November 2014. doi: 10.1111/pbi.12288
9. Fowler DB, Byrns BM, Greer KJ. Overwinter Low-Temperature Responses of Cereals: Analyses and Simulation. Crop Sci. 2014;54(6):2395-405. doi: 10.2135/cropsci2014.03.0196 PMID: WOS:000346571900001.
10. Fowler DB, Chauvin LP, Limin AE, Sarhan F. The regulatory role of vernalization in the expression of low-temperature-induced genes in wheat and rye. Theor Appl Genet. 1996;93(4):554-9. doi: 10.1007/Bf00417947 PMID: WOS:A1996VG22100010.
11. Fowler DB, Limin AE, Wang SY, Ward RW. Relationship between low-temperature tolerance and vernalization response in wheat and rye. Can J Plant Sci. 1996;76(1):37-42. PMID: WOS: A1996TZ71400007.
12. Galiba G, Vagujfalvi A, Li CX, Soltesz A, Dubcovsky J. Regulatory genes involved in the determination of frost tolerance in temperate cereals. Plant Sci. 2009;176(1):12-9. doi: 10.1016/j.plantsci.2008.09. 016 PMID: WOS:000261551900002.
13. Baga M, Fowler DB, Chibbar RN. Identification of genomic regions determining the phenological development leading to floral transition in wheat (Triticum aestivum L.). J Exp Bot. 2009;60(12):3575-85. doi: 10.1093/jxb/erp199 PMID: WOS:000269014600024
14. Baga M, Chodaparambil SV, Limin AE, Pecar M, Fowler DB, Chibbar RN. Identification of quantitative trait loci and associated candidate genes for low-temperature tolerance in cold-hardy winter wheat. Funct Integr Genomic. 2007;7(1):53-68. doi: 10.1007/s10142-006-0030-7 PMID: WOS:000245119600004.
15. Grant MN. Registration of Norstar Wheat. Crop Sci. 1980;20(4):552-. PMID: WOS: A1980KF63300042.
16. Campbell AB. Registration of Manitou Wheat. Crop Sci. 1967;7(4):406-&. PMID: WOS: A19679817300058.
17. Limin AE, Fowler DB. Developmental traits affecting low-temperature tolerance response in near-isogenic lines for the vernalization locus Vrn-A1 in wheat (Triticum aestivum L. em Thell). Ann Bot-London. 2002;89(5):579-85. doi: 10.1093/aob/mcf102 PMID: WOS:000175542000010.
18. Brule-Babel AL, Fowler DB. Genetic-Control of Cold Hardiness and Vernalization Requirement in Winter-Wheat. Crop Sci. 1988;28(6):879-84. PMID: WOS:A1988Q953900001.
19. Laurie DA, Reymondie S. High-Frequencies of Fertilization and Haploid Seedling Production in Crosses between Commercial Hexaploid Wheat-Varieties and Maize. Plant Breeding. 1991;106(3):182-9. doi: 10.1111/j.1439-0523.1991.tb00499.x PMID: WOS:A1991FW74500002.
20. Fowler DB. Cold acclimation threshold induction temperatures in cereals. Crop Sci. 2008;48(3):1147-54. doi: 10.2135/cropsci2007.10.0581 PMID: WOS:000256635400034.
21. Fowler DB. Influence of Date of Seeding on Yield and Other Agronomic Characters of Winter-Wheat and Rye Grown in Saskatchewan. Can J Plant Sci. 1983;63(1):109-13. PMID: WOS: A1983QD96300010.
22. Fowler DB, Gusta LV. Selection for Winterhardiness in Wheat.1. Identification of Genotypic Variability. Crop Sci. 1979;19(6):769-72. PMID: WOS:A1979JC84200004.
23. Wu YH, Bhat PR, Close TJ, Lonardi S. Efficient and Accurate Construction of Genetic Linkage Maps from the Minimum Spanning Tree of a Graph. Plos Genet. 2008;4(10). ARTN e1000212 doi: 10.1371/journal.pgen. 1000212 PMID: WOS:000261480900007.
24. Lorieux M. MapDisto: fast and efficient computation of genetic linkage maps. Mol Breeding. 2012;30(2):1231-5. doi: 10.1007/s11032-012-9706-y PMID: WOS:000307270900051.
25. Kosambi DD. The estimation of map distances from recombination values. Ann Eugenic. 1943;12:172-5. PMID: WOS:000200605700013.
26. Sosnowski O, Charcosset A, Joets J. BioMercator V3: an upgrade of genetic map compilation and quantitative trait loci meta-analysis algorithms. Bioinformatics. 2012;28(15):2082-3. doi: 10.1093/bioinformatics/bts313 PMID: WOS:000306686400026.
27. Wu YH, Close TJ, Lonardi S. Accurate Construction of Consensus Genetic Maps via Integer Linear Programming. Ieee Acm T Comput Bi. 2011;8(2):381-94. doi: 10.1109/Tcbb.2010.35 PMID: WOS:000286146600011.
28. Jackson BN, Aluru S, Schnable PS. Consensus genetic maps: A graph theoretic approach. 2005 IEEE Computational Systems Bioinformatics Conference, Proceedings. 2005:35-43. doi: 10.1109/Csb. 2005.26 PMID: WOS:000231800100007.
29. Jackson BN, Schnable PS, Aluru S. Consensus genetic maps as median orders from inconsistent sources. Ieee Acm T Comput Bi. 2008;5(2):161-71. doi: 10.1109/Tcbb.2007.70221 PMID: WOS:000255443900001.
30. Yap IV, Schneider D, Kleinberg J, Matthews D, Cartinhour S, McCouch SR. A graph-theoretic approach to comparing and integrating genetic, physical and sequence-based maps. Genetics. 2003;165(4):2235-47. PMID: WOS:000187805300046.
31. Munoz-Amatriain M, Moscou MJ, Bhat PR, Svensson JT, Bartos J, Suchankova P, et al. An Improved Consensus Linkage Map of Barley Based on Flow-Sorted Chromosomes and Single Nucleotide Polymorphism Markers. Plant Genome-Us. 2011;4(3):238-49. doi: 10.3835/plantgenome2011.08.0023 PMID: WOS:000312661700008.
32. Close TJ, Bhat PR, Lonardi S, Wu YH, Rostoks N, Ramsay L, et al. Development and implementation of high-throughput SNP genotyping in barley. Bmc Genomics. 2009;10. Artn 582 doi: 10.1186/1471-2164-10-582 PMID: WOS:000272983700001.
33. Joehanes R, Nelson JC. QGene 4.0, an extensible Java QTL-analysis platform. Bioinformatics. 2008;24(23):2788-9. doi: 10.1093/bioinformatics/btn523 PMID: WOS:000261168600024.
34. Yang J, Hu CC, Hu H, Yu RD, Xia Z, Ye XZ, et al. QTLNetwork: mapping and visualizing genetic architecture of complex traits in experimental populations. Bioinformatics. 2008;24(5):721-3. doi: 10.1093/bioinformatics/btm494 PMID: WOS:000253746400021.
35. Bauer A, Frank AB, Black AL. Estimation of Spring Wheat Leaf Growth-Rates and Anthesis from Air-Temperature. Agron J. 1984;76(5):829-35. PMID: WOS:A1984TJ82400027.
36. McMaster GS. Phenology, development, and growth of the wheat (Triticum aestivum L) shoot apex: A review. Adv Agron. 1997;59:63-118. doi: 10.1016/S0065-2113 (08) 60053-X PMID: WOS: A1997BH28N00003.
37. Zanke C, Ling J, Plieske J, Kollers S, Ebmeyer E, Korzun V, et al. Genetic architecture of main effect QTL for heading date in European winter wheat. Front Plant Sci. 2014;5. ARTN 217 doi: 10.3389/fpls. 2014.00217 PMID: WOS:000339044800001.
38. Fowler DB, Limin AE, Ritchie JT. Low-temperature tolerance in cereals: Model and genetic interpretation. Crop Sci. 1999;39(3):626-33. PMID: WOS:000080943700002.
39. Fowler DB, Gusta LV, Tyler NJ. Selection for Winter-Hardiness in Wheat.3. Screening Methods. Crop Sci. 1981;21(6):896-901. PMID: WOS:A1981MY38600022.
40. Duggan BL, Fowler DB. Yield structure and kernel potential of winter wheat on the Canadian prairies. Crop Sci. 2006;46(4):1479-87. doi: 10.2135/cropsci2005.06-0126 PMID: WOS:000239054100006.
41. Aspinall D. Water deficit in wheat. In: Pearson CJ, editor. Control of Crop Productivity. Australia: Academic Press Inc.; 1984. p. 91-110.
42. Entz MH, Fowler DB. Critical Stress Periods Affecting Productivity of No-Till Winter-Wheat in Western Canada. Agron J. 1988;80(6):987-92. PMID: WOS:A1988R009300028.
43. Gilliland DJ, Fowler DB. Effect of a Rht Gene Conditioning the Semidwarf Character on Winterhardiness in Winter-Wheat (Triticum-aestivum L Em Thell). Can J Plant Sci. 1988;68(2):301-9. PMID: WOS:A1988N358000002.
44. Fisher JE. Developmental Morphology of Inflorescence in Hexaploid Wheat Cultivars with and without Cultivar Norin 10 in Their Ancestry. Can J Plant Sci. 1973;53(1):7-15. PMID: WOS: A1973O780300002.
45. Muchero W, Diop NN, Bhat PR, Fenton RD, Wanamaker S, Pottorff M, et al. A consensus genetic map of cowpea [Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPs. P Natl Acad Sci USA. 2009;106(43):18159-64. doi: 10.1073/pnas.0905886106 PMID: WOS:000271222500024.
46. Groos C, Gay G, Perretant MR, Gervais L, Bernard M, Dedryver F, et al. Study of the relationship between pre-harvest sprouting and grain color by quantitative trait loci analysis in a whitexred grain bread-wheat cross. Theor Appl Genet. 2002;104(1):39-47. doi: 10.1007/s001220200004 PMID: WOS:000173851500005.
47. Ganal M, Roder MS. Microsatellite and SNP Markers in Wheat Breeding. In: Varshney RK, Tuberosa R, editors. Genomic Assisted Crop Improvement. Vol 2: Genomics Applications in Crops: Springer Netherlands; 2007. p. 1-24.
48. Cui F, Fan XL, Zhao CH, Zhang W, Chen M, Ji J, et al. A novel genetic map of wheat: utility for mapping QTL for yield under different nitrogen treatments. Bmc Genet. 2014;15. Artn 57 doi: 10.1186/1471-2156-15-57 PMID: WOS:000336862300001.
49. Gao LF, Jing RL, Huo NX, Li Y, Li XP, Zhou RH, et al. One hundred and one new microsatellite loci derived from ESTs (EST-SSRs) in bread wheat. Theor Appl Genet. 2004;108(7):1392-400. doi: 10. 1007/s00122-003-1554-z PMID: WOS:000220988400025.
50. Somers DJ, Isaac P, Edwards K. A high-density microsatellite consensus map for bread wheat (Triticum aestivum L.). Theor Appl Genet. 2004;109(6):1105-14. doi: 10.1007/s00122-004-1740-7 PMID: WOS:000224614100001.
51. Xue SL, Zhang ZZ, Lin F, Kong ZX, Cao Y, Li CJ, et al. A high-density intervarietal map of the wheat genome enriched with markers derived from expressed sequence tags. Theor Appl Genet. 2008;117(2):181-9. doi: 10.1007/s00122-008-0764-9 PMID: WOS:000257125700005.
52. McCartney CA, Somers DJ, Humphreys DG, Lukow O, Ames N, Noll J, et al. Mapping quantitative trait loci controlling agronomic traits in the spring wheat cross RL4452 x 'AC Domain'. Genome. 2005;48(5):870-83. PMID: WOS:000234082400012.
53. Vagujfalvi A, Galiba G, Cattivelli L, Dubcovsky J. The cold-regulated transcriptional activator Cbf3 is linked to the frost-tolerance locus Fr-A2 on wheat chromosome 5A. Mol Genet Genomics. 2003;269(1):60-7. doi: 10.1007/s00438-003-0806-6 PMID: WOS:000183032400007.
54. Laudencia-Chingcuanco D, Ganeshan S, You F, Fowler B, Chibbar R, Anderson O. Genome-wide gene expression analysis supports a developmental model of low temperature tolerance gene regulation in wheat (Triticum aestivum L.). Bmc Genomics. 2011;12. Artn 299 doi: 10.1186/1471-2164-12-299 PMID: WOS:000292930000001.
55. Borojevic K, Borojevic K. The transfer and history of "reduced height genes" (Rht) in wheat from Japan to Europe. J Hered. 2005;96(4):455-9. doi: 10.1093/jhered/esi060 PMID: WOS:000230847000024.
56. Verma V, Worland AJ, Sayers EJ, Fish L, Caligari PDS, Snape JW. Identification and characterization of quantitative trait loci related to lodging resistance and associated traits in bread wheat. Plant Breeding. 2005;124(3):234-41. doi: 10.1111/j.1439-0523.2005.01070.x PMID: WOS:000229903100005.
57. Zhang LY, Liu DC, Guo XL, Yang WL, Sun JZ, Wang DW, et al. Genomic Distribution of Quantitative Trait Loci for Yield and Yield-related Traits in Common Wheat. J Integr Plant Biol. 2010;52(11):996-1007. doi: 10.1111/j.1744-7909.2010.00967.x PMID: WOS:000283599100006.
58. Bogard M, Allard V, Martre P, Heumez E, Snape JW, Orford S, et al. Identifying wheat genomic regions for improving grain protein concentration independently of grain yield using multiple inter-related populations. Mol Breeding. 2013;31(3):587-99. doi: 10.1007/s11032-012-9817-5 PMID: WOS:000315516400008.
59. Heidari B, Sayed-Tabatabaei BE, Saeidi G, Kearsey M, Suenaga K. Mapping QTL for grain yield, yield components, and spike features in a doubled haploid population of bread wheat. Genome. 2011;54(6):517-27. doi: 10.1139/G11-017 PMID: WOS:000291994900008.
60. Raman R, Allen H, Diffey S, Raman H, Martin P, McKelvie K. Localisation of quantitative trait loci for quality attributes in a doubled haploid population of wheat (Triticum aestivum L.). Genome. 2009;52(8):701-15. doi: 10.1139/G09-045 PMID: WOS:000269761300004.
61. Long Y, Shi J, Qiu D, Li R, Zhang C, Wang J, et al. Flowering time quantitative trait loci analysis of oilseed Brassica in multiple environments and genomewide alignment with Arabidopsis. Genetics. 2007;177(4):2433-44. doi: 10.1531/genetics.107.080705 PMID: WOS:000251949800038.
62. Sutka J, Snape JW. Location of a Gene for Frost-Resistance on Chromosome-5A of Wheat. Euphytica. 1989;42(1-2):41-4. doi: 10.1007/Bf00042613 PMID: WOS:A1989AF16200005.