Genome-wide linkage mapping of QTL for yield components, plant height and yield-related physiological traits in the Chinese wheat cross Zhou 8425B/Chinese spring

Frontiers in Plant Science

Volumn 6, Issue DEC, 2015, Pages

  Gao, Fengmei ^a,b,c   Wen, Weie ^b   Liu, Jindong ^b   Rasheed, Awais ^b   Yin, Guihong ^d   Xia, Xianchun ^b   Wu, Xiaoxia ^a   He, Zhonghu ^b  

^a NORTHEAST AGRICULTURAL UNIVERSITY   (China)

^b INSTITUTE OF PLANT PROTECTION   (China)

^c HEILONGJIANG ACADEMY OF AGRICULTURAL SCIENCES   (China)

^d Zhoukou Academy of Agriculture Sciences   (China)

Author keywords

Linkage analysis; Molecular marker; QTL; Triticum aestivum; Wheat 90K SNP array

Indexed keywords

EID: 84950325280     PISSN: None     EISSN: 1664462X     Source Type: Journal    
DOI: 10.3389/fpls.2015.01099     Document Type: Article

References (63)

1. Akhunov, E., Nicolet, C., and Dvorak, J. (2009). Single nucleotide polymorphism genotyping in polyploid wheat with the Illumina Golden-Gate assay. Theor. Appl. Genet. 119,507-517. doi: 10.1007/s00122-009-1059-5
2. Ali, M. L., Baenziger, P. S., Ajlouni, Z. A., Campbell, B. T., Gill, K. S., Eskridge, K. M., et al. (2011). Mapping QTL for agronomic traits on wheat chromosome 3A and a comparison of recombinant inbred chromosome line populations. Crop Sci. 51,553-566. doi: 10.2135/cropsci2010.06.0359
3. Aranzana, M. J., Kim, S., Zhao, K. Y., Bakker, E., Horton, M., Jakob, K., et al. (2005). Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet. 1:e60. doi: 10.1371/journal.pgen.0010060
4. Ariyadasa, R., Mascherm, M., Nussbaumer, T., Schulte, D., Frenkel, Z., Poursarebani, N., et al. (2014). A sequence-ready physical map of barley anchored genetically by two million single-nucleotide polymorphisms. Plant Physiol. 164, 412-423. doi: 10.1104/pp.113.228213
5. Bagge, M., Xia, X. C., and Lubberstedt, T. (2007). Functional markers in wheat. Curr. Opin. Plant Biol. 10, 211-216. doi: 10.1016/jpbi200701009
6. Birkhead, T. R., Ball, A., Stapleym, J., Dawson, D., Burke, T., and Slate, J. (2010). A comparison of SNPs and microsatellites as linkage mapping markers: lessons from the zebra finch (Taeniopygia guttata). BMC Genomics 11:218. doi: 10.1186/1471-2164-11-218
7. Barker, G. L. A., and Edwards, K. J. (2009). A genome-wide analysis of single nucleotide polymorphism diversity in the world's major cereal crops. Plant Biotechnol. J. 7, 318-325. doi: 10.1111/j.1467-7652.2009.00412.x
8. Bennett, D., Reynolds, M., Mullan, D., Izanloo, A., Kuchel, H., Langridge, P., et al. (2012). Detection of two major grain yield QTL in bread wheat (Triticum aestivum L.) under heat, drought and highyield potential environments. Theor. Appl. Genet. 125, 1473-1485. doi: 10.1007/s00122-012-1927-2
9. Blanco, A., Bellomo, M. P., Cenci, A., De Giovanni, C., D'Ovidio, R., Iacono, E., et al. (1998). A genetic linkage map of durum wheat. Theor. Appl. Genet. 97, 721-728. doi: 10.1007/s001220050948
10. Borner, A., Schumann, E., Furste, A., Coster, H., Leithold, B., Roder, M. S., et al. (2002). Mapping of quantitative trait loci determining agronomic important characters in hexapioid wheat (Triticum aestivum L.). Theor. Appl. Genet. 105, 921-936. doi: 10.1007/s00122-002-0994-1
11. Cabral, A. L., Jordan, M. C., McCartney, C. A., You, F. M., Humphreys, D. G., MacLachlan, R., et al. (2014). Identification of candidate genes, regions and markers for pre-harvest sprouting resistance in wheat (Triticum aestivum L.). BMC Plant Biol. 14:340.doi: 10.1186/s12870-014-0340-1
12. Colasuonno, P., Gadaleta, A., Giancaspro, A., Nigro, D., Giove, S., Incerti, O., et al. (2014). Development of a high-density SNP-based linkage map and detectionofyellowpigmentcontentQTLs in durumwheat. Mol. Breeding 34,1563-1578. doi: 10.1007/s11032-014-0183-3
13. Cook, J. P., McMullen, M. D., Holland, J. B., Tian, F., Bradbury, P., Ross-Ibarra, J., et al. (2012). Genetic architecture of maize kernel composition in the nested association mapping and inbred association panels. PlantPhysiol. 158,824-834. doi: 10.1104/pp.111.185033
14. Cuthbert, J. L., Somers, D. J., Brule-Babel, A. L., Brown, P. D., and Crow, G. H. (2008). Molecular mapping of quantitative trait loci for yield and yield components in spring wheat (Triticum aestivum L.). Theor. Appl. Genet. 117, 595-608. doi: 10.1007/s00122-008-0804-5
15. Edae, E. A., Byrne, P. F., Haley, S. D., Lopes, M. S., and Reynolds, M. P. (2014). Genome-wide association mapping of yield and yield components of spring wheat under contrasting moisture regimes. Theor. Appl. Genet. 127, 791-807. doi: 10.1007/s00122-013-2257-8
16. Ellis, M. H., Rebetzke, G. J., Azanza, F., Richards, R. A., and Spielmeyer, W. (2005). Molecular mapping of gibberellin-responsive dwarfing genes in bread wheat. Theor. Appl. Genet. 111,423-430.doi: 10.1007/s00122-005-2008-6
17. Golabadi, M., Arzani, A., Mirmohammadi Maibody, S. A. M., Tabatabaei, B. E. S., and Mohammadi, S. A. (2011). Identification of microsatellite markers linked with yield components under drought stress at terminal growth stages in durum wheat. Euphytica 177, 207-221. doi: 10.1007/s10681-010-0242-8
18. Green, A. J., Berger, G., Griffey, C. A., Pitman, R., Thomason, W., Balota, M., et al. (2012). Genetic yield improvement in soft red winter wheat in the Eastern United States from 1919 to 2009. Crop Sci. 52, 2097-2108. doi: 10.2135/cropsci2012010026
19. Gupta, P. K., Varshney, R. K., Sharma, P. C., and Ramesh, B. (1999). Molecular markers and their applications in wheat breeding. Plant Breeding 118, 369-390. doi: 10.1046/j1439-0523199900401x
20. Holland, J. B. (2007). Genetic architecture of complex traits in plants. Curr. Opin. PlantBiol. 10, 156-161. doi: 10.1016/jpbi200701003
21. Huang, X., Wei, X., Sang, T., Zhao, Q., Feng, Q., Zhao, Y., et al. (2010). Genome-wide association studies of 14 agronomic traits in rice landraces. Nat. Genet. 42, 961-967. doi: 10.1038/ng.695
22. Huang, X., Zhao, Y., Wei, X., Li, C., Wang, A., Zhao, Q., et al. (2011). Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat. Genet. 44, 32-39. doi: 10.1038/ng.1018
23. Huang, X. Q., Kempf, H., Ganal, M. W., and Roder, M. S. (2004). Advanced backcross QTL analysis in progenies derived from a cross between a German elite winter wheat variety and a synthetic wheat (Triticum aestivum L.). Theor. Appl. Genet. 109,933-943.doi: 10.1007/s00122-004-1708-7
24. Jia, G., Huang, X., Zhi, H., Zhao, Y., Zhao, Q., Li, W., et al. (2013). A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica). Nat. Genet. 45, 957-961. doi: 10.1038/ng.2673
25. Kumar, N., Kulwal, P. L., Balyan, H. S., and Gupta, P. K. (2007). QTL mapping for yield and yield contributing traits in two mapping populations of bread wheat. Mol. Breeding 19, 163-177. doi: 10.1007/s11032-006-9056-8
26. Lambel, S., Lanini, B., Vivoda, E., Fauve, J., Wechter, W. P., Harris-Shultz, K. R., et al. (2014). A major QTL associated with Fusarium oxysporum race resistance identified in genetic populations derived from closely related watermelon lines using selective genotyping and genotyping-by-sequencing for SNP discovery. Theor. Appl. Genet. 127, 2105-2115. doi: 10.1007/s00122-014-2363-2
27. Li, H., Peng, Z., Yang, X., Wang, W., Fu, J., Wang, J., et al. (2012). Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels. Nat. Genet. 45,43-50. doi: 10.1038/ng.2484
28. Li, H. H., Ye, G. Y., and Wang, J. K. (2007a). A modified algorithm for the improvement of composite interval mapping. Genetics 175, 361-374. doi: 10.1534/genetics.106.06681
29. Li, S. S., Jia, J. Z., Wei, X. Y., Zhang, X. C., Li, L. Z., Chen, H. M., et al. (2007b). An intervarietal genetic map and QTL analysis for yield traits in wheat. Mol. Breeding 20, 167-178. doi: 10.1007/s11032-007-9080-3
30. Li, X. M., Xia, X. C., Xiao, Y. G., He, Z. H., Wang, D. S., Trethowan, R., et al. (2015). QTL mapping for plant height and yield components in common wheat under water limited and full irrigation environments. Crop Pasture Sci. 67, 660-670. doi: 10.1071/CP14236
31. Li, Z. F., Zheng, T. C., He, Z. H., Li, G. Q., Xu, S. C., Li, X. P., et al. (2006). Molecular tagging of stripe rust resistance gene YrZH84 in Chinese wheat line Zhou 8425B. Theor. Appl. Genet. 112, 1098-1103. doi: 10.1007/s00122-006-0211-8
32. Liu, G., Li, J. J., Lu, L. H., Qin, D. D., Zhang, J. P., Guan, P. F., et al. (2014). Mapping QTLs of yield-related traits using RIL population derived from common wheat and Tibetan semi-wild wheat. Theor. Appl. Genet. 127, 2415-2432. doi: 10.1007/s00122-014-2387-7
33. Lopes, M. S., Reynolds, M. P., McIntyre, L., Mathews, K. L., Jalal Kamali, M. R., Mossad, M., et al. (2013). QTL for yield and associated traits in the Seri/Babax population grown across several environments in Mexico, in the West Asia, North Africa, and South Asia regions. Theor. Appl. Genet. 126, 971-984. doi: 10.1007/s00122-012-2030-4
34. Lupton, F. H. (1966). Translocation of photosynthetic assimilates in wheat. Ann. Appl. Biol. 57, 355-364. doi: 10.1111/j.1744-7348.1966.tb03829.x
35. Marone, D., Laido, G., Gadaleta, A., Colasuonno, P., Ficco, D. B. M., Giancaspro, A., et al. (2012). A high-density consensus map of A and B wheat genomes. Theor. Appl. Genet. 125, 1619-1638. doi: 10.1007/s00122-012-1939-y
36. McCartney, C. A., Somers, D. J., Humphreys, D. J., and Lukow, O. (2005). Mapping quantitative trait loci controlling agronomic traits in the spring wheat cross RL 4452 xAC ‘Domain'. Genome 48,870-883. doi: 10.1139/g05-055
37. Nachit, M. M., Elouafi, I., Pagnotta, M. A., Ei, S. A., Iacono, E., Labhilili, M., et al. (2001). Molecular linkage map for an intraspecific recombinant inbred population of durum wheat (Triticum turgidum L. var. durum). Theor. Appl. Genet. 102, 177-186. doi: 10.1007/s001220051633
38. Peng, Z. S., Li, X., Yang, Z. J., and Liao, M. L. (2011). A new reduced height gene found in the tetraploid semi-dwarf wheat landrace Aiganfanmai. Genet. Mol. Res. 10, 2349-2357. doi: 10.4238/2011.October.5.5
39. Pinto, R. S., and Reynolds, M. P. (2015). Common genetic basis for canopy temperature depression under heat and drought stress associated with optimized root distribution in bread wheat. Theor. Appl. Genet. 128, 575-585. doi: 10.1007/s00122-015-2453-9
40. Prashar, A., Hornyik, C., Young, V., McLean, K., Sharma, S. K., Dale, M. F. B., et al. (2014). Construction of a dense SNP map of a highlyheterozygous diploid potato population and QTL analysis of tuber shape and eye depth. Theor. Appl. Genet. 127, 2159-2171. doi: 10.1007/s00122-014-2369-9
41. Quarrie, S. A., Quarrie, S. P., Radosevic, R., Rancic, D., Kaminska, A., Barnes, J. D., et al. (2006). Dissecting a wheat QTL for yield present in a range of environments: from the QTL to candidate genes. J. Exp. Bot. 57, 2627-2637. doi: 10.1093/jxb/erl026
42. Rafalski, A. (2002). Applications of single nucleotide polymorphisms in crop genetics. Curr. Opin. Plant Biol. 5, 94-100. doi: 10.1016/S1369-5266(02)00240-6
43. Rebetzke, G. J., Condon, A. G., Farquhar, G. D., Appels, R., and Richards, R. A. (2008a). Quantitative trait loci for carbon isotope discrimination are repeatable across environments and wheat mapping populations. Theor. Appl. Genet. 118, 123-137. doi: 10.1007/s00122-008-0882-4
44. Rebetzke, G. J., van Herwaarden, A. F., Jenkins, C., Weiss, M., Lewis, D., Ruuska, S., et al. (2008b). Quantitative trait loci for water-soluble carbohydrates and associations with agronomic traits in wheat. Aust. J. Agric. Res. 59, 891-905. doi: 10.1071/AR08067
45. Reynolds, M., Bonnett, D., Chapman, S. C., Furbank, R. T., Manes, Y., Mather, D. E., et al. (2011). Raising yield potential of wheat. I. Overview of a consortium approach and breeding strategies. J. Exp. Bot. 62, 439-452. doi: 10.1093/jxb/erq311
46. Reynolds, M., and Tuberosam, R. (2008). Translational research impacting on crop productivity in drought-prone environments. Curr. Opin. Plant Biol. 11, 171-179. doi: 10.1016/j.pbi.2008.02.005
47. Schlotterer, C. (2004). The evolution of molecular markers - just a matter of fashion. Nat. Rev. Genet. 5, 63-69. doi: 10.1038/nrg1249
48. Sela, H., Ezratim, S., Ben-Yehuda, P., Manisterski, J., Akhunov, E., Dvorak, J., et al. (2014). Linkage disequilibrium and association analysis of stripe rust resistance in wild emmer wheat (Triticum turgidum ssp. dicoccoides) population in Israel. Theor. Appl. Genet. 127,2453-2463.doi: 10.1007/s00122-014-2389-5
49. Shiaoman, C., Zhang, W. J., Akhunov, E., Sherman, J., Ma, Y. Q., Luo, M. C., et al. (2009). Analysis of gene-derived SNP marker polymorphism in US wheat cultivars. Mol. Breeding 23,23-33. doi: 10.1007/s11032-008-9210-6
50. Sindhu, A., Ramsay, L., Sanderson, L. A., Stonehouse, R., Li, R., Condie, J., et al. (2014). Gene-based SNP discovery and genetic mapping in pea. Theor. Appl. Genet. 127,2225-2241.doi: 10.1007/s00122-014-2375-y
51. Song, Q., Hyten, D. L., Jia, G., Quigley, C. V., Fickus, E. W., Nelson, R. L., et al. (2013). Development and evaluation of Soy SNP 50K, a high-density genotyping array for soybean. PLoS ONE 8:e54985. doi: 10.1371/journal.pone.0054985
52. Stam, P. (1993). Construction of integrated genetic linkage maps by means of a new computer package: JoinMap. Plant J. 3, 739-744. doi: 10.1111/j.1365-313X.1993.00739.x
53. Sukumaran, S., Dreisigacker, S., Lopes, M., Chavez, P., and Reynolds, M. P. (2015). Genome-wide association study for grain yield and related traits in an elite spring wheat population grown in temperate irrigated environments. Theor. Appl. Genet. 128,353-363.doi: 10.1007/s00122-014-2435-3
54. Tian, F., Bradbury, P. J., Brown, P. J., Hung, H., Sun, Q., Flint-Garcia, S., et al. (2011). Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat. Genet. 43, 159-162. doi: 10.1038/ng.746
55. Wang, S. C., Wong, D., Forrest, K., Allen, A., Chao, S. M., Huang, B. E., et al. (2014). Characterization of polyploid wheat genomic diversity using a high-density 90000 single nucleotide polymorphism array. Plant Biotechnol. J. 12, 87-96. doi: 10.1111/pbi.12183
56. Xiao, Y. G., Yin, G. H., Li, H. H., Xia, X. C., Yan, J., Zheng, T. C., et al. (2011). Genetic diversity and genome-wide association analysis of stripe rust resistance among the core wheat parent Zhou 8425B and its derivatives. Sci. Agric. Sin. 44, 3919-3929. doi: 10.3864/j.issn.0578-1752.2011.19.001
57. Xu, Y. F., An, D. G., Liu, D. C., Zhang, A. M., Xu, H. X., and Li, B. (2012). Mapping QTLs with epistatic effects and QTLxtreatment interactions for salt tolerance at stage of wheat. Euphytica 186, 233-245. doi: 10.1007/s10681-012-0647-7
58. Yang, Q., Li, Z., Li, W. Q., Ku, L. X., Wang, C., Ye, J. R., et al. (2013). CACTA-like transposable element in ZmCCT attenuated photoperiod sensitivity and accelerated the postdomestication spread of maize. Proc. Natl. Acad. Sci. U.S.A. 110, 16969-16974. doi: 10.1073/pnas.1310949110
59. Yang, Z. B., Bai, Z. Y., Li, X. L., Wang, P., Wu, Q. X., Yang, L., et al. (2012). SNP identification and allelic-specific PCR markers development for TaGW2, a gene linked to wheat kernel weight. Theor. Appl. Genet. 125, 1057-1068. doi: 10.1007/s00122-012-1895-6
60. Yin, G. H., Wang, J. W., Wen, W. E., He, Z. H., Li, Z. F., Wang, H., et al. (2009). Mapping of wheat stripe rust resistance gene YrZH84 with RGAP markers and its application. Acta Agron. Sin. 35, 1274-1281. doi: 10.3724/SP.J.1006.2009.01274
61. Yu, H., Xie, W., Wang, J., Xing, Y., Xu, C., Li, X., et al. (2011). Gains in QTL detection using an ultra-high density SNP map based on population sequencing relative to traditional RFLP/SSR markers. PLoS ONE 6:e17595. doi: 10.1371/journal.pone.0017595
62. Zhao, K., Tung, C. W., Eizenga, G. C., Wright, M. H., Ali, M. L., Price, A. H., et al. (2011). Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat. Commun. 2:467. doi: 10.1038/ncomms1467
63. Zhao, X. L., Zheng, T. C., Xia, X. C., He, Z. H., Liu, D. Q., Yang, W. X., et al. (2008). Molecular mapping of leaf rust resistance gene LrZH84 in Chinese wheat line Zhou 8425B. Theor. Appl. Genet. 117, 1069-1075. doi: 10.1007/s00122-008-0845-9