Detection of donor effects in a rye introgression population with genome-wide prediction

Plant Breeding

Volumn 134, Issue 4, 2015, Pages 406-415

  Mahone, Gregory S ^a   Frisch, Matthias ^a   Bauer, Eva ^b   Haseneyer, Grit ^b   Miedaner, Thomas ^c   Falke, Karen Christin ^a,d  

^a JUSTUS LIEBIG UNIVERSITY   (Germany)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^c UNIVERSITY OF HOHENHEIM   (Germany)

^d UNIVERSITY OF MÜNSTER   (Germany)

Author keywords

Genome wide prediction; Heteroscedastic marker variances; Introgression line; Introgression population; RMLV; Rye5K SNP array; Secale cereale L.

Indexed keywords

SECALE CEREALE;

EID: 84938557047     PISSN: 01799541     EISSN: 14390523     Source Type: Journal    
DOI: 10.1111/pbr.12283     Document Type: Article

References (37)

1. Churchil, G. A., and R. W. Doerge, 1994: Empirical threshold values for quantitative trait mapping. Genetics 138, 963-971.
2. Dunnett, C., 1955: A multiple comparison procedure for comparing several treatments with a control. J. Am. Stat. Assoc. 50, 1096-1121.
3. Eshed, Y., and D. Zamir, 1994: Introgressions from Lycopersicon pennellii can improve the soluble-solids yield of tomato hybrids. Theor. Appl. Genet. 88, 891-897.
4. Eshed, Y., and D. Zamir, 1995: An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield- associated QTL. Genetics 141, 1147-1162.
5. Falke, K. C., and M. Frisch, 2011: Power and false-positive rate in QTL detection with near-isogenic line libraries. Heredity 106, 576-584.
6. Falke, K. C., Z. Sušić, B. Hackauf, V. Korzun, J. Schondelmaier, P. Wilde, P. Wehling, H. Wortmann, R. Mank, J. Rouppe van der Voort, H. P. Maurer, T. Miedaner, and H. H. Geiger, 2008: Establishment of introgression libraries in hybrid rye (Secale cereale L.) from an Iranian primitive accession as a new tool for rye breeding and genomics. Theor. Appl. Genet. 117, 641-652.
7. Falke, K. C., P. Wilde, H. Wortmann, H. H. Geiger, and T. Miedaner, 2009a: Identification of genomic regions carrying QTL for agronomic and quality traits in rye (Secale cereal L.) introgression libraries. Plant Breed. 128, 615-623.
8. Falke, K. C., Z. Sušić, P. Wilde, H. Wortmann, J. Möhring, H.-P. Piepho, H. H. Geiger, and T. Miedaner, 2009b: Testcross performance of rye introgression lines developed by marker-based backcrossing using an Iranian accession as donor. Theor. Appl. Genet. 118, 1225-1238.
9. Falke, K. C., P. Wilde, H. Wortmann, B. U. Müller, J. Möhring, H.-P. Piepho, and T. Miedaner, 2010: Correlation between per se and testcross performance in rye (Secale cereale L.) introgression lines estimated with a bivariate mixed linear model. Crop Sci. 50, 1863-1873.
10. Falke, K. C., G. S. Mahone, E. Bauer, G. Haseneyer, T. Miedaner, F. Breuer, and M. Frisch, 2014: Genome-wide prediction methods for detecting genetic effects of donor chromosome segments in introgression populations. BMC Genom. 15, 782.
11. Finkers, R., A. W. Van Heusden, F. Meijer-Dekens, J. A. L. Van Kan, P. Maris, and P. Lindhout, 2007: The construction of a Solanum habrochaites LYC4 introgression line population and the identification of QTLs for resistance to Botrytis cinerea. Theor. Appl. Genet. 114, 1071-1080.
12. Fisher, R. A., 1918: The correlation between relatives on the supposition of Mendelian inheritance. Transact. R. Soc. Edinburgh 52, 399-433.
13. Haseneyer, G., T. Schmutzer, M. Seidel, R. Zhou, M. Mascher, C. C. Schön, S. Taudien, U. Scholz, N. Stein, K. F. X. Mayer, and E. Bauer, 2011: From RNAseq to large-scale genotyping - genomics resources for rye (Secale cereale L.). BMC Plant Biol. 11, 131.
14. Hochberg, Y. A., 1988: A sharper Bonferroni procedure for multiple tests of significance. Biometrika 75, 800-803.
15. Hofheinz, N., and M. Frisch, 2014: Heteroscedastic ridge regression approaches for genome-wide prediction with a focus on computational efficiency and accurate effect estimation. G3 4, 539-546.
16. Ishikawa, S., N. Ae, and Y. Masahiro, 2005: Chromosomal regions with quantitative trait loci controlling cadmium concentration in brown rice (Oryza sativa). New Phytol. 168, 345-350.
17. 2 population. Theor. Appl. Genet. 116, 845-857.
18. Liu, S., R. Zhou, Y. Dong, P. Li, and J. Jia, 2006: Development, utilization of introgression lines using a synthetic wheat as donor. Theor. Appl. Genet. 112, 1360-1373.
19. Mahone, G. S., M. Frisch, T. Miedaner, P. Wilde, H. Wortmann, and K. C. Falke, 2013: Identification of quantitative trait loci in rye introgression lines carrying multiple donor chromosome segments. Theor. Appl. Genet. 126, 49-58.
20. Martis, M. M., R. Zhou, G. Haseneyer, T. Schmutzer, J. Vrána, M. Kubaláková, S. König, K. G. Kugler, U. Scholz, B. Hackauf, V. Korzun, C. C. Schön, J. Dolezel, E. Bauer, K. F. X. Mayer, and N. Stein, 2013: Reticulate evolution of the rye (Secale cereale L.) genome. Plant Cell 25, 3685-3698.
21. Miedaner, T., B. U. Müller, H.-P. Piepho, and K. C. Falke, 2011: Genetic architecture of plant height in winter rye introgression libraries. Plant Breed. 130, 209-216.
22. Miedaner, T., M. Hübner, V. Korzun, B. Schmiedchen, E. Bauer, G. Haseneyer, P. Wilde, and J. C. Reif, 2012: Genetic architecture of complex agronomic traits examined in two testcross populations of rye (Secale cereale L.). BMC Genom. 13, 706.
23. Patterson, H. D., and E. R. Williams, 1976: A new class of resolvable incomplete block designs. Biometrica 63, 83-92.
24. Pestsova, E. G., A. Börner, and M. S. Röder, 2006: Development and QTL assessment of Triticum aestivum - Aegilops tauschii introgression lines. Theor. Appl. Genet. 112, 634-647.
25. Pillen, K., A. Zacharias, and J. Léon, 2003: Advanced backcross QTL analysis in barley (Hordeum vulgare L.). Theor. Appl. Genet. 107, 340-352.
26. Ponting, R. C., M. C. Drayton, N. O. I Cogan, M. P. Dobrowolsk, G. C. Spangenberg, K. F. Smith, and J. W. Forster, 2007: SNP discovery, validation, haplotype structure and linkage disequilibrium in full-length herbage nutritive quality genes of perennial ryegrass (Lolium perenne L.). Mol. Genet. Genomics 278, 585-597.
27. Rafalski, A., 2002: Applications of single nucleotide polymorphisms in crop genetics. Curr. Opin. Plant Biol. 5, 94-100.
28. Ronin, Y., D. Mester, D. Minkov, R. Belotserkovski, B. N. Jackson, P. S. Schnable, S. Aluru, and A. Korol, 2012: Two-phase analysis in consensus genetic mapping. G3 2, 537-549.
29. Schmalenbach, I., J. Léon, and K. Pillen, 2009: Identification and verification of QTLs for agronomic traits using wild barley introgression lines. Theor. Appl. Genet. 118, 483-497.
30. Schmalenbach, I., T. J. March, T. Bringezu, R. Waugh, and K. Pillen, 2011: High-resolution genotyping of wild barley introgression lines and fine-mapping of the threshability locus thresh-1 using Illumina GoldenGate assay. G3 1, 187-196.
31. Schön, C. C., F. H. Utz, S. Groh, B. Truberg, S. Openshaw, and A. E. Melchinger, 2004: Quantitative trait locus mapping based on resampling in a vast maize testcross experiment and its relevance to quantitative genetics for complex traits. Genetics 167, 485-498.
32. Septiningsih, E. M., J. Prasetiyono, E. Lubis, T. H. Tai, T. Tjubaryat, S. Moeljopawiro, and S. R. McCouch, 2003: Identification of quantitative trait loci for yield and yield components in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon. Theor. Appl. Genet. 107, 1419-1432.
33. Szalma, S. J., B. M. Hostert, J. R. LeDeaux, C. W. Stuber, and J. B. Holland, 2007: QTL mapping with near-isogenic lines in maize. Theor. Appl. Genet. 114, 1211-1228.
34. Von Korff, M., H. Wang, J. Léon, and K. Pillen, 2006: AB-QTL analysis in spring barley: II. Detection of favourable exotic alleles for agronomic traits introgressed from wild barley (H. vulgare ssp. spontaneum). Theor. Appl. Genet. 112, 1221-1231.
35. Wang, Y., J. Yao, Z. Zhang, and Y. Zheng, 2006: The comparative analysis based on maize integrated QTL map and meta-analysis of plant height QTLs. Chin. Sci. Bull. 51, 2219-2230.
36. Wricke, G., 2002: Two major genes for kernel weight in rye. Plant Breed. 121, 26-28.
37. Zamir, D., 2001: Improving plant breeding with exotic genetic libraries. Nat. Rev. Genet. 2, 983-989.