Genomic prediction of biomass yield in two selection cycles of a tetraploid alfalfa breeding population

Plant Genome

Volumn 8, Issue 2, 2015, Pages

  Li, Xuehui ^a   Wei, Yanling ^e   Acharya, Ananta ^b   Hansen, Julie L ^c   Crawford, Jamie L ^c   Viands, Donald R ^c   Michaud, Réal ^d   Claessens, Annie ^d   Charles Brummer, E ^e  

^a NORTH DAKOTA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF GEORGIA   (United States)

^c Cornell Univ ^*  (United States)

^d AGRICULTURE AND AGRI FOOD CANADA   (Canada)

^e UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MEDICAGO SATIVA;

EID: 84937011034     PISSN: None     EISSN: 19403372     Source Type: Journal    
DOI: 10.3835/plantgenome2014.12.0090     Document Type: Article

References (51)

1. Asoro, F.G., M.A. Newell, W.D. Beavis, M.P. Scott, N.A. Tinker, and J.L. Jannink. 2013. Genomic, marker-assisted, and pedigree-BLUP selection methods for b-Glucan concentration in elite oat. Crop Sci. 53:1894–1906. doi:10.2135/cropsci2012.09.0526
2. Bates, D., M. Maechler, and B. Bolker. 2011. Welcome to lme4—Mixedeffects models project. R foundation for statistical computing, Vienna, Austria. http://lme4.r-forge.r-project.org/
3. Berge, L., C. Bouveyron, and S. Girard. 2012. HDclassif: An R package for model-based clustering and discriminant analysis of high-dimensional data. J. Stat. Softw. 46:1–29.
4. Bernardo, R., and J. Yu. 2007. Prospects for genome wide selection for quantitative traits in Maize. Crop Sci. 47:1082–1090.
5. Bradbury, P.J., Z. Zhang, D.E. Kroon, T.M. Casstevens, Y. Ramdoss, and E.S. Buckler. 2007. TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635. doi:10.1093/bioinformatics/btm308
6. Brummer, E.C. 1999. Capturing heterosis in forage crop cultivar development. Crop Sci. 39:943–954. doi:10.2135/cropsci1999.0011183X003900040001x
7. Brummer, E.C., and M.D. Casler. 2014. Cool-season forages. In: S. Smith, et al., editors, Yield gains in major U.S. field crops. ASA, CSSA, SSSA, Madison, WI. p. 33–52.
8. Choi, H.K., D. Kim, T. Uhm, E. Limpens, H. Lim, J.H. Mun, P. Kalo, R.V. Penmetsa, A. Seres, O. Kulikova, B.A. Roe, T. Bisseling, G.B. Kiss, and D.R. Cook. 2004. A sequence-based genetic map of Medicago truncatula and comparison of marker colinearity with M. sativa. Genetics 166:1463–1502. doi:10.1534/genetics.166.3.1463
9. Doyle, J.J., and J.I. Doyle. 1990. Isolation of plant DNA from fresh tissue. BRL Life Technologies: Focus 12:13–15.
10. Elshire, R.J., J.C. Glaubitz, Q. Sun, J.A. Poland, K. Kawamoto, E.S. Buckler, and S.E. Mitchell. 2011. A robust, simple Genotyping-by-Sequencing (GBS) approach for high diversity species. PLoS ONE 6:e19379. doi:10.1371/journal.pone.0019379
11. Endelman, J.B. 2011. Ridge regression and other kernels for genomic selection with R package rrBLUP. Plant Gen. 4:250. doi:10.3835/plantgenome2011.08.0024
12. Guo, Z., D.M. Tucker, D. Wang, C.J. Basten, E. Ersoz, W.H. Briggs, J. Lu, M. Li, and G. Gay. 2013. Accuracy of across-environment genome-wide prediction in maize nested association mapping populations. G3 (Bethesda) 3:263–272.
13. Han, Y., Y. Kang, I. Torres-Jerez, F. Cheung, C.D. Town, P.X. Zhao, M.K. Udvardi, and M.J. Monteros. 2011. Genome-wide SNP discovery in tetraploid alfalfa using 454 sequencing and high resolution melting analysis. BMC Genomics 12:350. doi:10.1186/1471-2164-12-350
14. Hayes, B.J., P.J. Bowman, A.J. Chamberlain, and M.E. Goddard. 2009. Invited review: Genomic selection in dairy cattle: Progress and challenges. J. Dairy Sci. 92:433–443. doi:10.3168/jds.2008-1646
15. Hayes, B.J., N.O.I. Cogan, L.W. Pembleton, M.E. Goddard, J.P. Wang, G.C. Spangenberg, and J.W. Forster. 2013. Prospects for genomic selection in forage plant species. Plant Breed. 132:133–143. doi:10.1111/pbr.12037
16. Heffner, E.L., J.L. Jannink, H. Iwata, E. Souza, and M.E. Sorrells. 2011. Genomic selection accuracy for grain quality traits in biparental wheat populations. Crop Sci. 51:2597–2606. doi:10.2135/cropsci2011.05.0253
17. Heffner, E.L., M.E. Sorrells, and J.L. Jannink. 2009. Genomic selection for crop improvement. Crop Sci. 49:1–12. doi:10.2135/cropsci2008.08.0512
18. Heslot, N., J. Rutkoski, J. Poland, J.L. Jannink, and M.E. Sorrells. 2013. Impact of marker ascertainment bias on genomic selection accuracy and estimates of genetic diversity. PLoS ONE 8:e74612. doi:10.1371/journal.pone.0074612
19. Hill, W.G., and B.S. Weir. 1988. Variances and covariances of squared linkage disequilibria in finite populations. Theor. Popul. Biol. 33:54–78. doi:10.1016/0040-5809(88)90004-4
20. Jannink, J.L. 2010. Dynamics of long-term genomic selection. Genet. Sel. Evol. 42:35. doi:10.1186/1297-9686-42-35
21. Kumar, S., D. Chagne, M.C. Bink, R.K. Volz, C. Whitworth, and C. Carlisle. 2012. Genomic selection for fruit quality traits in apple (Malus ´domestica Borkh.). PLoS ONE 7:e36674. doi:10.1371/journal.pone.0036674
22. Lamb, J.F.S., C.C. Sheaffer, L.H. Rhodes, R.M. Sulc, D.J. Undersander, and E.C. Brummer. 2006. Five decades of alfalfa cultivar improvement: Impact on forage yield, persistence, and nutritive value. Crop Sci. 46:902–909. doi:10.2135/cropsci2005.08-0236
23. Lande, R., and R. Thompson. 1990. Efficiency of marker-assisted selection in the improvement of quantitative traits. Genetics 124:743–756.
24. Li, X., A. Acharya, A.D. Farmer, J.A. Crow, A.K. Bharti, R.S. Kramer, Y. Wei, Y. Han, J. Gou, G.D. May, M.J. Monteros, and E.C. Brummer. 2012. Prevalence of single nucleotide polymorphism among 27 diverse alfalfa genotypes as assessed by transcriptome sequencing. BMC Genomics 13:568. doi:10.1186/1471-2164-13-568
25. Li, X., and E.C. Brummer. 2012. Applied genetics and genomics in alfalfa breeding. Agronomy 2:40–61. doi:10.3390/agronomy2010040
26. Li, X., Y. Han, Y. Wei, A. Acharya, A.D. Farmer, J. Ho, M.J. Monteros, and E.C. Brummer. 2014a. Development of an alfalfa SNP array and its use to evaluate patterns of population structure and linkage disequilibrium. PLoS ONE 9:e84329.
27. Li, X., X. Wang, Y. Wei, and E.C. Brummer. 2011a. Prevalence of segregation distortion in diploid alfalfa and its implications for genetics and breeding applications. Theor. Appl. Genet. 123:667–679. doi:10.1007/s00122-011-1617-5
28. Li, X., Y. Wei, A. Acharya, Q. Jiang, J. Kang, and E.C. Brummer. 2014b. A high-density genetic linkage map of autotetraploid alfalfa (Medicago sativa L.) developed using Genotyping-by-Sequencing is highly syntenous with the M. truncatula genome. G3 (Bethesda) 4:1971–1979. doi:10.1534/g3.114.012245
29. Li, X., Y. Wei, K.J. Moore, R. Michaud, D.R. Viands, J.L. Hansen, A. Acharya, and E.C. Brummer. 2011b. Association mapping of biomass yield and stem composition in a tetraploid alfalfa breeding population. Plant Gen. 4:24–35. doi:10.3835/plantgenome2010.09.0022
30. Lorenz, A.J., S. Chao, F.G. Asoro, E.L. Heffner, T. Hayashi, H. Iwata, K.P. Smith, M.E. Sorrells, and J.L. Jannink. 2011. Genomic selection in plant breeding: Knowledge and prospects. Adv. Agron. 110:77–123. doi:10.1016/B978-0-12-385531-2.00002-5
31. Lorenz, A.J., K.P. Smith, and J.L. Jannink. 2012. Potential and optimization of genomic selection for Fusarium head blight resistance in six-row barley. Crop Sci. 52:1609–1621. doi:10.2135/cropsci2011.09.0503
32. Lorenzana, R.E., and R. Bernardo. 2009. Accuracy of genotypic value predictions for marker-based selection in biparental plant populations. Theor. Appl. Genet. 120:151–161. doi:10.1007/s00122-009-1166-3
33. Lu, F., A.E. Lipka, J. Glaubitz, R. Elshire, J.H. Cherney, M.D. Casler, E.S. Buckler, and D.E. Costich. 2013. Switchgrass genomic diversity, ploidy, and evolution: Novel insights from a network-based SNP discovery protocol. PLoS Genet. 9:e1003215. doi:10.1371/journal.pgen.1003215
34. Ly, D., M. Hamblin, I. Rabbi, G. Melaku, M. Bakare, H.G. Gauch, R. Okechukwu, A.G.O. Dixon, P. Kulakow, and J.L. Jannink. 2013. Relatedness and genotype ´ environment interaction affect prediction accuracies in genomic selection: A study in Cassava. Crop Sci. 53:1312–1325. doi:10.2135/cropsci2012.11.0653
35. Massman, J.M., A. Gordillo, R.E. Lorenzana, and R. Bernardo. 2013. Genomewide predictions from maize single-cross data. Theor. Appl. Genet. 126:13–22. doi:10.1007/s00122-012-1955-y
36. Meuwissen, T.H., B.J. Hayes, and M.E. Goddard. 2001. Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819–1829.
37. Poland, J., J. Endelman, J. Dawson, J. Rutkoski, S.Y. Wu, Y. Manes, S. Dreisigacker, J. Crossa, H. Sanchez-Villeda, M. Sorrells, and J.L. Jannink. 2012. Genomic selection in wheat breeding using genotyping- by-sequencing. Plant Gen. 5:103–113. doi:10.3835/plantgenome2012.06.0006
38. R Development Core Team. 2012. R: A language and environment for statistical computing. R Foundation for Stat. Comput., Vienna, Austria.
39. Resende, M.F., Jr., P. Munoz, J.J. Acosta, G.F. Peter, J.M. Davis, D. Grattapaglia, M.D. Resende, and M. Kirst. 2012. Accelerating the domestication of trees using genomic selection: Accuracy of prediction models across ages and environments. New Phytol. 193:617–624. doi:10.1111/j.1469-8137.2011.03895.x
40. Resende, R.M.S., M.D. Casler, and M.D.V. Resende. 2014. Genomic selection in forage breeding: Accuracy and methods. Crop Sci. 54:143–156. doi:10.2135/cropsci2013.05.0353
41. Sakiroglu, M., S. Sherman-Broyles, A. Story, K.J. Moore, J.J. Doyle, and E.C. Brummer. 2012. Patterns of linkage disequilibrium and association mapping in diploid alfalfa (M. sativa L.). Theor. Appl. Genet. 125:577–590. doi:10.1007/s00122-012-1854-2
42. SAS Institute. 2010. The SAS system for Windows. Release 9.3. SAS Inst. Inc., Cary, NC.
43. Stekhoven, D.J., and P. Buhlmann. 2012. MissForest: Non-parametric missing value imputation for mixed-type data. Bioinformatics 28:112–118. doi:10.1093/bioinformatics/btr597
44. Sved, J.A. 1971. Linkage disequilibrium and homozygosity of chromosome segmens in finite populations. Theor. Popul. Biol. 2:125–141. doi:10.1016/0040-5809(71)90011-6
45. Teuber, L.R., K.L. Taggard, L.K. Gibbs, M.H. McCaslin, M.A. Peterson, and D.K. Barnes. 1998. Fall dormancy. In: Standard tests to characterize alfalfa cultivars, 3rd ed. (Amended 1998). North American Alfalfa Improvement Conference, Beltsville, MD. http://www.naaic.org/stdtests/Dormancy2.html (accessed 16 Dec. 2013).
46. Toosi, A., R.L. Fernando, and J.C.M. Dekkers. 2010. Genomic selection in admixed and crossbred populations. J. Anim. Sci. 88:32–46. doi:10.2527/jas.2009-1975
47. Uitdewilligen, J.G., A.M. Wolters, B. D’Hoop T.J. Borm, R.G. Visser, and H.J. van Eck. 2013. A next-generation sequencing method for genotyping- by-sequencing of highly heterozygous autotetraploid potato. PLoS ONE 8:e62355. doi:10.1371/journal.pone.0062355
48. Viands, D.R., C.C. Lowe, R.P. Murphy, and R.L. Millar. 1990. Registration of ‘Oneida VR’ alfalfa. Crop Sci. 30:955. doi:10.2135/cropsci1990.0011183X003000040042x
49. Yan, J., T. Shah, M.L. Warburton, E.S. Buckler, M.D. McMullen, and J. Crouch. 2009. Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers. PLoS ONE 4:e8451. doi:10.1371/journal.pone.0008451
50. Yang, S.S., Z.J. Tu, F. Cheung, W.W. Xu, J.F. Lamb, H.J. Jung, C.P. Vance, and J.W. Gronwald. 2011. Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems. BMC Genomics 12:199. doi:10.1186/1471-2164-12-199
51. Zhong, S., J.C. Dekkers, R.L. Fernando, and J.L. Jannink. 2009. Factors affecting accuracy from genomic selection in populations derived from multiple inbred lines: A barley case study. Genetics 182:355–364. doi:10.1534/genetics.108.098277