Association of single nucleotide polymorphisms with form traits in three New Zealand populations of radiata pine in the presence of genotype by environment interactions

Tree Genetics and Genomes

Volumn 12, Issue 4, 2016, Pages

  Li, Yongjun ^a   Wilcox, Phillip ^b   Telfer, Emily ^a   Graham, Natalie ^a   Stanbra, Lisa ^a  

^a SCION   (New Zealand)

^b UNIVERSITY OF OTAGO   (New Zealand)

Author keywords

Association study; Branch cluster frequency; G E interactions; Radiata pine; SNPs; Stem straightness

Indexed keywords

EID: 84976382103     PISSN: 16142942     EISSN: 16142950     Source Type: Journal    
DOI: 10.1007/s11295-016-1019-6     Document Type: Article

References (56)

1. Ade CP, Bemm F, Dickson JMJ, Walter C, Harris PJ (2014) Family 34 glycosyltransferase (GT34) genes and proteins in Pinus radiata (radiata pine) and Pinus taeda (loblolly pine). Plant J 78(2):305–318. doi:10.1111/tpj.12468
2. Akaike H (1973) Information theory and an extension of the maximum principle. In: The 2nd International Symposium on Information Theory, Budapest, Hungary, Akadémia Kiadó. 267–281
3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
4. Apiolaza LA (2012) Basic density of radiata pine in New Zealand: genetic and environmental factors. Tree Genet Genomes 8:87–96
5. Arcade A, Rampant PF, Guerroue BL, Paques LE, Prat D (1996) Quantitative traits and genetic markers: analysis of a factorial mating design in larch. In: Ahuja MR (ed) Somatic cell genetics and molecular genetics of trees. Kluwer Academic Publishers, Netherland, pp 211–216
6. Ball RD (2007a) Quantifying evidence for candidate gene polymorphisms: Bayesian analysis combining sequence-specific and quantitative trait loci colocation information. Genetics 177:2399–2416
7. Ball RD (2007b) Statistical analysis and experimental design. In: Oraguzie N, Rikkerink EHA, Gardiner SE, De Silva HN (eds) Association mapping in plants. Springer Verlag, New York, pp 133–196
8. Baltunis BS, Brawner JT (2010) Clonal stability in Pinus radiata across New Zealand and Australia. I. Growth and form traits. New Forests 40:305–322
9. Baltunis BS, Gapare WJ, Wu HX (2010) Genetic parameters and genotype by environment interaction in radiata pine for growth and wood quality traits in Australia. Silvae Genet 59:2–3
10. Beavis WD, Paterson AH (1997) QTL analyses: power, precision and accuracy. In: Molecular dissection of complex traits, Vol 1st. CRC Press LLC, p 145–159
11. Blackburn DP, Hamilton MG, Harwood CE, Baker TG, Potts BM (2013) Assessing genetic variation to improve stem straightness in Eucalyptus globulus. Ann For Sci 70:461–470
12. Burdon RD (1977) Genetic correlation as a concept for studying genotype-environment interaction in forest tree breeding. Silvae Genet 26:168–175
13. Burdon RD, Banister MH, Low CB (1992) Genetic survey of Pinus radiata. 4. variance structures and heritabilities in juvenile clones. N Z J For Sci 22:187–210
14. Carson MJ (1986) Control-pollinated seed orchards of best general combiners—a new strategy for radiata pine improvement. Plant Breed Symp 5:144–149
15. Carson MJ (1988) Long-internode or multinodal radiata pine—a financial analysis. FRI Bulletin No. 115. Forest Research Institute, Rotorua, New Zealand
16. Carson SD (1991) Genotype × environment interaction and optimal number of progeny test sites for improving Pinus radiata in New Zealand. N Z J For Sci 21:32–49
17. Codesido V, Fernández-López J (2009) Implication of genotype × site interaction on Pinus radiata breeding in Galicia. New Forests 37:17–34
18. Collard BCY, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philos Trans R Soc B 363:557–572. doi:10.1098/rstb.2007.2170
19. Cumbie WP (2010) Association genetics for growth, carbon isotope discrimination, and stem quality in loblolly pine. PhD thesis, Department of Forestry, North Carolina State University
20. Del Río M, Bravo F, Pando V, Sanz G, Sierra de Grado R (2004) Influence of individual tree and stand attributes in stem straightness in Pinus pinaster Ait. stands. Ann For Sci 61:141–148
21. Dillon SK, Nolan M, Li W, Bell C, Wu HX, Southerton SG (2010) Allelic variation in cell wall candidate genes affecting solid wood properties in natural populations and land races of Pinus radiata. Genetics 185:1477–1487. doi:10.1534/genetics.110.116582
22. Dungey HS, Brawner JT, Burger F, Carson M, Henson M, Jefferson P, Matheson AC (2009) A new breeding strategy for Pinus radiata in New Zealand and New South Wales. Silvae Genet 58:28–38
23. Falconer D, Mackay T (1996) Introduction to quantitative genetics. Longmans Green, New York, Harlow
24. FOA, MPI (2012) New Zealand forest industry facts and figures 2011/2012. New Zealand Forest Owners Association & Ministry of Primary Industries. www.mpigovt.nz or www.nzfoa.org.nz, Wellington, New Zealand
25. Gapare WJ, Ivković M, Dutkowski GW, Spencer DJ, Buxton P, Wu HX (2012) Genetic parameters and provenance variation of Pinus radiata D. Don. ‘Eldridge collection’ in Australia 1: growth and form traits. Tree Genet Genomes 8:391–407
26. Garrick D, Taylor J, Fernando R (2009) Deregressing estimated breeding values and weighting information for genomic regression analyses. Genet Sel Evol 41:55
27. Gilmour AR, Cullis BR, Gogel BJ, Thompson R (2009) ASREML user guide release 3.0. VSN International Ltd, Hemel Hempstead HP2 4TP England, Hemel Hempstead
28. Goddard ME (1998) Consensus and debate in the definition of breeding objectives. J Dairy Sci 81:6–18
29. Howarth JM, Goddard ME, Kinghorn BP (1997) Breeding strategies for targeting different breeding objectives. Paper presented at the Association for the Advancement of Animal Breeding and Genetics, Vol 12, Dubbo, NSW Australia, 6–10 April 1997
30. Jayawickrama KJS, Carson MJ (2000) A breeding strategy for the New Zealand Radiata Pine Breeding Cooperative. Silvae Genet 49:82–90
31. Johnston GR, Burdon RD (1990) Family-site interaction in Pinus radiata: implications for progeny testing strategy and regionalised breeding in New Zealand. Silvae Genet 39:55–62
32. Kumar S, Echt C, Wilcox PL, Richardson TE (2004) Testing for linkage disequilibrium in the New Zealand radiata pine breeding population. Theor Appl Genet 108:292–298
33. Lepoittevin C, Harvengt L, Plomion C, Garnier-Géré P (2012) Association mapping for growth, straightness and wood chemistry traits in the Pinus pinaster Aquitaine breeding population. Tree Genet Genomes 8:113–126. doi:10.1007/s11295-011-0426-y
34. Matheson AC, Raymond CA (1984) The impact of genotype × environment interactions on Australian Pinus radiata breeding programs. Aust For Res 14:11–25
35. McDonald TM, Apiolaza LA (2009) Genotype by environment interaction of Pinus radiata in New Zealand. In: Second Australasian Forest Genetics Conference, Perth, Australia
36. Mead DJ (2013) Sustainable management of Pinus radiata plantations. FAO Forestry Paper No. 170. Rome, FAO
37. Möller R, Steward D, Phillips L, Flint H, Wagner A (2005) Gene silencing of cinnamyl alcohol dehydrogenase in Pinus radiata callus cultures. Plant Physiol Biochem 43(12):1061–1066
38. Muir W, Nyquist WE, Xu S (1992) Alternative partitioning of the genotype-by-environment interaction. Theor Appl Genet 84:193–200. doi:10.1007/BF00224000
39. Murray BG (1998) Nuclear DNA amounts in gymnosperms. Ann Bot 82:3–15
40. Neale DB, Savolainen O (2004) Association genetics of complex traits in conifers. Trends Plant Sci 9:325–330
41. Pederick LA (1990) Family × site interaction in Pinus radiata in Victoria, Australia, and implications for breeding strategy. Silvae Genet 39:3–4
42. Raymond CA (2011) Genotype by environment interactions for Pinus radiata in New South Wales, Australia. Tree Genet Genomes 7:819–833. doi:10.1007/s11295-011-0376-4
43. Resende MF Jr et al (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
44. Shelbourne CJA (1972) Genotype-environment interaction: its study and its implications in forest tree improvement. In: proceedings of IUFRO Genetics and SABRAO Joint Symposium, Vol B-1 (i). Tokyo, Japan, p 1–28
45. Silva FF et al (2014) Sire evaluation for total number born in pigs using a genomic reaction norms approach. J Anim Sci 92:3825–3834. doi:10.2527/jas.2013-6486
46. Sutton WRJ (1999) The need for planted forests and the example of radiata pine. New Forests 17:95–110. doi:10.1023/A:1006567221005
47. Tabor HK, Risch NJ, Myers RM (2002) Candidate-gene approaches for studying complex genetic traits: practical considerations. Nat Rev Genet 3:391–397
48. Telfer E, Graham N, Stanbra L, Manley T, Wilcox P (2013) Extraction of high purity genomic DNA from pine for use in a high-throughput genotyping platform. N Z J For Sci 43:3
49. Via S, Hawthorne D (2005) Back to the future: genetic correlations, adaptation and speciation. Genetica 123:147–156. doi:10.1007/s10709-004-2731-y
50. White TL, Adams WT, Neale DB (2007) Forest genetics. CAB International, Cambridge
51. Wilcox PL, Richardson TE, Carson SD (1997) Nature of quantitative trait variation in Pinus radiata: insights from QTL detection experiments. Paper presented at the IUFRO ‘97 Genetics of Radiata Pine, Rotorua, New Zealand
52. Wilcox PL, Echt CE, Burdon RD (2007) Gene-assisted selection: applications of association genetics for forest tree breeding. In: Oraguzie NC, Rikkerink EHA, Gardiner SE, De Silva NH (eds) Assocaition mapping in plants. Springer, New York, pp 211–247
53. Wu HX, Matheson AC (2005) Genotype by environment interactions in an Australia-wide radiata pine diallel mating experiment: implications for regionalized breeding. For Sci 51:29–40
54. Wu HX, Ivković M, Gapare WJ, Matheson AC, Baltunis BS, Powell MB, McRae TA (2008) Breeding for wood quality and profit in radiata pine: a review of genetic parameters. N Z J For Sci 38:56–87
55. Xiong J (2010) Genetic analysis of forking defects in loblolly pine. PhD thesis, North Carolina State University, Raleigh NC, USA
56. Zeller SL, Kalinina O, Brunner S, Keller B, Schmid B (2010) Transgene × environment interactions in genetically modified wheat. PLoS One 5:7