Paternity recovery in two maritime pine polycross mating designs and consequences for breeding

Tree Genetics and Genomes

Volumn 11, Issue 5, 2015, Pages

  Vidal, Marjorie ^a,b,c   Plomion, Christophe ^a,b   Harvengt, Luc ^c   Raffin, Annie ^a,b   Boury, Christophe ^a,b   Bouffier, Laurent ^a,b  

^a UMR 1202 BIOGECO   (France)

^b UNIVERSITÉ DE BORDEAUX   (France)

^c FCBA   (France)

Author keywords

Breeding strategies; Paternal reproductive success; Pedigree reconstruction; Pinus pinaster Ait; Pollen contamination; SNP markers

Indexed keywords

EID: 84942522736     PISSN: 16142942     EISSN: 16142950     Source Type: Journal    
DOI: 10.1007/s11295-015-0932-4     Document Type: Article

References (44)

1. Adams WT, Neale DB, Loopstra CA (1988) Verifying controlled crosses in conifer tree-improvement programs. Silvae Genet 37:147–152
2. Aronen T, Nikkanen T, Harju A, Tiimonen H, Haggman H (2002) Pollen competition and seed-siring success in Picea abies. Theor Appl Genet 104:638–642. doi:10.1007/s00122-001-0789-9
3. Burdon RD, Shelbourne CJA (1971) Breeding populations for recurrent selection: conflicts and possible solutions. N Z J For Sci 1:174
4. Canales J, Bautista R, Label P, Gomez-Maldonado J, Lesur I, Fernandez-Pozo N, Rueda-Lopez M, Guerrero-Fernandez D, Castro-Rodriguez V, Benzekri H, Canas RA, Guevara MA, Rodrigues A, Seoane P, Teyssier C, Morel A, Ehrenmann F, Le Provost G, Lalanne C, Noirot C, Klopp C, Reymond I, Garcia-Gutierrez A, Trontin JF, Lelu-Walter MA, Miguel C, Cervera MT, Canton FR, Plomion C, Harvengt L, Avila C, Gonzalo Claros M, Canovas FM (2014) De novo assembly of maritime pine transcriptome: implications for forest breeding and biotechnology. Plant Biotechnol J 12:286–299. doi:10.1111/pbi.12136
5. Chancerel E, Lamy JB, Lesur I, Noirot C, Klopp C, Ehrenmann F, Boury C, Le Provost G, Label P, Lalanne C, Leger V, Salin F, Gion JM, Plomion C (2013) High-density linkage mapping in a pine tree reveals a genomic region associated with inbreeding depression and provides clues to the extent and distribution of meiotic recombination. BMC Biol 11:19. doi:10.1186/1741-7007-11-50
6. Doerksen TK, Herbinger CM (2008) Male reproductive success and pedigree error in red spruce open-pollinated and polycross mating systems. Can J For Res-Rev Can Rech For 38:1742–1749. doi:10.1139/x08-025
7. Doerksen TK, Herbinger CM (2010) Impact of reconstructed pedigrees on progeny—test breeding values in red spruce. Tree Genet Genomes 6:591–600. doi:10.1007/s11295-010-0274-1
8. Durel CE, Bertin P, Kremer A (1996) Relationship between inbreeding depression and inbreeding coefficient in maritime pine (Pinus pinaster). Theor Appl Genet 92:347–356
9. El-Kassaby YA, Cappa EP, Liewlaksaneeyanawin C, Klapste J, Lstiburek M (2011) Breeding without breeding: is a complete pedigree necessary for efficient breeding? PLoS One 6:11. doi:10.1371/journal.pone.0025737
10. Funda T, Liewlaksaneeyanawin C, El-Kassaby YA (2014) Determination of paternal and maternal parentage in lodgepole pine seed: full versus partial pedigree reconstruction. Can J For Res-Rev Can Rech For 44:1122–1127. doi:10.1139/cjfr-2014-0145
11. Gaspar MJ, de-Lucas A, Alia R, Paiva JAP, Hidalgo E, Louzada J, Almeida H, Gonzalez-Martinez SC (2009) Use of molecular markers for estimating breeding parameters: a case study in a Pinus pinaster Ait. progeny trial. Tree Genet Genomes 5:609–616. doi:10.1007/s11295-009-0213-1
12. Gauzere J, Oddou-Muratorio S, Pichot C, Lefevre F, Klein E (2013) Biases in quantitative genetic analyses using open-pollinated progeny tests from natural tree populations. Acta Bot Gall 160:225–236. doi:10.1080/12538078.2013.822827
13. Gilmour AR, Gogel BJ, Cullis BR, Thompson R (2009) ASReml user fuide release 3.0. VSN International Ltd, Hemel Hempstead, HP1 1ES, UK
14. Glaubitz JC, Rhodes OE, Dewoody JA (2003) Prospects for inferring pairwise relationships with single nucleotide polymorphisms. Mol Ecol 12:1039–1047. doi:10.1046/j.1365-294X.2003.01790.x
15. Gonzalez-Martinez SC, Gerber S, Cervera MT, Martinez-Zapater JM, Alia R, Gil L (2003) Selfing and sibship structure in a two-cohort stand of maritime pine (Pinus pinaster Ait.) using nuclear SSR markers. Ann For Sci 60:115–121. doi:10.1051/forest:2003003
16. Grattapaglia D, Diener PSD, dos Santos GA (2014) Performance of microsatellites for parentage assignment following mass controlled pollination in a clonal seed orchard of loblolly pine (Pinus taeda L.). Tree Genet Genomes 10:1631–1643. doi:10.1007/s11295-014-0784-3
17. Hallingback HR, Jansson G (2013) Genetic information from progeny trials: a comparison between progenies generated by open pollination and by controlled crosses. Tree Genet Genomes 9:731–740. doi:10.1007/s11295-012-0588-2
18. Hansen OK, McKinney LV (2010) Establishment of a quasi-field trial in Abies nordmanniana—test of a new approach to forest tree breeding. Tree Genet Genomes 6:345–355. doi:10.1007/s11295-009-0253-6
19. Hansen OK, Nielsen UB (2010) Microsatellites used to establish full pedigree in a half-sib trial and correlation between number of male strobili and paternal success. Ann For Sci 67:10. doi:10.1051/forest/2010028
20. Illy G (1966) Recherches sur l’amélioration génétique du pin maritime. Ann Sci Forest 23:765–948. doi:10.1051/forest/19660401
21. Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 16:1099–1106. doi:10.1111/j.1365-294X.2007.03089.x
22. Kimura M, Crow JF (1963) The measurement of effective population number. Evolution 17:279–288
23. Klapste J, Lstiburek M, El-Kassaby YA (2014) Estimates of genetic parameters and breeding values from western larch open-pollinated families using marker-based relationship. Tree Genet Genomes 10:241–249. doi:10.1007/s11295-013-0673-1
24. Korecky J, Klapste J, Lstiburek M, Kobliha J, Nelson CD, El-Kassaby YA (2013) Comparison of genetic parameters from marker-based relationship, sibship, and combined models in Scots pine multi-site open-pollinated tests. Tree Genet Genomes 9:1227–1235. doi:10.1007/s11295-013-0630-z
25. Kumar S, Gerber S, Richardson TE, Gea L (2007) Testing for unequal paternal contributions using nuclear and chloroplast SSR markers in polycross families of radiata pine. Tree Genet Genomes 3:207–214. doi:10.1007/s11295-006-0056-y
26. Kumar S, Richardson TE (2005) Inferring relatedness and heritability using molecular markers in radiata pine. Mol Breed 15:55–64. doi:10.1007/s11032-004-2059-4
27. Lai BS, Funda T, Liewlaksaneeyanawin C, Klapste J, Van Niejenhuis A, Cook C, Stoehr MU, Woods J, El-Kassaby YA (2010) Pollination dynamics in a Douglas-fir seed orchard as revealed by pedigree reconstruction. Ann For Sci 67:8. doi:10.1051/forest/2010044
28. Lambeth C, Lee BC, O’Malley D, Wheeler N (2001) Polymix breeding with parental analysis of progeny: an alternative to full-sib breeding and testing. Theor Appl Genet 103:930–943. doi:10.1007/s001220100627
29. Lynch M, Walsh B (1998) Genetics and analysis of quantitative traits. Sinauer Associates, Inc., Sunderland, MA, USA, 980 p
30. Mangin B, Siberchicot A, Nicolas S, Doligez A, This P, Cierco-Ayrolles C (2012) Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness. Heredity 108:285–291. doi:10.1038/hdy.2011.73
31. Marshall TC, Slate J, Kruuk LEB, Pemberton JM (1998) Statistical confidence for likelihood-based paternity inference in natural populations. Mol Ecol 7:639–655. doi:10.1046/j.1365-294x.1998.00374.x
32. Moriguchi Y, Ishiduka D, Kaneko T, Itoo S, Taira H, Tsumura Y (2009) The contribution of pollen germination rates to uneven paternity among polycrosses of Cryptomeria japonica. Silvae Genet 58:139–144
33. Nakamura RR, Wheeler NC (1992) Pollen competition and paternal success in Douglas-fir. Evolution 46:846–851. doi:10.2307/2409655
34. Parantainen A, Pasonen HL (2004) Pollen-pollen interactions in Pinus sylvestris. Scand J Forest Res 19:199–205. doi:10.1080/02827580410029336
35. Pasonen HL, Pulkkinen P, Kapyla M, Blom A (1999) Pollen-tube growth rate and seed-siring success among Betula pendula clones. New Phytol 143:243–251. doi:10.1046/j.1469-8137.1999.00451.x
36. Plomion C, Chancerel E, Endelman J, Lamy JB, Mandrou E, Lesur I, Ehrenmann F, Isik F, Bink M, van Heerwaarden J, Bouffier L (2014) Genome-wide distribution of genetic diversity and linkage disequilibrium in a mass-selected population of maritime pine. BMC Genomics 15:16. doi:10.1186/1471-2164-15-171
37. RCoreTeam (2013) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org/.
38. Snow AA, Spira TP (1996) Pollen-tube competition and male fitness in Hibiscus moscheutos. Evolution 50:1866–1870. doi:10.2307/2410744
39. Squillace AE (1974) Average genetic correlations among offspring from open-pollinated forest trees. Silvae Genetica 23:149–156
40. Wheeler N, Payne P, Hipkins V, Saich R, Kenny S, Tuskan G (2006) Polymix breeding with paternity analysis in Populus: a test for differential reproductive success (DRS) among pollen donors. Tree Genet Genomes 2:53–60. doi:10.1007/s11295-005-0033-x
41. White T (1987) A conceptual framework for tree improvement programs. New For 1:325–342. doi:10.1007/BF00031742
42. Wiselogel AE, Vanbuijtenen JP (1988) Probability of equal mating in polymix pollinations of loblolly pine (Pinus taeda L.). Silvae Genet 37:184–187
43. Zhao P, Zhang SX, Woeste K (2013) Genotypic data changes family rank for growth and quality traits in a black walnut (Juglans nigra L.) progeny test. New For 44:357–368. doi:10.1007/s11056-012-9343-7
44. Zobel BJ, Talbert JT (1984). Applied forest tree improvement (p. 528). New York: Wiley.