The influence of parental effects on transcriptomic landscape during early development in brook charr (Salvelinus fontinalis, Mitchill)

Heredity

Volumn 110, Issue 5, 2013, Pages 484-491

  Bougas, B ^a   Audet, C ^b   Bernatchez, L ^a  

^a UNIVERSITÉ LAVAL   (Canada)

^b INSTITUT DES SCIENCES DE LA MER DE RIMOUSKI   (Canada)

Author keywords

Hybrid; Microarray; Parental effects; Salvelinus fontinalis; Transcriptome

Indexed keywords

EMBRYONIC DEVELOPMENT; FEEDING BEHAVIOR; GENE; GENE EXPRESSION; HATCHING; HYBRIDIZATION; LANDSCAPE; METABOLISM; NUCLEIC ACID; ONTOGENY; PARENTAL CARE; PHENOTYPE; PROTEIN; SALMONID;

ANIMAL; ANIMAL EMBRYO; ARTICLE; BODY SIZE; CHIMERA; DNA MICROARRAY; EMBRYO DEVELOPMENT; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; MALE; PHENOTYPE; PHYSIOLOGY; PRENATAL DEVELOPMENT; TROUT; YOLK SAC;

ANIMALS; BODY SIZE; CHIMERA; EMBRYO, NONMAMMALIAN; EMBRYONIC DEVELOPMENT; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; MALE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHENOTYPE; TROUT; YOLK SAC;

SALMONIDAE; SALVELINUS FONTINALIS;

EID: 84878738709     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/hdy.2012.113     Document Type: Article

References (53)

1. Badyaev A, Uller T (2009). Parental effects in ecology and evolution: mechanisms, processes and implications. Philos Trans R Soc Lond B Biol Sci 364: 1169-1177.
2. Bai J, Solberg C, Fernandes J, Johnston I (2007). Profiling of maternal and developmentalstage specific mRNA transcripts in Atlantic halibut Hippoglossus hippoglossus. Gene 386: 202-210. (Pubitemid 44918243)
3. Baroux C, Autran D, Gillmor C, Grimanelli D, Grossniklaus U (2008). The maternal to zygotic transition in animals and plants. Cold Spring Harb Symp Quant Biol 73: 89-100.
4. Bougas B, Granier S, Audet C, Bernatchez L (2010). The transcriptional landscape of cross-specific hybrids and its possible link with growth in brook charr (Salvelinus fontinalis Mitchill). Genetics 186: 97-107.
5. Brooks S, Tyler CR, Sumpter JP (1997). Egg quality in fish: what makes a good egg? Rev Fish Biol and Fish 7: 387-416. (Pubitemid 127508874)
6. Cassimeris L (2002). The oncoprotein 18/stathmin family of microtubule destabilizers. Curr Opin Cell Biol 14: 18-24. (Pubitemid 34131652)
7. Churchill G (2002). Fundamentals of experimental design for cDNA microarrays. Nat Genet 32: 490-495. (Pubitemid 35435151)
8. Cui X, Hwang J, Qiu J, Blades N, Churchill G (2005). Improved statistical tests for differential gene expression by shrinking variance components estimates. Biostatistics 6: 59-75. (Pubitemid 41240370)
9. Domazet-Lošo T, Tautz D (2010). A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature 468: 815-818.
10. Donelson J, Munday P, McCormick M (2009). Parental effects on offspring life histories: when are they important? Biol Lett 5: 262-265.
11. Eilertsen E, Bardsen B, Liljedal S, Rudolfsen G, Folstad I (2009). Experimental evidence for paternal effects on offspring growth rate in arctic charr (Salvelinus alpinus). Philos Trans R Soc Lond B Biol Sci 276: 129-136.
12. Einum S, Fleming I (1999). Maternal effects of egg size in brown trout (Salmo trutta): norms of reaction to environmental quality. Proc R Soc Lond B Biol Sci 266: 2095-2100. (Pubitemid 29511880)
13. Einum S, Fleming I (2000). Selection against late emergence and small offspring in atlantic salmon (Salmo salar). Evolution 54: 628-639. (Pubitemid 30263936)
14. Falconer D, Mackay T (1996). Introduction to Quantitative Genetics, 4th edn. Longman: Essex.
15. Gibson G, Riley-Berger R, Harshman L, Kopp A, Vacha S, Nuzhdin S et al. (2004). Extensive sex-specific nonadditivity of gene expression in Drosophila melanogaster. Genetics 167: 1791-1799. (Pubitemid 39265915)
16. Green B (2008). Maternal effects in fish populations. Adv Mar Biol 54: 1-105.
17. Heath D, Fox C, Heath J (1999). Maternal effects on offspring size: variation through early development of chinook salmon. Evolution 53: 1605-1611. (Pubitemid 29524154)
18. Heath DD, Blouw DM (1998). Maternal effects in fish: are they adaptive or merely physiological side-effects? In: Mousseau TA, Fox CW (Eds) Adaptive Maternal Effects. Oxford University Press: Oxford, pp 178-201.
19. Huang DW, Sherman BT, Lempicki RA (2009a). Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nat Protoc 4: 44-57.
20. Huang DW, Sherman BT, Lempicki RA (2009b). Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37: 1-13.
21. Inchausti P, Ginzburg L (2009). Maternal effects mechanism of population cycling: a formidable competitor to the traditional predator-prey view. Philos Trans R Soc Lond B Biol Sci 364: 1117-1124.
22. Johnson R, Shrimpton J, Cho G, Heath D (2007). Dosage effects on heritability and maternal effects in diploid and triploid chinook salmon (Oncorhynchus tshawytscha). Heredity 98: 303-310. (Pubitemid 46674473)
23. Kanaya S, Kudo Y, MokiToda S, Katsura K, DelCarpio C (1996). Synchronous gene expressions during embryogenesis of Oncorhynchus masou (Yamame). Biochem Mol Biol Int 39: 261-266. (Pubitemid 26202741)
24. Kerr M, Afshari C, Bennett L, Bushel P, Martinez J, Walker NJ et al. (2002). Statistical analysis of a gene expression microarray experiment with replication. Stat Sinica 12: 203-217.
25. Kerr M, Martin M, Churchill G (2000). Analysis of variance for gene expression microarray data. J Comput Biol 7: 819-837.
26. Koop B, von Schalburg K, Leong J, Walker N, Lieph R, Cooper GA et al. (2008). A salmonid EST genomic study: genes, duplications, phylogeny and microarrays. BMC Genomics 9: 545.
27. Li N, Das K, Wu R (2009). Functional mapping of human growth trajectories. J Theor Biol 261: 33-42.
28. Lindholm A, Hunt J, Brooks R (2006). Where do all the maternal effects go? Variation in offspring body size through ontogeny in the live-bearing fish Poecilia parae. Biol Lett 2: 586-589. (Pubitemid 44935438)
29. Loppin B, Lepetit D, Dorus S, Couble P, Karr T (2005). Origin and neofunctionalization of a drosophila paternal effect gene essential for zygote viability. Curr Biol 15: 87-93.
30. Løvoll M, Kilvik T, Boshra H, Bøgwald J, Sunyer J, Dalmo RA (2006). Maternal transfer of complement components c3-1, c3-3, c3-4, c4, c5, c7, bf, and df to offspring in rainbow trout (Oncorhynchus mykiss). Immunogenetics 58: 168-179.
31. MAPAQ (2010). Les pêches et aquaculture commerciales. Bilan 2008 et perspectives (les). Bibliothèque et archives du Québec (Ed.): Québec, QC, CANADA.
32. Martin S, Savaria J, Audet C, Bernatchez L (1997). Microsatellites reveal no evidence for inbreeding effects but low inter-stock genetic diversity among brook charr stocks used for production in Quebec. Bull Aquacult Assoc Can 97: 21-23.
33. Mathavan S, Lee S, Mak A, Miller L, Murthy K, Govindarajan K et al. (2005). Transcriptome analysis of zebrafish embryogenesis using microarrays. PLoS Genet 1: 269-276.
34. Mavarez J, Audet C, Bernatchez L (2009). Major disruption of gene expression in hybrids between young sympatric anadromous and resident populations of brook charr (Salvelinus fontinalis Mitchill). J Evol Biol 22: 1708-1720.
35. Mousseau T, Fox C (Eds) (1998). Maternal Effects as Adaptations. Oxford University Press: New York.
36. Nichols K, Broman K, Sundin K, Young J, Wheeler P, Thorgaard G (2007). Quantitative trait loci x maternal cytoplasmic environment interaction for development rate in Oncorhynchus myhiss. Genetics 175: 335-347. (Pubitemid 46168577)
37. Nolte A, Renaut S, Bernatchez L (2009). Divergence in gene regulation at young life history stages of whitefish (Coregonus sp.) and the emergence of genomic isolation. BMC Evol Biol 9: 59.
38. Perry G, Audet C, Bernatchez L (2005). Maternal genetic effects on adaptive divergence between anadromous and resident brook charr during early life history. J Evolution Biol 18: 1348-1361. (Pubitemid 41725685)
39. Perry G, Audet C, Laplatte B, Bernatchez L (2004). Shifting patterns in genetic control at the embryo-alevin boundary in brook charr. Evolution 58: 2002-2012. (Pubitemid 39348501)
40. Petersson E, Jarvi T (2007). Characteristics of brown trout males influence growth and survival of their offspring. J Fish Biol 71: 493-509. (Pubitemid 47125304)
41. Quinn G, Keough M (2005). Experimental Design and Data Analysis for Biologists, 4th edn Cambridge University Press: Cambridge, (UK).
42. Refstie T, Steine T (1978). Selection experiments with salmon. III. Genetic and environmental sources of variation in length and weight of Atlantic salmon in freshwater phase. Aquaculture 14: 221-234.
43. Renaut S, Bernatchez L (2011). Transcriptome-wide signature of hybrid breakdown associated with intrinsic reproductive isolation in lake whitefish species pairs (Coregonus spp. salmonidae). Heredity 106: 1003-1011.
44. Roff D (1996). Evolutionary Quantitative Genetics. Chapman & Hall(Ed.). New York.
45. Roff D, Sokolovska N (2004). Extra-nuclear effects on growth and development in the sand cricket Gryllus firmus. J Evol Biol 17: 663-671. (Pubitemid 38571960)
46. Saavedra C, Amat F (2005). Maternal effects on encystment in crosses between two geographic strains of Artemia franciscana. J Hered 96: 713-717. (Pubitemid 41668792)
47. Sauvage C, Derome N, Normandeau E, St-Cyr J, Audet C, Bernatchez L (2010). Fast transcriptional responses to domestication in the brook charr Salvelinus fontinalis. Genetics 185: 105-112.
48. von Schalburg K, Rise M, Cooper G, Brown G, Gibbs A, Nelson C et al. (2005). Fish and chips: various methodologies demonstrate utility of a 16,006-gene salmonid microarray. BMC Genomics 6: 126.
49. Wedekind C, Jacob A, Evanno G, Nusslé S, Müller R (2008). Viability of brown trout embryos positively linked to melanin-based but negatively to carotenoid-based colours of their fathers. Proc Biol Sci 275: 1737-1744. (Pubitemid 351839874)
50. Wittkopp P, Haerum B, Clark A (2006). Parent-of-origin effects on mRNA expression in Drosophila melanogaster not caused by genomic imprinting. Genetics 173: 1817-1821. (Pubitemid 44127679)
51. Wolf J, Wade M (2009). What are maternal effects (and what are they not)? Philos Trans R Soc Lond B Biol Sci 364: 1107-1115.
52. Wolfinger R, Gibson G, Wolfinger E, Bennett L, Hamadeh H, Bushel P et al. (2001). Assessing gene significance from cDNA microarray expression data via mixed models. J Comput Biol 8: 625-637. (Pubitemid 34053500)
53. Xu P, McIntyre LM, Scardina J, Wheeler P, Thorgaard G, Nichols K (2010). Transcriptome profiling of embryonic development rate in rainbow trout advanced backcross introgression lines. Mar Biotechnol 13: 215-231.