Quantifying the genetic component of phenotypic variation in unpedigreed wild plants: Tailoring genomic scan for within-population use

Molecular Ecology

Volumn 18, Issue 12, 2009, Pages 2602-2614

  Herrera, C M ^a   Bazaga, P ^a  

^a DEPARTMENT OF CONSERVATION BIOLOGY   (Spain)

Author keywords

Ecological genomics; Environmental variance; Fecundity hierarchy; Genetic variance; Genomic scan; Genotype by environment interaction; Viola cazorlensis

Indexed keywords

PLANT DNA;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ARTICLE; BIOLOGICAL MODEL; ENVIRONMENT; FERTILITY; GENETIC MARKER; GENETIC POLYMORPHISM; GENETICS; METHODOLOGY; MOLECULAR EVOLUTION; PHENOTYPE; PLANT GENOME; POPULATION GENETICS; QUANTITATIVE TRAIT; STATISTICAL MODEL; VIOLACEAE;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM ANALYSIS; DNA, PLANT; ENVIRONMENT; EVOLUTION, MOLECULAR; FERTILITY; GENETIC MARKERS; GENETICS, POPULATION; GENOME, PLANT; LINEAR MODELS; MODELS, GENETIC; PHENOTYPE; POLYMORPHISM, GENETIC; QUANTITATIVE TRAIT, HERITABLE; VIOLA;

VIOLA CAZORLENSIS; VIOLACEAE;

EID: 66749156625     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2009.04229.x     Document Type: Article

References (83)

1. Agresti A (2007) An Introduction to Categorical Data Analysis, 2nd edn. Wiley, Hoboken, New Jersey.
2. Andreasen K, Baldwin BG (2001) Unequal evolutionary rates between annual and perennial lineages of checker mallows (Sidalcea, Malvaceae): evidence from 18S-26S rDNA internal and external transcribed spacers. Molecular Biology and Evolution, 18, 936 944. (Pubitemid 32520465)
3. Andrew RL, Peakall R, Wallis IR et al 2005) Marker-based quantitative genetics in the wild?: the heritability and genetic correlation of chemical defenses in Eucalyptus. Genetics, 171, 1989 1998.
4. Antlfinger AE, Curtis WF, Solbrig OT (1985) Environmental and genetic determinants of plant size in Viola sororia. Evolution, 39, 1053 1064. (Pubitemid 17247586)
5. Applied Biosystems (2005) AFLP Plant Mapping Protocol. Applied Biosystems, Foster City, California.
6. ST tell us? Trends in Ecology & Evolution, 20, 435 440. (Pubitemid 41026729)
7. Beaumont MA, Balding DJ (2004) Identifying adaptive genetic divergence among populations from genome scans. Molecular Ecology, 13, 969 980. (Pubitemid 38390600)
8. Beaumont MA, Nichols RA (1996) Evaluating loci for use in the genetic analysis of population structure. Proceedings of the Royal Society B: Biological Sciences, 263, 1619 1626. (Pubitemid 27055553)
9. Bennett MD, Leitch IJ (2004) Angiosperm DNA C-Values Database (release 5.0. Dec. 2004). Available from URL: http://www.kew.org/cvalues/homepage.html.
10. Black WC, Baer CF, Antolin MF, DuTeau NM (2001) Population genomics: genome-wide sampling of insect populations. Annual Review of Entomology, 46, 441 469. (Pubitemid 32304996)
11. Bonin A, Bellemain E, Eidesen PB, Pompanon F, Brochmann C, Taberlet P (2004) How to track and assess genotyping errors in population genetics studies. Molecular Ecology, 13, 3261 3273. (Pubitemid 39415663)
12. Bonin A, Taberlet P, Miaud C, Pompanon F (2006) Explorative genome scan to detect candidate loci por adaptation along a gradient of altitude in the common frog (Rana temporaria). Molecular Biology and Evolution, 23, 773 783.
13. Bonin A, Ehrich D, Manel S (2007) Statistical analysis of amplified fragment length polymorphism data: a toolbox for molecular ecologists and evolutionists. Molecular Ecology, 16, 3737 3758. (Pubitemid 47397323)
14. Burdon JJ, Harper JL (1980) Relative growth rates of individual members of a plant population. Journal of Ecology, 68, 953 957.
15. Cameron ND, van Eijk MJT, Brugmans B, Peleman J (2003) Discrimination between selected lines of pigs using AFLP markers. Heredity, 91, 494 501. (Pubitemid 37399260)
16. Castiglioni P, Ajmone-Marsan P, van Wijk R, Motto M (1999) AFLP markers in a molecular linkage map of maize: codominant scoring and linkage group distribution. Theoretical and Applied Genetics, 99, 425 431. (Pubitemid 29432491)
17. Falconer DS (1989) Introduction to Quantitative Genetics, 3rd edn. Longman, Harlow, Essex, UK.
18. Falush D, Stephens M, Pritchard JK (2007) Inference of population structure using multilocus genotype data: dominant markers and null alleles. Molecular Ecology Notes, 7, 574 578. (Pubitemid 47035522)
19. Farrall M (2004) Quantitative genetic variation: a post-modern view. Human Molecular Genetics, 13, R1 R7.
20. Fernández J, Toro MA (2006) A new method to estimate relatedness from molecular markers. Molecular Ecology, 15, 1657 1667.
21. Gange AC, Brown VK (1989) Insect herbivory affects size variability in plant populations. Oikos, 56, 351 356. (Pubitemid 20424087)
22. Garant D, Kruuk LEB (2005) How to use molecular marker data to measure evolutionary parameters in wild populations. Molecular Ecology, 14, 1843 1859. (Pubitemid 40772407)
23. Geber MA, Griffen LR (2003) Inheritance and natural selection on functional traits. International Journal of Plant Sciences, 164, S21 S42.
24. Gillespie JH, Turelli M (1989) Genotype-environment interactions and the maintenance of polygenic variation. Genetics, 121, 129 138. (Pubitemid 19026326)
25. Gottlieb LD (1977) Genotypic similarity of large and small individuals in a natural population of the annual plant Stephanomeria exigua ssp. coronaria (Compositae). Journal of Ecology, 65, 127 134.
26. Herrera CM (1989) Biología y ecología de Viola cazorlensis. II. Uso de sustratos, reproducción y consumo por los herbívoros. Anales del Jardín Botánico de Madrid, 47, 125 138.
27. Herrera CM (1990a) The adaptedness of the floral phenotype in a relict endemic, hawkmoth-pollinated violet. 1. Reproductive correlates of floral variation. Biological Journal of the Linnean Society, 40, 263 274.
28. Herrera CM (1990b) The adaptedness of the floral phenotype in a relict endemic, hawkmoth-pollinated violet. 2. Patterns of variation among disjunct populations. Biological Journal of the Linnean Society, 40, 275 291.
29. Herrera CM (1991) Dissecting factors responsible for individual variation in plant fecundity. Ecology, 72, 1436 1448.
30. Herrera CM (1993) Selection on floral morphology and environmental determinants of fecundity in a hawk moth-pollinated violet. Ecological Monographs, 63, 251 275.
31. Herrera CM, Bazaga P (2008) Population-genomic approach reveals adaptive floral divergence in discrete populations of a hawk moth-pollinated violet. Molecular Ecology, 17, 5378 5390.
32. Herselman L, Thwaites R, Kimmins FM et al 2004) Identification and mapping of AFLP markers linked to peanut (Arachis hypogaea L.) resistance to the aphid vector of groundnut rosette disease. Theoretical and Applied Genetics, 109, 1426 1433. (Pubitemid 40059265)
33. Heywood JS, Levin DA (1984) Genotype-environment interactions in determining fitness in dense, artificial populations of Phlox drummondii. Oecologia, 61, 363 371. (Pubitemid 16276952)
34. Hill WG, Goddard ME, Visscher PM (2008) Data and theory point to mainly additive genetic variance for complex traits. PLoS Genetics, 4, e1000008. doi.
35. Jump AS, Peñuelas J, Rico L et al 2008) Simulated climate change provokes rapid genetic change in the Mediterranean shrub Fumana thymifolia. Global Change Biology, 14, 637 643.
36. Klappert K, Butlin RK, Reinhold K (2007) The attractiveness fragment - AFLP analysis of local adaptation and sexual selection in a caeliferan grasshopper, Chorthippus biguttulus. Naturwissenschaften, 94, 667 674. (Pubitemid 47036767)
37. van Kleunen M, Ritland K (2005) Estimating heritabilities and genetic correlations with marker-based methods: an experimental test in Mimulus guttatus. Journal of Heredity, 96, 368 375. (Pubitemid 41399398)
38. Leinonen T, O'Hara RB, Cano JM, Merilä J (2008) Comparative studies of quantitative trait and neutral marker divergence: a meta-analysis. Journal of Evolutionary Biology, 21, 1 17. (Pubitemid 350256623)
39. Littell RC, Milliken GA, Stroup WW, Wolfinger RD, Schabenberger O (2006) SAS for Mixed Models, 2nd edn. SAS Institute, Cary, North Carolina.
40. Luikart G, England PR, Tallmon D, Jordan S, Taberlet P (2003) The power and promise of population genomics: from genotyping to genome typing. Nature Reviews Genetics, 4, 981 994. (Pubitemid 37474645)
41. Lynch M, Walsh B (1998) Genetics and Analysis of Quantitative Traits. Sinauer & Associates, Sunderland, Masachusetts.
42. Mackay TFC (2001) The genetic architecture of quantitative traits. Annual Review of Genetics, 35, 303 339. (Pubitemid 34032979)
43. Mazer SJ, Wolfe LM (1992) Planting density influences the expression of genetic variation in seed mass in wild radish (Raphanus sativus L. Brassicaceae). American Journal of Botany, 79, 1185 1193.
44. Merilä J, Sheldon BC (1999) Genetic architecture of fitness and nonfitness traits: empirical patterns and development of ideas. Heredity, 83, 103 109. (Pubitemid 29452118)
45. Møller AP, Jennions MD (2002) How much variance can be explained by ecologists and evolutionary biologists? Oecologia, 132, 492 500. (Pubitemid 36059163)
46. Mousseau TA, Roff DA (1987) Natural selection and the heritability of fitness components. Heredity, 59, 181 197.
47. Ojha BR (2005) Comparison of Eco-Mse and Pst-Mse primer combinations in generating AFLP map of tomato. Journal of the Institute of Agriculture and Animal Sciences, 26, 27 35.
48. Olsen KM, Purugganan MD (2004) Plant population genomics, linkage disequilibrium mapping, and the genetics of adaptation. In : Plant Adaptation: Molecular Genetics and Ecology (eds Cronk QCB, Whitton J, Ree RH, Taylor IEP pp. 45 52. National Research Council, Ottawa, Canada.
49. Orr HA (1998) The population genetics of adaptation: the distribution of factors fixed during adaptive evolution. Evolution, 52, 935 949. (Pubitemid 28417879)
50. Papa R, Bellucci E, Rossi M et al 2007) Tagging the signatures of domestication in common bean (Phaseolus vulgaris) by means of pooled DNA samples. Annals of Botany, 100, 1039 1051. (Pubitemid 47614328)
51. Parisod C, Christin PA (2008) Genome-wide association to fine-scale ecological heterogeneity within a continuous population of Biscutella laevigata (Brassicaceae). New Phytologist, 178, 436 447.
52. Peakall R, Smouse PE (2006) Genalex 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6, 288 295. (Pubitemid 43373825)
53. Prati D, Schmid B (2000) Genetic differentiation of life-history traits within populations of the clonal plant Ranunculus reptans. Oikos, 90, 442 456.
54. Pritchard JK, Wen X, Falush D (2007) Documentation for Structure Software: Version 2.2. Department of Human Genetics, University of Chicago, Chicago, Illinois. Available at http://pritch.bsd.uchicago.edu/structure.html.
55. ST comparisons for natural populations meaningful? Molecular Ecology, 17, 4782 4785.
56. Raman H, Moroni JS, Sato K, Read BJ, Scott BJ (2002) Identification of AFLP and microsatellite markers linked with an aluminium tolerance gene in barley (Hordeum vulgare L.). Theoretical and Applied Genetics, 105, 458 464. (Pubitemid 36072799)
57. Ritland K (1996) A marker-based method for inferences about quantitative inheritance in natural populations. Evolution, 50, 1062 1073.
58. Ritland K (2000) Detecting inheritance with inferred relatedness in nature. In : Adaptive Genetic Variation in the Wild (eds Mousseau TA, Sinervo B, Endler J pp. 187 199. Oxford University Press, Oxford, UK.
59. Ritland K (2005) Multilocus estimation of pairwise relatedness with dominant markers. Molecular Ecology, 14, 3157 3165. (Pubitemid 43919355)
60. Ritland K, Ritland C (1996) Inferences about quantitative inheritance based on natural population structure in the yellow monkeyflower, Mimulus guttatus. Evolution, 50, 1074 1082.
61. Roff DA (1997) Evolutionary Quantitative Genetics. Chapman & Hall, New York.
62. SAS Institute (2004) SAS/STAT 9.1. User's Guide. SAS Institute, Cary, North Carolina.
63. SAS Institute (2006) Preliminary Capabilities for Bayesian Analysis in SAS/STAT Software. SAS Institute, Cary, North Carolina.
64. Smith SA, Donoghue MJ (2008) Rates of molecular evolution are linked to life history in flowering plants. Science, 322, 86 89.
65. Solbrig OT (1981) Studies on the population biology of the genus Viola. 2. The effect of plant size on fitness in Viola sororia. Evolution, 35, 1080 1093.
66. Solbrig OT, Solbrig DJ (1984) Size inequalities and fitness in plant populations. Oxford Surveys in Evolutionary Biology, 1, 141 159.
67. Stanton ML (1985) Seed size and emergence time within a stand of wild radish (Raphanus raphanistrum L.): the establishment of a fitness hierarchy. Oecologia, 67, 524 531. (Pubitemid 17245858)
68. Stanton ML, Thiede DA (2005) Statistical convenience vs biological insight: consequences of data transformation for the analysis of fitness variation in heterogeneous environments. New Phytologist, 166, 319 337.
69. Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proceedings of the National Academy of Sciences, USA, 100, 9440 9445. (Pubitemid 37033947)
70. Storz JF (2005) Using genome scans of DNA polymorphism to infer adaptive population divergence. Molecular Ecology, 14, 671 688. (Pubitemid 40346460)
71. Stratton DA, Bennington CC (1998) Fine-grained spatial and temporal variation in selection does not maintain genetic variation in Erigeron annuus. Evolution, 52, 678 691. (Pubitemid 28324498)
72. Thomas SC, Bazzaz FA (1993) The genetic component in plant size hierarchies: norms of reaction to density in a Polygonum species. Ecological Monographs, 63, 231 249.
73. Turelli M, Barton NH (2004) Polygenic variation maintained by balancing selection: pleiotropy, sex-dependent allelic effects and GxE interactions. Genetics, 166, 1053 1079. (Pubitemid 38391761)
74. Vasemägi A, Primmer CR (2005) Challenges for identifying functionally important genetic variation: the promise of combining complementary research strategies. Molecular Ecology, 14, 3623 3642. (Pubitemid 43919918)
75. Vekemans X, Beauwens T, Lemaire M, Roldán-Ruiz I (2002) Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size. Molecular Ecology, 11, 139 151. (Pubitemid 34108478)
76. Visscher PM, Hill WG, Wray NR (2008) Heritability in the genomics era - concepts and misconceptions. Nature Reviews Genetics, 9, 255 266.
77. Vos P, Hogers R, Bleeker M et al 1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Research, 23, 4407 4414.
78. Vuylsteke M, Mank R, Antonise R et al 1999) Two high-density AFLP linkage maps of Zea mays L. analysis of distribution of AFLP markers. Theoretical and Applied Genetics, 99, 921 935. (Pubitemid 29527040)
79. Waller DM (1985) The genesis of size hierarchies in seedling populations of Impatiens capensis Meerb. New Phytologist, 100, 243 260. (Pubitemid 17244355)
80. Weiner J, Thomas SC (1986) Size variability and competition in plant monocultures. Oikos, 47, 211 222. (Pubitemid 18280977)
81. Young HJ, Stanton ML, Ellstrand NC, Clegg JM (1994) Temporal and spatial variation in heritability and genetic correlations among floral traits in Raphanus sativus, wild radish. Heredity, 73, 298 308. (Pubitemid 2137956)
82. Young WP, Schupp JM, Keim P (1999) DNA methylation and AFLP marker distribution in the soybean genome. Theoretical and Applied Genetics, 99, 785 792. (Pubitemid 29464025)
83. Yuan L, Dussle CM, Muminovic J, Melchinger AE, Lubberstedt T (2004) Targeted BSA mapping of Scmv1 and Scmv2 conferring resistance to SCMV using PstI/MseI compared with EcoRI/MseI AFLP markers. Plant Breeding, 123, 434 437. (Pubitemid 39448115)