Phenotypic landscapes: phenological patterns in wild and cultivated barley

Phenotypic variation in natural populations is the outcome of the joint effects of environmentally induced adaptations and neutral processes on the genetic architecture of quantitative traits. In this study, we examined the role of adaptation in shaping wild barley phenotypic variation along different environmental gradients. Detailed phenotyping of 164 wild barley (Hordeum spontaneum) accessions from Israel (of the Barley1K collection) and 18 cultivated barley (H. vulgare) varieties was conducted in common garden field trials. Cluster analysis based on phenotypic data indicated that wild barley in this region can be differentiated into three ecotypes in accordance with their ecogeographical distribution: north, coast and desert. Population differentiation (QST) for each trait was estimated using a hierarchical Bayesian model and compared to neutral differentiation (FST) based on 42 microsatellite markers. This analysis indicated that the three clusters diverged in morphological but not in reproductive characteristics. To address the issue of phenotypic variation along environmental gradients, climatic and soil gradients were compared with each of the measured traits given the geographical distance between sampling sites using a partial Mantel test. Flowering time and plant growth were found to be differentially correlated with climatic and soil characteristic gradients, respectively. The H. vulgare varieties were superior to the H. spontaneum accessions in yield components, yet resembled the Mediterranean types in vegetative characteristics and flowering time, which may indicate the geographical origin of domesticated barley.

[1]  A. Flavell,et al.  Islands and streams: clusters and gene flow in wild barley populations from the Levant , 2012, Molecular ecology.

[2]  A. Hughes,et al.  Evolution of adaptive phenotypic traits without positive Darwinian selection , 2011, Heredity.

[3]  S. Volis.  Adaptive genetic differentiation in a predominantly self-pollinating species analyzed by transplanting into natural environment, crossbreeding and Q(ST)-F(ST) test. , 2011, The New phytologist.

[4]  S. Ullrich,et al.  Barley: Production, Improvement, and Uses , 2011 .

[5]  Joy Bergelson,et al.  Towards identifying genes underlying ecologically relevant traits in Arabidopsis thaliana , 2010, Nature Reviews Genetics.

[6]  H. Piepho,et al.  DNA polymorphisms and haplotype patterns of transcription factors involved in barley endosperm development are associated with key agronomic traits , 2010, BMC Plant Biology.

[7]  M. Whitlock,et al.  Testing for Spatially Divergent Selection: Comparing QST to FST , 2009, Genetics.

[8]  P. Craufurd,et al.  Climate change and the flowering time of annual crops. , 2009, Journal of experimental botany.

[9]  A. Graner,et al.  Strong correlation of wild barley (Hordeum spontaneum) population structure with temperature and precipitation variation , 2009, Molecular ecology.

[10]  R. Waugh,et al.  The emergence of whole genome association scans in barley. , 2009, Current opinion in plant biology.

[11]  F. Bonhomme,et al.  Ecological genetics in the North Atlantic: environmental gradients and adaptation at specific loci. , 2008, Ecology.

[12]  E. Nevo,et al.  Habitat‐specific natural selection at a flowering‐time QTL is a main driver of local adaptation in two wild barley populations , 2008, Molecular ecology.

[13]  David N. Reznick,et al.  Adaptive versus non‐adaptive phenotypic plasticity and the potential for contemporary adaptation in new environments , 2007 .

[14]  Adrian E. Raftery,et al.  Model-based Methods of Classification: Using the mclust Software in Chemometrics , 2007 .

[15]  Dimitris Rizopoulos,et al.  ltm: An R Package for Latent Variable Modeling and Item Response Analysis , 2006 .

[16]  Arndt von Haeseler,et al.  Haplotype structure at seven barley genes: relevance to gene pool bottlenecks, phylogeny of ear type and site of barley domestication , 2006, Molecular Genetics and Genomics.

[17]  J. Goudet,et al.  The Effects of Dominance, Regular Inbreeding and Sampling Design on QST, an Estimator of Population Differentiation for Quantitative Traits , 2006, Genetics.

[18]  P. Langridge,et al.  Extreme Population-Dependent Linkage Disequilibrium Detected in an Inbreeding Plant Species, Hordeum vulgare , 2006, Genetics.

[19]  D. Ward,et al.  Distinguishing adaptive from nonadaptive genetic differentiation: comparison of QST and FST at two spatial scales , 2005, Heredity.

[20]  R. O’Hara,et al.  Bias and Precision in QST Estimates: Problems and Some Solutions , 2005, Genetics.

[21]  Mattias Jakobsson,et al.  The Pattern of Polymorphism in Arabidopsis thaliana , 2005, PLoS biology.

[22]  P. Morrell,et al.  Low levels of linkage disequilibrium in wild barley (Hordeum vulgare ssp. spontaneum) despite high rates of self-fertilization. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[23]  R. Ellis,et al.  Identification of Hordeum spontaneum QTL alleles improving field performance of barley grown under rainfed conditions , 2004 .

[24]  R. O’Hara,et al.  Latitudinal divergence of common frog (Rana temporaria) life history traits by natural selection: evidence from a comparison of molecular and quantitative genetic data , 2003, Molecular ecology.

[25]  N. Ellstrand.  Current knowledge of gene flow in plants: implications for transgene flow. , 2003, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[26]  C. Schlötterer,et al.  microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets , 2003 .

[27]  R. Varshney,et al.  Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.) , 2003, Theoretical and Applied Genetics.

[28]  D. Ward,et al.  Differentiation in populations of Hordeum spontaneum along a gradient of environmental productivity and predictability: life history and local adaptation , 2002 .

[29]  M. Friendly.  Corrgrams , 2002 .

[30]  Andrea Brandolini,et al.  Genetics and geography of wild cereal domestication in the near east , 2002, Nature Reviews Genetics.

[31]  D. Zamir.  Improving plant breeding with exotic genetic libraries , 2001, Nature Reviews Genetics.

[32]  J. Merilä,et al.  Comparison of genetic differentiation at marker loci and quantitative traits , 2001 .

[33]  T. Komatsuda,et al.  Construction of a genetic map of barley (Hordeum vulgare L.) cross 'Azumamugi' x 'Kanto Nakate Gold' using a simple and efficient amplified fragment-length polymorphism system. , 2001, Genome.

[34]  Andrew Thomas,et al.  WinBUGS - A Bayesian modelling framework: Concepts, structure, and extensibility , 2000, Stat. Comput..

[35]  K. Ritland.  Marker‐inferred relatedness as a tool for detecting heritability in nature , 2000, Molecular ecology.

[36]  Burt,et al.  Natural selection in the wild. , 2000, Trends in ecology & evolution.

[37]  F. Salamini,et al.  On the origin and domestication history of Barley (Hordeum vulgare). , 2000, Molecular biology and evolution.

[38]  E. Nevo.  Genetic diversity in wild cereals: regional and local studies and their bearing on conservation ex situ and in situ , 1998, Genetic Resources and Crop Evolution.

[39]  B. Charlesworth,et al.  The effects of local selection, balanced polymorphism and background selection on equilibrium patterns of genetic diversity in subdivided populations. , 1997, Genetical research.

[40]  E. Nevo,et al.  Estimating variance effect of QTL: an important prospect to increase the resolution power of interval mapping , 1996 .

[41]  K. Spitze.  Population structure in Daphnia obtusa: quantitative genetic and allozymic variation. , 1993, Genetics.

[42]  K. R. Clarke,et al.  Non‐parametric multivariate analyses of changes in community structure , 1993 .

[43]  M. Turelli.  PHENOTYPIC EVOLUTION, CONSTANT COVARIANCES, AND THE MAINTENANCE OF ADDITIVE VARIANCE , 1988, Evolution; international journal of organic evolution.

[44]  S. Jana,et al.  Comparative assessment of genetic diversity in wild and primitive cultivated barley in a center of diversity. , 1988, Genetics.

[45]  E. Nevo,et al.  Genetic resources of wild cereals in Israel and vicinity. II. Phenotypic variation within and between populations of wild barley, Hordeum spontaneum , 1984, Euphytica.

[46]  B. Weir,et al.  ESTIMATING F‐STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE , 1984, Evolution; international journal of organic evolution.

[47]  R. Lande.  NATURAL SELECTION AND RANDOM GENETIC DRIFT IN PHENOTYPIC EVOLUTION , 1976, Evolution; international journal of organic evolution.

[48]  D. Zohary,et al.  Distribution of Wild Wheats and Barley , 1966, Science.

[49]  S. Wright,et al.  Isolation by Distance. , 1943, Genetics.

[50]  Dimitrios Rizopoulos.  ltm: An R Package for Latent Variable Modeling and Item Response Theory Analyses , 2006 .

[51]  K. Yao,et al.  G-box binding coincides with increased Solanum melongena cysteine proteinase expression in senescent fruits and circadian-regulated leaves , 2004, Plant Molecular Biology.

[52]  A. Konstantinos,et al.  A Comparative Assessment , 2003 .

[53]  D. C. Gordon,et al.  Wild barley: a source of genes for crop improvement in the 21st century? , 2000, Journal of experimental botany.

[54]  Xuewen Lu,et al.  Genotype × Region Interaction for Two-Row Barley Yield in Canada , 2000 .

[55]  P. Burrough,et al.  Principles of geographical information systems , 1998 .

[56]  N. Ellstrand,et al.  POPULATION GENETIC CONSEQUENCES OF SMALL POPULATION SIZE: Implications for Plant Conservation , 1993 .

[57]  P. Shewry,et al.  Origin, evolution, population genetics and resources for breeding of wild barley, Hordeum spontaneum, in the Fertile Crescent. , 1992 .