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Pages 205-224

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From page 205...
... We discuss the suc cesses, advantages, and challenges of each, but we conclude that bottom-up approaches to understanding domestication as an adaptive process hold greater promise both for the study of Department of ecology and evolutionary Biology, University of California, irvine, CA 92697-2525.
From page 206...
... 20 / Jeffrey Ross-Ibarra et al. adaptation and as a means to identify genes that contribute to agronomically important traits.
From page 207...
... We conclude by arguing that an appreciation of domestication as an adaptive process has the potential to reveal far more about the genes contributing to agronomic traits than has been learned to date.
From page 208...
... divided human-mediated selection into two components: methodi cal selection, ‘‘systematically endeavor[ing] to modify a breed according to some predetermined standard,'' and unconscious selection, ‘‘that which follows from men naturally preserving the most valued and destroying the less valued individuals, without any thought of altering the breed.'' Unconscious selection, he posited, was no different from natural selection.
From page 209...
... Plant Domestication / 20 of the domestication syndrome are larger fruit or grain, reduced branch ing, gigantism, the loss or reduction of seed dispersal, the loss of seed dormancy, changes in photoperiod sensitivity, and the loss or reduction of toxic compounds (hammer, 1984; Gepts, 2004)
From page 210...
... 20 / Jeffrey Ross-Ibarra et al. FiGUre 11.1 schematic of the phenotype–genotype hierarchy as represented by top-down and bottom-up approaches.
From page 211...
... Moreover, the rate at which such genes are identified will continue to increase as genomic data become available for more spe cies; this increase is already evident in the 2006 publication year, which witnessed an explosion of the isolation of genes contributing to major phenotypic differences between domesticates and their wild ancestors. Although not solely attributable to QTl approaches, genes isolated in 2006 included two rice shattering genes (Konishi et al., 2006; li et al., 2006b)
From page 212...
... The first, like most QTl approaches, aims to identify genome-wide variation that associates with phenotypic variation. This requires measures of genetic variability in markers representing most of the genome and tests of phenotype–genotype association for each marker.
From page 213...
... Plant Domestication / 2 which a genotype is associated with a geographic region rather than a phenotype. This will become especially problematic for phenotypes that vary by geographic region, such as flowering time or photoperiod sensi tivity.
From page 214...
... one early example successfully linked phenotypic variation in malting quality in barley to haplotype variation at the β-amylase2 gene, a locus involved in starch hydrolysis. Differences in the coding region of barley β-amylase2 affect thermostability of the enzyme (Ma et al., 2001; Clark et al., 2003)
From page 215...
... Conceptually, the approach is simple: under the selection scenario described in Fig. 11.2, one expects that genes contributing to adaptive traits will have low genetic variation relative to nonselected genes.
From page 216...
... here we briefly introduce some of the methods and outline the challenges involved in identifying candidate genes using population genetics. Fitting a Demographic Model ideally, bottom-up approaches begin by assaying genetic diversity in hundreds of loci, preferably from a sample of ≈100 individuals representing both the domesticate and its wild ancestor.
From page 217...
... one way is to develop a demographic model that provides a reasonable fit to available data and then apply statistical tests of selection under that demographic model. The estimation of demographic history from DnA sequence data was first applied to maize (eyre-Walker et al., 1998; hilton and Gaut, 1998)
From page 218...
... The list of selected genes is enriched for functions related to transcription factors, genes implicated in plant growth, and genes involved in amino acid biosynthesis. Moreover, genes identified as targets of selection clustered nonrandomly around previously identified QTls for domestication traits (Wright et al., 2005)
From page 219...
... Plant Domestication / 2 and the number of sampled loci used. simulations show that the false discovery rate of this method may be high for recessive genes, for genes selected from standing variation, and for populations that have undergone demographic change (Teshima et al., 2006)
From page 220...
... Boxes represent the central 50% of the data, and lines extend out to 3/2 of the interquantile range. From Gene to Phenotype via Molecular Genetics The biggest drawback to bottom-up approaches is that the candidate genes are not associated with a phenotype.
From page 221...
... . QTl and lD approaches that do not include wild populations are likely to miss many of the genes contributing to agronomic traits that were important during early domestication.
From page 222...
... 222 / Jeffrey Ross-Ibarra et al. that contribute to adaptive traits and that will be useful in an agronomic context.
From page 223...
... Plant Domestication / 22 this last step, connecting a candidate gene to a phenotype via functional studies, is often not much easier for top-down approaches than for candi date genes identified by using population genetics. over the past 25 years, top-down approaches have yielded a list of ≈30 genes with well characterized phenotypic effects in plants (Doebley et al., 2006)


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