Quantitative Trait Locus Analysis of the Early Domestication of Sunflower

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ABSTRACT

Genetic analyses of the domestication syndrome have revealed that domestication-related traits typically have a very similar genetic architecture across most crops, being conditioned by a small number of quantitative trait loci (QTL), each with a relatively large effect on the phenotype. To date, the domestication of sunflower (Helianthus annuus L.) stands as the only counterexample to this pattern. In previous work involving a cross between wild sunflower (also H. annuus) and a highly improved oilseed cultivar, we found that domestication-related traits in sunflower are controlled by numerous QTL, typically of small effect. To provide insight into the minimum genetic changes required to transform the weedy common sunflower into a useful crop plant, we mapped QTL underlying domestication-related traits in a cross between a wild sunflower and a primitive Native American landrace that has not been the target of modern breeding programs. Consistent with the results of the previous study, our data indicate that the domestication of sunflower was driven by selection on a large number of loci, most of which had small to moderate phenotypic effects. Unlike the results of the previous study, however, nearly all of the QTL identified herein had phenotypic effects in the expected direction, with the domesticated allele producing a more crop-like phenotype and the wild allele producing a more wild-like phenotype. Taken together, these results are consistent with the hypothesis that selection during the post-domestication era has resulted in the introduction of apparently maladaptive alleles into the modern sunflower gene pool.

PLANT domestication typically involves intense directional selection, which produces large changes in quantitative traits, often accompanied by some degree of reproductive isolation between wild and domesticated taxa. Crop evolution thus allows for the investigation of basic evolutionary phenomena such as the phenotypic response of populations to long-term directional selection, the genetic consequences of recent selective sweeps, and the limitations imposed on selection response by genetic architecture (e.g., STUBER et al. 1980; WANG et al. 1999; BOST et al. 2001). Unlike researchers studying most wild systems, students of domestication often enjoy historical insights into the likely timing of selection, as well as the types of traits that have been subjected to selection. Common domestication traits include: increased seed or fruit size, more determinate growth and flowering, suppression of natural seed dispersal, and loss of self-incompatibility. Termed the ''domestication syndrome'' (HARLAN 1992), these traits make crop plants easier to cultivate and result in more valuable products for human use.

Genetic analyses of the domestication syndrome have revealed that these traits have a similar genetic architecture across most crops (e.g., DOEBLEY et al. 1990; DOEBLEY and STEC 1991, 1993; PATERSON et al. 1991; KOINANGE et al. 1996; XIONG et al. 1999). More specifically, crop-related traits are typically conditioned by a small number of quantitative trait loci (QTL), each with a relatively large effect on the phenotype (reviewed in ROSS-IBARRA 2005). Perhaps the most well-known example of this is maize, wherein just five genomic regions account for the majority of the phenotypic differentiation between teosinte and maize (DOEBLEY and STEC 1991, 1993). DOEBLEY and STEC (1991, p. 294) argued that if ''evolution is opportunistic, one would predict that major shifts in the morphological traits of plants could be controlled by the full range of genetic mechanisms from few genes with large effects to many genes with small effects.'' They further argued that ''The relative importance in plant evolution of these contrasting modes of inheritance remains to be determined.''

Although wild populations have been shown to respond to selection in a variety of ways (e.g., BRADSHAW et al. 1998; FISHMAN et al. …