DISCUSSION

Perhaps the most surprising result of this study was the paucity of major QTL detected. Only 4 of 78 QTL (corresponding to only 3 of 18 traits) explained >25% of the phenotypic variation in the mapping population (Table 2; Figure 1). In contrast, other recent studies on the genetic basis of domestication have revealed that domestication traits often have a relatively simple genetic basis. In maize, for example, 6 of the 10 domestication traits analyzed by Doebley and Stec (1991) were conditioned by one major QTL each, accompanied by 3–6 modifiers of minor to intermediate effect. Similarly, Koinange et al. (1996) identified major QTL for 8 of 10 traits involved in the domestication of the common bean. The observed lack of major QTL in our study suggests that the phenotypic transition from wild to domesticated sunflower was relatively smooth, with very few (if any) major leaps. Moreover, this lack of dependence on major alleles suggests that sunflower domestication may have occurred much more readily than if it had required the fortuitous occurrence of multiple major mutations.

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Figure 2.

Distribution of the mode of gene action for the 78 QTL detected in this study. U, underdominant; R, recessive; r, partially recessive; A, additive; d, partially dominant; D, dominant; and O, overdominant. Criteria used in defining the mode of gene action of each QTL are outlined in materials and methods.

The observed lack of major QTL is also somewhat surprising given the results of prior studies in sunflower (reviewed in Miller and Fick 1993). For example, Putt (1940) identified a single, dominant gene (Br) that controls branching. Two decades later, Putt (1964) reported recessive control of branching due to alleles at another locus (b1). Hockett and Knowles (1970) reported the existence of two additional duplicate genes (Br2 and Br3) with dominant effects, as well as two complementary genes (b2 and b3) that produce a fully branched plant when both are homozygous recessive. More recently, Kovacik and Skaloud (1990) verified the existence of two genes that exhibit dominant control of branching, as well as two additional genes that produce a branched plant when either is homozygous recessive. Finally, Gentzbittel et al. (1999) found that top branching and basal branching are controlled by two different loci, both of which are located on the same linkage group. Thus, although there is some support for the existence of major genes, our results suggest that the control of branching is genetically complex.

Of the three traits influenced by major QTL in this mapping population, the number of selfed seeds is conditioned by two such loci that are linked on the lower half of LG17. Although cultivated sunflower is generally self-compatible and wild sunflower is self-incompatible, it is unclear if either (or both) of these QTL correspond to loci involved in the recognition and rejection of self-pollen. Rather, the selection of a self-compatible F₁ may have led to the founding of a completely self-compatible mapping population. Because the heads were left unmanipulated, it thus is possible that these regions correspond to loci that influence autogamy independent of the self-incompatibility system. Along these lines, George and Klungness (1980) reported that variation in selfing ability can be influenced by factors such as floret density and stigma orientation, which alter the degree of contact between the anthers and stigmas of adjacent flowers on a head. Pollen agglutination (i.e., the tendency of pollen to form sticky masses) also influences selfing rate in sunflower through its effects on pollen mobility (Segalaet al. 1980). The issue of locating and identifying self-incompatibility loci is an important one in that patterns of variation at these highly variable loci may provide a great deal of information on the dynamics of sunflower domestication as well as insight into the question of multiple origins.

Given that the QTL magnitudes presented here contrast so strongly with those from other studies of domestication, alternative explanations must be considered. One possibility is that, because QTL magnitudes were expressed in terms of the percentage of phenotypic variation explained (PVE), increased variation due to environmental effects would lead to a reduction in QTL magnitude. As discussed in materials and methods, however, environmental variation was controlled for in two ways. First, plants were rotated among greenhouse beds early in their development. Second, all traits were tested for variation among blocks and, where necessary, subsequent analyses were performed on the residuals after accounting for block effects, rather than the raw trait values. Environmental variation is not, therefore, a likely explanation for the paucity of major QTL. Another possibility is that numerous major QTL exist, but were missed due to incomplete genome coverage. The map covers an estimated 84% of the sunflower genome, however, making this explanation also unlikely. Finally, it is possible that defining the magnitude of QTL on the basis of PVE is somewhat misleading. Rather, it may be more appropriate to express effects in terms of the proportion of the phenotypic difference between the parental taxa that is explained by a given QTL. In this case, however, the overall conclusions that can be drawn from such a comparison are much the same. For example, the two QTL detected for achene length (located on LG05 and LG10) account for 16.9 and 10.7% of the phenotypic variance in the mapping population, respectively (Table 2). By comparison, the phenotypic effects of these loci correspond to ~10 and 5% of the phenotypic gap between cultivated and common sunflower (Table 1). Thus, it appears that the lack of major QTL is a biologically real phenomenon. Although it is possible that a substantial amount of the phenotypic variance is conditioned by epistasis, significant interactions among QTL were detected for only two traits, heads per branch and ray size (data not shown). In both cases, the interactions accounted for only a small proportion of the total variance (5.2 and 4.7%, respectively). It therefore seems likely that most traits are controlled by the additive effects of numerous loci of small to moderate effect.

Because domestication presumably results from strong selection, the expectation would be for cultivar alleles to produce a cultivar-like phenotype and wild alleles to produce a wild-like phenotype. Although our data largely conform to this expectation, there are exceptions. At over one-third of all QTL detected (27 of 78), the cmsHA89 allele had a wild-like phenotypic effect and, perhaps most notably, three traits (height, number of branches, and ray size) had a minority of QTL in the expected direction (Table 2). The fact that many wild alleles have crop-like effects suggests that common sunflower may be a rich source of germplasm for continued crop improvement. The occurrence of numerous crop-like alleles in the wild also supports our contention that sunflower may have been readily domesticated. Indeed, if large reserves of suitable variation were already present in the ancestral population(s), then sunflower domestication needed only the intervention of humans to proceed.

The presence of crop-like alleles in the wild also suggests that there may be multiple paths to the domesticated phenotype. This, in turn, makes multiple origins all the more feasible. In contrast, if domesticated taxa are built on novel variation, mutation will be the rate-limiting step, and the recurrent evolution of domesticated taxa will be relatively unlikely (e.g., Doebley 1990). It would therefore be interesting to compare the genetic architecture of domestication (more specifically, the directionality of allelic effects) in taxa with single vs. multiple origins of domestication. Multiple independent origins of domesticated plants have been documented in barley, bitter vetch, lima beans, common beans, chili peppers, and rice (Blumler 1992; van Raamsdonk 1993; Diamond 1997; Zohary 1999; reviewed in Levin 2001). Unfortunately, the data necessary for such a comparison do not currently exist.

The frequent occurrence of QTL with effects in the “wrong” direction, combined with the relatively low magnitudes described above, indicates that, at least for some traits, a large fraction of the phenotypic difference between cultivated and common sunflower cannot be accounted for. One possible explanation is that there may have been QTL of small effect that went undetected (Beavis 1994). Alternatively, incomplete sampling of the wild genome may have created this effect. Common sunflower is highly heterozygous, but the crossing design employed here permitted the introduction of only a single wild allele per locus into the mapping population. All possible alleles from the wild parent, as well as the interactions among these alleles, were therefore not represented. Thus, additional crosses between the same parental lines might reveal additional QTL, thereby accounting for a greater proportion of the phenotypic difference between cultivated and common sunflower.

Although the genomic locations of QTL identified in this study are relatively widespread, a considerable amount of clustering is apparent (Figure 1). Clearly, some of this clustering is due to the inclusion of multiple measures of what might be considered a single trait. For example, achene length, width, and weight might all be considered measures of “achene size,” and QTL for these traits sometimes coincide (see LG03, LG06, LG09, and LG10). However, there is also considerable clustering of QTL across apparently unrelated traits. This pattern of genetic correlations across traits has been documented in other cases of domestication as well. In the common bean and maize, QTL underlying domestication traits are largely restricted to three and five genomic regions, respectively (Doebleyet al. 1990; Doebley and Stec 1991, 1993; Koinangeet al. 1996). Although linkage among QTL influencing domestication traits is predicted to evolve under strong selection, especially in allogamous species (Le Thierry D'Ennequin et al. 1999), relatively little attention has been paid to the role of pleiotropy in domestication. Thus, further characterization of the genetic basis of these correlations (i.e., linkage vs. pleiotropy) would be illuminating.

Regardless of the ultimate cause of genetically correlated traits, the end result is much the same. Antagonistic correlations will constrain adaptive evolution, whereas concordant effects will facilitate adaptation (Lande 1979; Lande and Arnold 1983). The main difference is that under physical linkage, as opposed to pleiotropy, unfavorable relationships can be disrupted, potentially freeing up advantageous alleles that were previously housed in maladaptive chromosomal blocks. This issue is especially interesting in light of the observed directionality of allelic effects. Although the majority of trait correlations were concordant, there were numerous instances of antagonistic correlations across the genome (Figure 1). For example, 7 of the 10 QTL on LG06 have effects in the wrong direction, including 2 QTL affecting achene size, a trait that was clearly under selection during domestication (see below). This pattern could result from either the chance fixation of a maladaptive chromosomal block during domestication or strong selection favoring one or a few QTL that have antagonistic effects on other domestication traits. With respect to the former, chance fixation would be more likely if sunflower experienced a strong domestication bottleneck (i.e., a period of restricted population size during domestication). Although little is known about the dynamics of sunflower domestication, this sort of bottleneck has been documented in maize (Eyre-Walkeret al. 1998). In the latter case, one might expect such selectively important QTL to be of relatively major effect. It is therefore possible that the trait driving the evolution of this region was not included in the present analysis. One possibility is that this region harbors one or more loci with effects on seed oil content or composition.

The ratio of alleles with effects in the “right” vs. “wrong” direction can also be used to investigate the role of selection in trait divergence (Orr 1998). The mere existence of alleles in one direction or the other is not, however, sufficient to implicate the effects of selection. For example, because cultivated sunflower has larger achenes than its wild progenitor, we know a priori that the cultivar must harbor at least some “plus” alleles. Thus, we must ask if the ratio of plus:minus alleles is more extreme than expected by chance, given the observed phenotypic difference (Orr 1998). In this case, 14 QTL affect some aspect of achene size (length, width, or weight). Of these, 12 have the expected effect (i.e., the cmsHA89 allele produces larger achenes). Inspection of Figure 1 reveals that these 14 QTL map to only 10 unique chromosomal regions. Of these 10 regions, 9 produce the expected effect. Applying Orr's (1998) test to these data, our results are consistent with directional selection favoring increased achene size (P = 0.04). In view of the fact that sunflower is a seed crop, this result is not necessarily surprising. What is more interesting is that none of the other traits analyzed show similar evidence of selection. Traits relating to plant architecture, for example, may not have been targets of strong directional selection. This conclusion must be tempered with the realization that the power of this test is closely associated with the number of QTL detected. For traits such as shattering, therefore, we fail to reject the null hypothesis of neutral divergence even though all of the QTL detected (in this case only 2) had effects in the expected direction.

Finally, our data contradict the view that domestication traits are largely under recessive genetic control (e.g., Ladizinsky 1985). Inspection of Figure 2 reveals that the majority of QTL are, in fact, nonrecessive. These findings are in accord with those of Paterson et al. (1991) in tomato and Doebley et al. (1994) in maize. Once again, this finding suggests that sunflower was readily domesticated and that selection during domestication likely resulted in a rapid phenotypic response.

The goal of this study was to examine the genetic basis of traits that differentiate cultivated and wild sunflower. The lack of major QTL, combined with both the occurrence of numerous wild alleles with cultivar-like effects and largely nonrecessive gene action, suggests that sunflower was readily domesticated. Moreover, our data suggest that wild sunflower may be an important source of germplasm for continued crop improvement. Looking across the genome, there was a considerable amount of clustering among QTL influencing multiple, apparently unrelated traits. Whether this pattern results from linkage or pleiotropy remains unclear. The first step to resolving this issue will be fine mapping these regions in an attempt to further refine QTL locations. Finally, a major sunflower cDNA sequencing effort is currently underway. The logical next step in the study of sunflower domestication will therefore be to begin identifying and mapping candidate genes underlying the traits of interest. The characterization of nucleotide variation at these adaptively important loci promises to provide a wealth of information on factors such as the strength and timing of selection during domestication. This approach will also open the door for comparative analyses of the domestication syndrome across widely disparate taxa.