Quantitative Trait Locus Analysis of the Early Domestication of Sunflower

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.

Contributions of Flowering Time Genes to Sunflower Domestication and Improvement

“…Genetic mapping: Map positions were obtained for 30 candidate genes by genotyping markers on subsets of one of six mapping panels: 94 of 214 NMS373 3 (NMS373 3 Ann1811) BC 1 individuals (Gandhi et al 2005); 96 of 378 Hopi 3 Ann1238 F 2 individuals (Wills and Burke 2007); 96 of 374 CMSHA89 3 Ann1238 F 3 individuals ; 48 of 94 RHA280 3 RHA801 recombinant inbred lines (RILs) Lai et al 2005); 94 of 262 PHC 3 PHD RILs (S. Knapp, unpublished results); and 94 of 94 NMS801 3 Arg1805 F 1 's (Heesacker et al 2009). Portions of the genes were amplified by PCR with gene-specific primers (Table S1).…”

“…Defining candidates by mapping: As a first criterion for choosing flowering time homologs as candidate domestication or improvement genes, we tested whether genes colocalized with previously identified flowering time QTLs Wills and Burke 2007;. Markers polymorphic in one of the six mapping panels available to us were identified (Table 1, Figure 2); of the 30 genes mapped, 18 mapped to LGs containing flowering time QTLs (Figure 3).…”

“…QTL regions, shown as 1-LOD intervals and detected in an elite 3 wild population in the greenhouse and the wild , are shown as solid and shaded bars, respectively. QTL regions detected in a landrace 3 wild population grown in the greenhouse (Wills and Burke 2007) are shown as white bars.…”

“…Individuals of this population have a short-day-sensitive photoperiod response in flowering, unlike CMSHA89, which is longday-sensitive and flowers earlier than Ann1238 in both inductive and non-inductive photoperiods (Blackman et al 2010). Since no genes mapped to the LG containing the single QTL unique to the landrace 3 wild panel (Wills and Burke 2007), we did not include the landrace parent of that panel in our analysis. Expression of candidates was assayed by RT-PCR in leaf and/or shoot apex tissue, depending on the gene's expression domain(s) in other species.…”

“…QTL studies performed on a landrace 3 wild H. annuus cross (Wills and Burke 2007) and an elite 3 wild H. annuus cross have found that the genetic architecture of flowering time differences between wild and domesticated sunflower is oligogenic. In each case, one major and several minor flowering time QTLs were detected, and QTLs concordant between these crosses were detected in two regions.…”