Genetic architecture of spatially complex color patterning in hybrid Mimulus

Hybridization generates inter-genomic interactions, which may result in unique traits not seen in either parent species. Here we explore the genetic basis of both carotenoid and anthocyanin floral pigmentation in hybrids between monkeyflower species Mimulus cupreus and M. luteus var. variegatus. Mimulus cupreus has abundant yellow carotenoid pigmentation in its petal lobes, while M. l. variegatus has a derived reduction in carotenoid intensity. Thus, as expected, carotenoid intensity segregates in an F2 hybrid population. More surprisingly, both species appear to have petal lobes solidly and identically covered in magenta anthocyanin pigment (which, when overlaid on the bright yellow carotenoid background, leads to an orange color in M. cupreus), yet F1 and F2 hybrids exhibit novel and complex spatial patterns of anthocyanin spotting. A rare yellow morph of M. cupreus, which lacks petal anthocyanins, also generates spatially patterned offspring when hybridized with M. l. variegatus. We use this cross, together with newly developed high-quality genome assembly of M. l. luteus and image analysis tools, to investigate the genetic architecture of color and pattern variation in an F2 hybrid population. We report a single QTL, containing the Beta-carotene hydroxylase (BCH) gene, associated with the non-patterned carotenoid reduction in M. l. variegatus. HPLC shows that relative beta-carotene abundance differs between dark yellow and light yellow petals, supporting a causal role for BCH. The presence versus absence of petal lobe anthocyanin segregates in a 3:1 ratio, and we report (as expected) an associated QTL encompassing the anthocyanin activator MYB5a/NEGAN which has previously been shown to be both necessary and sufficient to activate petal lobe anthocyanins in M. l. variegatus. Anthocyanin patterning was more complex, with seven QTLs associated with five quantitative patterning traits on the upper petals; 11 on the lower petals; and three qualitative whole-flower patterning traits. Although power was too limited to effectively test for epistatic interactions in this cross, the QTLs provide candidate genomic regions for further investigating the molecular mechanisms of spatially complex floral color patterning, and multiple candidate genes are identified including anthocyanin activators and an anthocyanin repressor.