Genetic Control and Comparative Genomic Analysis of Flowering Time in Setaria (Poaceae)

Abstract

We report the first study on the genetic control of flowering in Setaria, a panicoid grass closely related to switchgrass, and in the same subfamily as maize and sorghum. A recombinant inbred line mapping population derived from a cross between domesticated Setaria italica (foxtail millet) and its wild relative Setaria viridis (green millet), was grown in eight trials with varying environmental conditions to identify a small number of quantitative trait loci (QTL) that control differences in flowering time. Many of the QTL across trials colocalize, suggesting that the genetic control of flowering in Setaria is robust across a range of photoperiod and other environmental factors. A detailed comparison of QTL for flowering in Setaria, sorghum, and maize indicates that several of the major QTL regions identified in maize and sorghum are syntenic orthologs with Setaria QTL, although the maize large effect QTL on chromosome 10 is not. Several Setaria QTL intervals had multiple LOD peaks and were composed of multiple syntenic blocks, suggesting that observed QTL represent multiple tightly linked loci. Candidate genes from flowering time pathways identified in rice and Arabidopsis were identified in Setaria QTL intervals, including those involved in the CONSTANS photoperiod pathway. However, only three of the approximately seven genes cloned for flowering time in maize colocalized with Setaria QTL. This suggests that variation in flowering time in separate grass lineages is controlled by a combination of conserved and lineage specific genes.

Beyond the single gene: How epistasis and gene-by-environment effects influence crop domestication

“…Two field, two greenhouse, and one growth chamber trial were performed at Oklahoma State University; two field trials took place at the University of Georgia (Athens, GA); and one growth chamber trial was at the Boyce Thompson Institute (Ithaca, NY). Trials varied in photoperiod, seed pretreatment, light intensity, time of year, and experimental design (58). All eight trials were phenotyped for flowering time (58); one field trial (F2_OK, field, OK) was phenotyped for seed shattering.…”

“…We searched for QTL and epistatic interactions for flowering time across eight trials that differed in environmental conditions, including photoperiod differences from short day (12 h light and dark) to long day (16 h light and 8 h dark) (58). We had previously reported stable QTL associations across trials, together with evidence of QTL × environment interactions (58) (Figs. S1 and S2).…”

Molecular Regulation of Flowering Time in Grasses

“…The most extensively gene studied in Arabidopsis flowering is CO that confers LD responses. CO encodes a B-box zinc finger transcription factor and CCT domain genes that promote flowering under LD conditions and activate the expression of FT [33][34][35], a major component of the florigen that induces flower differentiation [29]. Its inactivation causes flowering delay, while its over-expression induces early flowering.…”

“…The plant circadian system consists of biochemical timing mechanisms that temporarily modulate the function of several signalling pathways to measures changes in day-length and promote suitable timing of flowering to maximize reproductive success [2,3,6,7,9,10,[13][14][15]21,24,26,28,29,31,36,38,41,42,46,48,49,[56][57][58][59][60][61][62][63][64][65][66]. The photoperiod response on flowering time varies among grasses.…”

“…Grasses have multiple pathways to control flowering time but only some of them are conserved in Arabidopsis thaliana (L.) Heynh. [29]. These studies have been crucial in establishing the multiple pathways that control flowering, of which the photoperiod pathway is of major importance [30].…”