GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

Abstract

Background Transition to flowering at the right time is critical for local adaptation and to maximize grain yield in crops. Canola is an important oilseed crop with extensive variation in flowering time among varieties. However, our understanding of underlying genes and their role in canola productivity is limited. Results We report our analyses of a diverse GWAS panel (300–368 accessions) of canola and identify SNPs that are significantly associated with variation in flowering time and response to photoperiod across multiple locations. We show that several of these associations map in the vicinity of FLOWERING LOCUS T ( FT ) paralogs and its known transcriptional regulators. Complementary QTL and eQTL mapping studies, conducted in an Australian doubled haploid population, also detected consistent genomic regions close to the FT paralogs associated with flowering time and yield-related traits. FT sequences vary between accessions. Expression levels of FT in plants grown in field (or under controlled environment cabinets) correlated with flowering time. We show that markers linked to the FT paralogs display association with variation in multiple traits including flowering time, plant emergence, shoot biomass and grain yield. Conclusions Our findings suggest that FT paralogs not only control flowering time but also modulate yield-related productivity traits in canola. Electronic supplementary material The online version of this article (10.1186/s12864-019-5964-y) contains supplementary material, which is available to authorized users.

QTL mapping reveals genomic regions for yield based on incremental tolerance index to drought stress and related agronomic traits in canola

“…These results are consistent with a previous study, which reported a multi-trait QTL (flanked by markers 3110489 and 3075574) for plant emergence, shoot biomass, flowering time, and seed yield mapped on chromosome A07 in the vicinity of the FT [30]. PRC2 is involved in trimethylation of histone H3 lysine 27 and regulates VERNALISATION INSENSTIVE 3 (VIN3) and plays an important role in epigenetic repression of FLC [35].…”

“…This observed clustering of different QTL is consistent with genetic correlation among different traits in the RADH population (SupplementaryTable 1). In a previous study, Raman et al[30] found moderate to high genetic correlations for flowering time, early vigour, plant biomass and seed yield in an Australian DH population from Skipton/Ag-Spectrum//Skipton. Flowering time is an adaptive trait and shows pleiotropy with seed yield and other plant architectural traits in B. juncea and winter/spring crosses of B. napus[19,23,[30][31][32][33][34].…”

“…In a previous study, Raman et al[30] found moderate to high genetic correlations for flowering time, early vigour, plant biomass and seed yield in an Australian DH population from Skipton/Ag-Spectrum//Skipton. Flowering time is an adaptive trait and shows pleiotropy with seed yield and other plant architectural traits in B. juncea and winter/spring crosses of B. napus[19,23,[30][31][32][33][34]. However, in the present study, we used Australian spring type genotypes to minimise the effect of vernalisation genes on flowering time and seed yield.We attempted to locate the candidate genes within 1Mbp from significant trait-marker associations; however these genes may not be causative for trait variations and require further validation studies.…”

Linkage mapping and QTL analysis of flowering time using ddRAD sequencing with genotype error correction inBrassica napus

“…However, the QTL LOD peaks identified here are distant from this location. Among the known flowering time genes on C2, FT (40), FLC (41) and FY (42) may have particularly substantial effects.FT has been implicated in B. napus flowering time divergence(28,43) and FLC has been found to explain ~23% of flowering time variation in B. napus(44). FY is a suppressor of the transcription factor FLC (42, 45), and lies in close physical proximity to the LOD peaks identified in this study.…”

Linkage mapping and QTL analysis of flowering time using ddRAD sequencing with genotype error correction in Brassica napus

“…Flowering time genetic pathways have been elucidated in Arabidopsis and most flowering time genes are known to be conserved between Arabidopsis and B. napus [21][22][23]. On this basis, many QTL and associated SNPs for flowering time have been detected in B. napus [24][25][26][27][28][29][30][31]. However, despite progress in understanding the genetic underpinnings of B. napus flowering time, a substantial proportion of flowering time variation remains to be explained.…”