Capturing sequence variation among flowering-time regulatory gene homologs in the allopolyploid crop species Brassica napus

Abstract

Flowering, the transition from the vegetative to the generative phase, is a decisive time point in the lifecycle of a plant. Flowering is controlled by a complex network of transcription factors, photoreceptors, enzymes and miRNAs. In recent years, several studies gave rise to the hypothesis that this network is also strongly involved in the regulation of other important lifecycle processes ranging from germination and seed development through to fundamental developmental and yield-related traits. In the allopolyploid crop species Brassica napus, (genome AACC), homoeologous copies of flowering time regulatory genes are implicated in major phenological variation within the species, however the extent and control of intraspecific and intergenomic variation among flowering-time regulators is still unclear. To investigate differences among B. napus morphotypes in relation to flowering-time gene variation, we performed targeted deep sequencing of 29 regulatory flowering-time genes in four genetically and phenologically diverse B. napus accessions. The genotype panel included a winter-type oilseed rape, a winter fodder rape, a spring-type oilseed rape (all B. napus ssp. napus) and a swede (B. napus ssp. napobrassica), which show extreme differences in winter-hardiness, vernalization requirement and flowering behavior. A broad range of genetic variation was detected in the targeted genes for the different morphotypes, including non-synonymous SNPs, copy number variation and presence-absence variation. The results suggest that this broad variation in vernalization, clock and signaling genes could be a key driver of morphological differentiation for flowering-related traits in this recent allopolyploid crop species.

Targeted capture in evolutionary and ecological genomics

“…Although targeted capture has primarily been applied to protein-coding exons (Hodges et al 2007), regulatory regions such as UTR, miRNA, promoter regions, and other non-coding elements can also be targeted in a highly parallel fashion (Bainbridge et al 2011; Hebert et al 2013; Linnen et al 2013; Carneiro et al 2014a; Carneiro et al 2014b; Schiessl et al 2014). In addition, non-coding regions flanking exons and other baited regions are often indirectly targeted (Samuels et al 2013).…”

“…Finally, the uniformity in coverage across targeted loci may be leveraged to infer copy number variation (CNV) based on relative coverage (Saintenac et al 2011; Schiessl et al 2014; Jiang et al 2015). The utility of targeted capture in this respect is a tremendous advantage because structural variation (e.g., whole genome or gene duplications and chromosomal rearrangements) can play an important role in adaptation and speciation (Lowry & Willis 2010; Kondrashov 2012), yet identifying and characterizing structural variation is often difficult.…”

The fusion of genomes leads to more options: A comparative investigation on the desulfo-glucosinolate sulfotransferases of Brassica napus and homologous proteins of Arabidopsis thaliana

“…Due to genome triplication and alloploidization of B. napus, three homologs from each ancestor genome can theoretically be expected, but in average there are 4.4 functional gene copies present (Parkin et al, 2010). Variation of the gene copy number in B. napus was previously reported for several proteins, such as proline dehydrogenase (Faes et al, 2014), cytokinin receptors (Kuderova et al, 2015), and flowering-time regulatory genes (Schiessl et al, 2014). In the process of polyploidization, B. napus has undergone a high degree of genome and gene duplications and genome rearrangements (Zmienko et al, 2014), including homoeologous recombination, which leads to gene copy variation and presence/absence variation (Gaeta and Chris Pires, 2010;Udall et al, 2006).…”

“…The high number of homologous genes leads to higher robustness against mutation and loss of function risks (Bekaert et al, 2011) and a better adaption to the environment (Chen, 2010). Simultaneous transcription enables a faster and increased reaction capacity and a better fine tuning in physiological pathways (Schiessl et al, 2014).…”

Oilseed rape: learning about ancient and recent polyploid evolution from a recent crop species

“…On average, 4.4 expressed gene copies in B. napus have been identified genome-wide for every Arabidopsis gene (Parkin et al 2010). However, Lloyd et al (2014) observed that genes involved in meiosis tend to be retained in single copies after polyploidisation, while Schiessl et al (2014) found additional duplication/deletion events between the A and C genomes of B. napus also influenced gene copy number. A probable effect of human-directed genomic selection was also observed by Chalhoub et al (2014): all glucosinolate catabolism gene copies were retained in B. napus from diploid B. rapa and B. oleracea, putatively as a result of selection for low glucosinolates in this domesticated crop species.…”