Comparative Analysis of FLC Homologues in Brassicaceae Provides Insight into Their Role in the Evolution of Oilseed Rape

Zou, Xuefeng; Suppanz, Ida; Raman, Harsh; Hou, Jilun; Wang, Jing; Long, Yan; Jung, Christian; Meng, Jinling

doi:10.1371/journal.pone.0045751

Cited by 72 publications

(86 citation statements)

References 65 publications

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“…The fact that indel I in the upstream region of BnFLC.A10 cosegregated with flowering phenotype in the TN DH population but in only some of the diverse cultivars might be due to the contribution of other flowering time QTLs, including other BnFLC s, with very small genetic effects. For examples, one of the BnFLC paralogs, which was located in linkage group A3 ( BnFLC.A3b ), colocalized with the flowering time QTL and thus might contribute to the vernalization response in certain cultivars [43]. In fact, at least nine copies of Bn.FLC genes exist in rapeseed [43].…”

Section: Discussionmentioning

confidence: 99%

“…For examples, one of the BnFLC paralogs, which was located in linkage group A3 ( BnFLC.A3b ), colocalized with the flowering time QTL and thus might contribute to the vernalization response in certain cultivars [43]. In fact, at least nine copies of Bn.FLC genes exist in rapeseed [43]. Other genes, such as FRIGIDA , also regulate FLC expression in rapeseed; BnaA.FRI.a , one of orthologs of FRIGIDA in Arabidopsis , contributes to flowering time variation in rapeseed, which may partly explain why indel I did not totally cosegregated with flowering time in the association analysis [33].…”

Section: Discussionmentioning

confidence: 99%

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A Tourist-like MITE insertion in the upstream region of the BnFLC.A10 gene is associated with vernalization requirement in rapeseed (Brassica napus L.)

et al. 2012

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BackgroundRapeseed (Brassica napus L.) has spring and winter genotypes adapted to different growing seasons. Winter genotypes do not flower before the onset of winter, thus leading to a longer vegetative growth period that promotes the accumulation and allocation of more resources to seed production. The development of winter genotypes enabled the rapeseed to spread rapidly from southern to northern Europe and other temperate regions of the world. The molecular basis underlying the evolutionary transition from spring- to winter- type rapeseed is not known, however, and needs to be elucidated.ResultsWe fine-mapped the spring environment specific quantitative trait locus (QTL) for flowering time, qFT10-4,in a doubled haploid (DH) mapping population of rapeseed derived from a cross between Tapidor (winter-type) and Ningyou7 (semi-winter) and delimited the qFT10-4 to an 80-kb region on chromosome A10 of B. napus. The BnFLC.A10 gene, an ortholog of FLOWERING LOCUS C (FLC) in Arabidopsis, was cloned from the QTL. We identified 12 polymorphic sites between BnFLC.A10 parental alleles of the TN-DH population in the upstream region and in intron 1. Expression of both BnFLC.A10 alleles decreased during vernalization, but decreased more slowly in the winter parent Tapidor. Haplotyping and association analysis showed that one of the polymorphic sites upstream of BnFLC.A10 is strongly associated with the vernalization requirement of rapeseed (r2 = 0.93, χ2 = 0.50). This polymorphic site is derived from a Tourist-like miniature inverted-repeat transposable element (MITE) insertion/deletion in the upstream region of BnFLC.A10. The MITE sequence was not present in the BnFLC.A10 gene in spring-type rapeseed, nor in ancestral ‘A’ genome species B. rapa genotypes. Our results suggest that the insertion may have occurred in winter rapeseed after B. napus speciation.ConclusionsOur findings strongly suggest that (i) BnFLC.A10 is the gene underlying qFT10-4, the QTL for phenotypic diversity of flowering time in the TN-DH population, (ii) the allelic diversity caused by MITE insertion/deletion upstream of BnFLC.A10 is one of the major causes of differentiation of winter and spring genotypes in rapeseed and (iii) winter rapeseed has evolved from spring genotypes through selection pressure at the BnFLC.A10 locus, enabling expanded cultivation of rapeseed along the route of Brassica domestication.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

A Tourist-like MITE insertion in the upstream region of the BnFLC.A10 gene is associated with vernalization requirement in rapeseed (Brassica napus L.)

et al. 2012

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“…For example, several DArT markers were related to the positions of QTLs associated with flowering and quality components in the TN and SAS populations [9,15,27,37,40]. Two QTLs for flowering time were mapped in the genomic regions harbouring homoeologues of FLOWERING TIME LOCUS C of Arabidopsis, BnFLC.A3 on chromosomes A3 and Bn.FLC.A10 on chromosome A10 [15,27,40]. In the LM population, we identified four QTLs associated with 16:0, 18:1, 18:2 and 18:3 fatty acids on chromosomes A1, A5 and C4 (Table 4).…”

Section: Discussionmentioning

confidence: 99%

A consensus map of rapeseed (Brassica napus L.) based on diversity array technology markers: applications in genetic dissection of qualitative and quantitative traits

Raman

Kilian³

et al. 2013

BMC Genomics

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BackgroundDense consensus genetic maps based on high-throughput genotyping platforms are valuable for making genetic gains in Brassica napus through quantitative trait locus identification, efficient predictive molecular breeding, and map-based gene cloning. This report describes the construction of the first B. napus consensus map consisting of a 1,359 anchored array based genotyping platform; Diversity Arrays Technology (DArT), and non-DArT markers from six populations originating from Australia, Canada, China and Europe. We aligned the B. napus DArT sequences with genomic scaffolds from Brassica rapa and Brassica oleracea, and identified DArT loci that showed linkage with qualitative and quantitative loci associated with agronomic traits.ResultsThe integrated consensus map covered a total of 1,987.2 cM and represented all 19 chromosomes of the A and C genomes, with an average map density of one marker per 1.46 cM, corresponding to approximately 0.88 Mbp of the haploid genome. Through in silico physical mapping 2,457 out of 3,072 (80%) DArT clones were assigned to the genomic scaffolds of B. rapa (A genome) and B. oleracea (C genome). These were used to orientate the genetic consensus map with the chromosomal sequences. The DArT markers showed linkage with previously identified non-DArT markers associated with qualitative and quantitative trait loci for plant architecture, phenological components, seed and oil quality attributes, boron efficiency, sucrose transport, male sterility, and race-specific resistance to blackleg disease.ConclusionsThe DArT markers provide increased marker density across the B. napus genome. Most of the DArT markers represented on the current array were sequenced and aligned with the B. rapa and B. oleracea genomes, providing insight into the Brassica A and C genomes. This information can be utilised for comparative genomics and genomic evolution studies. In summary, this consensus map can be used to (i) integrate new generation markers such as SNP arrays and next generation sequencing data; (ii) anchor physical maps to facilitate assembly of B. napus genome sequences; and (iii) identify candidate genes underlying natural genetic variation for traits of interest.

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“…The B. napus A n and C n subgenomes are largely colinear to the corresponding diploid A r and C o 950 22 fig. S13).…”

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confidence: 92%

“…S19 and table S51). These loci correspond to important QTLs for vernalization requirement and flowering time (22).…”

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Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

Chalhoub

Denœud

et al. 2014

Science

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Oilseed rape (Brassica napus L.) was formed~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent A n and C n subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.T he Brassicaceae are a large eudicot family (1) and include the model plant Arabidopsis thaliana. Brassicas have a propensity for genome duplications ( Fig. 1) and genome mergers (2). They are major contributors to the human diet and were among the earliest cultigens (3).B. napus (genome A n A n C n C n ) was formed by recent allopolyploidy between ancestors of B. oleracea (Mediterranean cabbage, genome C o C o ) and B. rapa (Asian cabbage or turnip, genome A r A r ) and is polyphyletic (2, 4), with spontaneous formation regarded by Darwin as an example of unconscious selection (5). Cultivation began in Europe during the Middle Ages and spread worldwide. Diversifying selection gave rise to oilseed rape (canola), rutabaga, fodder rape, and kale morphotypes grown for oil, fodder, and food (4, 6).The homozygous B. napus genome of European winter oilseed cultivar 'Darmor-bzh' was assembled with long-read [>700 base pairs (bp)] 454 GS-FLX+ Titanium (Roche, Basel, Switzerland) and Sanger sequence (tables S1 to S5 and figs. S1 to S3) (7). Correction and gap filling used 79 Gb of Illumina (San Diego, CA) HiSeq sequence. A final assembly of 849.7 Mb was obtained with SOAP (8) and Newbler (Roche), with 89% nongapped sequence (tables S2 and S3). Unique mapping of 5× nonassembled 454 sequences from B. rapa ('Chiifu') or B. oleracea (' TO1000') assigned most of the 20,702 B. napus scaffolds to either the A n (8294) or the C n (9984) subgenomes (tables S4 and S5 and fig. S3). The assembly covers~79% of the 1130-Mb genome and includes 95.6% of Brassica expressed sequence tags (ESTs) (7). A single-nucleotide polymorphism (SNP) map (tables S6 to S9 and figs. S4 to S8) genetically anchored 712.3 Mb (84%) of the genome assembly, yielding pseudomolecules for the 19 chromosomes (table S10).The assembled C n subgenome (525.8 Mb) is larger than the A n subgenome (314.2 Mb), consistent with the relative sizes of the assembled C o genome of B. oleracea (540 Mb, 85% of thẽ 630-Mb genome) and the A r genome of B. rapa (312 Mb, 59% of the~530-Mb genome) (9-11). The B. napus assembly contains 34.8% transposable elements (TEs), less than the 40% estimated from raw reads (table...

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Comparative Analysis of FLC Homologues in Brassicaceae Provides Insight into Their Role in the Evolution of Oilseed Rape

Cited by 72 publications

References 65 publications

A Tourist-like MITE insertion in the upstream region of the BnFLC.A10 gene is associated with vernalization requirement in rapeseed (Brassica napus L.)

A Tourist-like MITE insertion in the upstream region of the BnFLC.A10 gene is associated with vernalization requirement in rapeseed (Brassica napus L.)

A consensus map of rapeseed (Brassica napus L.) based on diversity array technology markers: applications in genetic dissection of qualitative and quantitative traits

Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

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