natural variation in brachypodium links vernalization and ... · 182 vernalization periods showed...

1 Short title:

2 Natural variation in B. distachyon flowering time

3

4

5

6 Corresponding authors:

7 John H. Doonan

8 Institute of Biological, Environmental and Rural Sciences

9 Aberystwyth University

10 Aberystwyth

11 SY23 3DA

12 United Kingdom

13 Tel: +44 (0) 1970 823080

14 Email: [email protected]

15

16 Matthew J. Moscou

17 The Sainsbury Laboratory

18 Norwich Research Park

19 Norwich

20 NR4 7UH

21 United Kingdom

22 Tel: +44 (0)1603 450296

23 Email: [email protected]

mailto:[email protected]


24 Title:

25 Natural variation in Brachypodium links vernalization and flowering time loci as major

26 flowering determinants

27

28

29 Authors:

30 Jan Bettgenhaeuser1, Fiona M.K. Corke

2,3, Magdalena Opanowicz

3, Phon Green

1, Inmaculada

31 Hernández-Pinzón1, John H. Doonan

2,3, Matthew J. Moscou

1,4

32

33 Affiliations:

34 1The Sainsbury Laboratory, Norwich, NR4 7UH, United Kingdom

35 2Institute of Biological, Environmental and Rural Sciences, Aberystwyth University,

36 Aberystwyth, SY23 3DA, United Kingdom

37 3John Innes Centre, Norwich, NR4 7UH, United Kingdom

38 4School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United

39 Kingdom

40

41

42

43 One sentence summary:

44 Standing genetic variation for flowering time in a non-domesticated grass encompasses

45 known and novel regulators.

46 Footnotes:

47

48 Author contributions

49 JB, FC, MO, JD, and MM conceived the study, and participated in its design and

50 coordination. PG and IHP participated in the experiments. JB, FC, JD, and MM wrote the

51 manuscript. All authors read and approved the final manuscript.

52

53

54 Funding information

55 The work was funded by the Biotechnology and Biological Sciences Research Council

56 Doctoral Training Programme (BB/F017294/1) and Institute Strategic Programme

57 (BB/J004553/1), the Gatsby Charitable Foundation, the Leverhulme Trust (Grant reference

58 10754), the 2Blades Foundation, and the Human Frontiers Science Program

59 (LT000218/2011).

60

61

62 Present addresses

63 Magdalena Opanowicz

64 Thermo Fisher Scientific, Paisley, PA4 9RF, United Kingdom

65

66

67 Corresponding authors email addresses

68 John H. Doonan – [email protected]

69 Matthew J. Moscou – [email protected]



70 Abstract

71 The domestication of plants is underscored by the selection of agriculturally favorable

72 developmental traits, including flowering time, which resulted in the creation of varieties

73 with altered growth habits. Research into the pathways underlying these growth habits in

74 cereals has highlighted the role of three main flowering regulators: VRN1, VRN2, and FT.

75 Previous reverse genetic studies suggested that the roles of VRN1 and FT are conserved in

76 Brachypodium distachyon, yet identified considerable ambiguity surrounding the role of

77 VRN2. To investigate the natural diversity governing flowering time pathways in a non-

78 domesticated grass, the reference B. distachyon accession Bd21 was crossed with the

79 vernalization-dependent accession ABR6. Resequencing of ABR6 allowed the creation of a

80 SNP-based genetic map at the F4 stage of the mapping population. Flowering time was

81 evaluated in F4:5 families in five environmental conditions and three major loci were found to

82 govern flowering time. Interestingly, two of these loci colocalize with the B. distachyon

83 homologs of the major flowering pathway genes VRN2 and FT, whereas no linkage was

84 observed at VRN1. Characterization of these candidates identified sequence and expression

85 variation between the two parental genotypes, which may explain the contrasting growth

86 habits. However, the identification of additional QTLs suggests that greater complexity

87 underlies flowering time in this non-domesticated system. Studying the interaction of these

88 regulators in B. distachyon provides insights into the evolutionary context of flowering time

89 regulation in the Poaeceae, as well as elucidates the way humans have utilized the natural

90 variation present in grasses to create modern temperate cereals.

91 Introduction

92 Coordination of flowering time with geographic location and seasonal weather patterns has a

93 profound effect on flowering and reproductive success (Amasino, 2010). The mechanisms

94 underpinning this coordination are of great interest for understanding plant behavior and

95 distribution within natural ecosystems (Wilczek et al., 2010). Plants that fail to flower at the

96 appropriate time are unlikely to be maximally fertile and therefore will be less competitive in

97 the longer term. Likewise, optimal flowering time in crops is important for yield and quality:

98 seed and fruit crops need to flower early enough to allow ripening or to utilize seasonal rains,

99 while delayed flowering may be advantageous for leaf and forage crops (Distelfeld et al.,

100 2009; Jung and Müller, 2009).

101

102 Although developmental progression towards flowering can be modulated in several ways,

103 many plants have evolved means to detect seasonal episodes of cold weather and adjust their

104 flowering time accordingly, a process known as vernalization (Ream et al., 2012). Despite the

105 importance of flowering time, the molecular and genetic mechanisms underlying this

106 dependency have been studied in only a few systems, notably the Brassicaceae, Poaceae, and

107 Amaranthaceae (Andrés and Coupland, 2012; Ream et al., 2012). Three major

108 VERNALIZATION (VRN) genes appear to act in a regulatory loop in temperate grasses. The

109 wheat VRN1 gene is a MADS-box transcription factor, which is induced in the cold (Yan et

110 al., 2003; Andrés and Coupland, 2012). This gene is related to the Arabidopsis thaliana genes

111 APETALA1 and FRUITFUL (Yan et al., 2003; Andrés and Coupland, 2012). VRN2 encodes a

112 small CCT-domain protein (Yan et al., 2004) that is repressed by VRN1 and in turn represses

113 FLOWERING LOCUS T (FT), a strong universal promoter of flowering (Kardailsky et al.,

114 1999; Yan et al., 2006; Andrés and Coupland, 2012; Ream et al., 2012). In cereals, active

115 VRN2 alleles are necessary for a vernalization requirement. Spring barley and spring wheat

116 varieties, which do not require vernalization to flower, either lack VRN2 (Dubcovsky et al.,

117 2005; Karsai et al., 2005; von Zitzewitz et al., 2005), have point mutations in the conserved

118 CCT domain (Yan et al., 2004), or possess dominant constitutively active alleles of VRN1

119 (repressor of VRN2) (Yan et al., 2003; Fu et al., 2005) or FT (repressed by VRN2) (Yan et al.,

120 2006).

121

122 Investigations on the regulation of flowering in the Poaceae have focused on rice (Oryza

123 sativa), wheat (Triticum aestivum), and barley (Hordeum vulgare), all domesticated species

124 that have been heavily subjected to human selection over the past 10,000 years. Little

125 information is available on wild species within this family that have not been subjected to

126 human selection. Such a study could provide additional insights into the standing variation

127 present within wild systems and its likely pre-domestication adaptive significance in the

128 Poaceae (Schwartz et al., 2010). A favorable species for such a study is Brachypodium

129 distachyon, a small, wild grass, with a sequenced and annotated genome. B. distachyon was

130 originally developed as a model system for the agronomically important temperate cereals

131 (Draper et al., 2001; Opanowicz et al., 2008; The International Brachypodium Initiative,

132 2010; Catalán et al., 2014). With the recent availability of geographically dispersed diversity

133 collections, we can ask how wild grasses have adapted to different climatic zones.

134

135 Previous studies have begun to explore the molecular basis of vernalization in this system.

136 Higgins et al. (2010) identified homologs of the various flowering pathway genes in B.

137 distachyon, and several mainly reverse genetic studies have focused on characterizing these

138 genes further (Schwartz et al., 2010; Lv et al., 2014; Ream et al., 2014; Woods et al., 2014;

139 Woods et al., 2016). Schwartz et al. (2010) did not find complete correlation between

140 expression of VRN1 and flowering and hypothesized that VRN1 could therefore have

141 different activity or roles that are dependent on the genetic background. Yet, Ream et al.

142 (2014) found low VRN1 and FT levels in B. distachyon accessions with delayed flowering,

143 suggesting a conserved role of these homologs. Further support for a conserved role of VRN1

144 and FT comes from the observation that overexpression of these genes leads to extremely

145 early flowering (Lv et al., 2014; Ream et al., 2014) and RNAi-based silencing of FT and

146 amiRNA-based silencing of VRN1 prevent flowering (Lv et al., 2014; Woods et al., 2016).

147 The role of VRN2 in B. distachyon is less clear. Higgins et al. (2010) failed to identify a

148 homolog of VRN2 in B. distachyon; however, other studies identified Bradi3g10010 as the

149 best candidate for the B. distachyon VRN2 homolog (Schwartz et al., 2010; Ream et al.,

150 2012). Recent research supports the functional conservation of VRN2 in the role as a

151 flowering repressor, but suggests that the regulatory interaction between VRN1 and VRN2

152 evolved after the diversification of the Brachypodieae and the core Pooideae (e.g. wheat and

153 barley) (Woods et al., 2016).

154

155 To date most studies on the regulation of flowering time of B. distachyon have used reverse

156 genetic approaches to implicate the role of previously characterized genes from other species

157 (Higgins et al., 2010; Lv et al., 2014; Ream et al., 2014; Woods et al., 2016), while only few

158 studies have used the natural variation present among B. distachyon accessions to identify

159 flowering loci (Tyler et al., 2016; Wilson et al., 2016). Currently lacking is the

160 characterization of loci that control variation in flowering time in a biparental B. distachyon

161 mapping population. The Iraqi reference accession Bd21 does not require vernalization

162 (Vogel et al., 2006; Garvin et al., 2008) and in addition, vernalization does not greatly reduce

163 time to flowering in a 16 h or 20 h photoperiod (Schwartz et al., 2010; Ream et al., 2014). In

164 contrast, the Spanish accession ABR6 can be induced to flower following a six-week

165 vernalization period (Draper et al., 2001; Routledge et al., 2004).

166

167 In this paper, we report on the genetic architecture underlying flowering time in a mapping

168 population developed from ABR6 and Bd21. We observed the segregation of vernalization

169 dependency during population advancement (Figure 1) and characterized the genetic basis of

170 this dependency in detail at the F4:5 stage in multiple environments. The ability to flower

171 without vernalization was linked to three major loci, two of which colocalize with the B.

172 distachyon homologs of VRN2 and FT. Notably, our results further support the role of the

173 VRN2 locus as a conserved flowering time regulator in B. distachyon.

174

175

176

177 Results

178

179 Development of a B. distachyon mapping population between geographically and

180 phenotypically distinct accessions

181 Initial investigations into the flowering time of ABR6 and Bd21 in response to different

182 vernalization periods showed contrasting effects on the two accessions (Figure 1 and Figure

183 2). ABR6 responded strongly to increasing vernalization times with a reduction in flowering

184 by 93 days, ranging from 117 days for a two-week vernalization period to 24 days for an

185 eight-week vernalization period. This reduction in flowering time for ABR6 was not linear

186 and the greatest drop of 43 days occurred between four and five weeks of vernalization

187 (Figure 2). In contrast, no statistically significant difference was found with respect to the

188 vernalization response of Bd21, although a consistent trend towards a reduced flowering time

189 was observed. A cross was generated from these phenotypically diverse accessions for the

190 creation of a recombinant inbred line population. To develop a SNP-based genetic map,

191 ABR6 was resequenced and reads were aligned to the reference genome. A total of 1.36

192 million putative SNPs were identified between ABR6 and Bd21, of which 711,052

193 constituted non-ambiguous polymorphisms based on a minimum coverage of 15x and a strict

194 threshold for SNP calling (i.e. 100% of reads with an ABR6 allele, 0% of reads with a Bd21

195 allele). Following iterative cycles of marker selection, the final genetic map consists of 252

196 non-redundant markers and has a cumulative size of 1,753 cM (Supplemental Figure S1).

197 This size is comparable to the previously characterized Bd3-1 x Bd21 mapping population

198 (Huo et al., 2011) and confirms that B. distachyon has a high rate of recombination compared

199 to other grass species. The quality of the genetic map was verified by assessing the two-way

200 recombination fractions for all 252 markers (Supplemental Figure S2). All five chromosomes

201 were scanned for segregation distortion by comparing observed and expected genotype

202 frequencies for each marker. The expected heterozygosity at the F4 stage is 12.50% and the

203 expected parental allele frequencies are 43.75% for ABR6 and Bd21 alleles, respectively.

204 Although all five chromosomes contained regions of potential segregation distortion (Figure

205 3), only two loci on chromosomes Bd1 (peak at 474.1 cM) and Bd4 (peak at 77.0 cM)

206 deviated significantly from these expected frequencies.

207

208 Multiple QTLs control flowering in the ABR6 x Bd21 mapping population

209 We evaluated the ABR6 x Bd21 F4:5 population in a number of environments to identify the

210 genetic architecture underlying flowering time (Supplemental Table S1 and Supplemental

211 Data S1). Four sets of the population were grown without vernalization, whereas in one

212 additional set flowering was scored in response to six weeks of vernalization. In all

213 experiments, the population was exposed to natural light, although in three experiments

214 supplemental light was used to ensure a minimum 16 h or 20 h growth period. In addition,

215 two experiments did not have any temperature control (i.e. plants were exposed to the natural

216 temperature in the greenhouse), three experiments had the temperature controlled at

217 22°C/20°C during light/dark cycles, and one experiment had the temperature maintained at a

218 minimum of 18°C/11.5°C during light/dark cycles. Analysis of the non-vernalized

219 environments revealed a bimodal distribution between families that flowered and families

220 that did not flower (Figure 4). However, considerable residual variation in flowering time

221 existed among the flowering families. For example, in Environment 5 flowering occurred

222 over a 42-day period from 63 days to 105 days after germination (Figure 4E). Flowering in

223 the other non-vernalized environments occurred over a similar time period (Figure 4).

224 Interestingly, transgressive segregation for early and late flowering phenotypes was observed

225 in Environment 4 (Figure 4D). Phenotypes in the vernalized environment were heavily

226 skewed towards early flowering (Figure 4B). Only limited residual variation existed among

227 the vernalized F4:5 families and all plants flowered within 11 days from the first observation

228 of flowering in the population. The variation in flowering time for all five environments was

229 found to be not normally distributed. Among these diverse environments, QTL analyses

230 using binary and non-parametric models were conservative in detecting QTLs controlling

231 flowering time (qFLT) (Supplemental Table S2 and Supplemental Table S3), whereas

232 transformation of flowering time consistently identified QTLs between environments

233 (Supplemental Table S4 and Supplemental Table S5; Table 1 and Table 2). Three major

234 QTLs were identified on chromosomes Bd1 and Bd3 that were robustly observed using

235 parametric and non-parametric mapping approaches (Table 1 and Table 2; Figure 5). The

236 QTL on Bd1 (qFLT1, peak marker Bd1_47808182) appeared to be the major locus governing

237 flowering time in this population, as it was the major QTL in all five environments,

238 explaining the most phenotypic variation (phenotypic variance explained; PVE) compared to

239 any other QTL (Table 2). PVE values for this locus ranged from 15.9% to 37.5%. Another

240 QTL on Bd3 (qFLT6, peak marker Bd3_8029207) was also detected in all five studies,

241 though its contribution was only significant in three environments. PVE values for the

242 statistically significant QTLs ranged from 11.8% to 18.7%. Bd21 alleles at these two loci

243 promoted early flowering, whereas individuals with ABR6 alleles at both loci had maximal

244 flowering time or did not flower within the timescale of the experiment (Figure 6).

245 Interestingly, in the two environments where this former locus did not have a significant

246 contribution, two other QTLs were identified. A QTL on Bd3 (qFLT7, peak marker

247 Bd3_44806296) explained 13.6% and 14.0% of the variation observed in these studies and a

248 QTL on Bd2 (qFLT3, peak marker Bd2_53097824) was identified through a combination of

249 non-parametric and parametric analyses of Environments 4 and 5. Additional QTLs on Bd1

250 (qFLT2), Bd2 (qFLT4), Bd3 (qFLT5), and Bd4 (qFLT8) were not significant in more than

251 one of the environments tested (Table 1).

252

253 Previous studies identified the B. distachyon homologs of flowering regulators from

254 Arabidopsis, wheat, barley, and rice (Higgins et al., 2010; Ream et al., 2014). The one-LOD

255 support intervals of all statistically significant QTLs were combined to identify the maximal

256 one-LOD support interval for each QTL. Several of the previously identified B. distachyon

257 homologs of flowering regulators are candidate genes underlying these QTLs (Table 3).

258 Although several homologs fall within the one-LOD support intervals of qFLT1 on Bd1

259 (292.1 - 305.6 cM) and qFLT6 on the short arm of Bd3 (72.9 - 97.0 cM), these loci also

260 harbor the B. distachyon homologs of FT (Bradi1g48830) and VRN2 (Bradi3g10010), which

261 have been previously implicated in flowering time regulation in B. distachyon through a

262 series of mainly reverse genetic studies (Lv et al., 2014; Ream et al., 2014; Woods et al.,

263 2014; Woods et al., 2016).

264

265 Natural variation in FT and VRN2

266 Analysis of the resequencing and RNAseq data allowed an initial evaluation of candidate

267 genes underlying these QTLs. A de novo assembly was created from the ABR6 resequencing

268 reads and the resulting contigs were probed with the Bd21 sequences of FT (Bradi1g48830)

269 and VRN2 (Bradi3g10010), enabling the identification of structural variation between ABR6

270 and Bd21 (Figure 7; Supplemental Table S6). Spliced alignment of RNAseq reads permits

271 further characterization of candidate genes underlying an identified QTL through the

272 confirmation of polymorphisms between two parental genotypes, verification of annotated

273 candidate gene models, qualitative assessment of expression of candidate genes in the

274 sampled tissue, and discovery of potential splice variants.

275

276 No polymorphisms were found in the coding sequence of Bradi1g48830, the B. distachyon

277 homolog of FT. However, two indels (two and four bp, respectively) and a SNP mapped to

278 the 3’-UTR. Additionally, two SNPs and three indels (including a 33 bp indel 590 bps

279 upstream of Bradi1g48830) were found in the promoter region (2 kb upstream). The

280 terminator region (2 kb downstream) contained three SNPs and four indels. Bradi1g48830

281 was not expressed in ABR6 and barely detectable in Bd21 (only two reads mapped to the

282 gene). Owing to the low expression, it was not possible to confirm the published gene model

283 with our RNAseq data.

284

285 Greater sequence variation was observed at Bradi3g10010, the B. distachyon homolog of

286 VRN2, and its flanking regions. Only 1.9 kb of the promoter region is present on the

287 Bradi3g10010 contig, but this region contains 29 SNPs and three indels (including an 84 bp

288 indel 1.4 kb upstream of Bradi3g10010). The 2 kb terminator region contains 14 SNPs and

289 three 1 bp indels. Additionally, 11 SNPs and four indels (including a 37 bp and a 22 bp indel)

290 were localized in the intron, two SNPs in the coding sequence, and four SNPs in the 3’-UTR.

291 Bradi3g10010 was expressed in leaves from both Bd21 and ABR6 and spliced alignment of

292 RNAseq reads confirmed the published annotation of Bradi3g10010 for both ABR6 and

293 Bd21. Moreover, the six SNPs predicted in the exons were supported by the RNAseq data

294 and these may contribute to the observed effect on flowering time in this mapping population.

295 Two SNPs map to the annotated coding sequence and four SNPs map to the 3’-UTR. One of

296 the two SNPs in the annotated coding sequence is predicted to cause a non-synonymous

297 mutation (Figure 7).

298

299 Expression of VRN1, VRN2, and FT in response to vernalization

300 To understand the transcriptional dynamics of VRN1, VRN2, and FT in response to

301 vernalization, we assessed steady state levels of mRNA expression in plants at the fourth leaf

302 stage after exposure to two, four, and six weeks of vernalization at 5C or to no vernalization

303 (Figure 8). VRN1 and FT had a similar pattern in steady state levels of gene expression in

304 response to vernalization (Figure 8A and 8C). For both genes, very low levels of expression

305 were observed in ABR6, whereas Bd21 had fairly high levels of transcript abundance. After

306 experiencing four weeks of vernalization, ABR6 had similar levels of VRN1 transcript as

307 Bd21 without vernalization treatment. In contrast, FT expression had a marginal increase

308 after four and six weeks of vernalization in ABR6 relative to no vernalization or two weeks

309 of vernalization. FT expression levels were significantly lower than Bd21 across all periods

310 of vernalization. Both VRN1 and FT expression increased significantly between Bd21

311 examples vernalized for two or four weeks. VRN2 expression in ABR6 was inversely

312 correlated with the length of vernalization, with similar levels of expression after no

313 vernalization and two weeks vernalization and increasingly lower levels of expression after

314 four and six weeks of vernalization (Figure 8B). Bd21 exhibited a similar reduction in VRN2

315 expression, although lower levels of expression were observed without vernalization

316 compared to ABR6 with six weeks vernalization. The trends of all three genes highlighted the

317 importance of four weeks of vernalization as the inflection point in transcriptional abundance,

318 which coincides with a significant reduction in days to flowering in ABR6 (Figure 2).

319

320

321

322 Discussion

323

324 In our advancement of the ABR6 x Bd21 RIL population, we observed substantial variation

325 in flowering time. To define the genetic architecture of flowering time, we developed a

326 comprehensive genetic map and assessed F4:5 families in multiple environments. We

327 uncovered three major QTLs, with two QTLs coincident with the B. distachyon homologs of

328 VRN2 and FT. Interestingly, VRN1 was not associated with flowering time and was found to

329 have no mutations within the transcribed sequence (Supplemental Table S6). Further minor

330 effect QTLs were identified, suggesting that additional regulators play a role in controlling

331 flowering time in B. distachyon.

332

333 Segregation distortion in the ABR6 x Bd21 population

334 Segregation distortion is a common observation in the development of mapping populations

335 in plants, including grasses such as rice, Aegilops, maize, or barley (Xu et al., 1997; Faris et

336 al., 1998; Lu et al., 2002; Muñoz-Amatriaín et al., 2011). In the ABR6 x Bd21 population,

337 significant deviation from expected genotype frequencies was observed at two loci on

338 chromosomes Bd1 and Bd4 (Figure 3). Interestingly, heterozygosity was not affected at these

339 loci, but the ABR6 allele was overrepresented. It is likely that these loci are linked to traits

340 that were inadvertently selected during population advancement based on genetic and/or

341 environmental factors. Several genetic mechanisms can contribute to segregation distortion in

342 intraspecific crosses, including hybrid necrosis (Bomblies and Weigel, 2007), genes involved

343 in vernalization requirement and flowering time (such as the vrn2 locus in the Haruna Nijo x

344 OHU602 doubled-haploid barley population (Muñoz-Amatriaín et al., 2011)), or preferential

345 transmission of a specific parental genotype. While segregation distortion at these loci was

346 not associated with the identified flowering time QTLs, canonical resistance genes encoding

347 nucleotide-binding, leucine-rich repeat proteins are present at the Bd4 locus (Bomblies et al.,

348 2007; Tan and Wu, 2012).

349

350 The genetic architecture of flowering time in B. distachyon

351 In Arabidopsis, natural variation has been used as a complementary forward genetics-based

352 approach for investigating flowering time (Koornneef et al., 2004). In our work, we identified

353 two major QTLs controlling flowering time (qFLT1 and qFLT6; Figure 6) in both vernalized

354 and non-vernalized environments that colocalized with the B. distachyon homologs of FT

355 (Bradi1g48830) and VRN2 (Bradi3g10010). These observations are consistent with previous

356 reverse genetic studies on the role of FT and VRN2 in controlling flowering time (Lv et al.,

357 2014; Ream et al., 2014; Woods et al., 2014; Woods et al., 2016). Two additional QTLs on

358 chromosomes Bd2 (qFLT3) and Bd3 (qFLT7) were detected in two environments, whereas

359 three minor effect QTLs (qFLT2, qFLT4, qFLT5, and qFLT8) were found in individual

360 environments only. Two recent genome-wide association studies (GWAS) used the natural

361 variation found within B. distachyon germplasm to identify SNPs associated with flowering

362 time (Tyler et al., 2016; Wilson et al., 2016). Tyler et al. (2016) identified nine significant

363 marker-trait associations, none of which overlap with the QTLs identified in our study. In

364 contrast, Wilson et al. (2016) identified a much simpler genetic architecture consisting of

365 three significant marker-trait associations, one of which could be linked to FT. These

366 additional QTLs and marker-trait associations identified in our study and the GWAS studies

367 could either correspond to one of the identified homologs of flowering genes in B. distachyon

368 (Table 3; compare Higgins et al. 2010) or constitute novel loci as hypothesized by Schwartz

369 et al. (2010). With the exception of the proximal QTL on Bd2 (qFLT3), all QTLs in our study

370 were contributed by ABR6 (Table 1). Bd21 has previously been classified as a “spring

371 annual” (Schwartz et al., 2010) or “extremely rapid flowering” (Ream et al., 2014). However,

372 increased vernalization times still led to a modest reduction in flowering time (Figure 2),

373 which is explained by the detection of a QTL contributed by Bd21.

374

375 We hypothesized that structural variation between ABR6 and Bd21 would underlie the

376 observed variation in flowering time. No structural variation in FT was observed between

377 ABR6 and Bd21 in the coding sequence, however, several indels map to the promoter region

378 (Figure 7). These polymorphisms may explain expression differences between these two

379 accessions. As expected, no FT expression was found in ABR6 seedlings, and only two Bd21

380 RNAseq reads mapped to this gene. Steady-state expression levels of FT in the fourth leaf

381 were significantly lower in ABR6 relative to Bd21 without vernalization (Figure 8C). After

382 four weeks vernalization, FT expression levels increased in ABR6, although they were

383 significantly lower than Bd21 steady-state levels after any level of vernalization. It was

384 previously shown that in barley, wheat, and B. distachyon, FT expression is upregulated after

385 vernalization (Sasani et al., 2009; Chen and Dubcovsky, 2012; Ream et al., 2014). Our

386 observations indicate that FT is expressed in Bd21 and increases less than VRN1 in response

387 to vernalization. In contrast, FT in ABR6 only increases marginally after four weeks of

388 vernalization and remains significantly below the levels observed in Bd21 after no

389 vernalization.

390

391 Interestingly, an intact copy of the flowering repressor VRN2 is also present in Bd21 (Ream

392 et al., 2012), which does not have a strong vernalization response (Vogel et al., 2006; Garvin

393 et al., 2008). The lack of vernalization requirement in some B. distachyon accessions cannot,

394 therefore, be explained by an absence of VRN2 (Ream et al., 2014). Intriguingly, early-

395 flowering mutants identified in genetic screens have thus far not mapped in the VRN2 region

396 (Ream et al., 2014). Moreover, expression levels for VRN2 also did not vary among early and

397 late flowering accessions and VRN2 mRNA levels are likely not rate limiting (Ream et al.,

398 2014). An earlier study by Schwartz et al. (2010) described potential correlation between

399 different VRN2 alleles and flowering time. The authors did not rule out the effects of

400 population structure and proposed that elucidating the role of VRN2 in B. distachyon will

401 require more in-depth genetic studies. A recent comprehensive analysis of population

402 structure in B. distachyon collections revealed that flowering time, and not geographic origin,

403 is indeed the major distinguishing factor between genotypically distinct clusters (Tyler et al.,

404 2016). Our results confirm VRN2 as an important flowering regulator in the ABR6 x Bd21

405 mapping population and highlight structural and expression variation between parental

406 accessions. However, none of the SNPs identified in the coding sequence map to the CCT

407 domain. A point mutation in this domain results in a spring growth habit in cultivated

408 Triticum monococcum accessions (Yan et al., 2004). It is unclear whether the structural

409 variation surrounding VRN2 corresponds to the allelic variation observed by Schwartz et al.

410 (2010). Woods and Amasino (2016) hypothesize that even though VRN2 may not be involved

411 in vernalization control in B. distachyon, it may still possess an ancestral role in flowering

412 regulation. This is further supported by the observation that VRN2 expression is not

413 controlled by VRN1 in B. distachyon, yet VRN2 was found to be a functional repressor of

414 flowering in this species (Woods et al., 2016). We observed a negative correlation between

415 VRN2 transcript accumulation and vernalization period in ABR6 and Bd21 (Figure 8B).

416 Similar decreases were observed for ABR6 and Bd21, although transcript abundance in Bd21

417 were significantly lower than ABR6 under any vernalization period. Therefore, our

418 identification of natural variation in VRN2 among geographically diverse B. distachyon

419 accessions further supports VRN2 as a core flowering regulator in this non-domesticated

420 grass.

421

422 In our study of the natural variation between two morphologically and geographically diverse

423 B. distachyon accessions we failed to implicate VRN1 as a flowering regulator. However,

424 VRN1 expression during and after cold treatment and the failure of VRN1 silenced lines to

425 flower suggests a conserved role of VRN1 as a promoter of flowering (Woods and Amasino,

426 2016; Woods et al., 2016). Interestingly, a QTL in the Bd21 x Bd1-1 B. distachyon mapping

427 population colocalized with VRN1 and the light receptor PHYTOCHROME C (PHYC)

428 (Woods et al., 2016). Between ABR6 and Bd21, sequence variation was found in the

429 promoter and terminator regions of VRN1 and a strong positive correlation was observed with

430 extended periods of vernalization (Figure 8A), particularly at four weeks vernalization, which

431 was a critical inflection point for flowering time in ABR6. Despite this sequence and

432 expression variation, VRN1 was not found to contribute to flowering time in the ABR6 x

433 Bd21 mapping population. Interestingly, an assessment of allelic variation in 53 B.

434 distachyon accessions currently available in Phytozome (Version 11.0.2,

435 https://phytozome.jgi.doe.gov) found that none of these accessions possess structural

436 variation in the VRN1 annotated coding sequence. These findings suggest that VRN1 is a

437 crucial regulator of flowering in B. distachyon and under strong selection pressure.

438

439

440 Conclusions

441

442 Thanks to their economic and evolutionary importance, flowering time pathways are of

443 particular interest in the cereals and related grasses. Our report adds to this body of research

444 by using natural variation to map vernalization dependency in a B. distachyon mapping

445 population. Since B. distachyon is partly sympatric with the wild relatives of wheat and

446 barley, it seems likely that the species would have been subject to similar selective pressure

447 and therefore is a useful model for understanding pre-domestication or standing variation. We

448 investigated this standing variation by assessing segregation of flowering regulators in a

449 mapping population derived from two geographically diverse accessions of B. distachyon.

450 Notably, we found additional support for the roles of FT and VRN2 in controlling flowering

451 in wild temperate grasses. Additionally, allelic variation may explain the ambiguity around

452 the role of the VRN2 homolog observed in B. distachyon. Further fine-mapping will be

453 required to confirm the roles of these genes in B. distachyon flowering time. However, we

454 also detected novel components in the form of additional QTLs, which reflects the power of

455 studying natural variation in mapping populations derived from phenotypically diverse

456 parents. During population advancement, we have observed a variety of additional

457 morphological and pathological characteristics segregating in this population and it will serve

458 as a useful resource for other researchers investigating standing variation in non-domesticated

459 grasses.

460

461

462 Materials and Methods

463

464 Plant growth for assessing ABR6 and Bd21 vernalization response

465 Six seeds for ABR6 and Bd21 were germinated on paper (in darkness at room temperature)

466 and transferred to an equal mixture of the John Innes Cereal Mix and a peat and sand mix

467 (Vain et al., 2008) four days after germination. Vernalization was initiated 14 days after

468 germination for either two, three, four, five, six, seven, or eight weeks (8 h day length; 1.2

469 klux light intensity; 5°C). The different sets were staggered to ensure that all sets left

470 vernalization on the same date. After vernalization plants were grown in a Sanyo Versatile

471 Environmental Test Chamber (Model MLR-351; 16 h photoperiod; 8.0 klux light intensity;

472 22°C/20°C day/night temperatures) for 35 days and then transferred to a greenhouse without

473 light and temperature control (late April to mid July 2013; Norwich, UK). Days to flowering

474 was measured from the end of vernalization until the emergence of the first spike and was

475 averaged across all six biological replicates (only five replicates were available for Bd21 after

476 7 weeks of vernalization). Statistical significances were assessed by pairwise comparisons

477 using t-tests with pooled standard deviations and Bonferroni correction for multiple

478 comparisons.

479

480 Resequencing of ABR6

481 Seedlings were grown in a Sanyo Versatile Environmental Test Chamber (16h photoperiod;

482 8.0 klux light intensity; 22°C) in an equal mixture of the John Innes Cereal Mix and a peat

483 and sand mix. Seven-week-old plants were placed in darkness for three days prior to

484 collecting tissue. Genomic DNA was extracted using a standard CTAB protocol and a library

485 of 800 bp inserts was constructed and sequenced with 100 bp paired-end reads and an

486 estimated coverage of 25.8x on an Illumina HiSeq 2500. Library preparation and sequencing

487 was performed at The Genome Analysis Centre (Norwich, UK). The resulting reads were

488 mapped to the Bd21 reference sequence (Version 1)

489 (The International Brachypodium Initiative, 2010) with the Galaxy wrapper, which used the

490 BWA (Version 0.5.9) aln and sampe options (Li and Durbin, 2009). Polymorphisms between

491 ABR6 and Bd21 were identified with the mpileup2snp and mpileup2indel tools of VarScan

492 (Version 2.3.6) using default settings (Koboldt et al., 2009). A de novo assembly was created

493 from the raw ABR6 reads using default settings of the CLC Assembly Cell (Version 4.2.0)

494 and default parameters. Potential structural variation between ABR6 and Bd21 was

495 investigated by performing a BLAST search with the Bd21 regions of interest against the

496 ABR6 de novo assembly and mapping contigs for hits with at least 95% identity and an E-

497 value under 1e-20

to the Bd21 reference sequence (Version 3).

498

499 Development of the ABR6 x Bd21 F4 population and genetic map

500 The B. distachyon accessions ABR6 and Bd21 were crossed and three ABR6 x Bd21 F1

501 individuals, confirmed as hybrid by SSR marker analysis (data not shown), were allowed to

502 self-pollinate to generate a founder F2 population comprised of 155 individuals. After single

503 seed descent, DNA was extracted from leaf tissue of 114 independent F4 lines using a CTAB

504 gDNA extraction protocol modified for plate-based extraction (Dawson et al., 2016). SNPs

505 for genetic map construction were selected based on a previously characterized Bd21 x Bd3-1

506 F2 genetic map to ensure an even distribution of markers relative to physical and genetic

507 distances (Huo et al., 2011). SNPs without additional sequence variation in a 120 bp window

508 were selected every 10 cM. The Agena Bioscience MassARRAY design suite was used to

509 develop 17 assays that genotyped 449 putative SNPs using the iPLEX Gold assay at the Iowa

510 State University Genomic Technologies Facility (Supplemental Data S2). Markers were

511 excluded for being monomorphic (106), dominant (34), or for missing data for the parental

512 controls (33). Heterozygous genotype calls for some markers were difficult to distinguish and

513 classified as missing data. Additional SNPs between ABR6 and Bd21 in six markers

514 developed for the Bd21 x Bd3-1 F2 genetic map (Barbieri et al., 2012) were converted into

515 CAPS markers (Konieczny and Ausubel, 1993) (Supplemental Table S7). The integrity of

516 these 282 markers was evaluated using R/qtl (Version 1.33-7) recombination fraction plots

517 (Broman et al., 2003). Two markers were removed for not showing linkage and one marker

518 was moved to its correct position based on linkage. Genetic distances were calculated using

519 the Kosambi function in MapManager QTX (Version b20) (Manly et al., 2014). Removal of

520 unlinked and redundant markers produced a final ABR6 x Bd21 F4 genetic map consisting of

521 252 SNP-based markers (Supplemental Data S3). Segregation distortion was assessed using a

522 chi-square test with Bonferroni correction for multiple comparisons.

523

524 Plant growth and phenotyping of flowering time in the ABR6 x Bd21 F4:5 families

525 Three to five plants for each of the 114 ABR6 x Bd21 F4:5 families were grown under five

526 different environmental conditions as detailed in Supplemental Table S1. For the

527 phenotyping performed in Aberystwyth, individual seeds were sown in 6 cm pots with a

528 mixture of 20% grit sand and 80% Levington F2 peat-based compost. Seeds were grown for

529 2 weeks in greenhouse conditions (22°C/20°C, natural light supplemented with 20 h lighting)

530 and then either maintained in the greenhouse or transferred to a vernalization room for six

531 weeks (16 h day length, 5°C). Plants were returned to the greenhouse following vernalization

532 and grown to maturity. Flowering time was defined as the emergence of the first

533 inflorescence and was measured from the first day that flowering was observed in the entire

534 mapping population. Flowering time was averaged across the individuals of an F4:5 family.

535 For the phenotyping performed in Norwich, plants were first subjected to growth conditions

536 and pathogen assays as described in Dawson et al. 2015. Plants were germinated in a peat-

537 based compost in 1 L pots and grown for six weeks in a controlled environment room

538 (18°C/11°C, 16 h light period). Six weeks post germination, the fourth or fifth leaf of each

539 plant was cut off for pathological assays. The plants were transplanted into 9 cm pots with an

540 equal mixture of the John Innes Cereal Mix and a peat and sand mix (Vain et al., 2008) and

541 transferred to the respective growth environments for flowering assessment (Supplemental

542 Table S1). Flowering time was defined as the emergence of the first inflorescence within an

543 F4:5 family and was measured from the first day that flowering was observed in the entire

544 mapping population. Families that did not flower 60 days after emergence of the first

545 inflorescence in the mapping population were scored as not flowering.

546

547 Quantitative trait locus analysis for flowering time

548 Flowering phenotypes were assessed for normality using the Shapiro-Wilk test (Royston,

549 1982). In an initial analysis, phenotypic values were converted into a binary classification

550 based on whether families flowered (F) or did not flower (NF). Interval mapping was

551 performed with the scanone function in R/qtl under a binary model with conditional genotype

552 probabilities computed with default parameters and the Kosambi map function (Xu and

553 Atchley, 1996; Broman et al., 2006). Simulation of genotypes was performed with a fixed

554 step distance of 2 cM, 128 simulation replicates, and a genotyping error rate of 0.001.

555 Statistical significance for QTLs was determined by performing 1,000 permutations and

556 controlled at = 0.05 (Doerge and Churchill, 1996). Non-parametric interval mapping was

557 performed with similar parameters in R/qtl under an np model (Kruglyak and Lander, 1995).

558 For parametric mapping, flowering time data was transformed (T) using the following

559 approaches: (T1) the removal of all F4:5 families that did not flower within the timescale of

560 the experiment, (T2) transforming all non-flowering phenotypic scores to one day above the

561 maximum observed, and (T3) transforming by ranking families according to their flowering

562 time. For the third transformation approach (T3), the earliest flowering family was given a

563 rank score of 1 and subsequent ordered families given incremental scores based on rank (2, 3,

564 4, etc.). When two or more families had shared flowering time, they were given the same

565 rank and the next ranked family was given an incremental rank score based on the number of

566 preceding shared rank families. Non-flowering families were given the next incremental rank

567 after the last flowering rank. For all three transformations, composite interval mapping was

568 performed under an additive model (H0:H1) using QTL Cartographer (Version 1.17j) with the

569 selection of five background markers, a walking speed of 2 cM, and a window size of 10 cM

570 (Zeng, 1993, 1994; Basten et al., 2004). Statistical significance for QTLs was determined by

571 performing 1,000 permutations with reselection of background markers and controlled at =

572 0.05 (Doerge and Churchill, 1996; Lauter et al., 2008). One-LOD support intervals were

573 estimated based on interval mapping (Lander and Botstein, 1989).

574

575 RNAseq of ABR6 and Bd21

576 Plants were grown in a controlled environment room with 16 h light at 22°C and fourth and

577 fifth leaves were harvested as soon as the fifth leaf was fully expanded (roughly 28 days after

578 germination). RNA was extracted using the TRI Reagent (Sigma-Aldrich®

) according to the

579 manufacturer’s specifications. TruSeq libraries were generated from total RNA and mean

580 insert sizes were 251 bp and 254 bp for ABR6 and Bd21, respectively. Library preparation

581 and sequencing was performed at The Genome Analysis Centre (Norwich, UK). Sequencing

582 was carried out using 150 bp paired-end reads on an Illumina HiSeq 2500 and ABR6 and

583 Bd21 yielded 38,867,987 and 37,566,711 raw reads, respectively. RNAseq data quality was

584 assessed with FastQC and reads were removed using Trimmomatic (Version 0.32) (Bolger et

585 al., 2014) with parameters set at ILLUMINACLIP:TruSeq 3-PE.fa:2:30:10, LEADING:3,

586 TRAILING:3, SLIDINGWINDOW:4:15, and MINLEN:100. These parameters will remove

587 all reads with adapter sequence, ambiguous bases, or a substantial reduction in read quality.

588 The sequenced reads were mapped to the Bd21 reference genome using the TopHat (Version

589 2.0.9) spliced alignment pipeline (Trapnell et al., 2009).

590

591 RT-qPCR analyses

592 ABR6 and Bd21 seeds were surface sterilized (70% ethanol for 30 seconds, washed in

593 autoclaved dH2O, 1.3% sodium hypochlorite for 4 minutes, washed in autoclaved H2O three

594 times), transferred to moistened Whatman filter paper, left at room temperature in darkness

595 overnight, and vernalized for either two, four, or six weeks (in darkness at 5°C). A control set

596 was surface sterilized and transferred to filter paper overnight, but not vernalized. Following

597 vernalization, plants were transferred to soil and grown in a Sanyo Versatile Environmental

598 Test Chamber in conditions similar to Environment 2 (20h photoperiod; 4.0 klux light

599 intensity; 22°C/20°C). Once fully expanded, fourth leaves were collected in the middle of the

600 photoperiod and flash frozen in liquid nitrogen.

601

602 Total RNA was extracted using TRI reagent according to manufacturer’s instructions (Sigma-

603 Aldrich®

). RNA samples were treated with DNase I (Roche) prior to cDNA synthesis.

604 Quality and quantity of RNA samples were assessed using a NanoDrop spectrophotometer

605 followed by agarose electrophoresis. First-strand cDNA was synthesized according to

606 manufacturer’s instructions (Invitrogen). Briefly, 1 g of total RNA, 1 L of 0.5 M poly-T

607 primers, and 1 L of 10 mM dNTP were incubated at 65C for 5 min and 4C for 2 min, with

608 subsequent reverse transcription reactions performed using 2 L of 10x reverse transcription

609 buffer, 4 L of 25 mM MgCl2, 2 L of 0.1 M DTT, 1 L of RNaseOUT (40 U/L), and 1 L

610 of SuperScript III reverse transcriptase (200 U/L) at 50C for 50 min. Reverse transcription

611 was inactivated by incubating at 85C for 5 min and residual RNA was removed with the

612 addition of 1 L Rnase H (2 U/L) and incubation at 37C for 20 min.

613

614 Quantitative real time PCR was performed in 20 L reaction volumes using 10 L of SYBR-

615 Green mix (Sigma-Aldrich), 1 L of 10 M forward and reverse primers, 4 L water, and 4

616 L of cDNA diluted 10-fold. The program for PCR amplification involved an initial

617 denaturation at 95C for 3 min and then 40 cycles of 94C for 10 sec, 60C for 15 sec, and

618 72C for 15 sec. Fluorescence data was collected at 72C at the extension step and during the

619 melting curve program on a CFX96 Real-Time system (Bio-Rad).

620

621 Relative gene expression was determined using the 2-CT

method described by Livak and

622 Schmittgen (2001) using UBIQUITIN-CONJUGATING ENZYME18 (Brachypodium

623 distachyon; (Hong et al., 2008); Schwartz et al. 2010) for normalization. All primers were

624 previously used by Ream et al. (2014) and had PCR efficiency ranging from 95 to 110%.

625 Statistical analysis of gene expression was performed using R (Version 3.2.3). Comparisons

626 between all genotype by treatment combinations were made with pairwise t-tests using log

627 transformed relative expression levels, with p-values corrected for multiple hypothesis testing

628 based on the Benjamini-Hochberg approach.

629

630 Accession numbers for data in public repositories

631 Raw resequencing reads of ABR6 have been submitted to the NCBI Short Read Archive

632 under the BioProject ID PRJNA319372 and SRA accession SRX1720894. The ABR6 de

633 novo assembly has been deposited at DDBJ/ENA/GenBank under the accession

634 LXJM00000000. The version described in this paper is version LXJM01000000. Raw

635 RNAseq reads have been submitted to the NCBI Short Read Archive under the BioProject ID

636 PRJNA319373 and SRA accessions SRX1721358 (ABR6) and SRX1721359 (Bd21).

637

638

639 Acknowledgements

640 We thank John Vogel for sharing preliminary sequencing data, Burkhard Steuernagel for

641 assistance with the de novo assembly of the ABR6 genome, David Garvin and Luis Mur for

642 providing seed, and Claire Collett, Ray Smith, Tom Thomas, and Aliyah Debbonaire for

643 assistance with population progression. MassARRAY genotyping was performed at the

644 Genomic Technologies Facility at Iowa State University. The work was funded by the

645 Biotechnology and Biological Sciences Research Council Doctoral Training Programme

646 (BB/F017294/1) and Institute Strategic Programme (BB/J004553/1), the Gatsby Charitable

647 Foundation, the Leverhulme Trust (Grant reference 10754), the 2Blades Foundation, and the

648 Human Frontiers Science Program (LT000218/2011).

649 Tables

650

651 Table 1. Significant flowering time QTLs (qFLT) in the different environments identified

652 using several binary, non-parametric, and parametric approaches.

Locus Chra

cM Alleleb

E1c

E2 E3 E4 E5

qFLT1 Bd1 297.6 Bd21

B, T2, T1, T3, T2, T3, T2, T3

T1, T2,

qFLT7 Bd3 294.6 Bd21 - - - NP T3, NP

qFLT8 Bd4 90.1 Bd21 - - - NP -

653 aChromosome

654 bAllele that reduces flowering time

655 cEnvironment (see Supplemental Table S1)

656 dQTL analyses were performed with interval mapping using binary classification (B) and

657 non-parametric analysis (NP), and composite interval mapping using transformed data (T1,

658 T2, and T3).

qFLT2

Bd1

465.2

Bd21

T3, NPd

T2

NP

-

NP

-

-

T3, NP

-

qFLT3 Bd2 338.3 ABR6 - - - NP T2, T3

qFLT4 Bd2 409.0 Bd21 - T1, T3 - - -

qFLT5 Bd3 60.8 Bd21 - - - T1 -

qFLT6 Bd3 91.2 Bd21 T2, T3 T1, T3 T2, T3 -

T2, T3,

-

B, T2,

659 Table 2. Significant QTLs from composite interval mapping of transformed flowering time

660 phenotypes (T3) in the ABR6 x Bd21 F4:5 families.

ENVa

Locus Chrb cM EWT

c LOD AEE

d PVE

e 1-LOD SI

f

1 qFLT1 Bd1 297.6 3.06 12.96 2.87 36.3% 296.1 - 305.6

1 qFLT6 Bd3 91.2 3.06 4.51 1.64 11.8% ND

2 qFLT1 Bd1 297.6 3.09 7.59 0.82 20.0% 296.1 - 305.6

2 qFLT4 Bd2 409.0 3.09 3.20 0.47 6.7% 403.2 - 411.0

2 qFLT6 Bd3 93.2 3.09 6.64 0.79 18.2% 72.9 - 97.0

3 qFLT1 Bd1 297.6 3.20 8.61 1.50 31.1% 292.1 - 303.6

3 qFLT6 Bd3 91.2 3.20 5.69 1.20 18.7% 74.9 - 97.0

4 qFLT1 Bd1 297.6 3.19 3.49 1.77 15.9% 292.1 - 305.6

4 qFLT7 Bd3 294.6 3.19 3.79 1.59 14.0% 273.9 - 300.7

5 qFLT1 Bd1 297.6 3.17 8.62 3.43 37.5% 294.1 - 301.6

5 qFLT3 Bd2 338.3 3.17 3.70 -1.75 9.9% 323.7 - 348.0

5 qFLT7 Bd3 294.6 3.17 5.61 2.02 13.6% 275.9 - 302.0

661 aEnvironment (see Supplemental Table S1)

662 bChromosome

663 cExperiment-wide permutation threshold

664 dAdditive effect estimate for transformed phenotypes

665 ePercent of phenotypic variance explained

666 fOne-LOD support interval (cM); ND denotes QTLs not detected using standard interval

667 mapping.

668 Table 3. Previously identified B. distachyon homologs of flowering regulators in Arabidopsis

669 (At), hexaploid and diploid wheat (Ta and Tm), barley (Hv), and rice (Os) within the one-

670 LOD support intervals of the statistically significant QTLs under transformation T3.

671 aChromosome

672 bCombined maximal one-LOD support interval (cM) from all significant QTLs

673 cIdentified in Higgins et al. 2010 and Ream et al. 2012

Locus Chra 1-LOD SI

b B. distachyon gene Homologous genes

c

qFLT1

qFLT3

Bd1

Bd2

292.1 - 305.6

323.7 - 348.0

Bradi1g45810

Bradi1g46060

Bradi1g48340

Bradi1g48830

Bradi2g53060

AtAGL24, TaVRT2, OsMADS55

AtABF1

AtCLF, OsCLF

AtTSF, HvFT1, OsHd3a/OsFTL2

AtFDP

qFLT4

Bd2

403.2 - 411.0

Bradi2g54200

Bradi2g55550

Bradi2g60820

AtNF-YB10

AtbZIP67

AtFY, OsFY

qFLT6

Bd3

72.9 - 97.0

Bradi2g62070

Bradi3g08890

AtLUX, OsLUX

OsFTL13

qFLT7

Bd3

273.9 - 300.7

Bradi3g10010

Bradi3g12900

Bradi3g41300

TaVRN2, TmCCT2, OsGhd7

AtHUA2

OsMADS37

Bradi3g42910

Bradi3g44860

AtSPY, OsSPY

OsRCN2

674 Figures

675

676 Figure 1. Flowering behavior within the ABR6 x Bd21 mapping population. Three months

677 after a six-week vernalization period, ABR6 (left) is not flowering, whereas Bd21 (center) is

678 flowering and an individual in the ABR6 x Bd21 mapping population displays an

679 intermediate flowering phenotype (right).

680

681 Figure 2. Effect of vernalization on flowering time in ABR6 and Bd21. Days to flowering

682 was measured from the end of vernalization for seven different vernalization periods. After

683 vernalization plants were grown in a growth chamber (16 h photoperiod) for 35 days and then

684 transferred to a greenhouse without light and temperature control (late April to mid July

685 2013; Norwich, UK). Mean days to flowering and standard error are based on six biological

686 replicates. Different letters represent statistically significant differences based on pairwise

687 comparisons using t-tests with pooled standard deviations and Bonferroni correction for

688 multiple comparisons.

689

690 Figure 3. Segregation distortion in the ABR6 x Bd21 F4 population. For each marker of the

691 genetic map the frequencies of F4 individuals with homozygous ABR6 genotype (solid

692 magenta), homozygous Bd21 genotype (dashed green), or heterozygous genotype (solid

693 black) were calculated (scale on left). Data coverage (percent of F4 individuals with genotype

694 calls per marker) is represented by the gray line (scale on right).

695

696 Figure 4. Frequency distribution of flowering time in the ABR6 x Bd21 population.

697 Flowering time was measured from the first day that flowering was observed in the entire

698 population. (A) Environment 1 (April to July, natural light supplemented for 20h, 22°C/20°C,

699 no vernalization), (B) Environment 2 (April to July, natural light supplemented for 20h,

700 22°C/20°C, six weeks vernalization), (C) Environment 3 (May to July, natural light and

701 temperatures, no vernalization), (D) Environment 4 (September to November, natural light

702 supplemented for 16h, minimum 18°C/11.5°C, no vernalization), (E) Environment 5 (March

703 to May, natural light and temperatures, no vernalization). Flowering times for the parental

704 lines are indicated by arrows (no data for Environment 3). NF = not flowering.

705

706 Figure 5. Linkage mapping of flowering time in the ABR6 x Bd21 population. Time to

707 flowering for 114 F4:5 families of the population was transformed into ordered rank values,

708 QTL analysis performed using composite interval mapping under an additive model

709 hypothesis test (H0:H1), and plotted based on normalized permutation thresholds. The blue

710 horizontal line represents the threshold of statistical significance based on 1,000

711 permutations. Orange = Environment 1(April to July, natural light supplemented for 20h,

712 22°C/20°C, no vernalization), blue = Environment 2 (April to July, natural light

713 supplemented for 20h, 22°C/20°C, six weeks vernalization), red = Environment 3 (May to

714 July, natural light and temperatures, no vernalization), yellow = Environment 4 (September to

715 November, natural light supplemented for 16h, minimum 18°C/11.5°C, no vernalization),

716 green = Environment 5 (March to May, natural light and temperatures, no vernalization). See

717 Supplemental Table S1 for full environmental details. The genetic positions of the previously

718 identified homologs of VRN1, VRN2, and FT are indicated (compare Higgins et al. 2010 and

719 Ream et al. 2012).

720

721 Figure 6. Phenotype by genotype plot for the two major loci controlling flowering time in the

722 ABR6 x Bd21 mapping population. Days to flowering in Environment 3 for the ABR6 x

723 Bd21 F4:5 families homozygous at qFLT1 and qFLT6 shows that the Bd21 alleles at these two

724 loci promote early flowering. Error bars represent one standard error; NF = not flowering.

725

726 Figure 7. Comparison of the flowering regulators FT and VRN2 between the B. distachyon

727 accessions Bd21 and ABR6. Contigs of the ABR6 de novo assembly were aligned to the

728 Bd21 reference sequence (Version 3) and polymorphisms were identified in the genes of

729 interest and 2kb promoter and terminator sequence (1.9kb promoter for VRN2). Red ticks

730 represent SNPs and black ticks represent indels. The length of indels (bp) is shown with + for

731 insertion and – for deletion. The amino acid change of the non-synonymous SNP in VRN2 is

732 indicated. s = synonymous SNP; dashed line = promoter or terminator; white box = 5’-UTR

733 or 3’-UTR; black box = exon; black line = intron; M = methionine/translation start; star =

734 translation stop; black bar under VRN2 = CCT domain.

735

736 Figure 8. VRN1, VRN2, and FT expression in fourth leaf of ABR6 and Bd21 after varying

737 periods of cold treatment. Seeds were imbibed with water and not vernalized or vernalized

738 for two, four, or six weeks, and transferred to a growth chamber with parameters similar to

739 Environment 2. Fully expanded fourth leaves were harvested in the middle of the

740 photoperiod. Relative gene expression of VRN1 (A), VRN2 (B), and FT (C) was determined

741 using RT-qPCR and analyzed using the 2-Ct

method. All genes were normalized to 1

based

742 on Bd21 expression with no cold treatment (0 weeks) and UBQ18 was used as internal

743 control. Bars represent the mean of three biological replicates with error bars showing 1

744 standard error. Different letters represent statistically significant differences based on

745 pairwise t-tests using a multiple hypothesis corrected p-value threshold of 0.05 with the

746 Benjamini-Hochberg approach.

747 Supplemental Material

748

749 Supplemental Figure S1. Linkage groups of ABR6 x Bd21 genetic map.

750 Supplemental Figure S2. Two-way recombination fraction plot for the ABR6 x Bd21 F4

751 population.

752 Supplemental Table S1. Summary of the environmental conditions tested.

753 Supplemental Table S2. Significant QTLs from interval mapping of binary classification of

754 flowering time phenotypes in the ABR6 x Bd21 F4:5 families.

755 Supplemental Table S3. Significant QTLs from interval mapping using a non-parametric

756 model for flowering time phenotypes in the ABR6 x Bd21 F4:5 families (NP).

757 Supplemental Table S4. Significant QTLs from composite interval mapping of transformed

758 flowering time phenotypes in the ABR6 x Bd21 F4:5 families (T1).



761 Supplemental Table S6. Summary of the structural variation between Bd21 and ABR6 for

762 the flowering regulators Bradi1g48830 (FT), Bradi3g10010 (VRN2), and Bradi1g08340

763 (VRN1).

764 Supplemental Table S7. Five cleaved amplified polymorphic sequences (CAPS) markers

765 included in the ABR6 x Bd21 genetic map design.

766 Supplemental Data S1. Raw, binary, and transformed flowering time data for the ABR6 x

767 Bd21 F4:5 families in the five environments tested.

768 Supplemental Data S2. Sequence information used to develop iPLEX assays for the 247

769 MassARRAY markers in the ABR6 x Bd21 genetic map design.

770 Supplemental Data S3. ABR6 x Bd21 genetic map.

771

772

773 Supplemental Figure S1. Linkage groups of ABR6 x Bd21 genetic map. Cumulative cM

774 distances and SNP marker names are shown to the left and right of each chromosome,

775 respectively. cM distance at the F4 stage was estimated using the Kosambi function. SNP

776 marker names consist of the corresponding chromosome and physical position in the Bd21

777 reference genome (Version 3).

778

779 Supplemental Figure S2. Two-way recombination fraction plot for the ABR6 x Bd21 F4

780 population.

781

782 Supplemental Table S1. Summary of the environmental conditions tested.

783

784 Supplemental Table S2. Significant QTLs from interval mapping of binary classification of

785 flowering time phenotypes in the ABR6 x Bd21 F4:5 families.

786

787 Supplemental Table S3. Significant QTLs from interval mapping using a non-parametric

788 model for flowering time phenotypes in the ABR6 x Bd21 F4:5 families (NP).

789



792



795

796 Supplemental Table S6. Summary of the structural variation between Bd21 and ABR6 for

797 the flowering regulators Bradi1g48830 (FT), Bradi3g10010 (VRN2), and Bradi1g08340

798 (VRN1).

799

800 Supplemental Table S7. Five cleaved amplified polymorphic sequences (CAPS) markers

801 included in the ABR6 x Bd21 genetic map design. Marker names consist of the

802 corresponding chromosome and physical position in the Bd21 reference genome (Version 3).

803 Synonymous names refer to Barbieri et al. 2012.

804

805 Supplemental Data S1. Raw, binary, and transformed flowering time data for the ABR6 x

806 Bd21 F4:5 families in the five environments tested.

807

808 Supplemental Data S2. Sequence information used to develop iPLEX assays for the 247

809 MassARRAY markers in the ABR6 x Bd21 genetic map design. Marker names consist of the

810 corresponding chromosome and physical position in the Bd21 reference genome (Version 3)

811 and SNPs are indicated in square brackets.

812

813 Supplemental Data S3. ABR6 x Bd21 genetic map. “A” genotype calls refer to ABR6, “B”

814 genotype calls to Bd21, “H” genotype calls to heterozygous markers and “-“ to missing data

815 points.

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http://www.ncbi.nlm.nih.gov/pubmed?term=Xu%20Y%2C%20Zhu%20L%2C%20Xiao%20J%2C%20Huang%20N%2C%20McCouch%20SR%20%281997%29%20Chromosomal%20regions%20associated%20with%20segregation%20distortion%20of%20molecular%20markers%20in%20F2%2C%20backcross%2C%20doubled%20haploid%2C%20and%20recombinant%20inbred%20populations%20in%20rice%20%28Oryza%20sativa%20L%29%2E%20Molecular%20and%20General%20Genetics%20253%3A%20535%2D545&dopt=abstract

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http://scholar.google.com/scholar?as_q&num=10&btnG=Search%2BScholar&as_occt=any&as_sauthors=Xu&as_ylo=1997&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Yan%20L%2C%20Fu%20D%2C%20Li%20C%2C%20Blechl%20A%2C%20Tranquilli%20G%2C%20Bonafede%20M%2C%20Sanchez%20A%2C%20Valarik%20M%2C%20Yasuda%20S%2C%20Dubcovsky%20J%20%282006%29%20The%20wheat%20and%20barley%20vernalization%20gene%20VRN3%20is%20an%20orthologue%20of%20FT%2E%20Proceedings%20of%20the%20National%20Academy%20of%20Sciences%2C%20USA%20103%3A%2019581%2D19586&dopt=abstract

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http://www.ncbi.nlm.nih.gov/pubmed?term=Yan%20L%2C%20Loukoianov%20A%2C%20Blechl%20A%2C%20Tranquilli%20G%2C%20Ramakrishna%20W%2C%20SanMiguel%20P%2C%20Bennetzen%20JL%2C%20Echenique%20V%2C%20Dubcovsky%20J%20%282004%29%20The%20wheat%20VRN2%20gene%20is%20a%20flowering%20repressor%20down%2Dregulated%20by%20vernalization%2E%20Science%20303%3A%201640%2D1644&dopt=abstract

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http://www.ncbi.nlm.nih.gov/pubmed?term=Yan%20L%2C%20Loukoianov%20A%2C%20Tranquilli%20G%2C%20Helguera%20M%2C%20Fahima%20T%2C%20Dubcovsky%20J%20%282003%29%20Positional%20cloning%20of%20the%20wheat%20vernalization%20gene%20VRN1%2E%20Proceedings%20of%20the%20National%20Academy%20of%20Sciences%2C%20USA%20100%3A%206263%2D6268&dopt=abstract

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natural variation in brachypodium links vernalization and ... · 182 vernalization periods showed...

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