ORIGINAL PAPER

Integrated consensus genetic and physical maps of flax(Linum usitatissimum L.)

Sylvie Cloutier • Raja Ragupathy • Evelyn Miranda •

Natasa Radovanovic • Elsa Reimer • Andrzej Walichnowski •

Kerry Ward • Gordon Rowland • Scott Duguid • Mitali Banik

Received: 28 March 2012 / Accepted: 21 July 2012 / Published online: 14 August 2012

� The Author(s) 2012. This article is published with open access at Springerlink.com

Abstract Three linkage maps of flax (Linum usitatissi-

mum L.) were constructed from populations CDC Bethune/

Macbeth, E1747/Viking and SP2047/UGG5-5 containing

between 385 and 469 mapped markers each. The first

consensus map of flax was constructed incorporating 770

markers based on 371 shared markers including 114 that

were shared by all three populations and 257 shared

between any two populations. The 15 linkage group map

corresponds to the haploid number of chromosomes of this

species. The marker order of the consensus map was lar-

gely collinear in all three individual maps but a few local

inversions and marker rearrangements spanning short

intervals were observed. Segregation distortion was present

in all linkage groups which contained 1–52 markers

displaying non-Mendelian segregation. The total length of

the consensus genetic map is 1,551 cM with a mean marker

density of 2.0 cM. A total of 670 markers were anchored to

204 of the 416 fingerprinted contigs of the physical map

corresponding to *274 Mb or 74 % of the estimated flax

genome size of 370 Mb. This high resolution consensus

map will be a resource for comparative genomics, genome

organization, evolution studies and anchoring of the whole

genome shotgun sequence.

Introduction

Flax (Linum usitatissimum L., 2n = 2x = 30), is an annual

self-pollinated crop that is commercially grown as a source

of stem fibre and seed oil. Flax seed oil is utilized for the

fabrication of various biodegradable products such as high

quality drying oil, paints, varnishes and linoleum flooring.

Flax oil is a rich source of omega-3 fatty acids used as

nutraceuticals and also as a functional food for both humans

and animals. Fibre and oilseed flax belong to the same

species but are morphologically different. Oilseed type flax

plants (linseed) are more branched and shorter than the fibre

type (Gill 1987). Fibre flax is grown mainly in Northern

Europe, Russia and China but linseed is the primary type

grown in Canada, USA, Argentina and India as well as

Russia and China (Gill 1987; Marchenkov et al. 2003).

Development and characterization of flax genetic

resources and assessment of genetic variability are essen-

tial for germplasm conservation and breeding. Flax germ-

plasm collections contain thousands of accessions of

L. usitatissimum and related species, of which, subsets

were assessed for the extent of genetic diversity for mor-

phological characteristics (Diederichsen and Hammer

1995; Diederichsen 2001; Diederichsen and Raney 2006;

Communicated by R. Visser.

Electronic supplementary material The online version of thisarticle (doi:10.1007/s00122-012-1953-0) contains supplementarymaterial, which is available to authorized users.

S. Cloutier (&) � R. Ragupathy � E. Miranda �N. Radovanovic � E. Reimer � A. Walichnowski �K. Ward � M. Banik

Cereal Research Centre, Agriculture and Agri-Food Canada,

195 Dafoe Road, Winnipeg, MB R3T 2M9, Canada

e-mail: sylvie.j.cloutier@agr.gc.ca

S. Cloutier

Department of Plant Science, University of Manitoba,

66 Dafoe Road, Winnipeg, MB R3T 2N2, Canada

G. Rowland

Crop Development Centre, University of Saskatchewan,

51 Campus Drive, Saskatoon, SK S7N 5A8, Canada

S. Duguid

Morden Research Station, Agriculture and Agri-Food Canada,

101 Route 100, Unit 100, Morden, MB R6M 1Y5, Canada

123

Theor Appl Genet (2012) 125:1783–1795

DOI 10.1007/s00122-012-1953-0

Saeidi 2008). A variety of molecular markers including

random amplified polymorphic DNA (RAPD), restriction

fragment length polymorphism (RFLP), amplified fragment

length polymorphism (AFLP) and simple sequence repeat

(SSR) have been developed and used in assessing flax

genetic diversity (Spielmeyer et al. 1998; Oh et al. 2000;

Wiesner et al. 2001; Fu et al. 2003; Adugna et al. 2006; Fu

2006, Roose-Amsaleg et al. 2006; Cloutier et al. 2009,

2012; Uysal et al. 2010; Deng et al. 2010, 2011; Bickel et al.

2011; Kale et al. 2012; Rachinskaya et al. 2011; Soto-Cerda

et al. 2011a, 2011b). While the reports are numerous, the

number of informative markers in each of the studies is

somewhat limited with the majority reporting between 9

and 60 markers only (Cloutier et al. 2012).

SSRs are stretches of DNA consisting of a variable

number of short tandem repeats that are generally co-

dominant, highly polymorphic, multi-allelic, relatively

abundant, heritable, reproducible and reliable (Powell et al.

1996; Hwang et al. 2009). They also show cross-species

usefulness and can be used in closely related species

(Powell et al. 1996; Collard et al. 2005; Varshney et al.

2005). SSRs have been developed from genomic sequences

or Expressed Sequence Tags (ESTs). In flax, Ragupathy

et al. (2011) identified 4,064 putative SSRs from bacterial

artificial chromosome (BAC) end sequences (BES). SSR

markers have also been developed from various flax EST

libraries (Cloutier et al. 2009; Soto-Cerda et al. 2011b) and

from SSR-enriched genomic libraries or other genomic

sequences (Roose-Amsaleg et al. 2006; Deng et al. 2010,

2011; Bickel et al. 2011; Kale et al. 2012; Rachinskaya et al.

2011). There are currently 1,326 SSR markers published in

flax (Cloutier et al. 2012). SSR markers have been used for

the construction of genetic maps of many plant species and

provide dependable landmarks throughout the genome

(Cheng et al. 2009; Studer et al. 2010). In flax, genetic maps

and genetic diversity assessment were achieved with this

type of marker (Fu and Peterson 2010; Cloutier et al. 2011;

Soto-Cerda et al. 2011b). Genetic maps are useful for

evolutionary and comparative studies as they provide both

intra- and inter-species genome wide insights on recombi-

nation rates and gene rearrangements within or across

chromosomes (Ball et al. 2010; Wang et al. 2011).

Only three individual flax linkage maps (Spielmeyer et al.

1998; Oh et al. 2000; Cloutier et al. 2011) have been pub-

lished to date. The linkage map developed by Cloutier et al.

(2011) had 113 markers, mostly SSRs, grouped into 24

linkage groups, while those of Spielmeyer et al. (1998) and

Oh et al. (2000) were based on 213 AFLP markers forming

18 linkage groups and 94 RFLP/RAPD markers grouped into

15 linkage groups, respectively. The limitations of these

maps reside in either or both the type and limited number of

markers. Hence the need exists for a reliable, high density

genetic map of flax that would serve as reference for a wide

variety of applications such as QTL mapping, map based

gene cloning, marker assisted crop improvement, linkage

disequilibrium (LD) mapping, phylogenetic analysis and

anchoring of the whole genome shotgun sequence assembly.

Consensus genetic linkage maps have been constructed for

various plant species including Arabidopsis (Hauge et al.

1993), Brassica (Xu et al. 2010, Wang et al. 2011), barley

(Langridge et al. 1995; Varshney et al. 2007), sorghum

(Mace et al. 2009), wheat (Somers et al. 2004), rice (Antonio

et al. 1996), maize (Cone et al. 2002), red clover (Isobe et al.

2009), lettuce (Truco et al. 2007), rye (Gustafson et al. 2009),

soybean (Hwang et al. 2009), melon (Diaz et al. 2011),

grapevine (Vezzulli et al. 2008), cowpea (Muchero et al.

2009), chickpea (Millan et al. 2010), potato (Danan et al.

2011), eucalyptus (Brondani et al. 2006), Cucurbita pepo

(Zraidi et al. 2007) and Zoysia species (Li et al. 2010). High

density consensus maps are well suited as references for the

incorporation of information from genetically diverse indi-

viduals or multiple populations thus facilitating comparative

analyses across germplasm.

Whole genome physical maps have been constructed for

maize (Messing et al. 2004), Brachypodium (Gu et al.

2009), melon (Gonzalez et al. 2010), grapevine (Scalabrin

et al. 2010), Arabidopsis (Mozo et al. 1999), Brassica rapa

(Mun et al. 2008), soybean (Wu et al. 2004), apple (Han

et al. 2011) and flax (Ragupathy et al. 2011). BAC-based

physical maps have been anchored to genetic maps in a

number of plants such as rice (Chen et al. 2002), maize

(Wei et al. 2009), papaya (Yu et al. 2009), Medicago (Mun

et al. 2006), bean (Cordoba et al. 2010), poplar (Kelleher

et al. 2007), grapevine (Scalabrin et al. 2010) and melon

(Gonzalez et al. 2010), where they were used to order

physical maps and provide a framework for genome

sequence assemblies.

The physical map of the flax genome cv. CDC Bethune,

an oilseed flax variety, consists of 416 fingerprinted contigs

(FPC) spanning *368 Mb, very close to the estimated

genome size of CDC Bethune of approximately 370 Mb

(Ragupathy et al. 2011). The present study was intended to:

(1) construct three independent genetic maps, (2) create an

integrated consensus genetic map and (3) anchor the con-

sensus genetic and physical maps of flax to provide the

backbone information for ordering the whole genome

shotgun (WGS) sequence assembly.

Materials and methods

Plant material, DNA extraction and marker

amplification

Three segregating populations were used for mapping.

CDC Bethune/Macbeth (BM) is comprised of 243 F6-

1784 Theor Appl Genet (2012) 125:1783–1795

123

derived recombinant inbred lines (RILs). The two parents

are current varieties termed ‘conventional’ oilseed types

because they contain 55–57 % linolenic acid, a ‘‘standard’’

amount for oilseed flax varieties. E1747/Viking (EV)

received from S. Knapp (University of Georgia, USA)

consists of 90 F6-derived RILs generated from a cross

between the low linolenic acid line E1747 and the Euro-

pean fibre flax variety Viking. SP2047/UGG5-5 (SU) is an

F1-derived doubled haploid (DH) population of 78 indi-

viduals. SP2047 is a solin breeding line characterized by its

2–4 % linolenic acid content and yellow seeds while

UGG5-5 is a ‘‘high-lin’’ line with 65–70 % linolenic acid

(Banik et al. 2011; Cloutier et al. 2011).

Genomic DNA was extracted from lyophilized leaf tis-

sue (*100 mg fresh) of individual seedlings of all the

segregating and parental lines of the three mapping popu-

lations using the DNeasy 96 plant kit according to manu-

facturer’s instructions (Qiagen Inc, Toronto, ON, Canada).

The genomic DNA was quantified by fluorometer and re-

suspended to a final concentration of 6 ng/ll. Amplification

of template DNA with SSR primers was performed in 384–

well plates in a final volume of 10 ll. The amplification

products were resolved on an ABI 3130xl Genetic analyzer

(Applied Biosystems, Foster City, CA, USA) and scored for

segregation of parental alleles at each SSR locus. A total of

five SNPs and seven genes (fad2A, fad2B, fad3A, fad3B,

dgatA, dgatB and ysc1) were also positioned on the maps

(Cloutier et al. 2011). Protocols and primer information for

SSR markers Lu4 to Lu1193, Lu2097 to Lu2300 and

Lu2331 to Lu3291 were previously described (Cloutier

et al. 2009, 2011, 2012). In addition, SSR markers Lu2001

to Lu2096 were from previously published reports (Roose-

Amsaleg et al. 2006; Deng et al. 2010, 2011) while Lu2301

to Lu2330 were designed from scaffold 505 of the flax

WGS sequence assembly (http://www.phytozome.net), as

previously described (Cloutier et al. 2009, 2012). Refer-

ences for individual markers of the consensus map are listed

(Supplementary Table S1).

Anchoring the genetic and physical maps

Genetic and physical map anchoring was performed using

complementary strategies. First, the CDC Bethune BAC

library was screened with a subset of the SSR primers

positioned on the genetic maps to identify BAC addresses

and their corresponding FPC contigs (Ragupathy et al.

2011). SSR markers Lu2097-Lu2300 and Lu2331-Lu3291

were derived directly from BESs and, as such, were

directly assigned BAC addresses and corresponding FPC

contigs. These BES anchors were confirmed by performing

BLASTn searches of the SSR primer sequences against the

flax WGS sequence assembly (http://www.phytozome.net).

Only perfect matches of both primer sequences to the same

scaffold were considered for anchoring. BLASTn searches

were also performed using the BESs from which the SSRs

were derived and matches with an e value \1e-25 were

considered scaffold anchors. Similarly, primer BLAST and

BLASTn were performed for SSR markers Lu4 to Lu1193

derived from ESTs (Cloutier et al. 2009, 2012). The marker

name convention ‘‘marker name_FPC contig number’’ (e.g.

Lu3156_405) was adopted to indicate positioning of the

markers on the physical map. Markers not anchored to an

FPC contig were labelled ‘0’ (e.g. Lu2312_0). Markers

amplifying two or three loci were labelled with a single

contig number but likely belong to paralogous contigs.

Map construction and linkage analysis

Linkage analysis was carried out independently for each

mapping population using JoinMap 4.0 (Van Ooijen 2006)

with a LOD of 4.0 and a maximum recombination fre-

quency of 40. Marker segregation was tested against the

expected Mendelian ratio of 1:1 using the Chi-square

goodness-of-fit test. For conversion of recombination fre-

quency into map distances expressed in centiMorgans

(cM), the Kosambi mapping function which accounts for

genetic interference from double cross over was used

(Kosambi 1944).

The consensus linkage map was constructed based on

the principle illustrated by Stam (1993) using JoinMap 4.0

(Van Ooijen 2006). LOD scores and pairwise recombina-

tion frequencies were computed for all linkage groups

(LGs) of individual populations. They were then combined

into a single group node in the navigation tree using the

‘grouping node’ command. Consensus LGs were obtained

using the ‘combine groups for map integration’ function

that is based on the presence of a minimum of two marker

loci common to at least two populations on the basis of the

mean recombination frequencies and combined LOD

scores of pairwise data from the three segregating popu-

lations. The consensus map was constructed according to

Alheit et al. (2011) and Gong et al. (2008) using the fol-

lowing parameters: Kosambi mapping function, regression

mapping option, maximum recombination frequency of 40,

LOD[1.0, ripple = 1, third round = yes and goodness-of-

fit jump threshold for removal of loci = 5.0. Comparative

analyses of marker distance and marker order were per-

formed across individual maps and with the consensus map

by visualization of the four final maps obtained as descri-

bed above. The individual homologous LGs from the three

populations were integrated using commonly mapped

markers based on 411 segregating lines (243 RILs from

BM, 90 RILs from EV and 78 DHs from SU). The 15

consensus LGs were numbered LG1 to LG15, in decreas-

ing size order (cM). The population specific LGs were

described using the population acronyms and the same

Theor Appl Genet (2012) 125:1783–1795 1785

123

number as in the consensus map (BMLG1-BMLG16,

EVLG1-EVLG18 and SULG1-SULG15).

Results

Individual genetic linkage maps

CDC Bethune/Macbeth

A total of 389 segregating marker loci were polymorphic in

the BM population, of which, 385 marker loci assembled

into 16 LGs spanning 2,007 cM, for an average density of

one marker locus every 5.2 cM, and 4 marker loci

remained unlinked (Table 1). LGs ranged from 27 to

187 cM and contained 9–40 markers. The dgatA and dgatB

genes were mapped in this population. The population

showed segregation distortion for 56 loci (P \ 0.05) with

equal numbers of loci skewed towards each parent (Sup-

plementary Table S2).

E1747/Viking

The EV population was assayed with 443 polymorphic

marker loci, 442 of which grouped into 18 LGs leaving a

single marker unlinked (Table 1). The length of the LGs

and number of marker loci per LG varied from 10 to

168 cM and 2–46, respectively. The total length of the map

was 1,731 cM with a mean marker density of 3.9 cM

between loci. 77 of the 442 loci diverged significantly from

the expected 1:1 segregation ratio with 33 skewed towards

E1747 and 44 skewed towards Viking (Supplementary

Table S2).

SP2047/UGG5-5

The previously published SU map was based on 125

marker loci assembled in 24 linkage groups spanning

834 cM (Cloutier et al. 2011). The SU map constructed

herein is more saturated and comprehensive with 477

polymorphic marker loci, of which 8 remained unlinked

and the remaining 469 formed 15 LGs totalling 3,044 cM

(Table 1). The length of the LGs and the number of loci

per LG varied from 136 to 362 cM and 20–47, respec-

tively. The approximate average marker density was one

every 6.5 cM. A total of 168 loci showed segregation

distortion (Supplementary Table S2). All LGs contained

distorted markers except SULG13 which contained a

single polymorphic marker in the SU population and

SULG14 (Supplementary Table S2). A total of seven

genes including six from fatty acid biosynthetic pathways

(fad2A, fad2B, fad3A, fad3B, dgatA and dgatB) were also

mapped.

Consensus map

A total of 795 markers generated 821 loci for a locus per

marker ratio of 1.03 because 18 markers identified two loci

and four markers identified three loci. Of the 821 loci

scored in the three populations, 114 were common to all

three populations and another 257 were common to two of

the three populations (Supplementary Table S3). A total of

770 marker loci were assembled into the 15 LGs consti-

tuting the consensus map (Fig. 1; Table 1). Four additional

LGs contained 19 marker loci ordered based on a single

mapping population and 32 markers remained unlinked

(Table 1; Supplementary Table S2). The total length of the

consensus genetic linkage map was 1,551 cM and LGs

ranged from 60 to 170 cM. The consensus map had an

average marker density of one per 2.0 cM. Assuming a

genome size of 370 Mb for CDC Bethune (Ragupathy et al.

2011), the genome wide ratio of physical to genetic dis-

tance averaged 239 Kb/cM, equivalent to an average of one

marker per 481 Kb.

The length of the consensus map was shorter than the

individual population specific maps (Table 1). All LGs of

Table 1 Mapping statistics for the three individual and the consensus genetic maps of flax

Populations No.

individuals

Total no.

marker loci

No. marker

loci in LGsaLength

(cM)

No.

LGsaNo. unlinked

marker loci

No. marker loci in

the consensus map

Percent marker loci

in the consensus map

CDC Bethune/

Macbeth (BM)

243 389 385 2,007 16 4 373 95.9

E1747/Viking (EV) 90 443 442 1,731 18 1 419 94.6

SP2047/UGG5-5 (SU) 78 477 469 3,044 15 8 463 97.1

Consensus 411 821 770 (19) 1,551 15 (4) 32 770 93.8

a Numbers in brackets represent marker loci and LGs belonging to a single population and that did not incorporate in the 15 LGs of the

consensus map

1786 Theor Appl Genet (2012) 125:1783–1795

123

*Lu2857_00.0*Lu25_18720.8*Lu2089_18721.6*Lu3235_53722.2*Lu2026_56022.9*Lu2853_18724.5*Lu2861_18726.6*Lu2091_027.3*Lu2858_18732.1*Lu1066_161_28536.1*Lu49B_036.6*Lu3020_28537.2*Lu427_16139.0*Lu2390_5140.8*Lu2807_16141.8*Lu2808_16142.4*Lu987_044.8*Lu2803_16146.2*Lu2802_161 *Lu955_046.9*Lu1160b_58647.6*Lu56_051.1*fad2A_32551.2*Lu869_052.4*Lu3283_88753.7*Lu2392a_5158.4*Lu2392b_5158.8*Lu2387_5160.5*Lu299_51 *Lu866_063.2*Lu796_5163.3*Lu2393_5163.9*Lu2388_5164.2*Lu2053_5165.4*Lu3220_51270.2*Lu3222_51272.8*Lu1160a_58674.5*Lu2589_9376.8*Lu2597_9478.3*Lu2592_9381.6*Lu2895b_20391.2*Lu2055_11992.0*Lu998_27592.9*Lu2712_12694.4*Lu2698_11998.6*Lu868_119100.9*Lu2374b_45106.2*Lu870_0109.7*Lu2010c_0111.3*Lu2184a_12113.3*Lu2183a_12118.8*Lu3053_297121.9*Lu2010b_0123.5*Lu999_550125.4*Lu1148_550129.8*Lu3231_550130.8*Lu3279_856131.3*Lu46_0132.3*Lu47_0132.8*Lu2687_112136.8*Lu114_181147.1*Lu981_222148.8*Lu943_222150.0*Lu2681_0170.0

LG1

*Lu747b_00.0*Lu2799_1600.1*Lu2794_1601.1*Lu2795_16011.0*Lu2796_16012.7*Lu2800_16022.1*Lu2113_128.5*Lu129_135.1*Lu906_138.9*Lu2115_143.4*Lu2250_2846.6*Lu2247_2850.9*Lu2469_10853.5*Lu344_2855.7*Lu3291_110856.7*Lu2137_4 *Lu2370_4456.8*Lu2188_1457.1*Lu859_1057.4*Lu2135_4 *Lu257_23958.0*Lu2139_458.4*Lu910_458.7*Lu3238_56858.9*Lu3023_28659.0*Lu2144_4 *Lu3022_286*Lu840_286 *Lu3256_67659.1

*Lu3269_77159.3*Lu2067a_059.7*Lu2145_4 *Lu532_459.8*Lu2457a_6660.5*Lu824_460.6*Lu2366_4460.8*Lu2959_23761.7*Lu926Ba_062.9*Lu128_20667.0*Lu209_20668.3*Lu2907_20670.0*Lu2908_20670.5*Lu2909_20671.3*Lu2340_3972.4*Lu2351_3974.3*Lu2349_3978.0*Lu2347_3982.0*Lu2341_3982.5*Lu2346_3983.5*Lu125_3985.9*Lu3068_31386.4*Lu3276_81387.8*Lu2344_3989.1*Lu2352_3992.5*Lu900_3998.1*Lu1028_9099.2*Lu2027_475 *Lu2007_475*Lu2021a_475105.0

*Lu3206_475105.8*Lu324_51106.5*Lu2718_134109.2*Lu2720_134113.3*Lu3205_475122.9*Lu1115_134137.5

LG2

*Lu342_1010.0*Lu445_5425.1*Lu318_4139.2*Lu1039_010.5*Lu3024_28712.3*Lu1161_10115.4*Lu2628_10115.6*Lu452_018.6*Lu2625a_10120.4*Lu899_15038.0*Lu774_15048.1*Lu2764_15049.0*Lu2767_15049.4*Lu821_15051.0*Lu3262_72955.7*Lu64_060.9*Lu2777b_15662.7*Lu373_1664.4*Lu139_1666.0*Lu787a_069.3*Lu2194_1672.3*Lu2689_11373.3*Lu2161_773.6*Lu2047_0 *Lu2044_074.3*Lu2040_0 *Lu2049_0*Lu3117_37474.4

*Lu2063_0 *Lu2163_775.2*Lu3223_51975.7*Lu2164_776.5*Lu3199a_444 *Lu2635_10279.1*Lu106_10282.2*Lu105_10282.5*Lu2633_10283.2*Lu2631_10284.8*Lu3195_44487.7*Lu104_10291.4*Lu3111_36992.5*Lu3151_40197.0*Lu3153_40198.3*Lu3152_40198.8*Lu933_099.5*Lu638_401 *Lu639_401100.1*Lu1144_0103.3*Lu2706_119107.0*Lu3290_1078107.1*dgatA_400108.1*Lu2038_0108.9*Lu658_400110.7*Lu3148_400111.6*Lu3150_400113.4*Lu3146_400117.4*Lu3144_400120.4*Lu2838b_177121.1*Lu509_118122.0*Lu558_118122.4*Lu2693_115127.4*Lu2775b_156127.5*Lu450_115127.8*Lu422a_115128.7

LG3

*Lu3281_8650.0*Lu2966_2439.1*Lu996_24317.4*Lu2006_0 *Lu2004_32*Lu2002_24327.3

*Lu2968_24327.4*Lu2073_67332.4*Lu722B_67334.4*Lu2025_32441.8*Lu2008_32441.9*Lu2059_32442.5*Lu2207_48747.2*Lu3228_54549.2*Lu3229_54550.2*Lu2399_5550.9*Lu2396_5553.8*Lu3252_65953.9*Lu3213_48754.1*Lu2087_48754.2*Lu717_23157.8*Lu2397_5558.4*Lu2942_23158.8*Lu2944_23158.9*Lu2940_23159.3*Lu2943_23166.4*Lu989_67568.7*Lu207_67570.2*Lu3113_37175.5*Lu3116_37176.5*Lu2983_26178.2*Lu2980_26181.2*Lu587_082.8*Lu833_26183.4*Lu1049_084.5*Lu2984_26186.6*Lu851_26187.8*Lu2981_26188.9*Lu2239_2489.5*Lu2043_26191.8*Lu2054_26192.0*Lu2237_2494.6*Lu2031_2494.9*Lu2233_2497.8*Lu2230_24102.2*Lu919_0109.0*Lu2235_24110.4*Lu2076_24111.2*Lu2286_35119.4*Lu2287_35121.2*Lu2009_0 *Lu2011_0121.7*Lu2024_0121.8

LG4

*s18B10_00.0*Lu227_1307.4*Lu643_1309.1*Lu361_13010.7*Lu274B_13013.5*Lu3201_44724.1*Lu223_44724.2*Lu2037b_025.9*Lu2014_028.2*Lu2295_3628.9*Lu505_030.9*Lu176_3634.2*Lu1182_037.1*Lu2288_3642.0*Lu2291_3643.1*Lu2411_5844.1*Lu2292_3645.7*Lu744_3646.9*Lu2297_3648.3*Lu2293_3649.3*Lu2704_11950.2*dgatB_11951.2*Lu2086_051.6*Lu2304_0 *Lu2305_051.8*Lu2752_14651.9*Lu3225_53752.2*Lu922_052.4*Lu2362_4352.5*Lu2365_4352.8*Lu2364_4353.2*Lu2017_053.5*Lu2466_7053.9*Lu2700_11954.7*Lu3132_38554.9*Lu2884_202 *Lu2889_20255.2*Lu2318_0 *Lu2886_20255.3*Lu2885_20255.4*Lu2883_20255.9*Lu2887_20256.1*Lu623_20256.3*Lu3248_59656.4*Lu2890_20256.6*Lu41_20257.1*Lu164_3057.6*Lu2255_3058.0*Lu266_3058.5*Lu2403_5870.4*Lu2408_5873.5*Lu738_5876.2*Lu652_5879.1*Lu2409_5880.7*Lu2405_5885.7*Lu2512_7698.8*Lu968_55101.6*Lu330_76104.8*Lu2509_76108.0*Lu2516a_76108.7*Lu682_76110.4*Lu2068_76112.4

LG5

*Lu1006_590.0*Lu1177_00.9*Lu3287_9982.5*Lu2420_596.5*Lu2418_598.7*Lu2917b_2149.6*Lu2084_5910.4*Lu1179_5910.8*Lu502_8616.3*Lu699_38026.3*Lu1094_38026.6*Lu1107_197 *Lu944_19730.7*Lu2608_9732.3*Lu3014_28037.1*Lu3013_28039.2*Lu2545_8139.8*Lu442a_044.3*Lu2169_945.8*Lu2544_8146.6*Lu2548_8148.1*Lu2972_24848.2*Lu1178_2748.6*Lu456_775 *Lu2550_8149.2*Lu457_775 *Lu2242_2749.4*Lu2072_2749.8*Lu2039_2749.9*Lu2613_9750.8*Lu918_051.0*Lu3267_75751.3*Lu728b_2751.5*Lu69_0 *Lu2542_81*Lu2549_81 *Lu2543_8152.2

*Lu2071_81 *Lu2064_8152.6*Lu836_053.4*Lu2975_24853.7*Lu2974_24854.9*Lu2971_24857.5*Lu2556_8262.5*Lu1002B_8262.6*Lu2561b_8263.2*Lu2560_8263.4*Lu2564_8264.1*Lu2565_8267.5*Lu2553_8268.6*Lu2554_8269.4*Lu2555_8272.0*Lu2557_8272.6*Lu3057a_30373.0*Lu60_073.7*Lu861_59184.1*Lu1112_17184.8*Lu3091_32996.6*Lu2078_329_10107.3

LG6

*Lu260_790.0*Lu2532_792.7*Lu2535_793.6*Lu2536_795.7*Lu2534_795.8*Lu2083_796.7*Lu2540_797.2*Lu402_797.9*Lu675_7910.6*Lu2533_7910.8*Lu511_7910.9*Lu2032_011.6*Lu741_7913.3*Lu1146a_7913.7*Lu2825b_17518.3*Lu2832_17521.1*Lu146_17523.9*Lu138_175 *Lu151_17524.0*Lu235_23024.9*Lu2810_16627.3*Lu2827_17528.8*Lu1055_7738.2*Lu3181_43640.2*Lu296_43640.8*Lu1022_43642.3*Lu3180_43642.7*Lu672_43643.4*Lu3184_43644.1*Lu3178b_43646.0*Lu2815_17051.7*Lu2812a_17052.5*Lu585B_10853.7*Lu2065_054.7*Lu2651_10855.6*Lu2652_10856.2*Lu2654_10856.3*Lu557_45460.8*Lu3100a_35366.8*Lu1124_8471.2*Lu2571_8476.6*Lu2658_10880.0*Lu2648_10880.9*fad3A_8483.8*Lu44E4_8484.7*Lu2003_28190.0*Lu566_28191.6*Lu449_28192.1*Lu3016_28192.5*Lu3017_28196.6*Lu3266_73399.6*Lu58a_257104.3

LG7

*Lu595_1080.0*Lu2561c_8212.0*Lu2659_10814.8*Lu2649_10818.9*Lu2840_17824.8*Lu339_17825.7*Lu1171_17827.6*Lu2561a_8229.0*Lu265_73637.1*Lu2030_8238.2*Lu3057b_30340.1*Lu3059_30344.0*Lu2563_8245.4*Lu3157_40547.9*Lu3156_40551.9*Lu633_053.2*Lu2428_6053.4*Lu2957_235 *Lu2268_3154.7*Lu2056_21756.0*Lu2923_21756.3*Lu2578_8856.6*Lu2203_1857.1*Lu2103_4664.9*Lu857_4665.3*Lu2918_21566.1*Lu2921_21567.6*Lu2082_4670.2*Lu2098_4670.8*Lu2105_4672.1*Lu2102_4672.7*Lu2306_4673.0*Lu2313_073.5*Lu2312_0 *ysc1_0*Lu2307_073.6

*Lu2316_4674.2*Lu928_0 *Lu2106_4674.3*Lu2317_074.8*Lu2320_075.1*Lu2326_075.3*Lu2330_076.4*Lu447_21576.5*Lu2329_077.2*Lu178_4678.5*Lu2424_6079.8*Lu2618_9880.8*Lu2101_4683.5*Lu2431_6084.5*Lu2430_6084.6*Lu2156_584.7*Lu2429_6085.2*Lu3189_44187.9*Lu625_6088.7*Lu1077_17488.8*Lu2425_6090.0*Lu2820_17491.0*Lu2823_17493.0*Lu2822_17493.8*Lu3280_86494.2*Lu2745_14194.7*Lu2587_9195.7*Lu2714_13098.0*Lu963_9199.0*Lu2515_76100.4*Lu1103_60103.0*Lu2338a_38103.9

LG8

Fig. 1 Consensus genetic map

of flax integrated from three

mapping populations. Numbers

to the left of each linkage group

represent Kosambi map units

(cM). Locus names followed by

their FPC contig anchor

separated by an underscore are

on the right. Linkage groups are

in decreasing size order

Theor Appl Genet (2012) 125:1783–1795 1787

123

the consensus map were constructed based on markers

shared among the three populations except LG13 which

was constructed mostly with markers from the BM and EV

populations because all markers, with the exception of

Lu850, were monomorphic in the SU population. The

consensus map displayed a few gaps that were mostly

smaller than 10 cM. The largest gap of 20.8 cM is in LG1

(Fig. 1; Supplementary Table S1). The marker orders were

consistent between the three independent genetic maps

with some local inversions.

*Lu2917a_2140.0*Lu628_786.5*Lu14_08.0*Lu927_7812.0*Lu891_7812.7*Lu140_267 *Lu1041_013.4*Lu756_26715.1*Lu2991_26716.6*Lu2041_018.0*Lu2042_018.2*Lu2694_11518.7*Lu2997_26719.9*Lu2992_3623.9*Lu2996_26727.0*Lu220_26727.3*Lu2779_15630.0*Lu2780_15630.6*Lu2096_031.6*Lu867_031.7*Lu926Bb_032.4*Lu2774_15633.4*Lu2880_19734.7*Lu2778_15637.0*Lu2775a_15637.7*Lu2985_038.3*Lu2773_15639.7*Lu2090_040.2*Lu2081_7340.5*Lu2482_7340.9*Lu2486_7341.5*Lu2600_9741.7*Lu2787_15641.9*Lu2485_7342.4*Lu2127a_242.7*Lu2183b_1243.0*Lu2183c_1243.3*Lu1135_7344.1*Lu263_9744.5*Lu896_044.8*Lu439_73 *Lu728a_16145.5*Lu2612_9746.8*Lu787b_15654.7*fad3B_20757.2*Lu58b_25758.8*Lu2914_20761.7*Lu2913_20764.9*Lu275_068.6*Lu206b_30669.7*Lu1052_070.0*Lu203b_30670.7*Lu765Bb_30672.9*Lu3063_30673.3*Lu2574_8475.3*Lu2911_207 *Lu803_076.6*Lu3064_30677.4*Lu1151_079.0*Lu381_20183.4*Lu3289_106484.4

LG12

*Lu2046_380.0*Lu2333_382.1*Lu2332_383.5*Lu2331_386.7*Lu2867_1889.5*Lu11_010.6*Lu2019_11111.0*Lu2676_11113.5*Lu2679a_11120.7*Lu2673_11121.0*Lu83_11121.4*Lu291_023.9*Lu575_11127.5

*Lu3218_49745.2*Lu935_32148.6*Lu3217_49750.6*Lu2850_18751.4*Lu568_052.0*Lu512_32155.1*Lu785_32155.8*Lu13_32157.9*Lu3078_32159.1*Lu325_32160.1*Lu934_061.1*Lu292_061.2*Lu2580_8969.1*Lu3003_26971.5

*Lu2127b_282.2*Lu2118_284.2*Lu2123_285.6*Lu1165_286.2

LG11

*Lu2472_710.0*Lu1158_712.1*Lu668_713.7*Lu2149_510.0*Lu685_512.9*Lu2155_515.1*Lu2157_517.2*Lu2154a_518.8*Lu2162_727.5*Lu2901_20430.5*Lu3099_353 *Lu2052_3231.5*Lu3100b_35331.7*Lu273_3234.4*Lu3007_26934.8*Lu657_3234.9*Lu1168_10435.8*Lu3120_37936.4*Lu2725_13740.1*Lu2728_13742.1*Lu2732_13742.5*Lu458_13742.7*Lu2731_13746.0*Lu2051_13747.1*Lu2929_22153.0*Lu2928_22155.0*Lu2926_22155.2*Lu483_22156.0*Lu37b_22158.6*Lu1117_059.4*Lu1116_059.6*Lu1176_22160.6*Lu2092b_062.3*Lu2265_3164.9*Lu2016_067.5*Lu2050_068.5*Lu2264a_3169.7*Lu2270_3173.0*Lu1043_78074.2*Lu1136_3174.4*Lu1042_78075.4*Lu2272_3176.2*Lu371B_3781.7*Lu2360_4282.6*Lu804_14184.6*Lu2746_14187.7

LG10

*Lu2437_610.0*Lu2451_611.5*Lu213_6110.8*Lu2262_3114.4*Lu2438_6117.4*Lu2453_6118.7*Lu2443_6120.0*Lu2447_2825.3*Lu2758_14925.4*Lu2936_23026.1*Lu2450_6127.2*Lu2448_2827.5*Lu2058_029.4*Lu801_6129.6*Lu181_3130.1*Lu2446_2831.6*Lu519_77 *Lu526_7731.7*Lu2523_7732.4*Lu3097_33832.8*Lu2524_7733.0*Lu2739_14036.0*Lu2741_14136.5*Lu3082_32339.1*Lu3083_32339.3*Lu144b_0 *Lu3085_32339.6*Lu2809a_16641.9*Lu2361_4242.4*Lu2449_7743.0*Lu3199a_44447.7*Lu2828_175 *Lu2824_17552.1*Lu757_230 *Lu798_23056.2*Lu2939a_23056.5*Lu895_061.5*Lu2168_964.0*Lu2878_19664.9*Lu1146b_19670.0*Lu2538_7985.8*Lu3244_59287.5*Lu932_490 *Lu1125_84190.6*Lu283_84192.0*Lu3216_49093.4*Lu91_49094.6

LG9

*Lu2621_990.0*Lu897_02.1*Lu3251_6305.0*Lu3209_4825.6*Lu3210_4825.8*Lu3212_4826.1*Lu2045_08.1*Lu2373_4513.0*Lu2377_4514.9*Lu808_015.3*Lu3043_29017.2*Lu3040_29020.5*Lu850_29025.0*Lu793_29026.2*Lu3033_29026.7*Lu514_29026.9*Lu3046_29027.9*Lu3219a_49728.8*Lu9_029.8*Lu813_29030.1*Lu3038_29032.2*Lu3036_29032.4*Lu786_10133.1*Lu3103_35533.4*Lu225_35540.3*Lu2679b_11141.0*Lu601b_35543.0*Lu2625b_10143.6*Lu444_18847.1*Lu476_18847.9*Lu461_18848.3*Lu2863_18851.0*Lu684_18851.6*Lu2865_18853.0*Lu613_18853.3*s7F06_056.7*Lu2862_18861.6*Lu2020_8964.1*s16E2_067.8*s19C1c3_068.5*Lu701_8968.7*Lu1044_8970.1*Lu1044B_8970.2*Lu959_8970.8*s19C1c1_076.0

LG14

*Lu2219_210.0

*Lu2223_2111.8

*Lu2216_2122.0*Lu2074_0 *Lu197_2125.9*Lu2468a_7027.4*Lu2639_10327.6*Lu2638_10328.1*Lu650_2028.9*Lu2459_70 *Lu2467_7029.3*Lu2196_1629.5*Lu2463_7030.8*Lu485_032.6*Lu2279_3237.2*Lu2771_15442.1*Lu805_1146.5*Lu2468b_7049.4

*Lu2176_1166.0

*Lu2012_90 *Lu2021b_9076.2

LG13

*Lu2697b_1180.0*fad2B_4052.1*Lu113_1186.6*Lu2695_1187.4*Lu2696_1187.8*Lu462a_21210.9*Lu838_21211.0*Lu1172_11811.7*Lu1007_4013.5*Lu2354_4017.1*Lu359_017.9

*Lu2010a_19031.9*Lu2001_034.3*Lu1127_12134.9*Lu2965_24335.4*Lu2382_5035.9*Lu357_4236.0*Lu2057_69236.8*Lu1163_12137.7*Lu2383_5039.0*Lu2707_12140.7*Lu3028_28742.6*Lu3185_44045.2*Lu3026_28746.4*Lu3186_44048.0*Lu510_44051.2*Lu2931_22652.8*Lu271_22653.6*Lu637_22657.2*Lu1001_7457.9*Lu451_058.4*Lu2497_7459.9

LG15

Fig. 1 continued

1788 Theor Appl Genet (2012) 125:1783–1795

123

The percentages of distorted loci in BM, EV and SU

populations were 15, 17 and 36 %, respectively (Supple-

mentary Table S2). Out of the 770 loci of the consensus

map, 292 (38 %) loci exhibited segregation distortion in at

least one of the three mapping populations (Supplemen-

tary Table S2). The presence of a large number of dis-

torted loci seems to have caused the large gap in LG11.

Although LG8 carried the most distorted loci (76 %),

the length of that LG was not affected as compared to the

bi-parental populations where marker segregation was

Mendelian, although some local rearrangements of closely

linked markers were observed. Overall, only a few

ambiguities were identified with respect to marker posi-

tion compared to individual maps. Markers Lu359_0 and

Lu2354_40, common to all three populations, mapped at

the proximal end of each individual population LG15.

However, these markers were placed at internal positions

(41.977 and 42.829 cM) in the consensus LG15 (Supple-

mentary Table S1).

Anchoring genetic and physical maps

Of the 770 loci in the consensus genetic map, 670 were

anchored to 204 of the 416 FPC contigs of the physical

map (Ragupathy et al. 2011) corresponding to 274 Mb or

74 % of the flax genome (Fig. 2). Twenty-one of the 204

FPC contigs were anchored at more than one map location

because some markers amplified two or three polymorphic

loci (labelled with a small a, b or c suffix in Fig. 1). FPC

contigs were anchored with 1–14 markers. Examples of

FPC contigs anchored with 14 markers include FPC

contigs 79 and 82 estimated at 2.836 Mb with 205 BAC

clones and 3.192 Mb with 265 BAC clones, respectively.

The largest FPC contig (21), estimated at 5.562 Mb,

consisted of 437 BAC clones and was anchored with four

markers. Sixty-seven FPC contigs contained a single

marker.

Discussion

Comparison of individual and consensus maps

Three genetic maps of flax have been published to date: a

213 AFLP marker-based map of 18 LGs covering

1,400 cM (Spielmeyer et al. 1998), a 1,000 cM RFLP/

RAPD map with 94 markers assembled into 15 LGs (Oh

et al. 2000) and a 113 marker map containing EST-SSRs,

SNPs, genes and one phenotypic trait grouped into 24 LGs

and spanning 834 cM (Cloutier et al. 2011). Major QTL for

fusarium wilt (Spielmeyer et al. 1998), for fatty acid

composition and seed coat colour (Cloutier et al. 2011)

were identified using these genetic maps. The increased

marker density of the SU map from 113 (Cloutier et al.

2011) to 469 (this publication) significantly improved the

map by bridging gaps and thereby reducing the number of

LGs from 24 to 15 while increasing the map coverage from

834 to 3,044 cM which promises to enhance QTL detec-

tion. Collinearity with two additional genetic maps (BM

and EV) further confirmed the accuracy of the groupings.

The three maps were largely collinear with few marker

inversions. Although some LGs or portions thereof were

fixed in some of the individual populations (e.g. LG4,

LG13 and LG15 in SU; LG7, LG9 and LG15 in BM; LG15

in EV), the consensus map successfully bridged LGs and

resulted in good coverage across the genome with few

gaps. Some local inconsistencies of marker order such as

small inversions or local rearrangements between individ-

ual and consensus maps were observed, particularly in

closely linked markers and markers located at the distal

ends of LGs as previously reported for rye (Studer et al.

2010), cotton (Xu et al. 2008), Zoysia (Li et al. 2010),

grapevine (Vezzulli et al. 2008) and Eucalyptus (Brondani

et al. 2006). The single most striking discrepancy resided in

the total length of the SU map which exceeded the size of

the BM and EV maps by more than 1,000 cM. The higher

Fig. 2 Distribution of the genetic markers of the consensus map

across the FPC contigs of the physical map (Ragupathy et al. 2011). A

total of 204 of the 416 FPC contigs (x axis) were anchored by 670

marker loci (dots). The length of the contigs (Mb) is on the left y axis.

From 1 to 14 marker loci (dots) were anchored onto each FPC contig

represented on the right y axis

Theor Appl Genet (2012) 125:1783–1795 1789

123

percentage (36 %) of distorted markers of this DH popu-

lation, i.e. at least twice as high as the other two popula-

tions, may be responsible for the artifactual expansion of

the genetic map length (Garcia-Dorado and Gallego 1992;

Zhu et al. 2007; Li et al. 2011).

Comparative and consensus mapping are advantageous

to obtain an unbiased linkage map representing the genome

under investigation. As discussed above, mapping of

markers employing multiple populations provides

increased genome coverage because it is unlikely that

multiple parents would all be fixed (monomorphic) in the

same genomic regions. Also, overall population size

afforded by multiple populations increases the chances of

capturing recombination events, the foundation of genetic

mapping. Reports of overrepresentation of localized

crossover promoting 13mer motifs (Myers et al. 2008) in

recombination hot spots of 1–2 kb (Ptak et al. 2005), and

the influence of highly polymorphic trans-acting loci such

as PRDM9 on the activation of those recombination hot-

spots in human (Baudat et al. 2010; Paigen and Petkov

2010) indicates the importance of the genomic background

in crossover frequencies. Considering crossing over as a

fundamental cellular process conserved across eukaryotes,

variability for distribution of recombination hot spots and

its genetic determinants can be determined using multiple

populations. Comparative mapping can also offer evidence

for duplications or chromosomal rearrangements (Sewell

et al. 1999). As a consequence of merging of datasets from

three populations, the consensus map had fewer and

smaller gaps compared to the individual genetic maps,

hence it was more comprehensive. Fatty acid desaturase

genes fad2A, fad2B, fad3A and fad3B, diacyl glycerol

transferase genes dgatA and dgatB and seed coat color gene

ysc1 were positioned to seven different LGs of the con-

sensus map. The majority were polymorphic in a single

population but common neighbouring polymorphic mark-

ers permitted their integration in the consensus map,

illustrating another advantage of consensus mapping. Flax

has a relatively low level of genetic polymorphism, indi-

cating a lower degree of genome divergence (Deng et al.

2010; Cloutier et al. 2011; Kale et al. 2012), unlike crops

like maize where extensive molecular variation has been

reported, primarily due to the activity of transposable ele-

ments (Llaca et al. 2011). The use of multiple populations

followed by consensus mapping greatly increases marker

saturation, a valuable feature for all mapping applications,

for understanding the LD structure across genomes and

germplasm characterization by association mapping (Soto-

Cerda and Cloutier 2012).

The present consensus map of 770 SSR markers repre-

sents a major improvement over the low resolution phy-

logenetic analyses published to date with other marker

types (McDill et al. 2009; Fu and Allaby 2010) and those

published with few SSR markers within Linum usitatissi-

mum (Wiesner et al. 2001; Cloutier et al. 2009) and across

Linum species (Fu and Peterson 2010; Soto-Cerda et al.

2011b). Pale flax (Linum bienne Mill, L. angustifolia Huds)

is the wild progenitor of cultivated flax. Both have similar

karyotypes bearing equal numbers of chromosomes

(2n = 2x = 30) (Muravenko et al. 2003) and interspecific

crosses between them produce fertile progeny (Gill and

Yermanos 1967; Diederichsen and Hammer 1995). Pale

and cultivated flax have been inferred to differ by a single

translocation event (Gill and Yermanos 1967). The

exceptionally high transferability (97 %) of EST-SSRs

from cultivated flax to L. bienne supports the assignment of

pale flax to the primary gene pool (Diederichsen 2007; Fu

and Peterson 2010; Soto-Cerda et al. 2011b). A genetic

map for pale flax or an interspecific cross map has yet to be

produced. The current availability of SSR markers com-

bined with their cross applicability should allow for an in-

depth analysis of genetic diversity in L. bienne which

should be useful to explore its potential to widen the gene

pool of cultivated flax to meet breeding objectives.

Linum usitatissimum is a self-pollinated diploid species

which, like a number of crop genomes, is an ancient

polyploid (Blanc and Wolfe 2004; Paterson et al. 2004;

Pfeil et al. 2005; Sterck et al. 2005; Gong et al. 2008; Soltis

et al. 2009; Schmutz et al. 2010; Jiao et al. 2011; Lin and

Paterson 2011). The remnant of ancestral whole genome

duplication is reflected by the fact that a subset of SSR

markers amplified two paralogous loci, although in most

cases, only one was polymorphic (Cloutier et al. 2009,

2012). Mapping of the markers that amplified multiple

polymorphic loci revealed ancestral chromosomal rear-

rangements resulting from paleopolyploidization events as

noticed in LG6 and LG8. The existence of duplicated

regions in consensus linkage groups LG6 and LG8

delimited by Lu2561 and Lu3057 markers indicate signa-

tures of ancient duplication (Supplementary Figure 1).

Analyses of a large collection of flax ESTs also corroborate

the ancient duplication of flax (Venglat et al. 2011), as

exemplified by the duplicate nature of the genes of the fatty

acid biosynthetic pathway (Cloutier et al. 2011). Global

comparative analysis of the scaffolds of the WGS sequence

assembly promises a more comprehensive picture of the

events that have shaped the flax genome through evolution.

Distorted markers

The segregation distortion in the three populations ranged

from 15 to 36 %, an intermediate level, comparable to

extent of distorted markers reported in common bean

(37.3 %, de Campos et al. 2011), maize (19–36 %, Lu et al.

2002), red clover (5.8–45 %, Isobe et al. 2009), Medicago

truncatula (27 %, Thoquet et al. 2002) and peanut

1790 Theor Appl Genet (2012) 125:1783–1795

123

(8.5–22.8 %, Hong et al. 2010) but higher than C. pepo

(3.7 %, Zraidi et al. 2007; Gong et al. 2008), Brassica rapa

(2.6 %, Song et al. 1991), grapevine (7–11 %, Doligez

et al. 2006) and globe artichoke (13 %, Portis et al. 2009).

Species such as Arabidopsis (43.0 %, Reiter et al. 1992),

cotton (71 %, Lacape et al. 2009), tomato (68 %, Paterson

et al. 1988), perennial ryegrass (32–63 %, Anhalt et al.

2008), Zoysia (43.7 %, Li et al. 2010) and cowpea (41 %,

Muchero et al. 2009), all displayed substantially higher

percentages of markers deviating from the expected seg-

regation ratios.

Non-Mendelian segregation ratios arise from chromo-

somal rearrangements, gametic competition, embryo via-

bility and various physiological causes (Xu et al. 1997;

Gonzalo et al. 2005; Portis et al. 2009) and, inadvertently,

also from sampling errors (Lorieux et al. 2000). Segrega-

tion distortion has been associated more strongly with

genetic effects as opposed to population structure or mar-

ker type (Anhalt et al. 2008).

Among the three flax populations reported here, the DH

SU population had the highest proportion of distorted loci,

similar to DH populations of rice (31.8 %, Xu et al. 1997)

and Brassica (22–49 %, Wang et al. 2011), but lower than

alfalfa (68 %, Li et al. 2011). The higher proportion of non-

Mendelian markers in DH populations may be attributed to

selection for tissue culture responsiveness loci (Xu et al.

1997; Alheit et al. 2011). Even though they were located on

all LGs, distorted markers were not randomly distributed

but were clustered within LGs (Cloutier et al. 2011;

Cordoba et al. 2010; Li et al. 2011) supporting the cause of

selection rather than experimental errors (Li et al. 2011), a

view further emphasized by higher proportions of distorted

markers on specific LGs such as LG2 (36/65), LG8 (52/68)

and LG10 (32/46). Chromosome specific uneven distribu-

tion of markers has been reported for triticale chromosome

2A and 1R (Alheit et al. 2011); LG1, LG2 and LG3 of

Medicago truncatula (Studer et al. 2010) and M20 and M32

of Zoysia (Li et al. 2010). Clustering of distorted markers

was also documented in lettuce (Truco et al. 2007), Euca-

lyptus (Brondani et al. 2006) and peanut (Hong et al. 2010).

Map distance and map order can both be affected by

segregation distortion (Lyttle 1991; Zhu et al. 2007) as was

observed in the SU population where large gaps were

observed between blocks of non-Mendelian markers adja-

cent to blocks of markers with non-skewed segregation,

which accounted in part for the overestimation of the map

length for this population. Elimination of non-Mendelian

marker loci was suggested to improve mapping accuracies

(Zhu et al. 2007; Xu 2008). However, such an approach

would decrease the number of markers available and

reduce coverage of some genomic regions, hence dimin-

ishing the map saturation (Zhu et al. 2007; Xu 2008). Here,

we clearly demonstrated that consensus mapping was a

powerful way to correct for mapping inaccuracies caused

by non-Mendelian markers because consensus mapping

takes into account segregation data from multiple popula-

tions including common markers with Mendelian segre-

gation in at least one population.

Anchoring genetic and physical maps

The physical map of flax is comprised of 416 FPC contigs

spanning *368 Mb (Ragupathy et al. 2011). A total of 670

markers were anchored to 204 FPC contigs representing

*274 Mb, i.e. 74 % of the estimated 370 Mb genome of

CDC Bethune, comparable to papaya (72.4 %, Yu et al.

2009), apple (60 %, Han et al. 2011) and grapevine (72 %,

Scalabrin et al. 2010) genomes and exceeding the extent of

anchoring reported in Medicago truncatula (32 %, Mun

et al. 2006), Populus trichocarpa (22 %, Kelleher et al.

2007), Prunus (15.5 %, Zhebentyayeva et al. 2008), bean

(8 %, Cordoba et al. 2010) and melon (12 %, Gonzalez

et al. 2010). Although sufficient to provide initial ordering

of the WGS sequence assembly into bins, the level of

anchoring of the physical and genetic maps of flax pre-

sented herein falls short of the requirement for high accu-

racy ordering and orienting of the scaffolds of genomic

sequence as was shown in maize (93 %, Wei et al. 2009)

and rice (91 %, Chen et al. 2002). Tens of thousands of

genome-wide SNPs currently being developed in our lab

from the three mapping populations, using the state of the

art ‘genotyping by sequencing (GBS)’ approach (Davey

et al. 2011) will likely provide the degree of saturation

necessary for the task of obtaining an accurate physical

map ordering and orientation, a prerequisite for a high

quality genome sequence assembly.

In conclusion, we reported on the construction of the

first consensus genetic map of flax using 411 individuals

from three populations and grouping and ordering 770

markers in 15 LGs spanning 1,551 cM. The vast majority

of the markers are SSRs, a highly reproducible marker

system which should prove its usefulness as an important

resource for the flax research community, especially flax

breeders. The overall map density averaged one marker

every 2.0 cM. The consensus genetic map has been

anchored to the flax physical map, a first step in the

ordering of the scaffolds that currently make up the WGS

sequence assembly of the flax genome. This integrated map

will enable structural and functional genomic studies

including fine mapping of genes of interest, marker-assis-

ted flax breeding, map-based gene cloning, comparative/

synteny mapping, QTL analysis and association mapping

in flax and other related species.

Acknowledgments We sincerely thank Rae-Ann Trudeau for

technical assistance, Joanne Schiavoni for manuscript editing and

Theor Appl Genet (2012) 125:1783–1795 1791

123

Michael Shillinglaw for figure preparation. This research is part of the

Total Utilization Flax GENomics (TUFGEN) project funded by

Genome Canada and co-funded in part by the Agriculture Develop-

ment Fund of Saskatchewan, the Governments of Manitoba and

Saskatchewan, the Flax Council of Canada and the Manitoba Flax

Growers Association. Project management and support by Genome

Prairie are also acknowledged.

Open Access This article is distributed under the terms of the

Creative Commons Attribution License which permits any use, dis-

tribution, and reproduction in any medium, provided the original

author(s) and the source are credited.

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