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Table 1 Positional candidate genes for Mt-FTQTL6

From: A tandem array of CBF/DREB1 genes is located in a major freezing tolerance QTL region on Medicago truncatula chromosome 6

Gene ID [reference]

BAC clone and/or WGS sequence

EST (1)

cDNA (1)

Number of splicing isoforms

Number of intron(s) in the coding sequence [intron size(s) in bp]

Putative gene product

Amino acid length [length of the acidic C-terminal domain] (2)

Theoretical molecular weight (KDa)

Theoretical pI [pI of the C-terminal domain] (2)

MtBAG - 1[40]

-

AW299190; BG646253; AW257319; AW256371; BI308136; AL369679; AW329645; AL373067; BF006595; AW694037; BF650244; AL373068; CA919955; AL373067; CA917144; BE325495; EX533119; BG588510; BE322176

-

1

-

Bcl-2-associated athanogene

355

39.9

9.37

MtCBF14

Scaffold065bis

-

-

-

-

CBF/DREB1 protein

230 [103]

25.74

5.55 [4.02]

MtCBF13

Scaffold065bis

-

-

-

-

CBF/DREB1 protein

-

-

-

MtCBF3[32]/MtDREB1C[14]

Scaffold065bis

CA920049; CF069650; BG581707; BF005835; BQ138271; BG582534

DQ267620; EU139868

1

-

CBF/DREB1 protein

227 [109]

25.99

5.64 [4.11]

MtCBF12

Scaffold065bis

GT136747; GT141343

BT134401

1

-

CBF/DREB1 protein

-

-

-

MtCBF11

Scaffold065bis

-

-

-

-

CBF/DREB1 protein

281 [103]

31.21

5.66 [4.07]

MtCBF2[32]

Scaffold065bis; mth2-221P20; mte1-60A22

BF520341

EU139867

1

-

CBF/DREB1 protein

230 [106]

26.07

5.8 [4.12]

MtCBF10

Scaffold065bis; mth2-221P20; mte1-60A22

-

-

-

-

CBF/DREB1 protein

198 [104]

22.58

5.39 [4.03]

MtCBF9

Scaffold065bis; mte1-60A22

CX528143

-

1

-

CBF/DREB1 protein

208 [114]

24.04

4.99 [3.94]

MtCBF8 (a)

Scaffold065bis; mte1-60A22

EY477920; BQ165478; CA921976; BF005540; AW573630; BQ165479; EY476564; BE999274; BE998545;BE999273; CB893700

DQ778006; BT146058

2

no intron/1 intron [316]

CBF/DREB1 protein

215 [100]/271 [156]

24.87/31.11

6.1 [4.27]/8.37 [4.92]

MtCBF7

Scaffold065bis; mte1-60A22

BF005905

-

1

1 intron [279]

CBF/DREB1 protein

245 [130]

27.88

6.66 [4.60]

MtCBF6

Scaffold065bis; mth2-92O15

CF069139; AW775188; BF006671;CA919708

-

2

no intron/1 intron [352]

CBF/DREB1 protein

216 [101]/248 [133]

24.67/28.23

6.31 [4.22]/8.41 [4.84]

MtCBF5

Scaffold065bis; mth2-92O15

BG648933; BF005756; CA920720

-

1

1 intron [380]

CBF/DREB1 protein

267 [152]

30.54

8.87 [5.04]

MtPERLD

Scaffold065bis; mth2-92O15

BF631847; EV255869; AL373022; CB892925; EY476043; BG449960; BG648146; BF639371; BG648635; CX527766; CX527793; CX527254; BI267056; BF521243; BF642637; CX523947; BE319009; AL373021; BF635170; BM779066; BQ152673; AW736243; BG646840

BT051744; BT139597

2

4 introns [2807;93;1008;2220]/ 5 introns [123; 2663; 93;1008;2220]

Per1-like family protein

342

39.48

7.6

MTR _050s0020[23]

Scaffold065bis; mth2-92O15; mth2-53l24 (GB acc AC229695) (b)

BF635955; GT141039; GT136423

-

1

15 introns [2336; 137; 162; 266; 470; 89; 86; 126; 80; 626; 88; 84; 86; 80; 450] (c)

ABC transporter B family member

715

78.37

9.07

MTR _050s0019[23]

Scaffold065bis; mth2-92O15; mth2-53l24 (GB acc AC229695)

EV258193; CX522284

BT147320

1

1 intron [721]

Conserved uncharacterized protein

242

26.45

8.56

MtZFWD

Scaffold065bis

CX520203; BE239869

-

1

8 introns [939; 162; 143; 306; 104; 78; 598; 759] (d)

Zinc finger CCCH and WD40 domain-containing protein

438

47.29

7.85

MTR _054s0001[23]

Scaffold065bis; mth2-12e18 (GB acc AC229727)

BQ138417

-

1

11 introns [1352; 982; 1537; 116; 110; > 418; 443; 1495; 27; 139; 627] (e)

DNA 3′- phosphoesterase

338

37.66

6.56

MTR _054s0019[23]

Scaffold065bis; mth2-12e18 (GB acc AC229727)

CB894631; CF068286; DW018377; BG647692; BE316675; EV256045; BF639952; CB893865; EV261994; BE322046; BI263625; AW691341; CX535182; BI265523; BE998615; CA918979; BI266410; CA858657; BF520558; BF637666; BI267231; AJ503890

BT051762; BT148189; BT136112

2

5 introns [938; 202; 1366; 511; 864]/ different translation start site and novel intron of 4532 bp

Sorbitol dehydrogenase-like protein

362

39

6.13

MTR _6g089580[23]

Scaffold065bis; mth2-50m10 (GB acc AC174372)

BG648131; AW685633; AW586532; AI974700; CA920607

-

1

no intron

unknown protein

628

71.8

8.38

  1. (1) Corresponding EST and cDNA were identified through BLAST searches against M. truncatula EST and nr/nt databases in GenBank [36] (January 2013), respectively. In case of alternate splicing, the sequence(s) corresponding to the less represented transcript isoform is(are) in italics; (2) similar to [41], the C-terminal domains of MtCBF2-3;5-11;14 were considered as the amino acid sequences that occur after the signature motif “DSAWR” and that up to the last amino acid of the protein; (a) a cDNA sequence corresponding to MtCBF8 was directly submitted to GenBank [36] by Chen JR, Guo L, Wang H in 2007. The respective locus was referred to as DREB1A; (b) In addition to MTR _050s0019 and MTR _050s0020, 7 other non-transposon genes could be identified on AC229695 but were not considered in this study. In fact, the corresponding genomic region for these latter, spanning 114,402 kb (1-19,425; 23,144-90,266; 147,607-159,557; 185,484-201,386 bp) is completely missing from Scaffold065bis. Because of its size exceeding 200 Kb, AC229695 seems to have resulted from sequencing inserts of at least two BAC clones, one of which did not originate from Mt-FTQTL6-containing region; (c) The intron/exon structure of MTR _050s0020 from M. truncatula Mt3.5 genome assembly has been revised and its corresponding coding sequence found to contain 15 introns instead of 16. M. truncatula EST and close protein sequences together with EST from other Papilionoideae species and notably a Pisum sativum L. sequence generated by RNAseq (Alves Carvalho et al. in preparation) were used for this purpose; (d) As related EST do not fully cover MtZFWD coding sequence, intron positions were predicted after multiple alignment with the coding sequences of Glyma16g32370 and Glyma09g27300 and EST sequences from Lathyrus odoratus L. (GO316201, GO317026, GO319782), L. japonicus (FS347722, FS346164, FS360001) and Phaseolus acutifolius A. Gray (HO781358); (e) As the EST BQ138417 does not cover the entire coding sequence of MTR _054s0001, highly similar EST sequences from L. japonicus (GO014516), Vigna unguiculata (L.) Walp. (FF549909) and G. max (AW184979, FK011826) were used for intron location. The positions and sizes of introns 9 and 10 are different from Mt3.5.
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BMC Genomics

ISSN: 1471-2164

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