Chr.1 Chr.2 Chr.3 Chr.4 Chr.5 Chr.6

2 Mb

43.2 Mb

35.9 Mb 36.2 Mb35.5 Mb

29.6 Mb30.7 Mb

Chr.8 Chr.9 Chr.10 Chr.11 Chr.12Chr.7

29.6 Mb

28.4 Mb

22.6 Mb 22.7 Mb

28.4 Mb 27.5 Mb

Introgression fragment of donor BG300 in K354

[37,39,40]

[41][37,40,43]

[41][42]

[34,44]

[34][34,37,38,39]

[37,43]

[40][34,43]

[38]

[36,38]

[34][36,38]

[35,37]

[34,45]

RM490

RM579

RM449

RM129

RM488

RM246RM443

RM297RM212

RM104RM5310

RM236

RM145

RM324

RM262

RM3355

RM263RM221RM183RM318RM240

RM112

RM523

RM175RM489

RM7RM251

RM7365

RM156

RM6832

RM186

RM148RM85

RM6487

RM307

RM6314

RM1155

RM252

RM317

RM255

RM348

RM280

RM1024

RM267

RM13

RM164

RM173

RM274

RM31 RM334

RM540RM469RM587RM510RM217RM253

RM136RM527

RM275

RM3

RM5463

RM295

RM432RM6011

RM346RM455

RM118

RM248

RM337

RM38

RM547

RM331

RM223

RM447

RM316

RM219

RM296

RM257RM288RM328RM215RM245

RM216

RM311

RM1375

RM304

RM286

RM1124

RM202

RM209RM21

RM206

RM224

RM3483RM19

RM247

RM101

RM277

RM7018

RM270

[*] Major CT related QTL reported in ref.*

Additional file 16. Genomic distribution of 17 introgression fragments in K354. A total of 100 polymorphic SSR markers between C418 and donor parent Bg300 were used to construct the recombination map of K354 based on the physical distance of SSR marker. Red rectangles on the chromosome indicate the introgression fragments. Vertical lines on the right side of chromosome indicate the intervals of previously reported QTLs underlying seedling cold tolerance in rice. The number in bracket is the number of reference. According to the polymorphism between the C418 and K354 showing by SSR markers and the position of each SSR marker annotated on GRAMENE database (www.gramene.org), we estimated the introgressed region roughly 2 Mb (~ 8 cM) for just single marker introgressed with flanking non-introgressed marker or the interval between multiple introgressed markers.