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Table 1 Genes ID, analyzed length and total polymorphisms found in 19 sunflower inbred lines

From: Identification of Single Nucleotide Polymorphisms and analysis of Linkage Disequilibrium in sunflower elite inbred lines using the candidate gene approach

Strategy of selection Gene Similarity (BLASTx searches)a Description STb N° Indelsc Total length (bp)d Coding region (bp)d Noncoding region (bp)d
Sunflower SSH-EST library survey GO Glycolate oxidase (Spinacia oleracea) Electron carrier ROS machinery [69] 2 1 (36) 608 300 308
  PGIP3 Poligalacturonase inhibitor protein precursor (Actidinia deliciosa) Plant defense against diverse pathogens that use polygalacturonase to breach the plant cell wall [70] 3 0 (0) 676 561 115
  LZP Leucine zipper protein putative (Triticum aestivum) Transcriptional factors involved in plant development, photomorphogenesis and responses to stress [71] 0 1 (8) 425 84 341
  GLP Germin-like protein (Oryza sativa) Apoplastic and glycosilated protein shown to be involved in plant defense [72] 0 3 (3) 876 648 228
Literature search MADSB-TF3 MADS-box transcription factor (Helianthus annuus) Transcription factors acting as regulators of various aspects of plant development [73] 13 11 (20) 1082 291 791
  AALP Arabidopsis Aleurain-like protease (Arabidopsis thaliana) Enzyme involved in macromolecular degradation and recycling, its expression is up-regulated during aging-related and harvesting-induced senescence [74] 10 2 (11) 269 189 80
  LIM LIM domain protein PLIM1b (H. annuus) Transcription factors that play important roles in construction of cytoskeleton and signal transduction [75] 6 2 (5) 319 150 169
in silico analysis with SNP Discovery RL41 60S ribosomal protein L41 (A. thaliana) Protein component of the Ribosomal 60S subunit, important for the translational apparatus and involved in apoptosis and cell cycle [76, 77] 3 0 (0) 100 66 34
  ANT Adenine nucleotide translocator, mitochondrial precursor (Gossypium hirsutum) Inner-membrane mitochondria carrier that plays roles in integrating celullar stress and regulating programmed cell death [78] 9 0 (0) 216 213 3
  RS16 40S ribosomal protein S16 (Euphorbia esula) Ribosomal S16 component retained during desiccation process in water stress tolerant plants [79] 7 0 (0) 448 405 43
  NsLTP Nonspecific lipid-transfer protein precursor (H. annuus) Participates in cutin formation, embryogenesis, defense reactions against phytopathogens, symbiosis and adaptation to various environmental conditions [80] 7 2 (13) 294 96 198
  SEM Probable 26S proteasome complex subunit sem1–2 (H. annuus) Complex involved in protein turnover pathway, helps to remove proteins that arise from synthetic errors, spontaneous denaturation, free-radical and enviromental stress induced damage [81] 3 0 (0) 226 87 139
  SAMC S-adenosylmethionine decarboxylase (Daucus carota) Key enzyme in PolyAmines (PAs) biosynthesis. PA synthesis is induced by high osmotic pressure, low temperature, low pH and oxidative stress. PAs are proposed to have resistance roles in plant-microbe interactions [82] 12 1 (3) 369 189 180
  GCvT Glycine cleavage symstem T protein (Flaveria trinervia) The glycine cleavage system catalyzes the oxidative decarboxylation of glycine in bacteria and in mitochondria of animals and plants [83] 3 0 (0) 183 180 3
  SBP Sedoheptulose-1,7-bisphosphatase, chloroplast (A. thaliana) Calvin Cycle's enzyme: branch point between regeneration of ribulose 1,5 biphosphate and export to starch biosynthesis. The overexpression of SBP increases photosynthetic carbon fixation and biomass in plants [84] 11 0 (0) 243 240 3
  LHCP Light-harvesting chlorophyll a/b-binding protein precursor (L. sativa)   8 0 (0) 362 348 14
  CPSI Photosystem I reaction center subunit V, chloroplast precursor (Camellia sinensis) Genes encoding components involved in photosynthesis which showed differential expression patterns under both chilling and salt stresses in sunflower [69] 4 0 (0) 168 144 24
  PSI-III-CAB Pothosystem I type III chlorophyll a/b-binding protein (A. thaliana)   1 1 (1) 710 387 323
  CAB Chlorophyll a/b-binding protein (Beta vulgaris)   7 2 (10) 537 393 144
Comparison purposes CAM Calmodulin (Morus nigra) Plays a central role in calcium-mediated signaling [46] 29 6 (93) 538 117 421
  CHS Chalcone synthase (Saussurea medusa) Plays an essential role in the biosynthesis of plant phenylpropanoids [46] and abiotic stress defense responses [85, 86] 0 0 (0) 1051 978 73
  GAPDH Glyceraldehyde-3-phosphate dehydrogenase (Glycine max) Tetrameric NAD1 binding protein that is involved in glycolysis and gluconeogenesis [46] 2 2 (3) 782 617 165
  GIA Gibbelleric acid insennsitive-like protein (Lactuca. sativa) Putative gibberellin response modulator [46] 2 1 (1) 749 504 245
  GPX Putative gluthathione peroxidase (Medicago truncatula) Antioxidant enzymes suggested as important factors in protection mechanisms against oxidative damage [46] 0 1 (6) 744 513 231
  GST Glutathione S-transferase (Pisum sativum)   40 0 (0) 561 351 210
  PGIC Cytosolic phosphoglucose isomerase (Stephanomeria tenuifolia) Catalyzes the reversible isomerization of 6-phosphoglucose and 6-phosphofructose, an essential reaction that precedes sucrose biosynthesis [46] 15 2 (4) 569 219 350
  SCR1 Scarecrow transcription factor type 1(Castanea sativa) SCARECROW-like gene regulators are known to be involved in asymmetric cell division in plants [46] 3 0 (0) 739 732 7
  SCR2 Scarecrow transcription factor type 2 (O. sativa)   7 0 (0) 504 504 0
Total     207 38 (217) 14,348 9,506 4,842
Average/locus     7.39 1.36    
Frequency     1/69 1/377.6    
  1. aGene coding regions and functions were determined by BLASTx searches.
  2. bTotal single nucleotide polymorphisms (ST).
  3. cNumber of indels counted according to blocks of insertions and deletions. The total bp length of indels is displayed in brackets.
  4. dTotal length, coding and non-coding region are displayed excluding indels.
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