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Table 5 Candidate genes for functional marker development

From: Recent advancements in molecular marker-assisted selection and applications in plant breeding programmes

Crop Trait/resistance Gene (s) Location in chromosome Sequence FW/REV References
Wheat Semi-dwarf stature Rht-B1 and Rht-D1 4B, 4D F-TCTCCTCCCTCCCCACCCCAAC
R-CCATGGCCATCTCGAGCTGC
&
F-CGCGCAATTATTGGCCAGAGATAG
R-CCCCATGGCCATCTCGAGCTGCTA
[105]
Grain weight TaSus2-2B 2 F-CGCCCTGAGCCG CATCCACA
R-CGCTCGCCCGC CATTTATTTCTCT
[106]
Grain weight TaGW2 6 F-ATGGGGAACAGAATAGGAGGGAGGA
R-CGAGTATGCCTAGAATGGAAAGAC
[107]
Photoperiod response Phd-H1 2 F-ACGCCTCCCACTACACTG
R-CACTGGTGGTAGCTGAGATT
[108]
Vernalization Vrn-D4 5 F-CATAATGCCAAGCCGGTGAGTAC
R-ATGTCTGCCAATTAGCTAGC
[109]
Low molecular weight glutenin Glu-D3 and Glu-B3 1D F-CAGCTAAACCCATGCAAGC
R-CAATGGAAGTCATCACCTCAA
[110]
Yellow pigment content Psy1 7A F-ACATGCCGCTACTCCTATCC
R-GTAGAGTGGCCAGACAAGGT
[111]
Lipoxygenase gene Talox-B1 4B F-ATGATACTGGGCGGGCTCGT
R-TCAGATGGAGATGCTGTTGGG
[112]
Powdery mildew Pm3 1A F-CAAGTACCAACCACAGCCAC
R-CCATTGCAACCACAGGAACA
[113]
Stem rust resistance Sr45 1D F-GTCCATTTTACGACGGTCCG
R-CTGGTCGGTAGGGAAGCTAG
[114]
Drought stress tolerance DREB1 3D F-GAATGGATCCCGGAAAGCAC
R-GGGAATGAACCAAGCCACAG
[115]
Rice Semi-dwarf sd1 1 F-CACGCACGGGTTCTTCCAGGTG
R-AGGAGAATAGGAGATGGTTTACC
[116]
Wide-compatibility gene S5n 6 F-CGTCTTGCTTCTTCATTCCC
R-GTAGGTAAACACAGGCAGAG
[117]
Photoperiod-thermo-sensitive genic male (PGMS and TGMS) sterility pms3 (p/tms12-1) 12 F-GAATGCCATCTAAACACT
R-ATTTTACTCTTGATGGATGGTC
[118]
Fragrance badh2 8 F-AGTTATGGTCTGGCTGGTGC
R-TTGTGTGCTACCCACCCTTC
[119]
Fragrance nksbad2 4 F-ATGGCAACATGGAAGGTAGC
R-CATCAGCAAGCTCCAAACAA
[120]
Low glutenin content Lgc1 10 F-TTCTACAATGAAGGCGATGC
R-CTGGGCTTTAACGGGACT
&
F-ACCGTGTTATGGCAGTTT
R-ATTCAAGGGCTATCGTCT
[121]
Fe and Zn OsNAS3, OsNRAMP1 7 F-TCCATCGCTTGCTACCTCAC
R-CCCGGAGATCGATCGAGACA
&
F-AGCACTCCCCCATCAATCAA
R-ACTACACGGGTGGCTCTTTG
[122]
Intermediate amylose content Wx-in 6 F-CAGCGTCGACGTAAGCCTAT
R-CAGGCCCCTGAAATCCATGT
[123]
Bacterial blight resistance Xa3 11 F-GAATGGGTGGGGTTGGGAAG
R-CCATGCACGCTTGTCGAATC
[124]
Brown planthopper resistance Bph14 3 F-CAATCCGAGCTTACGTGGTG
R-GGTGGAGAAGGCAAGAGTCT
[125]
Blast resistance Pit 1 F-GTGACGGAAGTGCATGGGTA
R-ACCAGGGAACCCGACAAGAA
[126]
Submergence tolerance SubA1 9 F-CTAGTTGGGCATACGATGGC
R-ACGCTTATATGTTACGTCAAC
[127]
Tolerance to phosphorus (P) deficiency Pup 1 12 F-CTGGACTTGACCCCAATGTA
R-TCTGATGGAGTGTTCGGAGT
[128]
Drought stress tolerance OsSAPK2 5 F-AAGGACATAGGGTCGGGGAA
R-TGGCCAAATGTGTGGGAGTT
[129]
Maize Plant stature tb1 1 F-CACATGAGCCCATGCCTCTC
R-AAAGCGGTAAGTCCATGGGG
[130]
Plant height Dwarf8 1 F-ACACTATCACCGCTCTATTG
R-ACTCTTTCCCTGACTTCATT
[131]
Oil content DGAT1-2 6 F-TGGCTCTGCAATCAGGAGAA
R-TGAAGCAGCAAACAACGAGC
[132]
Forage quality for digestibility Bm3 4 F-TTCAACAAGGCGTACGGGAT
R-AGTGGTTCTTCATGCCCTCG
[133]
Provitamin A ZmcrtRB3 2 F-GTCGGTACTGGCAAGTGGAA
R-TAGTACGTGGCCATGACGTG
[134]
Sweetness sugary1 4 F-TCCCGACTTCAGAACGGTTG
R-ACAACAGAGCAACCCCAACA
[135]
Drought tolerance MYBE1 5 F-GGTACCCTGTCAAGGTTCGG R-AATTACTGGCCCCAGGTTCG [136]
Barley Photoperiod response Phd-H1 7 F-CCTCTTCGCTATTAC GCCAG
R –GCCCTTCCCAACAGTTGCG
[137]
Vernalization requirements VRN-H 1 5 F-TTCATCATGGATCGCCAGTA
R-AAAGCTCCTGCCAACTACGA
[138]
Powdery mildew NBS–LRR 2 F-CGTTTTGTATGGCGTCCGAT
R-TTGTCGCTGAGGTCCATCTT
[139]
Leaf rust resistance Rph7 3H F-TGGAAACCACTGTACAGCCT
R-CAGGCATGGGAGTGAACCTA
[140]
Photoperiod response Phd-H1 2H F-GTTGAGATCGACAGTCCCCA
R-GGGCTCCTATCTCCAACTCC
[137]