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. 2020 Feb 10;133(5):1791–1810. doi: 10.1007/s00122-020-03560-w

Table 1.

List of QTL cloning and fine mapping studies reported during the pre-NGS and post-NGS era

Crop Study Trait Primary mappinga Fine mapping Population Size Markers usedb Refined Size References
Pre-NGS
 Arabidopsis QTL cloning Flowering (FRI and FIC) M2 lines Test cross lines 4500 SSR 15 kb Michaels and Amasino (1999)
QTL cloning Ascorbate biosynthesis (VTC2) F2 F2 3700 InDel 20 kb Jander et al. (2002)
 Rice QTL cloning Grain width and weight (GW2) F2 BC3F2 6013 RFLP 82 kb Song et al. (2007)
QTL cloning Grain number BIL NIL + × NIL − _F2 13,000 SNP 63 kb Ashikari et al. (2005)
QTL cloning Heading date RIL RIL + × P1_BC2F2 8400 SSR 2 Mb Xue et al. (2008)
QTL cloning Grain weight F2 BC2F2 674 STS 122 kb Guo et al. (2009)
QTL cloning Heading date (Hd1) F2 BC3F3 > 9000 RFLP, CAPS 71 kb Yano et al. (2000)
QTL cloning Submergence (Sub1A) F3 F2 2950 AFLP 182 kb Xu et al. (2006)
QTL cloning Photoperiodic flowering (Ehd1) BC2F1 NILs (BC6F2) >2500 RFLP, CAPS 115 kb Doi et al. (2004)
QTL cloning Seed hull color CSSL F2 (NIL) 3276 SSR, SNP 88 kb Zhu et al. (2011)
QTL cloning Rooting depth RIL NIL (BC3F2) 4560 SSR 60 kb Uga et al. (2013)
QTL cloning Grain weight (OsglHAT1) BIL F3 (NIL) 3012 SNP 12 kb Song et al. (2015)
Fine mapping Photoperiod sensitivity BCF4F2 BC3F3/BC4F3 2807 CAPS 264 kb Takahashi et al. (2001)
Fine mapping Stele transversal area F3 BC2F1 to BC2F4 8–160 InDel 359 kb Uga et al. (2011)
 Maize QTL cloning Plant architecture (tb1) F2 F1 and F2 26,000 and 42 RFLP 15 kb Doebley et al. (1997)
QTL cloning Leaf angle (ZmCLA4) F3 BC5F2 (BC3F1 to BC5F2) 10,628 SSR 48 kb Zhang et al. (2014)
QTL cloning Glume architecture (Tga1) F2 F2 3106 SNP 1042 bp Wang et al. (2005)
QTL cloning Flowering time (vgt1) NIL F2 (NIL) 4526 AFLP, CAPS, ASPCR 2 kb Salvi et al. (2007)
Fine mapping Maize streak virus resistance F3 F2 4725 SNP 762 Mb Nair et al. (2015)
Fine mapping Rough dwarf resistance (qMrdd1) HIF BC1F3 2685 SSR, SNP 12 Mb Tao et al. (2013)
QTL cloning Root initiation (RTCS) F2 F2 2000 SSR, CAPS 735 bp Taramino et al. (2007)
 Wheat QTL cloning Dormancy MAGIC HIF, NIL 5 NIL sets SNP 3 genes Barrero et al. (2015)
Fine mapping Grain weight BC2F3 BC4F2, BC4F3 118 and 264 SSR 76 cM Roder et al. (2008)
 Barley Fine mapping Frost resistance DH F2 1849 RFLP, SNP, CAPS 0.81 cM Francia et al. (2007)
Fine mapping Grain Threshability BC2DH BC4F2 7000 SSR, SNP 43 cM Schmalenbach et al. (2011)
QTL cloning Boron tolerance (Bot1) DH lines F3 6720 CAPS 0.05 cM Sutton et al. (2007)
 Soybean Fine mapping Seed number and leaflet shape BC3F2 BC3F3 4635 SSR 66 kb Jeong et al. (2012)
 Tomato QTL cloning Fruit weight (fw22) F2 F2 3472 RFLP, RAPD, CAPS 663 bp Frary et al. (2000)
QTL cloning Sugar content (brix9-2-5) NIL F2 7000 RFLP, RAPD, CAPS 484 bp Fridman et al. (2000)
QTL cloning Locule number (lc) F2 F2 9456 SNP, CAPS 1608 bp Munos et al. (2011)
Fine mapping Tomato yellow leaf curl virus resistance F3 F4 11,000 SSR 491 kb Yang et al. (2014)
Fine mapping Fruit mass and Brix IL IL 50 RFLP 32 and 12 cM Eshed and Zamir (1995)
Fine mapping Sugar content IL F2 (NIL) 7000 RFLP, SNP 484 bp Fridman et al. (2000)
Fine mapping Fruit mass IL NIL 3472 RFLP, RAPD 150 kb Alpert and Tanksley (1996)
Post-NGS
 Arabidopsis Fine mapping Flowering time F2 NA 192 GBS-SNP 9 kb Rowan et al. (2015)
Fine mapping Rosette leaf number (recq4a) F2 NA 192 GBS-SNP 269 kb Rowan et al. (2015)
 Rice Fine mapping Leaf width, aluminum tolerance RIL NA 176 GBS-SNP < 2 Mb Spindel et al. (2013)
Fine mapping Plant height RIL NA 150 WGRS-SNP 100 kb Huang et al. (2009)
Fine mapping Tillering and panicle branching F2 NA 1642 SSR, SNP 63 kb Yu et al. (2017)
Fine mapping Brown planthopper (BPH31) F2 NA 27 InDel 475 kb Prahalada et al. (2017)
Fine mapping Grain weight, grain length, grain width BIL NA 185 GBS-SNP 32–363 kb Bhatia et al. (2018)
 Maize Fine mapping Tassel and ear architecture F2 NA 708 GBS-SNP 08–566 Mb Chen et al. (2014)
 Wheat Fine mapping Grain protein content (GPC-B1) RSL F3 28 SNP 0.45 cM Trick et al. (2012)
Fine mapping Powdery mildew (PmTm4) resistance F2 NA 1499 SNP 066 cM Xie et al. (2017)
 Barley Fine mapping Awn length HIF NA 927 SNP < 0.9 cM Liller et al. (2017)
 Sorghum Fine mapping Grain weight F2 F3 307 SSR 101 kb Han et al. (2015)
Fine mapping Seed dormancy F2 F3 80 SSR 96 kb Li et al. (2016a)
 Common bean Fine mapping Angular leaf spot resistance (ALS41GS,UC) F4, Backcross lines NA 180 SSR, SNP 418 kb Keller et al. (2015)
 Chickpea Fine mapping Ascochyta blight RIL bulks NA 20 QTL-Seq SNP 15–64 Mb Deokar et al. (2019)
 Soybean Fine mapping Phytophthora resistance F2 F3 826 SSR, CAPS, SNP 36 kb, 151 kb Li et al. (2016b)
Fine mapping Root knot nematode resistance RIL NA 246 WGRS-SNP 297 kb Xu et al. (2013)
 Tomato Fine mapping Fruit shape (fs81) Backcross lines NA 3 SNP, dCAPS 303 Mb Sun et al. (2015)

aAbbreviations for primary population used: CSSLs chromosome segment substitution lines, HIFs heterogenous inbred families, RSLs recombinant substitution lines, MAGIC multi-parent advanced generation inter-cross, DH double haploid, BILs backcross inbred lines, NIL near-isogenic line, RIL recombinant inbred line, IL introgression line

bAbbreviations for markers used: RFLP restriction fragment length polymorphism, RAPD random amplified polymorphic DNA, AFLP amplified fragment length polymorphism, SSR simple sequence repeat, STS sequence-tagged site, SNP single-nucleotide polymorphism, CAPS cleaved amplified polymorphic sequence, dCAPS derived cleaved amplified polymorphic sequences, InDel insertion and deletion, ASPCR allele-specific polymorphic chain reaction, GBS-SNP SNPs derived from genotyping by sequencing, WGRS-SNP whole-genome resequencing, QTL-Seq QTL-Seq analysis