Table 2 Key allelic loci fine-mapped using the NGS method in rice
From: Application of resequencing to rice genomics, functional genomics and evolutionary analysis
Trait | QTL | Chromosome | Mapping materials | Reference | Allelic loci |
|---|---|---|---|---|---|
Tiller angle | qTA-9 | 9 | Nipponbare/93-11 | Wang et al. ([2011]) | TAC1 (Yu et al. [2007]) |
Plant height | qPH-1 | 1 | Nipponbare/93-11 | Wang et al. ([2011]) | SD1 (Sasaki et al. [2002]) |
Flag leaf width | qFLW-4 | 4 | Nipponbare/93-11 | Wang et al. ([2011]) | NAL1 (Qi et al. [2008]) |
Grain length | qGL-3 | 3 | Nipponbare/93-11; PA64s/93-11; Zhenshan 97/Minghui 63 | Wang et al. ([2011]), (Gao et al. [2013]), Yu et al. ([2011]) | GS3 (Fan et al. [2006]) |
Grain width | qGW-5 | 5 | Nipponbare/93-11 | Wang et al. ([2011]) | qSW5 (Shomura et al. [2008]) |
Heading date | qHD8 | 8 | PA64s/93-11 | (Gao et al. [2013]) | DTH8 (Wei et al. [2010]) |
Plant height | qPH5 | 5 | PA64s/93-11 | (Gao et al. [2013]) | EUI1 (Luo et al. [2006]) |
Plant height | qPH12 | 12 | PA64s/93-11 | (Gao et al. [2013]) | NRL1 (Hu et al. [2010]) |
Effective tiller number | qETN4 | 4 | PA64s/93-11 | (Gao et al. [2013]) | HTD1 (Zou et al. [2005]) |
Secondary panicle branch No. | qSPB1 | 1 | PA64s/93-11 | (Gao et al. [2013]) | LAX1 (Komatsu et al. [2001]) |
Seed set | qSS12 | 12 | PA64s/93-11 | (Gao et al. [2013]) | P/TMS12-1 (Zhou et al. [2012]) |
Hull color | Domesticaton sweeps | 4 | Natural population | Huang et al. ([2012a]) | Bh4 (Zhu et al. [2011]) |
Tiller angle | Domesticaton sweeps | 7 | Natural population | ||
Seed shattering | Domesticaton sweeps | 4 | Natural population | Huang et al. ([2012a]) | Sh4 (Li et al. [2006a]) |
Grain width | Domesticaton sweeps | 5 | Natural population | Huang et al. ([2012a]) | qSW5 (Shomura et al. [2008]) |
Leaf sheath color & apiculus color | Domesticaton sweeps | 6 | Natural population | Huang et al. ([2012a]) | OsC1 (Saitoh et al. [2004]) |
Seed shattering | Domesticaton sweeps | 1 | Natural japonica population | Huang et al. ([2012a]) | qSH1 (Konishi et al. [2006]) |
Grain quality | Domesticaton sweeps | 6 | Natural japonica population | Huang et al. ([2012a]) | Waxy (Wang et al. [1995]) |
Pericarp color | Domesticaton sweeps | 7 | Natural japonica population | Huang et al. ([2012a]) | Rc (Sweeney et al. [2006]) |
Grain width | gw5, kgw5 | 5 | Zhenshan 97/Minghui 63 | Yu et al. ([2011]) | GW5/qSW5 (Shomura et al. [2008]) |
Pigmentation | qPIG6 | 6 | Zhenshan 97/Minghui 63 | Yu et al. ([2011]) | OsC1 (Saitoh et al. [2004]) |
Gelatinization temperature | qGT6 | 6 | 517 rice landraces | Huang et al. ([2010]) | ALK (Gao et al. [2003]) |
Plant height | qPH1-3 | 1 | R1128/Nipponbare | Duan et al. ([2013]) | Sd1 (Sasaki et al. [2002]) |
Heading date | qPBN6-2 | 6 | R1128/Nipponbare | Duan et al. ([2013]) | Hd1 (Yano et al. [2000]) |
Early heading date | qPBN10-1 | 10 | R1128/Nipponbare | Duan et al. ([2013]) | Ehd1 (Doi et al. [2004]) |
Grain number 1 | qGN1-1 | 1 | R1128/Nipponbare | Duan et al. ([2013]) | Gn1 (Ashikari et al. [2005]) |
Ideal plant architecture | qPL8-1 | 8 | R1128/Nipponbare | Duan et al. ([2013]) | IPA1 (Jiao et al. [2010]) |