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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 Huang et al. ([2012a]), Xu et al. ([2012]) PROG1 (Jin et al. [2008]; Tan et al. [2008])
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])