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Table 1 Application and information of resequencing in rice

From: Application of resequencing to rice genomics, functional genomics and evolutionary analysis

Materials Depth of sequencing SNPs Research purposes References
132 RILs of a super hybrid rice >4× 171,847 Improving parental genome sequences (Gao et al. [2013])
Liang-You-Pei-Jiu >36× for parents   Dissecting yield-associated loci  
1083 cultivated rice* >1 ~ 50× 7,970,359 Domestication analysis of cultivated rice Huang et al. ([2012a])
446 wild rice    Identifying agronomic QTL  
40 cultivated rice > 15× 6,500,000 Identifying agronomic QTL Xu et al. ([2012])
10 wild rice    Domestication analysis  
950 cultivated rice >1× 4,109,366 GWAS study of flowering time and grain yield traits Huang et al. ([2012b])
517 rice landraces >1× 3,625,200 GWAS study of 14 agronomic traits Huang et al. ([2010])
150 RILs of Nipponbare/93-11 >20× 1,226,791 Large-scale gene discovery Huang et al. ([2009])
    Identifying 49 QTLs for 14 agronomic traits Wang et al. ([2011])
128 CSSLs of Nipponbare/93-11 >0.13× 7,680,000 QTL mapping for culm length Xu et al. ([2010])
    High-throughput genotyping  
5 cultivated rice >58× 1,154,063 Genetic diverse analysis (Jeong et al. [2013])
A restorer line 7302R >13× 307,627 Genetic variation identification (Li et al. [2012])
4 other cultivated rice     
241 RILs of a hybrid rice Shanyou 63 > 0.06× 270,820 QTL detection for grains Yu et al. ([2011])
40 RILs of Nortai/Hitomebore (bulked) >6× 161,563 Rapid QTL mapping Takagi et al. ([2013])
50 F2 lines of Dunghan Shali/Hitomebore     
781 F2 lines of R1128/Nipponbare >16× 74,329 Genetic analysis for super hybrid rice Duan et al. ([2013])
Koshihikari 15.7× 67,051 Evaluate the dynamics of the genome composition Yamamoto et al. ([2010])
  1. *1083 accessions of cultivated rice cultivars in the ref. of Huang et al. ([2012a]) include the 950 accessions of cultivated rice in the ref. of Huang et al. ([2012b]), which include the 517 accessions of rice landraces in the ref. of Huang et al. ([2010]).