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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]).