中国农业科学院 作物科学研究所
Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China

 

The Rice F2 population

 

1. Introduction

 

The F2 population consists of 180 individuals and was derived by the Rice Research Institute, Sichuan Agricultural University (Ye et al . 2005; Ye et al . 2007). The cross was made in Chengdu , China in July 2002 between the indica rice variety PA64s (Pei'Ai 64s in full name) and japonica rice variety Nipponbare. Nipponbare was completely sequenced in 2002, and PA64s was partially sequenced in the same year. The F 1 population was planted in Hainan , China in December 2002, and the F 2 population was planted in Chengdu , China in April 2003 for genotyping and phenotyping. A total of 137 SSR markers were screened for building the linkage map (Ye et al . 2005), and a number of agronomic traits were investigated in the field (Ye et al . 2005; Ye et al . 2007).

 

2. Number of markers on chromosome or linkage group

 

Chromosome   1a        4

Chromosome   1b      12

Chromosome   2        16

Chromosome   3a        4

Chromosome   3b      10

Chromosome   4          9

Chromosome   5        15

Chromosome   6a      11

Chromosome   6b        5

Chromosome   7          8

Chromosome   8a        3

Chromosome   8b        7

Chromosome   9           8

Chromosome 10a        5

Chromosome 10b        3

Chromosome 11        11

Chromosome 12           6

 

3. Linkage map represented by marker interval length ( RiceF2 LinkageMap)

 

4. Marker type (0, PA64s; 2, Nipponbare; -1, missing) (RiceF2 MarkerType)

 

5. Plant height (cm)

 

110.0 105.0 90.0 110.0 108.0 116.0 103.0 129.0 121.0 103.0 113.0 116.0 100.0 100.0 117.0 96.0 101.0 102.0 112.0 112.0

100.0 121.0 110.0 107.0 90.0 119.0 112.0 98.0 120.0 105.0 98.0 111.0 84.0 91.0 88.0 114.0 89.0 98.0 98.0 99.0

85.0 116.0 91.0 96.0 114.0 88.0 102.0 113.0 108.0 110.0 116.0 116.0 109.0 86.0 101.0 115.0 107.0 106.0 85.0 108.0

113.0 93.0 110.0 91.0 105.0 97.0 84.0 105.0 107.0 115.0 108.0 85.0 119.0 90.0 86.0 97.0 112.0 119.0 122.0 112.0

96.0 110.0 101.0 115.0 75.0 122.0 103.0 117.0 106.0 97.0 108.0 88.0 99.0 109.0 118.0 101.0 92.0 104.0 88.0 109.0

107.0 92.0 100.0 99.0 113.0 97.0 119.0 87.0 84.0 114.0 97.0 110.0 126.0 112.0 114.0 109.0 78.0 96.0 103.0 104.0

103.0 98.0 110.0 96.0 79.0 114.0 104.0 98.0 81.0 95.0 122.0 106.0 105.0 93.0 122.0 93.0 93.0 106.0 100.0 100.0

129.0 114.0 97.0 109.0 93.0 101.0 111.0 110.0 115.0 116.0 104.0 107.0 94.0 77.0 92.0 110.0 85.0 92.0 94.0 103.0

121.0 117.0 92.0 116.0 98.0 104.0 127.0 121.0 105.0 82.0 111.0 101.0 91.0 132.0 107.0 105.0 127.0 107.0 96.0 105.0

 

6. Input file for QTL mapping

 

6.1 Input file for Cartographer ( RiceF2.mcd)

 

6.2 Input file for IciMapping ( RiceF2.qtl)

 

6.3 Input file for R/qtlbim ( RiceF2. csv )

 

7. QTL analysis for plant height in rice

 

7.1 Results from Cartographer

 

 

 

7.2 Results from IciMapping

 

 

 

7.3 Results from R/qtlbim

 

          

 

8. References

 

Ye, S.-P., Q.-J. Zhang, J.-Q. Li, B. Zhao and P. Li, 2005 QTL mapping for yield component traits using (Pei'ai 64s/Nipponbare) F 2 population (in Chinese with English abstract). Acta Agronomica Sinica 31: 1620-1627.

Ye, S.-P., Q.-J. Zhang, J.-Q. Li, B. Zhao, D.-S. Yin and P. Li, 2007 Mapping of quantitative trait loci for six agronomic traits of rice in Pei'ai 64s/Nipponbare F 2 population (in Chinese with English abstract). Chinese J. Rice Sci. 21: 39-43.