Development and high-throughput genotyping of substitution lines carring the chromosome segments of indica 9311 in the background of japonica Nipponbare

Hua Zhang^{a, #},
Qiang Zhao^{b, #},
Zhi-Zhong Sun^a,
Chang-Quan Zhang^a,
Qi Feng^{b, c},
Shu-Zhu Tang^{a, c},
Guo-Hua Liang^{a, c},
Ming-Hong Gu^{a, c},
Bin Han^{b, c},
Qiao-Quan Liu^{a, c
, ,}

a.
Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of the Ministry of Education for Plant Functional Genomics, College of Agriculture, Yangzhou University, Yangzhou 225009, China
b.
National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
c.
National Center for Plant Gene Research (Shanghai), Shanghai 200032, China

More Information

Corresponding author: E-mail address: qqliu@yzu.edu.cn (Qiao-Quan Liu)

These authors contributed equally to this work.

摘要

- /
- /
Abstract: Chromosome segment substitution lines (CSSLs) are useful for the precise mapping of quantitative trait loci (QTLs) and dissection of the genetic basis of complex traits. In this study, two whole-genome sequenced rice cultivars, the japonica Nipponbare and indica 9311 were used as recipient and donor, respectively. A population with 57 CSSLs was developed after crossing and back-crossing assisted by molecular markers, and genotypes were identified using a high-throughput resequencing strategy. Detailed graphical genotypes of 38 lines were constructed based on resequencing data. These CSSLs had a total of 95 substituted segments derived fromindica 9311, with an average of about 2.5 segments per CSSL and eight segments per chromosome, and covered about 87.4% of the rice whole genome. A multiple linear regression QTL analysis mapped four QTLs for 1000-grain weight. The largest-effect QTL was located in a region on chromosome 5 that contained a cloned major QTL GW5/qSW5 for grain size in rice. These CSSLs with a background of Nipponbare may provide powerful tools for future whole-genome discovery and functional study of essential genes/QTLs in rice, and offer ideal materials and foundations for japonica breeding.
- Chromosome segment substitution lines (CSSLs) /
- Molecular marker-assisted selection /
- High-throughput resequencing
These authors contributed equally to this work.
注释:

HTML全文

参考文献(33)

[1]	Ebitani, T., Takeuchi, Y., Nonoue, Y. et al. Breed. Sci., 55 (2005),pp. 65-73
[2]	Feltus, F., Wan, J., Schulze, S. et al. Genome Res., 14 (2004),pp. 1812-1819
[3]	He, F., Xi, Z., Zeng, R.Z. et al. Acta Genet. Sin., 32 (2005),pp. 825-831
[4]	Huang, X.F., Feng, Q., Qian, Q. et al. High-throughput genotyping by whole-genome resequencing Genome Res., 19 (2009),pp. 1068-1076
[5]	International Rice Genome Sequencing Project The map-based sequence of the rice genome Nature, 436 (2005),pp. 793-800
[6]	Jiang, H., Liu, D., Gu, Z. et al. Rapid evolution in a pair of recent duplicate segments of rice J. Exp. Zool. (Mol. Dev. Evol.), 308B (2007),pp. 50-57
[7]	Li, W., Zeng, R., Zhang, Z. et al. Analysis of introgressed segments in near-isogenic lines for F1 pollen sterility in rice Chin. J. Rice Sci., 17 (2003),pp. 95-99
[8]	Liu, G., Li, W., Zeng, R. et al. Development of single segment substitution lines (SSSLs) of subspecies in rice Chin. J. Rice Sci., 17 (2003),pp. 201-204
[9]	McCouch, S., Teytelman, L., Xu, Y. et al. DNA Res., 9 (2002),pp. 199-207
[10]	Murray, M., Thompson, W. Rapid isolation of high molecular weight plant DNA Nucleic Acids Res., 8 (1980),pp. 4321-4325
[11]	Nadeau, J.H., Singer, J.B., Matin, A. et al. Analyzing complex genetic traits with chromosome substitution strains Nat. Genet., 24 (2000),pp. 221-225
[12]	Ookawa, T., Hobo, T., Yano, M. et al. New approach for rice improvement using a pleiotropic QTL gene for lodging resistance and yield Nat. Commun., 1 (2010),p. 132
[13]	Ouyang, S., Zhu, W., Hamilton, J. et al. The TIGR Rice Genome Annotation Resource: improvements and new features Nucleic Acids Res., 35 (2007),pp. D883-D887
[14]	Shen, Y., Jiang, H., Jin, J. et al. Development of genome-wide DNA polymorphism database for map-based cloning of rice genes Plant Physiol., 135 (2004),pp. 1198-1205
[15]	Shomura, A., Izawa, T., Ebana, K. et al. Deletion in a gene associated with grain size increased yields during rice domestication Nat. Genet., 40 (2008),pp. 1023-1028
[16]	Singer, J.B., Hill, A.E., Burrage, L.C. et al. Genetic dissection of complex traits with chromosome substitution strains of mice Science, 304 (2004),pp. 445-448
[17]	Tan, L., Zhang, P., Liu, F. et al. Genome, 51 (2008),pp. 692-704
[18]	Tian, F., Li, D., Fu, Q. et al. Theor. Appl. Genet., 112 (2006),pp. 570-580
[19]	Wang, X., Shi, X., Hao, B. et al. Duplication and DNA segmental loss in the rice genome: implications for diploidization New Phytol., 165 (2005),pp. 937-946
[20]	Wang, J., Wan, X., Crossa, J. et al. Genet. Res., 88 (2006),pp. 93-104
[21]	Wang, X., Zhao, X., Zhu, J. et al. DNA Res., 12 (2006),pp. 417-427
[22]	Weng, J., Gu, S., Wan, X. et al. Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight Cell Res., 18 (2008),pp. 1199-1209
[23]	Wu, X.J., Zuo, S., Chen, Z. et al. Theor. Appl. Genet., 122 (2010),pp. 915-923
[24]	Xu, H.S., Sun, Y.J., Zhou, H.J. et al. Development and characterization of contiguous segment substitution lines with background of an elite restorer line Acta Agron. Sin., 33 (2007),pp. 979-986
[25]	Xu, J.J., Zhao, Q., Du, P.N. et al. BMC Genomics, 11 (2010),p. 656
[26]	Ye, G., Liang, S., Wan, J.M. QTL mapping of protein content in rice using single chromosome segment substitution lines Theor. Appl. Genet., 121 (2010),pp. 741-750
[27]	Yu, B., Lin, Z., Li, H. et al. Plant J., 52 (2007),pp. 891-898
[28]	Yu, J., Wang, J., Lin, W. et al. PloS Biol., 3 (2005),p. e38
[29]	Zhang, H., Zhang, C.Q., Sun, Z.Z. et al. Theor. Appl. Genet., 123 (2011),pp. 1247-1256
[30]	Zhang, Q., Ye, S., Li, J. et al. Construction of a microsatellite linkage map with two sequenced rice varieties Acta Genet. Sin., 33 (2006),pp. 152-160
[31]	Zhang, Z., Deng, Y., Tan, J. et al. DNA Res., 14 (2007),pp. 37-45
[32]	Zhao, W., Wang, J., He, X. et al. BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics Nucleic Acids Res., 32 (2004),pp. D377-D382
[33]	Zhu, W., Lin, J., Yang, D. et al. Plant Mol. Biol. Rep., 27 (2009),pp. 126-131