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

Journal of Genetics and Genomics

Volumn 38, Issue 12, 2011, Pages 603-611

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

^a YANGZHOU UNIVERSITY   (China)

^b INSTITUTE OF PLANT PHYSIOLOGY AND ECOLOGY   (China)

^c National Center for Plant Gene Research Shanghai   (China)

Author keywords

Chromosome segment substitution lines (CSSLs); High throughput resequencing; Molecular marker assisted selection; Oryza sativa L.

Indexed keywords

MOLECULAR MARKER;

ARTICLE; CHROMOSOME 5; CHROMOSOME ANALYSIS; CHROMOSOME MAP; CHROMOSOME SUBSTITUTION STRAIN; CULTIVAR; GENE LOCATION; GENE SEQUENCE; GENOTYPE; GRAIN; JAPONICA NIPPONBARE; MOLECULAR CLONING; NONHUMAN; PLANT GENOME; QUANTITATIVE TRAIT LOCUS; RICE;

CHROMOSOME MAPPING; CHROMOSOMES, PLANT; CROSSES, GENETIC; GENETIC MARKERS; GENOTYPING TECHNIQUES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; ORYZA SATIVA; PLANTS, GENETICALLY MODIFIED; QUANTITATIVE TRAIT LOCI;

JAPONICA; ORYZA SATIVA;

EID: 84855205095     PISSN: 16738527     EISSN: 18735533     Source Type: Journal    
DOI: 10.1016/j.jgg.2011.11.004     Document Type: Article

References (33)

1. Ebitani T., Takeuchi Y., Nonoue Y., Yamamoto T., Takeuchi K., Yano M. Construction and evaluation of chromosome segment substitution lines carrying overlapping chromosome segments of indica rice cultivar " Kasalath" in a genetic background of japonica elite cultivar " Koshihikari" Breed. Sci. 2005, 55:65-73.
2. Feltus F., Wan J., Schulze S., Estill J., Jiang N., Paterson A. An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments. Genome Res. 2004, 14:1812-1819.
3. He F., Xi Z., Zeng R.Z., Talukdar A., Zhang G.Q. Developing single segment substitution lines (SSSLs) in rice (Oryza sativa L.) using advanced backcrosses and MAS. Acta Genet. Sin. 2005, 32:825-831.
4. Huang X.F., Feng Q., Qian Q., Zhao Q., Wang L., Wang A., Guan J., Fan D., Weng Q., Huang T., Dong G., Sang T., Han B. High-throughput genotyping by whole-genome resequencing. Genome Res. 2009, 19:1068-1076.
5. International Rice Genome Sequencing Project The map-based sequence of the rice genome. Nature 2005, 436:793-800.
6. Jiang H., Liu D., Gu Z., Wang W. Rapid evolution in a pair of recent duplicate segments of rice. J. Exp. Zool. (Mol. Dev. Evol.) 2007, 308B:50-57.
7. Li W., Zeng R., Zhang Z., Zhang G.Q. Analysis of introgressed segments in near-isogenic lines for F1 pollen sterility in rice. Chin. J. Rice Sci. 2003, 17:95-99. (in Chinese with an English abstract).
8. Liu G., Li W., Zeng R., Zhang G.Q. Development of single segment substitution lines (SSSLs) of subspecies in rice. Chin. J. Rice Sci. 2003, 17:201-204. (in Chinese with an English abstract).
9. McCouch S., Teytelman L., Xu Y., Lobos K., Clare K., Walton M., Fu B., Maghirang R., Li Z., Xing Y., Zhang Q., Kono I., Yano M., Fjellstrom R., DeClerck G., Schneider D., Cartinhour S., Ware D., Stein L. Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res. 2002, 9:199-207.
10. Murray M., Thompson W. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 1980, 8:4321-4325.
11. Nadeau J.H., Singer J.B., Matin A., Lander E.S. Analyzing complex genetic traits with chromosome substitution strains. Nat. Genet. 2000, 24:221-225.
12. Ookawa T., Hobo T., Yano M., Murata K., Ando T., Miura H., Asano K., Ochiai Y., Ikeda M., Nishitani R., Ebitani T., Ozaki H., Angeles E., Hirasawa T., Matsuoka M. New approach for rice improvement using a pleiotropic QTL gene for lodging resistance and yield. Nat. Commun. 2010, 1:132.
13. Ouyang S., Zhu W., Hamilton J., Lin H., Campbell M., Childs K., Thibaud-Nissen F., Malek R.L., Lee Y., Zheng L., Orvis J., Haas B., Wortman J., Buell C.R. The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res. 2007, 35:D883-D887.
14. Shen Y., Jiang H., Jin J., Zhang Z., Xi B., He Y., Wang G., Wang C., Qian L., Li X., Yu Q., Liu H., Chen D., Gao J., Huang H., Sh T., Yang Z. Development of genome-wide DNA polymorphism database for map-based cloning of rice genes. Plant Physiol. 2004, 135:1198-1205.
15. Shomura A., Izawa T., Ebana K., Ebitani T., Kanegae H., Konishi S., Yano M. Deletion in a gene associated with grain size increased yields during rice domestication. Nat. Genet. 2008, 40:1023-1028.
16. Singer J.B., Hill A.E., Burrage L.C., Olszens K.R., Song J., Justice M., O'Brien W.E., Conti D.V., Witte J.S., Lander E.S., Nadeau J.H. Genetic dissection of complex traits with chromosome substitution strains of mice. Science 2004, 304:445-448.
17. Tan L., Zhang P., Liu F., Wang G., Ye S., Zhu Z., Fu Y., Cai H., Sun C.Q. Quantitative trait loci underlying domestication-and yield-related traits in an Oryza sativa × Oryza rufipogon advanced backcross population. Genome 2008, 51:692-704.
18. Tian F., Li D., Fu Q., Zhu Z., Fu Y., Wang X., Sun C.Q. Construction of introgression lines carrying wild rice (Oryza rufipogon Griff.) segments in cultivated rice (Oryza sativa L.) background and characterization of introgressed segments associated with yield-related traits. Theor. Appl. Genet. 2006, 112:570-580.
19. Wang X., Shi X., Hao B., Ge S., Luo J. Duplication and DNA segmental loss in the rice genome: implications for diploidization. New Phytol. 2005, 165:937-946.
20. Wang J., Wan X., Crossa J., Crouch J., Weng J., Zhai H., Wan J.M. QTL mapping of grain length in rice (Oryza sativa L.) using chromosome segment substitution lines. Genet. Res. 2006, 88:93-104.
21. Wang X., Zhao X., Zhu J., Wu W.L. Genome-wide investigation of intron length polymorphisms and their potential as molecular markers in rice (Oryza sativa L.). DNA Res. 2006, 12:417-427.
22. Weng J., Gu S., Wan X., Gao H., Guo T., Su N., Lei C., Zhang X., Cheng Z., Guo X., Wang J., Jiang L., Zhai H.Q., Wan J.M. Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight. Cell Res. 2008, 18:1199-1209.
23. TQ, a major gene conferring resistance to rice stripe disease. Theor. Appl. Genet. 2010, 122:915-923.
24. Xu H.S., Sun Y.J., Zhou H.J., Yu S.B. Development and characterization of contiguous segment substitution lines with background of an elite restorer line. Acta Agron. Sin. 2007, 33:979-986.
25. Xu J.J., Zhao Q., Du P.N., Xu C.W., Wang B., Feng Q., Liu Q.Q., Tang S., Gu M.H., Han B., Liang G.H. Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice (Oryza sativa L.). BMC Genomics 2010, 11:656.
26. Ye G., Liang S., Wan J.M. QTL mapping of protein content in rice using single chromosome segment substitution lines. Theor. Appl. Genet. 2010, 121:741-750.
27. Yu B., Lin Z., Li H., Li X., Li J., Wang Y., Zhang X., Zhu Z., Zhai W., Wang X., Xie D., Sun C.Q. TAC1, a major quantitative trait locus controlling tiller angle in rice. Plant J. 2007, 52:891-898.
28. Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S., Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L., Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J., Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X., Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y., Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L., Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H., Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z., Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L., Fang L., Leil T., Chen C., Chen H., Xu Z., Li H., Huang H., Zhang F., Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q., Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J., Gao L., Zheng W., Hao B., Liu S., Wang W., Yuan L., Cao M., McDermott J., Samudrala R., Wang J., Wong G.K., Yang H. The genomes of Oryza sativa: a history of duplications. PloS Biol. 2005, 3:e38.
29. Zhang H., Zhang C.Q., Sun Z.Z., Yu W., Gu M.H., Liu Q.Q., Li Y.S. A major locus qS12, located in a duplicated segment of chromosome 12, causes spikelet sterility in an indica-japonica rice hybrid. Theor. Appl. Genet. 2011, 123:1247-1256.
30. Zhang Q., Ye S., Li J., Zhao B., Liang Y., Peng Y., Li P. Construction of a microsatellite linkage map with two sequenced rice varieties. Acta Genet. Sin. 2006, 33:152-160.
31. Zhang Z., Deng Y., Tan J., Hu S., Yu J., Xue Q. A genome-wide microsatellite polymorphism database for the indica and japonica rice. DNA Res. 2007, 14:37-45.
32. Zhao W., Wang J., He X., Huang X., Jiao Y., Dai M., Wei S., Fu J., Chen Y., Ren X., Zhang Y., Ni P., Zhang J., Li S., Wang J., Wong G.K.S., Zhao H., Yu J., Yang H., Wang J. BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics. Nucleic Acids Res. 2004, 32:D377-D382.
33. Zhu W., Lin J., Yang D., Zhao L., Zhang Y., Zhu Z., Chen T., Wang C.L. Development of chromosome segment substitution lines derived from backcross between two sequenced rice cultivars, indica recipient 93-11 and japonica donor Nipponbare. Plant Mol. Biol. Rep. 2009, 27:126-131.