Development of Oryza rufipogon and O. sativa Introgression Lines and Assessment for Yield-related Quantitative Trait Loci
Lubin Tan
Department of Plant Genetics and Breeding and State Key Laboratory of Agro-biotechnology, China Agricultural University, Beijing 100094, China
Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing 100094, China
Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, China Agricultural University, Beijing 100094, China
Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100094, China
Search for more papers by this authorFengxia Liu
Department of Plant Genetics and Breeding and State Key Laboratory of Agro-biotechnology, China Agricultural University, Beijing 100094, China
Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing 100094, China
Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, China Agricultural University, Beijing 100094, China
Search for more papers by this authorWei Xue
Department of Plant Genetics and Breeding and State Key Laboratory of Agro-biotechnology, China Agricultural University, Beijing 100094, China
Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing 100094, China
Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, China Agricultural University, Beijing 100094, China
Search for more papers by this authorGuijuan Wang
Department of Plant Genetics and Breeding and State Key Laboratory of Agro-biotechnology, China Agricultural University, Beijing 100094, China
Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing 100094, China
Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, China Agricultural University, Beijing 100094, China
Search for more papers by this authorSheng Ye
Department of Plant Genetics and Breeding and State Key Laboratory of Agro-biotechnology, China Agricultural University, Beijing 100094, China
Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing 100094, China
Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, China Agricultural University, Beijing 100094, China
Search for more papers by this authorZuofeng Zhu
Department of Plant Genetics and Breeding and State Key Laboratory of Agro-biotechnology, China Agricultural University, Beijing 100094, China
Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing 100094, China
Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, China Agricultural University, Beijing 100094, China
Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100094, China
Search for more papers by this authorYongcai Fu
Department of Plant Genetics and Breeding and State Key Laboratory of Agro-biotechnology, China Agricultural University, Beijing 100094, China
Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing 100094, China
Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, China Agricultural University, Beijing 100094, China
Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100094, China
Search for more papers by this authorXiangkun Wang
Department of Plant Genetics and Breeding and State Key Laboratory of Agro-biotechnology, China Agricultural University, Beijing 100094, China
Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing 100094, China
Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, China Agricultural University, Beijing 100094, China
Search for more papers by this authorCorresponding Author
Chuanqing Sun
Department of Plant Genetics and Breeding and State Key Laboratory of Agro-biotechnology, China Agricultural University, Beijing 100094, China
Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing 100094, China
Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, China Agricultural University, Beijing 100094, China
Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100094, China
*Author for correspondence. Tel (Fax): +86 (0)10 6273 1811; E-mail: <[email protected]>.Search for more papers by this authorLubin Tan
Department of Plant Genetics and Breeding and State Key Laboratory of Agro-biotechnology, China Agricultural University, Beijing 100094, China
Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing 100094, China
Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, China Agricultural University, Beijing 100094, China
Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100094, China
Search for more papers by this authorFengxia Liu
Department of Plant Genetics and Breeding and State Key Laboratory of Agro-biotechnology, China Agricultural University, Beijing 100094, China
Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing 100094, China
Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, China Agricultural University, Beijing 100094, China
Search for more papers by this authorWei Xue
Department of Plant Genetics and Breeding and State Key Laboratory of Agro-biotechnology, China Agricultural University, Beijing 100094, China
Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing 100094, China
Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, China Agricultural University, Beijing 100094, China
Search for more papers by this authorGuijuan Wang
Department of Plant Genetics and Breeding and State Key Laboratory of Agro-biotechnology, China Agricultural University, Beijing 100094, China
Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing 100094, China
Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, China Agricultural University, Beijing 100094, China
Search for more papers by this authorSheng Ye
Department of Plant Genetics and Breeding and State Key Laboratory of Agro-biotechnology, China Agricultural University, Beijing 100094, China
Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing 100094, China
Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, China Agricultural University, Beijing 100094, China
Search for more papers by this authorZuofeng Zhu
Department of Plant Genetics and Breeding and State Key Laboratory of Agro-biotechnology, China Agricultural University, Beijing 100094, China
Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing 100094, China
Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, China Agricultural University, Beijing 100094, China
Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100094, China
Search for more papers by this authorYongcai Fu
Department of Plant Genetics and Breeding and State Key Laboratory of Agro-biotechnology, China Agricultural University, Beijing 100094, China
Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing 100094, China
Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, China Agricultural University, Beijing 100094, China
Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100094, China
Search for more papers by this authorXiangkun Wang
Department of Plant Genetics and Breeding and State Key Laboratory of Agro-biotechnology, China Agricultural University, Beijing 100094, China
Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing 100094, China
Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, China Agricultural University, Beijing 100094, China
Search for more papers by this authorCorresponding Author
Chuanqing Sun
Department of Plant Genetics and Breeding and State Key Laboratory of Agro-biotechnology, China Agricultural University, Beijing 100094, China
Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing 100094, China
Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, China Agricultural University, Beijing 100094, China
Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100094, China
*Author for correspondence. Tel (Fax): +86 (0)10 6273 1811; E-mail: <[email protected]>.Search for more papers by this authorSupported by the Project of Conservation and Utilization of Agricultural Wild Plants of the Ministry of Agriculture of China and a Grant from High-Tech Research and Development (863) Program of China (2006AA100101), and the National Natural Science Foundation of China (30270803). Publication of this paper is supported by the National Natural Science Foundation of China (30624808).
Abstract
Introgression lines population was effectively used in mapping quantitative trait loci (QTLs), identifying favorable genes, discovering hidden genetic variation, evaluating the action or interaction of QTLs in multiple conditions and providing the favorable experimental materials for plant breeding and genetic research. In this study, an advanced backcross and consecutive selfing strategy was used to develop introgression lines (ILs), which derived from an accession of Oryza rufipogon Griff. collected from Yuanjiang County, Yunnan Province of China, as the donor, and an elite indica cultivar Teqing (O. sativa L.), as the recipient. Introgression segments from O. rufipogon were screened using 179 polymorphic simple sequence repeats (SSR) markers in the genome of each IL. Introgressed segments carried by the introgression lines population contained 120 ILs covering the whole O. rufipogon genome. The mean number of homozygous O. rufipogon segments per introgression line was about 3.88. The average length of introgressed segments was approximate 25.5 cM, and about 20.8% of these segments had sizes less than 10 cM. The genome of each IL harbored the chromosomal fragments of O. rufipogon ranging from 0.54% to 23.7%, with an overall average of 5.79%. At each locus, the ratio of substitution of O. rufipogon alleles had a range of 1.67-9.33, with an average of 5.50. A wide range of alterations in morphological and yield-related traits were also found in the introgression lines population. Using single-point analysis, a total of 37 putative QTLs for yield and yield components were detected at two sites with 7%-20% explaining the phenotypic variance. Nineteen QTLs (51.4%) were detected at both sites, and the alleles from O. rufipogon at fifteen loci (40.5%) improved the yield and yield components in the Teging background. These O. rufipogon -O. sativa introgression lines will serve as genetic materials for identifying and using favorable genes from common wild rice.
References
- Ahn SN, Suh JP, Oh CS, Lee SJ, Suh HS (2002). Development of introgression lines of weedy rice in the background of Tongil-type rice. Rice Genet. Newsl. 19, 14.
- Aida Y, Tsunematsu H, Doi K, Yoshimura A (1997). Development of a series of introgression lines of japonica in the background of indica rice. Rice Genet. Newsl. 14, 41–43.
- Alpert K, Tanksley SD (1996). High-resolution mapping and isolation of a yeast artificial chromosome contig containing fw2.2: A major fruit-weight quantitative trait locus in tomato. Proc. Natl. Acad. Sci. USA 93, 15503–15507.
- Bernacchi D, Beck-Bunn T, Emmatty D, Eshed Y, Inai S, Lopez J et al. (1998). Advanced back-cross QTL analysis of tomato. II. Evaluation of near-isogenic lines carrying single-donor introgressions for desirable wild QTL-alleles derived from Lycopersicon hirsutum an. L. pimpinellifolium. Theor. Appl. Genet. 97, 170–180.
- Brondani C, Rangel PHN, Brondani RPV, Ferreira ME (2002). QTL mapping and introgression of yield-related traits from Oryza glumaepatula to cultivated rice (Oryza sativa) using microsatellite markers. Theor. Appl. Genet. 104, 1192–1203.
- Chetelat RT, Meglic V (2000). Molecular mapping of chromosome segments introgressed from Solanum lycopersicoides into cultivated tomato (Lycopersicon esculentum). Theor. Appl. Genet. 100, 232–241.
- Doi K, Iwata N, Yoshimura A (1997). The construction of chromosome substitution lines of African rice (Oryza glaberrima Steud.) in the background of japonica (O. sativa L.). Rice Genet. Newsl. 14, 39–41.
- Eduardo I, Arus P, Monforte AJ (2005). Development of a genomic library of near isogenic lines (NILs) in melon (Cucumis melo L.) from the exotic accession PI161375. Theor. Appl. Genet. 112, 139–148.
- Eshed Y, Zamir D (1994). A genomic library of Lycopersicon pennellii in L. esculentum: A tool for fine mapping genes. Euphytica 79, 175–179.
- Eshed Y, Zamir D (1995). An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield associated QTL. Genetics 141, 1147–1162.
- Eshed Y, Zamir D (1996). Less-than-additive epistatic interactions of quantitative trait loci in tomato. Genetics 143, 1807–1817.
- Frary A, Nesbitt TC, Grandillo S, Knaap E, Cong B, Liu J et al. (2000). fw2.2: A quantitative trait locus key to the evolution of tomato fruit size. Science 289, 85–88.
- Fridman E, Pleban T, Zamir D (2000). A recombination hotspot delimits a wild species quantitative trait locus for tomato sugar content to 484 bp within an invertase gene. Proc. Natl. Acad. Sci. USA 97, 4718–4723.
- Grandillo S, Ku HM, Tanksley SD (1996). Characterization of fs8.1, a major QTL influencing fruit shape in tomato. Mol. Breeding 2, 251–260.
- He GM, Luo XJ, Tian F, Li KG, Su W, Zhu ZF et al. (2006). Haplo-type variation in structure and expression of a gene cluster associated with a quantitative trait locus for improved yield in rice. Genome Res. 16, 618–626.
- Howell PM, Marshall DF, Lydiate DJ (1996). Towards developing inter-varietal substitution lines in Brassica napus using marker-assisted selection. Genome 39, 348–358.
- Konishi S, Izawa T, Lin SY, Ebana K, Fukuta Y, Sasaki T et al. (2006). An SNP caused loss of seed shattering during rice domestication. Science 312, 1392–1396.
- Koumproglou R, Wilkes TM, Townson P, Wang XY, Beynon J, Pooni HS et al. (2002). STAIRS: A new genetic resource for functional genomic studies o. Arabidopsis. Plant J. 31, 355–364.
- Kubo T, Aida Y, Nakamura K, Tsunematsu H, Doi K, Yoshimura A (2002). Reciprocal chromosome segment substitution series derived from japonica and indica cross of rice (Oryza sativa L.). Breeding Sci. 52, 319–325.
- Kurakazu T, Sobrizal, Ikeda K, Sanchez PL, Doi K, Angeles ER et al. (2001). Oryza meridionalis chromosomal segment introgression lines in cultivated rice, O. sativa L. Rice Genet. Newsl. 18, 81–82.
- Li CB, Zhou AL, Sang T (2006). Genetic analysis of rice domestication syndrome with the wild annual species. Oryza nivara. New Phytol. 170, 185–194.
- Li DJ, Sun CQ, Fu YC, Chen L, Zhu ZF, Li C et al. (2002). Identification and mapping of genes for improving yield from Chinese common wild rice (O. rufipogon Griff.) using advanced back-cross QTL analysis. Chin. Sci. Bull. 18, 1533–1537.
- Li ZK, Fu BY, Gao YM, Xu JL, Ali J, Lafitte HR et al. (2005). Genome-wide introgression lines and their use in genetic and molecular dissection of complex phenotypes in rice (Oryza sativa L.. Plant Mol. Biol. 59, 33–52.
- Manly KF, Cudmore Jr RH, Meer JM (2001). Map Manager QTX, cross-platform software for genetic mapping. Mamm. Genome 12, 930–932.
- Matus I, Corey A, Filichkin T, Hayes PM, Vales MI, Kling J et al. (2003). Development and characterization of recombinant chromosome substitution lines (RCSLs) using Hordeum vulgare subsp. spontaneum as a source of donor alleles in a Hordeum vulgare subsp. vulgare background. Genome 46, 1010–1023.
- McCouch SR, Teytelman L, Xu YB, Lobos KB, Clare K, Walton M et al. (2002). Development of 2,240 new SSR markers for rice (Oryza sativa L.). DNA Res. 9, 199–207.
- Moncada P, Martinez CP, Borrero J, Chatel M, Gauch H, Guimaraes E et al. (2001). Quantitative trait loci for yield and yield components in an Oryza sativa×Oryza rufipogon BC2F2 population evaluated in an upland environment. Theor. Appl. Genet. 102, 41–52.
- Monforte AJ, Tanksley SD (2000a). Development of a set of near isogenic and backcross recombinant inbred lines containing most of the Lycopersicon hirsutum genome in a L. esculentum genetic background: A tool for gene mapping and gene discovery. Genome 43, 803–813.
- Monforte AJ, Tanksley SD (2000b). Fine mapping of a quantitative trait locus (QTL) from Lycopersicon hirsutum chromosome 1 affecting fruit characteristics and agronomic traits: Breaking linkage among QTLs affecting different traits and dissection of heterosis for yield. Theor. Appl. Genet. 100, 471–479.
-
Oka HI (1988). Origin of Cultivated Rice. Japan Scientific Society Press,
Tokyo
.
10.1016/B978-0-444-98919-2.50005-3 Google Scholar
- Panaud O, Chen X, McCouch SR (1996). Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.. Mol. Gen. Genet. 252, 597–607.
- Pang HH, Cai HW, Wang XK (1995). Morphological classification of common wild rice (Oryza rufipogon Griff.) in China. Acta Agron. Sin. 21, 17–24 (in Chinese with an English abstract).
- Pestsova EG, Borner A, Roder MS (2001). Development of a set of Triticum aestivum-Aegilops tauschii introgression lines. Heredi-tas 135, 139–143.
- Rogers OS, Bendich AJ (1988). Extraction of DNA from plant tissue, plant molecular. Bio. Man. A6, 1–10.
- Second G (1982). Origin of the genetic diversity of cultivated rice (Oryza spp.), study of the polymorphism scored at 40 isozyme loci. JPN J. Genet. 57, 25–57.
- Septiningsih EM, Prasetiyono J, Lubis E, Tai TH, Tjubaryat T, Moeljopawiro S et al. (2003). Identification of quantitative trait loci for yield and yield components in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relativ. O. rufipogon. Theor. Appl. Genet. 107, 1419–1432.
- Sobriza I, Ikeda K, Sanchez PL, Doi K, Doi K, Angles ER et al. (1999). Development of Oryza glumaepatula introgression line in rice, O. sativa L. Rice Genet. Newsl. 16, 107.
- Sun CQ, Wang XK, Yoshimura A, Iwata N (2001). Comparison of the genetic diversity of common wild rice (Oryza rufipogon Griff.) and cultivated rice (O. sativa L.) using RFLP markers. Theor. Appl. Genet. 102, 157–162.
- Sun CQ, Wang XK, Yoshimura A, Doi K (2002). Genetic differentiation for muclear, mitochondrial and chloroplast genomes in common wild rice (O. rufipogon Griff.) and cultivated rice (O. sativa L.). Theor. Appl. Genet. 104, 1335–1345.
- Tan LB, Zhang PJ, Fu YC, Liu FX, Wang XK, Sun CQ (2004). Identification of quantitative trait loci controlling plant height and days to heading from Yuanjiang common wild rice (Oryza rufipogon Griff.). Yi Chuan Xue Bao 31, 1123–1128 (in Chinese with an English abstract).
- Tanksley SD, McCouch SR (1997). Seed banks and molecular maps: Unlocking genetic potential from the wild. Science 277, 1063–1066.
- Tanksley SD, Nelson JC (1996). Advanced backcross QTL analysis: A method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor. Appl. Genet. 92, 191–203.
- Temnykh S, Park W, Ayres N, Cartinhour S, Hauck N, Lipovich L et al. (2000). Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor. Appl. Genet. 100, 697–712.
- Tian F, Li DJ, Fu Q, Zhu ZF, Fu YC, Wang XK et al. (2006a). Construction of introgression lines carrying wild rice (Oryza rufipogon Griff.) segments in cultivated rice (O. sativa L.) background and characterization of introgressed segments associated with yield-related traits. Theor. Appl. Genet. 112, 570–580.
- Tian F, Zhu ZF, Zhang BS, Tan LB, Fu YC, Wang XK et al. (2006b). Fine mapping of a quantitative trait locus for grain number per panicle from wild rice (Oryza rufipogon Griff.). Theor. Appl. Genet. 113, 619–629.
- Thomson MJ, Tai TH, McClung AM, Lai XH, Hinga ME, Lobos KB et al. (2003). Mapping quantitative trait loci for yield, yield components and morphological traits in an advanced backcross population between Oryza rufipogon and the Oryza sativa cultivar Jefferson. Theor. Appl. Genet. 107, 479–493.
- Van Berloo R (1999). GGT: Software for the display of graphical genotypes. J. Hered. 90, 328–329.
- Korff M, Wang H, Léon J, Pillen K (2004). Development of candidate introgression lines using an exotic barley accession (Hordeum vulgare ssp. spontaneum) as donor. Theor. Appl. Genet. 109, 1736–1745.
- Wang ZY, Second G, Tanksley SD (1992). Polymorphism and phy-logenetic relationships among species in the genus Oryza as determined by analysis of nuclear RFLPs. Theor. Appl. Genet. 83, 565–581.
- Xiao J, Grandillo S, Ahn SN, McCouch SR, Tanksley SD, Li J et al. (1996). Genes from wild rice improve yield. Nature 384, 223–224.
- Xiao J, Li J, Grandillo S, McCouch SR, Tanksley SD, Li J et al. (1998). Identification of trait-improving quantitative trait loci alleles from a wild rice relative. Oryza rufipogon. Genetics 150, 899–909.
- Yamamoto T, Kuboki Y, Lin SY, Sasaki T, Yano M (1998). Fine mapping of quantitative trait loci Hd-1, Hd-2 and Hd-3, controlling heading date of rice, as single Mendelian factor. Theor. Appl. Genet. 97, 37–44.
- Yamamoto T, Lin HY, Sasaki T, Yano M (2000). Identification of heading date quantitative trait loci Hd6 and characterization of its epistatic interaction with Hd2 in rice using advanced back-cross progeny. Genetics 154, 885–891.
- Yano M, Katayose Y, Ashikari M, Yamanouchi U, Monna L, Fuse T et al. (2000). Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gen. CONSTANS. Plant Cell 12, 2473–2483.
- Young ND, Tanksley SD (1989). Restriction fragment length polymorphism maps and the concept of graphical genotypes. Theor. Appl. Genet. 77, 95–101.
- Zamir D (2001). Improving plant breeding with exotic genetic libraries. Nat. Rev. Genet. 2, 983–989.
- Zhang YS, Luo LJ, Xu CG, Zhang QF, Xing YZ (2006). Quantitative trait loci for panicle size, heading date and plant height co-segregating in trait-performance derived near-isogenic lines of ric. (Oryza sativa). Theor. Appl. Genet. 113, 361–368.
