Abstract
To genetically dissect drought resistance associated with japonica upland rice, we evaluated a doubled haploid (DH) population from a cross between two japonica cultivars for seven root traits under three different growing conditions (upland, lowland and upland in PVC pipe). The traits included basal root thickness (BRT), total root number (RN), maximum root length (MRL), root fresh weight (RFW), root dry weight (RDW), ratio of root fresh weight to shoot fresh weight (RFW/SFW) and ratio of root dry weight to shoot dry weight (RDW/SDW). The BRT was significantly correlated with the index of drought resistance, which was defined as the ratio of yield under the stress of the upland condition to that under the normal lowland condition. A complete genetic linkage map with 165 molecular markers covering 1,535 cM was constructed. Seven additive quantitative trait loci (QTLs) and 15 pairs of epistatic loci for BRT and RN were identified under upland and lowland conditions, and 12 additive QTLs and 17 pairs of epistatic QTLs for BRT, RN, MRL, RFW, RFW/SFW and RDW/SDW were identified under the PVC pipe condition. Four additive QTLs and one pair of epistatic QTLs controlling IDR were also found. These QTLs individually explained up to 25.6% of the phenotypic variance. QTL × environment (Q × E) interactions were detected for all root traits, and the contributions of these interactions ranged from 1.1% to 19.9%. Five co-localized QTLs controlling RFW and RDW, RFW/SFW, RDW/SDW and IDR, BRT and RN, RN, MRL and IDR were found. Four types of QTLs governing BRT and RN were classified by their detection in the upland and lowland conditions. Some common QTLs for root traits across different backgrounds were also revealed. These co-localized QTLs and common QTLs will facilitate marker-assisted selection for root traits in rice breeding programs.
Similar content being viewed by others
References
Ali ML, Pathan MS, Zhang J, Bai G, Sarkarung S, Nguyen HT (2000) Mapping QTLs for root traits in a recombinant inbred population from two indica ecotypes in rice. Theor Appl Genet 101:756–766
Champoux MC, Wang G, Sarkarung S, Mackill DJ, O’Toole JC, Huang N, McCouch SR (1995) Locating genes associated with root morphology and drought avoidance in rice via linkage to molecular markers. Theor Appl Genet 90:969–981
Fukai S, Cooper M (1995) Development of drought-resistant cultivars using physio-morphological traits in rice. Field Crops Res 40:67–86
Ge SL (1992) The comparison and classification of several morphological criteria of root of paddy rice and upland rice in different cultural methods. PhD thesis, Beijing Agricultural University, Beijing
Kamoshita A, Wade LJ, Ali ML, Pathan MS, Zhang J, Sarkarung S, Nguyen HT (2002a) Mapping QTLs for root morphology of a rice population adapted to rainfed lowland conditions. Theor Appl Genet 104:880–893
Kamoshita A, Zhang JX, Siopongco J, Sarkarung S, Nguyen HT, Wade LJ (2002b) Effect of phenotyping environment on identification of quantitative trait loci for rice root morphology under anaerobic conditions. Crop Sci 42:255–265
Lander ES, Green P, Abraham SJ, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) mapmaker: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181
Li ZK, Yu SB, Lafitte HR, Huang N, Courtois B, Hittalmani S, Vijayakumar CHM, Liu GF, Wang GC, Shashidhar HE, Zhuang JY, Zheng KL, Singh VP, Sidhu JS, Srivantaneeyakul S, Khush GS (2003) QTL × environment interactions in rice. I. Heading date and plant height. Theor Appl Genet 108:141–153
Lincoln SE, Daly MJ, Lander ES (1993) Constructing genetic linkage maps with mapmaker/exp ver. 3.0: a tutorial and reference manual, 3rd edn. Technical Report, Whitehead Institute for Biomedical Research, Cambridge, Mass.
Ling ZM, Li ZC, Yu R, Mu P (2002) Agronomic root characters of upland rice and paddy rice (Oryza sativa L.). J Chin Agric Univ 7:7–11
McCouch SR, Kochert G, Yu Z, Wang ZY, Khush GS, Coffman WR, Tanksley SD (1988) Molecular mapping of rice chromosomes. Theor Appl Genet 76:815–829
McCouch SR, Temnykh S, Lukashova A, Coburn J, DeClerck G, Cartinhour S, Harrington S, Thomson M, Septiningsih E, Semon M, Moncada P, Li J (2001) Microsatellite markers in rice: abundance, diversity, and applications. In: Khush GS, Brar DS, Hardy B (eds) Rice genetics IV. Proc 4th Int Rice Genet Symp. Science Publ, New Delhi/ International Rice Research Institute, Los Baños, Philippines, pp 117–135
Nguyen HT, Babu RC, Blum A (1997) Breeding for drought resistance in rice: physiology and molecular genetics consideration. Crop Sci 37:1426–1434
Price AH, Tomos AD (1997) Genetic dissection of root growth in rice (Oryza sativa L.). II: mapping quantitative trait loci using molecular markers. Theor Appl Genet 95:143–152
Price AH, Virk DS, Tomos AD (1997) Genetic dissection of root growth in rice (Oryza sativa L.). I: a hydroponic screen. Theor Appl Genet 95:132–142
Ray JD, Yu L, McCouch SR, Wang G, Nguyen HT (1996) Mapping quantitative trait loci associated with root penetration ability in rice (Oryza sativa L.). Theor Appl Genet 92:627–636
Temnykh S, Park WD, Ayres N (2000) Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor Appl Genet 100:697–712
Toorchi M, Shashidhar HE, Gireesha TM, Hittalmani S (2003) Performance of backcrosses involving transgressant doubled haploid lines in rice under contrasting moisture regimes: yield components and marker heterozygosity. Crop Sci 43:1448–1456
Wang DL, Zhu J, Li ZK, Paterson AH (1999) A computer software for mapping quantitative trait loci with main effects, epistatic effects and QTL × environment interactions. User manual for qtlmapper ver.1.0. Texas A&M University, College Station
Wang HQ, Bouman BAM, Zhao DL, Wang CG, Moya PF (2002) Aerobic rice in northern China: opportunities and challenges. In: Bouman BAM, Hengsdijk H, Hardy B, Bindraban PS, Tuong TP, Ladha JK (eds) Water-wise rice production. International Rice Research Institute Los Baños, Philippines, pp 143–154
Yadav R, Courtois B, Huang N, McLaren G (1997) Mapping genes controlling root morphology and root distribution in a double-haploid population of rice. Theor Appl Genet 94:619–632
Zhang J, Zheng HG, Aarti A, Pantuwan G, Nguyen TT, Tripathy JN, Sarial AK, Robin S, Babu RC, Nguyen BD, Sarkarung S, Blum A, Nguyen HT (2001) Locating genomic regions associated with components of drought resistance in rice: comparative mapping within and across species. Theor Appl Genet 103:19–29
Zhu J (1998) Mixed model approaches for mapping quantitative trait loci. Hereditas 20[Suppl]:137–138
Acknowledgements
We thank Prof. Zuomin Yang for reading the manuscript. This work was supported by the State Key Basic Research and Development Plan of China (2003CB114301), the National Natural Science Foundation of China (30250009), the Hi-Tech Research and Development Program of China (2004AA211190 and 2003AA207040).
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by D.J. Mackill
Rights and permissions
About this article
Cite this article
Li, Z., Mu, P., Li, C. et al. QTL mapping of root traits in a doubled haploid population from a cross between upland and lowland japonica rice in three environments. Theor Appl Genet 110, 1244–1252 (2005). https://doi.org/10.1007/s00122-005-1958-z
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00122-005-1958-z