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Identification and characterization of quantitative trait loci for grain yield and its components under different nitrogen fertilization levels in rice (Oryza sativa L.)

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Abstract

A set of rice (Oryza sativa L.) recombinant inbred lines from a cross between Zhenshan 97 (indica) and HR5 (indica) was planted for four different growing seasons in two locations at three nitrogen (N) fertilization levels (N300, 300 kg urea/ha; N150, 150 kg urea/ha; and N0, 0 kg urea/ha). Grain yield and its components were evaluated, including grain yield per plant (GYPP), panicle number per plant (PNPP), grain number per panicle (GNPP), filled grains per panicle (FGPP), spikelet fertility percentage (SFP) and 100-grain weight (HGW). Correlation and path analysis indicated that SFP had the greatest contribution to GYPP at the N300 and N150 levels, but FGPP contributed the most to GYPP at the N0 level. Quantitative trait loci (QTL) were mapped based on a mixed linear model; genetic components (main effects, epistatic effects and QTL-by-environment interactions) were estimated separately. Six to 15 QTL with main effects were detected for each trait except SFP. Clusters of main-effect QTL associated with PNPP, GNPP, SFP and HGW were observed in regions on chromosomes 1, 2, 3, 5, 7 and 10. The main-effect QTL (qGYPP-4b and qGNPP-12) were only detected at the N0 level and explained 10.9 and 10.2% of the total phenotypic variation, respectively. A total of 33 digenic interactions among grain yield and its components were also identified. The identification of genomic regions associated with yield and its components at different nitrogen levels will be useful in marker-assisted selection for improving the nitrogen use efficiency of rice.

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Abbreviations

A:

Additive effect

AA:

Additive × additive epistasis

AE:

Additive × environment interaction

AAE:

Epistasis × environment interaction

M-QTL:

Main-effect QTL

E-QTL:

Epistatic QTL

Q × E:

QTL × environment interaction

RIL:

Recombinant inbred line

N0:

No nitrogen fertilization (0 kg urea/ha)

N150:

Medium nitrogen fertilization (150 kg urea/ha)

N300:

High nitrogen fertilization (300 kg urea/ha)

E1:

Summer of 2005 in Shanghai, China

E2:

Spring of 2006 in Hainan, China

E3:

Summer of 2006 in Shanghai, China

E4:

Spring of 2007 in Hainan, China

GYPP:

Grain yield per plant

PNPP:

Panicle number per plant

GNPP:

Grain number per panicle

FGPP:

Filled grains per panicle

SFP:

Spikelet fertility percentage

HGW:

100-grain weight

NUE:

Nitrogen use efficiency

QTL:

Quantitative trait locus

References

  • Agrama HAS, Zakaria AG, Said FB, Tuinstra MR (1999) Identification of quantitative trait loci for nitrogen efficiency in maize. Mol Breed 5:187–195

    Article  Google Scholar 

  • Andaya VC, Mackill DJ (2003) QTLs conferring cold tolerance at the booting stage of rice using recombinant inbred lines from a japonica × indica cross. Theor Appl Genet 106:1084–1090

    PubMed  CAS  Google Scholar 

  • Bao SD (2000) Analysis method for soil agrochemical. China Agriculture Press, Beijing (in Chinese)

    Google Scholar 

  • Bertin P, Gallais A (2001) Genetic variation for nitrogen use efficiency in a set of recombinant maize inbred lines: II. QTL detection and coincidences. Maydica 46:53–68

    Google Scholar 

  • Broadbent FE, De Datta SK, Laureles EV (1987) Measures of nitrogen utilization efficiency in rice genotypes. Agron J 79:786–791

    Article  Google Scholar 

  • Brondani C, Rangel N, Brondani V (2002) QTL mapping and introgression of yield-related traits from Oryza glumaepatula to cultivated rice (Oryza sativa L.) using microsatellite markers. Theor Appl Genet 104:1192–1203

    Article  PubMed  CAS  Google Scholar 

  • Cho YI, Jiang WZ, Chin JH, Piao ZZ, Cho YG, McCouch SR, Koh HJ (2007) Identification of QTLs associated with physiological nitrogen use efficiency in rice. Mol Cell 23:72–79

    CAS  Google Scholar 

  • Collins NC, Tardien F, Tuberosa R (2008) Quantitative trait loci and crop performance under abiotic stress: where do we stand? Plant Physiol 147:469–486

    Article  PubMed  CAS  Google Scholar 

  • Conway GR, Pretty JN (1988) Fertilizer risks in developing countries. Nature 334:207–208

    Article  PubMed  CAS  Google Scholar 

  • Cui KH, Peng SB, Xing YZ, Yu SB, Xu CG, Zhang QF (2003) Molecular dissection of the genetic relationship of source, sink and transport tissue with yield traits in rice. Theor Appl Genet 106:649–658

    PubMed  CAS  Google Scholar 

  • De Datta SK, Broadbent FE (1990) Nitrogen use efficiency of 24 rice genotypes on an N-deficient soil. Field Crop Res 23:81–92

    Article  Google Scholar 

  • De Datta SK, Buresh RJ (1989) Integrated nitrogen management in irrigated rice. Adv Soil Sci 10:143–169

    Article  Google Scholar 

  • Fan CC, Xing YZ, Mao HL, Lu TT, Han B, Xu CG, Li XH, Zhang QF (2006) GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet 112:1164–1171

    Article  PubMed  CAS  Google Scholar 

  • Fang P, Wu P (2001) QTL × N-level interaction for plant height in rice (Oryza sativa L.). Plant Soil 236:237–242

    Article  CAS  Google Scholar 

  • Fang P, Tao QN, Wu P (2001) QTLs underlying rice root to uptake NH4-N and NO3-N and rice N use efficiency at seedling stage. Plant Nutr Fertil Sci 7:159–165 (in Chinese with English abstract)

    Google Scholar 

  • Gerloff GG (1976) Plant efficiencies in the use of nitrogen, phosphorus and potassium. In: Wright MJ (ed) Plant adaptation to mineral stress in problem soils. Proceedings of the Beltsville, Maryland Workshop. Cornell University Agricultural Experiment Station, Ithaca, pp 161–173

    Google Scholar 

  • Ghesquiere A, Albar L, Lorieux M, Ahmadi N, Fargette D, Huang N, McCouch SR, Notteghem JL (1997) A major quantitative trait locus for rice yellow mottle virus resistance maps to a cluster of blast resistance genes on chromosome 12. Phytopathology 87:1243–1249

    Article  PubMed  CAS  Google Scholar 

  • Hirel B, Bertin P, Quillere I, Bourdoncle W, Attagnant C, Dellay C, Gouy A, Cadiou S, Retailliau C, Falque M (2001) Towards a better understanding of the genetic and physiological basis for nitrogen use efficiency in maize. Plant Physiol 125:1258–1270

    Article  PubMed  CAS  Google Scholar 

  • Hu FY, Tao DY, Sacks E, Fu BY, Xu P, Li J, Yang Y, McNally K, Khush GS, Paterson AH, Li ZK (2003) Convergent evolution of perenniality in rice and sorghum. Proc Natl Acad Sci USA 100:4050–4054

    Article  PubMed  CAS  Google Scholar 

  • Insightful Corporation (2001) S-plus 6.0 for Windows, User’s Guide. Seattle, WA, USA

  • Ishimaru K, Kobayashi N, Ono K, Yano M, Ohsugi R (2001) Are contents of Rubisco, soluble protein and nitrogen in flag leaves of rice controlled by the same genetics? J Exp Bot 52:1827–1833

    Article  PubMed  CAS  Google Scholar 

  • Jiang GH, He YQ, Xu CG, Li XH, Zhang QF (2004) The genetic basis of stay-green in rice analyzed in a population of doubled haploid lines derived from an indica by japonica cross. Theor Appl Genet 108:288–298

    Article  Google Scholar 

  • Kashiwagi T, Ishimaru K (2004) Identification and functional analysis of a locus for improvement of lodging resistance in rice. Plant Physiol 134:676–683

    Article  PubMed  CAS  Google Scholar 

  • Li JX, Yu SB, Xu CG, Tan YF, Gao YJ, Li XH, Zhang QF (2000) Analyzing quantitative trait loci for yield using a vegetatively replicated F2 population from a cross between the parents of an elite rice hybrid. Theor Appl Genet 101:248–254

    Article  CAS  Google Scholar 

  • Lian XM, Xing YZ, Yan H, Xu CG, Li XH, Zhang QF (2005) QTLs for low nitrogen tolerance at seedling stage identified using a recombinant inbred population derived from an elite rice hybrid. Theor Appl Genet 112:85–96

    Article  PubMed  CAS  Google Scholar 

  • Lincoln SE, Daly MJ, Lander E (1992). Constructing genetic maps with MAPMAKER/EXP 3.0. 3rd edn. Whitehead Institute Technical Report, Cambridge: Whitehead Institute

  • Loudet O, Chaillou S, Merigout P, Talbotec J, Daniel-Vedele F (2003) Quantitative trait loci analysis of nitrogen use efficiency in Arabidopsis. Plant Physiol 131:345–358

    Article  PubMed  CAS  Google Scholar 

  • Mao CZ, Yang L, Zheng BS, Wu YR, Liu FY, Wu P (2004) Comparative mapping of QTLs for Al tolerance in rice and identification of positional Al-induced genes. J Zhejiang Univ Sci 5:634–643

    Article  PubMed  CAS  Google Scholar 

  • Marri PR, Sarla N, Reddy LV, Siddiq EA (2005) Identification and mapping of yield and yield related QTLs from an Indian accession of Oryza rufipogon. BMC Genet 33:1–14

    Google Scholar 

  • McCouch SR, Cho YG, Yano M, Paul E, Blinstrub M, Morishima H, Kinoshita T (1997) Suggestion for QTL nomenclature. Rice Genet Newsl 14:11–13

    Google Scholar 

  • Mei HW, Luo LJ, Ying CS, Wang YP, Yu XQ, Guo LB, Paterson AH, Li ZK (2003) Gene actions of QTLs affecting several agronomic traits resolved in a recombinant inbred rice population and two testcross populations. Theor Apple Genet 107:89–101

    CAS  Google Scholar 

  • Naqvi NI, Chatto BB (1996) Development of a sequence characterized amplified region (SCAR) based indirect selection method for a dominant blast-resistance gene in rice. Genome 39:26–30

    Article  PubMed  CAS  Google Scholar 

  • Obara M, Kajiura M, Fukuta Y, Yano M, Hayashi M, Yamaya T, Sato T (2001) Mapping of QTLs associated with cytosolic glutamine synthetase and NADH-glutamate synthase in rice (Oryza sativa L.). J Exp Bot 52:1209–1217

    Article  PubMed  CAS  Google Scholar 

  • Obara M, Sato T, Sasaki S, Kashiba K, Nagano A, Nakamura I, Ebitani T, Yano M, Yamaya T (2004) Identification and characterization of a QTL on chromosome 2 for cytosolic glutamine synthetase content and panicle number in rice. Theor Appl Genet 110:1–11

    Article  PubMed  CAS  Google Scholar 

  • Senapathy S, Vinod KK, Malarvizhi P, Maheswaran M (2008) QTL and QTL × environment effects on agronomic and nitrogen acquisition traits in rice. J Integr Plant Biol 50:1108–1117

    Article  Google Scholar 

  • Septiningsih EM, Prasetiyono J, Lubis E, Tai TH, Tjubaryat T, Moeljopawiro S, McCouch SR (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 relative O. rufipogon. Theor Appl Genet 107:1419–1432

    Article  PubMed  CAS  Google Scholar 

  • Shan YH, Wang YL, Pan XB (2005) Mapping of QTLs for nitrogen use efficiency and related traits in rice (Oryza sativa L.). Agric Sci China 4:721–727

    Google Scholar 

  • Tong HH, Mei HW, Yu XQ, Xu XY, Li MS, Zhang SQ, Luo LJ (2006) Identification of related QTLs at late developmental stage in rice (Oryza sativa L.) under two nitrogen levels. Acta Genet Sin 5:458–467

    Article  Google Scholar 

  • Tong HH, Yu XQ, Mei HW, Cao YP, Zhang SQ, Luo LJ (2007) An effective method to identify high nitrogen use efficiency (NUE) genotype at seedling stage. J Zhejiang Agric Sci 5:537–541 (in Chinese with English abstract)

    Google Scholar 

  • Wang DL, Zhu J, Li ZK, Paterson AH (1999) Mapping QTLs with epistatic effects and QTL × environment interactions by mixed linear model approaches. Theor Appl Genet 99:1255–1264

    Article  Google Scholar 

  • Wissuwa M, Wegner J, Ae N, Yano M (2002) Substitution mapping of Pup1: a major QTL increasing phosphorus uptake of rice from a phosphorus-deficient soil. Theor Appl Genet 105:890–897

    Article  PubMed  CAS  Google Scholar 

  • Xiao J, Li JX, Yuan LP, Tanksley SD (1996) Identification of QTLs affecting traits of agronomic importance in a recombinant inbred population derived from a subspecific rice cross. Theor Appl Genet 92:230–244

    Article  CAS  Google Scholar 

  • Xing YZ, Tan YF, Hua JP, Sun XL, Xu CG, Zhang QF (2002) Characterization of the main effects, epistatic effects and their environmental interactions of QTLs on the genetic basis of yield traits in rice. Theor Appl Genet 105:248–257

    Article  PubMed  CAS  Google Scholar 

  • Yamaya T, Obara M, Nakajima H, Sasaki S, Hayakawa T, Sato T (2002) Genetic manipulation and quantitative-trait loci mapping for nitrogen recycling in rice. J Exp Bot 53:917–925

    Article  PubMed  CAS  Google Scholar 

  • Yu SB, Li JX, Xu CG, Tan YF, Gao YF, Li XH, Zhang QF (1997) Importance of epistasis as the genetic basis of heterosis in an elite rice hybrid. Proc Natl Acad Sci USA 94:9226–9231

    Article  PubMed  CAS  Google Scholar 

  • Zhang YS (2005) Analysis of QTLs affecting traits of agronomic importance and construction of near isogenic-lines with major QTL. PhD thesis, Huazhong Agricultural University, Wuhan, China

  • Zhang QF (2007) Strategies for developing green super rice. Proc Natl Acad Sci USA 104:16402–16409

    Article  PubMed  CAS  Google Scholar 

  • 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 line of rice. Theor Appl Genet 113:361–368

    Article  PubMed  CAS  Google Scholar 

  • Zhuang JY, Fan YY, Rao ZM, Wu JL, Xia YW, Zheng KL (2002) Analysis on additive effects and additive-by- additive epistatic effects of QTLs for yield traits in a recombinant inbred line population of rice. Theor Appl Genet 105:1137–1145

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

We are much indebted to the reviewers for their critical comments on the manuscript. This research was jointly supported by the National Natural Science Foundation of China (30830071), State Key Development Program of Basic Research of China (2010CB125901), Chinese Ministry of Science and Technology (863-2009AAQ04002), Chinese Ministry of Agriculture (948 plan, 2006-G1), National Special Program on the Research and Commercialization of Transgenic Plants (2010ZX08001-005, 2009ZX8009-007B) and Shanghai Municipal Science and Technology Commission (09DJ1400501).

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Authors and Affiliations

  1. College of Plant Science and Technology, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, China

    Han-hua Tong, Yong-zhong Xing & Li-jun Luo

  2. Shanghai Agrobiological Gene Center, 210016, Shanghai, China

    Han-hua Tong, Liang Chen, Wei-ping Li, Han-wei Mei, Xing-qiao Yu, Xiao-yan Xu & Li-jun Luo

  3. Chinese National Center for Rice Improvement, National Key Laboratory of Rice Biology, China National Rice Research Institute, 310006, Hangzhou, China

    Han-hua Tong & Shan-qing Zhang

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  1. Han-hua Tong
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Correspondence to Li-jun Luo.

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Han-hua Tong, Liang Chen and Wei-ping Li contributed equally to this paper.

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Tong, Hh., Chen, L., Li, Wp. et al. Identification and characterization of quantitative trait loci for grain yield and its components under different nitrogen fertilization levels in rice (Oryza sativa L.). Mol Breeding 28, 495–509 (2011). https://doi.org/10.1007/s11032-010-9499-9

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  • DOI: https://doi.org/10.1007/s11032-010-9499-9

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