Skip to main content
SpringerLink
Log in

Genetic dissection of leaf-related traits using 156 chromosomal segment substitution lines

  • Original Article
  • Published:
Journal of Plant Biology Aims and scope Submit manuscript

Abstract

A two-line super-hybrid rice (Oryza sativa L.) variety [Liangyoupei9 (LYP9)] demonstrated superiority over its both parents, viz. elite inbred lines 93-11 and Pei-ai64S (PA64S), as well as other conventional hybrids, and had long been exploited in China. However, the genetic basis of its leaf-related traits, supposed to be an important component for yield potential, remains elusive. Here, initially a set of chromosome segment substitution lines (CSSLs) was constructed, in which the genome of Pei-ai64S has been introgressed into the background of 93-11. This set was developed by marker aided selection, based on 123 polymorphic SSR markers. The introgressed chromosomal segments presented in the 156 CSSLs covered 96.46% of Pei-ai64S genome. Afterwards, the CSSLs were deployed to assess the genetic basis of leaf size (length and width) and chlorophyll content of top three leaves across five different environments. The CSSLs showed transgressive segregation for all of the traits, and significant correlations were detected among most of the traits. A total of 27 quantitative trait loci (QTL) were identified on ten chromosomes, and three QTL cluster affecting related traits were found on chromosome 3, 6, and 8, respectively. Remarkably, two key QTLs, qALW3-1 and qALW3-2, both controlling the antepenultimate leaf width, were identified in all five environments, and their effect were further validated by CSSLs harboring the two QTL alleles. Our results indicate that developing CSSLs is a powerful tool for genetic dissection of quantitative traits. Meanwhile, the QTLs controlling leaf-related traits uncovered here provide useful information for marker-assisted selection in improving the performance of leaf morphology and photosynthetic ability.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Bian J, He H, Shi H, Zhu G, Li C, Zhu C, Peng X, Yu Q, Fu J, He X, Chen X, Hu L, Ouyang L (2014) Quantitative trait loci mapping for flag leaf traits in rice using a chromosome segment substitution line population. Plant Breeding 133:203–209

    Article  CAS  Google Scholar 

  • Bian JM, Jiang L, Liu LL, Wei XJ, Xiao YH, Zhang LJ, Zhao ZG, Zhai HQ, Wan JM (2010) Construction of a new set of rice chromosome segment substitution lines and identification of grain weight and related traits QTLs. Breed Sci 60:305–313

    Article  Google Scholar 

  • Chen M, Luo J, Shao G, Wei X, Tang S, Sheng Z, Song J, Hu P (2012) Fine mapping of a major QTL for flag leaf width in rice, qFLW4, which might be caused by alternative splicing of NAL1. Plant Cell Rep 31:863–872

    Article  CAS  PubMed  Google Scholar 

  • Cheng SH, Zhuang JY, Fan YY, Du JH, Cao LY (2007) Progress in research and development on hybrid rice: a super-domesticate in China. Annals of Botany 100:959–966

    Article  PubMed Central  PubMed  Google Scholar 

  • Dong YJ, Yang Z, Xu J, Lin D, Sugimoto Y, Luo L, Mei H (2007) Quantitative trait loci for leaf chlorophyll content at two developmental stages of rice (Oryza sativa L.). Commun Biometry Crop Sci 1:1–7

    Google Scholar 

  • 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • Farooq M, Tagle AG, Santos RE, Ebron LA, Fujita D, Kobayashi N (2010) Quantitative trait loci mapping for leaf length and leaf width in rice cv. IR64 derived lines. J Integr Plant Biol 52:578–584

    Article  CAS  PubMed  Google Scholar 

  • Fujino K, Matsuda Y, Ozawa K, Nishimura T, Koshiba T, Fraaije MW, Sekiguchi H (2008) NARROW LEAF 7 controls leaf shape mediated by auxin in rice. Mol Genet Genomics 279:499–507

    Article  CAS  PubMed  Google Scholar 

  • Gladun IV, Karpov EA (1993a) Production and partitioning of assimilates between the panicle and vegetative organs of rice after flowering. Russ J Plant Physiol 40:728–773

    CAS  Google Scholar 

  • Gladun IV, Karpov EA (1993b) Distribution of assimilates from the flag leaf of rice during the reproductive period of development. Russ J Plant Physiol 40:215–219

    Google Scholar 

  • Hedden P (2003) The genes of the Green Revolution. Trends Genet 19:5–9

    Article  CAS  PubMed  Google Scholar 

  • Jiang G, Zeng J, He Y (2014) Analysis of quantitative trait loci affecting chlorophyll content of rice leaves in a double haploid population and two backcross populations. Gene 536:287–295

    Article  CAS  PubMed  Google Scholar 

  • Jiang S, Zhang X, Zhang F, Xu Z, Chen W, Li Y (2012) Identification and fine mapping of qCTH4, a quantitative trait loci controlling the chlorophyll content from tillering to heading in rice (Oryza sativa L.). J Hered 103:720–726

    Article  CAS  PubMed  Google Scholar 

  • Kubo T, Nakamura K, Yoshimura A (1999) Development of a series of Indica chromosome segment substitution lines in Japonica background of rice. Rice Genet Newsl 16:104–106

    Google Scholar 

  • Li H, Ye G, Wang J (2007) A modified algorithm for the improvement of composite interval mapping. Genetics 175:361–374

    Article  PubMed Central  PubMed  Google Scholar 

  • Li ZK (2001) QTL mapping in rice: a few critical considerations. Rice genetics IV. In: Khush GS, Brar DS, Hrady B (eds) Proceeding of the fourth international rice genetics symposium, 22-27 October 2000, Los Banos, Philippines, pp 153–171

    Google Scholar 

  • Lim JH, Yang HJ, Jung KH, Yoo SC, Paek NC (2014) Quantitative trait locus mapping and candidate gene analysis for plant architecture traits using whole genome re-sequencing in rice. Mol. Cells 37:149–160

    Article  PubMed Central  PubMed  Google Scholar 

  • Lin HX, Yamamoto T, Sasaki T, Yano M (2000) Characterization and detection of epistatic interactions of 3 QTLs, Hd-1, Hd-2 and Hd-3, controlling heading date of rice using nearly isogenic lines. Theor Appl Genet 101:1021–1028

    Article  CAS  Google Scholar 

  • McCouch SR, Cho YG, Yano M, Paul E, Blinstrub M (1997) Report on QTL nomenclature. Rice Genet Newslett 14:11–13

    Google Scholar 

  • McCouch SR, Teytelman L, Xu YB (2002) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res 9:199–207

    Article  CAS  PubMed  Google Scholar 

  • Mei H., 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 Appl Genet 107:89–101

    CAS  PubMed  Google Scholar 

  • Moose S, Mumm R (2008) Molecular plant breeding as the foundation for 21st century crop improvement. Plant Physiol 147:969–977

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4325

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Nadeau JH, Frankel WN (2000) The roads from phenotypic variation to gene discovery: mutagenesis versus QTLs. Nature Genetics 25:381–384

    Article  CAS  PubMed  Google Scholar 

  • Qi J, Qian Q, Bu Q, Li S, Chen Q, Sun J, Liang W, Zhou Y, Chu C, Li X, Ren F, Palme K, Zhao B, Chen J, Chen M, Li C (2008) Mutation of the rice Narrow leaf1 gene, which encodes a novel protein, affects vein patterning and polar auxin transport. Plant Physiol 147:1947–1959

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Takahashi Y, Shomura A, Sasaki T, Yano M (2001) Hd-6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes a subunit of protein kinase CK2. Proc Natl Acad Sci USA 98:7922–7927

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Takai T, Kondo M, Yano M, Yamamoto T (2010) A quantitative trait locus for chlorophyll content and its association with leaf photosynthesis in rice. Rice 3:172–180

    Article  Google Scholar 

  • Tian F, Bradbury PJ, Brown PJ, Hung H, Sun Q, Flint-Garcia S, Rocheford TR, McMullen MD, Holland JB, Buckler ES (2011) Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet 43:159–162

    Article  CAS  PubMed  Google Scholar 

  • Tomoshiro T, Mitsunori O, Waichi A (1983) Comparison of the formation of dry substance by the old and new type of rice cultivars. Japan J Crop Sci 52:299–305

    Article  Google Scholar 

  • Wang J, Wan X, Crossa J, Crouch J, Weng J, Zhai H, Wan J (2006) QTL mapping of grain length in rice (Oryza sativa L.) using chromosome segment substitution lines. Genet Res 88:93–104

    Article  CAS  PubMed  Google Scholar 

  • Wang J, Wan X, Li H, Pfeiffer WH, Crouch J, Wan J (2007) Application of identified QTL-marker associations in rice quality improvement through a design-breeding approach. Theor Appl Genet 115:87–100

    Article  PubMed  Google Scholar 

  • Wang P, Zhou G, Cui K, Li Z, Yu SB (2012) Clustered QTL for source leaf size and yield traits in rice (Oryza sativa L.). Mol Breed 29:99–113

    Article  CAS  Google Scholar 

  • Wang P, Zhou G, Yu H, Yu S (2011) Fine mapping a major QTL for flag leaf size and yield-related traits in rice. Theor Appl Genet 123:1319–1330

    Article  CAS  PubMed  Google Scholar 

  • Wang Q, Xie W, Xing H, Yan J, Meng X, Li X, Fu X, Xu J, Lian X, Yu S, Xing Y, Wang G (2015) Genetic architecture of natural variation in rice chlorophyll content revealed by a genome-wide association study. Mol Plant 8:946–957

    Article  CAS  PubMed  Google Scholar 

  • Xue W, Xing Y, Weng X, Zhao Y, Tang W, Wang L, Zhou H, Yu S, Xu C, Li X, Zhang Q (2008) Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet 40:761–767

    Article  CAS  PubMed  Google Scholar 

  • Yamamoto T, Lin HX, Sasaki T, Yano M (2000) Identification of heading date quantitative trait locus Hd-6 and characterization of its epistatic interactions with Hd-2 in rice using advanced backcross progeny. Genetics 154:885–891

    PubMed Central  CAS  PubMed  Google Scholar 

  • Yan J, Zhu J, He C, Benmoussa M, Wu P (1999) Molecular marker assisted dissection of genotype 9 environment interaction for plant type traits in rice (Oryza sativa L.). Crop Sci 39:538–544

    Article  Google Scholar 

  • Yang GH, Tu S, Li S, Feng L, Kong J, Li H, Li Y (2008) Analysis of quantitative trait loci underlying the traits related to chlorophyll content of the flag leaf in rice. Front Biol China 3:443–448

    Article  Google Scholar 

  • Yang W, Guo Z, Huang C, Wang K, Jiang N, Feng H, Chen G, Liu Q, Xiong L (2015) Genome-wide association study of rice (Oryza sativa L.) leaf traits with a high-throughput leaf scorer. J Exp Bot 66:5605–5615

    Article  PubMed Central  PubMed  Google Scholar 

  • Yano M, Katayose Y, Ashikari M, Yamanouchi U, Monna Lisa, Fuse T, Baba T, Yamamoto K, Umehara Y, Nagamura Y, Sasaki T (2000) Hd-1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell 12:2473–2483

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng YJ, Dai L, Zhou Y, Zhang XQ, Cao ML, Liu J, Sun JD, Tang JB, Chen YJ, Huang XB, Lin W, Ye C, Tong W, Cong LJ,et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79–92

    Article  CAS  PubMed  Google Scholar 

  • Yuan L (2003) Recent progress in breeding super hybrid rice in China, In Virmani S, Mao C, Hardy B, eds, Hybrid rice for food security, poverty alleviation and environmental protection. International Rice Research Institute (IRRI), Hanoi, pp 3–6

    Google Scholar 

  • Yue B, Xue WY, Luo LJ, Xing YZ (2006) QTL analysis for flag leaf characteristics and their relationships with yield and yield traits in rice. Acta Genet Sin 33:824–832

    Article  CAS  PubMed  Google Scholar 

  • Zhang GH, Li SY, Wang L, Ye WJ, Zeng DL, Rao YC, Peng YL, Hu J, Yang YL, Xu J, Ren DY, Gao ZY, Zhu L, Dong GJ, Hu XM, Yan MX, Guo LB, Li CY, Qian Q (2014) LSCHL4 from japonica cultivar, which is allelic to NAL1, increases yield of indica super rice 93-11. Mol Plant 7:1350–1364

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Zuo H, Xiao, Dong, Xu J, Li Z, Luo L, Mei H (2007) Molecular detection of quantitative trait loci for leaf chlorophyll content at different growth-stages of rice (Oryza sativa L.). Asian J Plant Sci 6:518–522

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, 210095, Nanjing, China

    Xi Liu, Linglong Liu, Yinhui Xiao, Shijia Liu, Yunlu Tian, Liangming Chen, Zhiquan Wang, Ling Jiang, Zhigang Zhao & Jianmin Wan

  2. Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081, Beijing, China

    Jianmin Wan

Authors
  1. Xi Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Linglong Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yinhui Xiao
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Shijia Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yunlu Tian
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Liangming Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Zhiquan Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Ling Jiang
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Zhigang Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Jianmin Wan
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Zhigang Zhao.

Additional information

These authors contributed equally to this work.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Liu, X., Liu, L., Xiao, Y. et al. Genetic dissection of leaf-related traits using 156 chromosomal segment substitution lines. J. Plant Biol. 58, 402–410 (2015). https://doi.org/10.1007/s12374-015-0402-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12374-015-0402-4

Keywords

Search

Navigation