Abstract
Jatropha curcas L. is a potential plant species for biodiesel production. However, its seed yield is too low for profitable production of biodiesel. To improve the productivity, genetic improvement through breeding is essential. Marker-assisted selection (MAS) has the huge potential to accelerate genetic improvement. We mapped 506 markers (216 microsatellites and 290 SNPs from ESTs) onto 11 linkage groups. However, genetic analysis of the yield traits has not been done in jatropha. Quantitative trait loci (QTL) mapping was conducted to identify genetic factors controlling growth and seed yield in jatropha. We identified a total of 28 QTLs for 11 growth and seed traits using a population of 296 backcrossing jatropha trees. QTL and expression QTL analyses were applied to identify genetic factors that are relevant to seed oil traits in jatropha. We screened key genes in auxin pathway including ARF and IAA families and downstream effectors to identify candidate genes controlling seed size in jatropha. JcARF19 was mapped in the major QTL region and significantly associated with seed length.
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Almeida J, Achten WMJ, Duarte MP, Mendes B, Muys B (2011) Benchmarking the environmental performance of the Jatropha biodieselsystem through a generic life cycle assessment. Environ Sci Technol 45:5447–5453
Bailis RE, Baka JE (2010) Greenhouse gas emissions and land use change from Jatropha curcas-based jet fuel in Brazil. Environ Sci Technol 44:8684–8691
Berleth T, Krogan NT, Scarpella E (2004) Auxin signals—turning genes on and turning cells around. Curr Opin Plant Biol 7(5):553–563
Brown JR (2007) Comparative genomics: basic and applied research. CRC Press, Boca Raton
Carvalho CR, Clarindo WR, Praça MM, Araújo FS, Carels N (2008) Genome size, base composition and karyotype of Jatropha curcas L., an important biofuel plant. Plant Sci 174(6):613–617. doi:10.1016/j.plantsci.2008.03.010
Chhetri AB, Tango MS, Budge SM, Watts KC, Islam MR (2008) Non-edible plant oils as new sources for biodiesel production. Int J Mol Sci 9(2):169–180
Costa GG, Cardoso KC, Del Bem LE, Lima AC, Cunha MA, de Campos-Leite L, Vicentini R, Papes F, Moreira RC, Yunes JA (2010) Transcriptome analysis of the oil-rich seed of the bioenergy crop Jatropha curcas L. BMC Genom 11(1):462
Durbak A, Yao H, McSteen P (2012) Hormone signaling in plant development. Curr Opin Plant Biol 15(1):92–96
Fairless D (2007) Biofuel: the little shrub that could–maybe. Nature 449(7163):652–655
Goldstein DB, Schlotterer C (eds) (1999) Microsatellites: evolution and applications
Gu K, Chiam H, Tian D, Yin Z (2011) Molecular cloning and expression of heteromeric ACCase subunit genes from Jatropha curcas. Plant Sci 180(4):642–649
Gu K, Yi C, Tian D, Sangha JS, Hong Y, Yin Z (2012) Expression of fatty acid and lipid biosynthetic genes in developing endosperm of Jatropha curcas. Biotechnol Biofuels 5(1):47
Guimarães EP (2007) Marker-assisted selection: current status and future perspectives in crops, livestock, forestry and fish. Food and Agriculture Organization, Rome (incomplete)
Harper JL, Lovell P, Moore K (1970) The shapes and sizes of seeds. Annu Rev Ecol Syst 1:327–356
Harushima Y, Yano M, Shomura A, Sato M, Shimano T, Kuboki Y, Yamamoto T, Lin SY, Antonio BA, Parco A (1998) A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics 148(1):479–494
Hayashi M, Miyahara A, Sato S, Kato T, Yoshikawa M, Taketa M, Hayashi M, Pedrosa A, Onda R, Imaizumi-Anraku H (2001) Construction of a genetic linkage map of the model legume Lotus japonicus using an intraspecific F2 population. DNA Res 8(6):301–310
Heller J (1996) Physic nut. Jatropha curcas L. promoting the conservation and use of underutilized and neglected crops, 1. IBPGR, Roma (in full)
Hwang T-Y, Sayama T, Takahashi M, Takada Y, Nakamoto Y, Funatsuki H, Hisano H, Sasamoto S, Sato S, Tabata S (2009) High-density integrated linkage map based on SSR markers in soybean. DNA Res:dsp010
Ioio RD, Nakamura K, Moubayidin L, Perilli S, Taniguchi M, Morita MT, Aoyama T, Costantino P, Sabatini S (2008) A genetic framework for the control of cell division and differentiation in the root meristem. Science 322(5906):1380–1384
Jain S, Sharma MP (2010) Biodiesel production from Jatropha curcas oil. Renew Sustain Energy Rev 14(9):3140–3147. doi:10.1016/j.rser.2010.07.047
Kumar S, Singh J, Nanoti SM, Garg MO (2012) A comprehensive life cycle assessment (LCA) of Jatropha biodiesel production in India. Bioresource Technol 110:723–729
Lee DJ, Park JW, Lee HW, Kim J (2009) Genome-wide analysis of the auxin-responsive transcriptome downstream of iaa1 and its expression analysis reveal the diversity and complexity of auxin-regulated gene expression. J Exp Bot 60(13):3935–3957
Li F, Kitashiba H, Inaba K, Nishio T (2009) A Brassica rapa linkage map of EST-based SNP markers for identification of candidate genes controlling flowering time and leaf morphological traits. DNA Res 16(6):311–323
Liu P, Wang CM, Li L, Sun F, Liu P, Yue GH (2011) Mapping QTLs for oil traits and eQTLs for oleosin genes in jatropha. BMC Plant Biol 11:132
Meksem K, Kahl G (eds) (2006) The handbook of plant genome mapping: genetic and physical mapping. Wiley, Oxford
Okushima Y, Fukaki H, Onoda M, Theologis A, Tasaka M (2007) ARF7 and ARF19 regulate lateral root formation via direct activation of LBD/ASL genes in Arabidopsis. Plant Cell Online 19(1):118–130
Okushima Y, Mitina I, Quach HL, Theologis A (2005a) AUXIN RESPONSE FACTOR 2 (ARF2): a pleiotropic developmental regulator. Plant J 43(1):29–46
Okushima Y, Overvoorde PJ, Arima K, Alonso JM, Chan A, Chang C, Ecker JR, Hughes B, Lui A, Nguyen D (2005b) Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19. Plant Cell Online 17(2):444–463
Openshaw K (2000) A review of Jatropha curcas: an oil plant of unfulfilled promise. Biomass Bioenergy 19(1):1–15
Panjabi P, Jagannath A, Bisht NC, Padmaja KL, Sharma S, Gupta V, Pradhan AK, Pental D (2008) Comparative mapping of Brassica juncea and Arabidopsis thaliana using intron polymorphism (IP) markers: homoeologous relationships, diversification and evolution of the A, B and C Brassica genomes. BMC Genom 9(1):113
Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5(2):94–100
Ren Y, Zhang Z, Liu J, Staub JE, Han Y, Cheng Z, Li X, Lu J, Miao H, Kang H (2009) An integrated genetic and cytogenetic map of the cucumber genome. PLoS One 4(6):e5795
Ruan Y-L, Patrick JW, Bouzayen M, Osorio S, Fernie AR (2012) Molecular regulation of seed and fruit set. Trends Plant Sci 17(11):656–665
Sanderson K (2009) Wonder weed plans fail to flourish. Nature 461:328–329
Sato S, Hirakawa H, Isobe S, Fukai E, Watanabe A, Kato M, Kawashima K, Minami C, Muraki A, Nakazaki N, Takahashi C, Nakayama S, Kishida Y, Kohara M, Yamada M, Tsuruoka H, Sasamoto S, Tabata S, Aizu T, Toyoda A, Shin-i T, Minakuchi Y, Kohara Y, Fujiyama A, Tsuchimoto S, Kajiyama S, Makigano E, Ohmido N, Shibagaki N, Cartagena JA, Wada N, Kohinata T, Atefeh A, Yuasa S, Matsunaga S, Fukui K (2011) Sequence analysis of the genome of an oil-bearing tree, Jatropha curcas L. DNA Res 18(1):65–76
Shah S, Sharma A, Gupta MN (2005) Extraction of oil from Jatropha curcas L. seed kernels by combination of ultrasonication and aqueous enzymatic oil extraction. Bioresour Technol 96(1):121–123. doi:10.1016/j.biortech.2004.02.026
Sladek R, Hudson TJ (2006) Elucidating cis-and trans-regulatory variation using genetical genomics. Trends Genet 22(5):245–250
Sun F, Liu P, Ye J, Lo LC, Cao S, Li L, Yue GH, Wang CM (2012) An approach for jatropha improvement using pleiotropic QTLs regulating plant growth and seed yield. Biotechnol Biofuels 5:1–10
Thumma BR, Naidu BP, Chandra A, Cameron DF, Bahnisch LM, Liu C (2001) Identification of causal relationships among traits related to drought resistance in Stylosanthes scabra using QTL analysis. J Exp Bot 52(355):203–214
Varshney RK, Tuberosa R (2007) Genomics-assisted crop improvement, vol 1. Springer, Berlin
Wang CM, Bai ZY, He XP, Lin G, Xia JH, Sun F, Lo LC, Feng F, Zhu ZY, Yue GH (2011a) A high-resolution linkage map for comparative genome analysis and QTL fine mapping in Asian seabass, Lates calcarifer. BMC Genom 12(1):174
Wang CM, Liu P, Yi C, Gu K, Sun F, Li L, Lo LC, Liu X, Feng F, Lin G (2011b) A first generation microsatellite-and SNP-based linkage map of Jatropha. PLoS One 6(8):e23632
Wang WY, Barratt BJ, Clayton DG, Todd JA (2005) Genome-wide association studies: theoretical and practical concerns. Nat Rev Genet 6(2):109–118
Wu J, Liu Y, Tang L, Zhang F, Chen F (2011) A study on structural features in early flower development of Jatropha curcas L. and the classification of its inflorescences. Afr J Agr Res 6:275–284
Xia JH, Liu F, Zhu ZY, Fu J, Feng J, Li J, Yue GH (2010) A consensus linkage map of the grass carp (Ctenopharyngodon idella) based on microsatellites and SNPs. BMC Genom 11(1):135
Xue L-J, Zhang J-J, Xue H-W (2009) Characterization and expression profiles of miRNAs in rice seeds. Nucleic Acids Res 37(3):916–930
Yang JH, Han SJ, Yoon EK, Lee WS (2006) Evidence of an auxin signal pathway, microRNA167-ARF8-GH3, and its response to exogenous auxin in cultured rice cells. Nucleic Acids Res 34(6):1892–1899
Ye J, Qu J, Bui HTN, Chua NH (2009) Rapid analysis of Jatropha curcas gene functions by virus-induced gene silencing. Plant Biotechnol J 7:964–976
Ye J, Hong Y, Qu J, Wang C (2012) Improvement of Jatropha oil bygenetic transformation. Springer Science Publishers, New York
Ye J, Liu P, Zhu CS, Qu J, Wang XH, Sun YW, Sun F, Jiang YL, Yue GH, Wang CM (2014) Identification of candidate genes JcARF19 and JcIAA9 associated with seed size traits in Jatropha. Funct Integr Genom 14(4):66–757
Yin Z, Meng F, Song H, Wang X, Xu X, Yu D (2010) Expression quantitative trait loci analysis of two genes encoding rubisco activase in soybean. Plant Physiol 152(3):1625–1637
Zhang Y, Wang Y, Jiang L, Xu Y, Wang Y, Lu D, Chen F (2007) Aquaporin JcPIP2 is involved in drought responses in Jatropha curcas. Acta Biochim Biophys Sin 39(10):787–794
Acknowledgements
The work is part of the project “Genetic Improvement of Jatropha” initiated and coordinated by Professor Nam-Hai Chua, Rockefeller University, USA. We thank Weijie Tang, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China, for his editing work on this chapter. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of this chapter.
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Ye, J., Wang, C., Yue, G. (2017). Linkage Mapping and QTL Analysis. In: Tsuchimoto, S. (eds) The Jatropha Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-319-49653-5_2
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DOI: https://doi.org/10.1007/978-3-319-49653-5_2
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