Please wait a minute...
Journal of Integrative Agriculture  2018, Vol. 17 Issue (08): 1727-1735    DOI: 10.1016/S2095-3119(17)61862-8
Crop Science Advanced Online Publication | Current Issue | Archive | Adv Search |
Identification of novel soybean oil content-related genes using QTLbased collinearity analysis from the collective soybean genome
XU Ming-yue1*, LIU Zhang-xiong2*, QIN Hong-tao1, QI Hui-dong1, WANG Zhong-yu1, MAO Xin-rui1, XIN Da-wei1, HU Zhen-bang1, WU Xiao-xia1, JIANG Hong-wei1, QI Zhao-ming1, CHEN Qing-shan1
1 Key Laboratory of Soybean Biology, Ministry of Education/College of Agriculture, Northeast Agricultural University, Harbin 150030, P.R.China
2 National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Germplasm Utilization, Ministry of Agriculture/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
Download:  PDF in ScienceDirect  
Export:  BibTeX | EndNote (RIS)      

Soybean is a global principal source of edible plant oil.  As more soybean oil-related quantitative trait loci (QTLs) have been located in the collective genome, it is urgent to establish a classification system for these distributed QTLs.  A collinear platform may be useful to characterize and identify relationships among QTLs as well as aid in novel gene discovery.  In this study, the collinearity MCScanX algorithm and collective soybean genomic information were used to construct collinearity blocks, to which soybean oil-related QTLs were mapped.  The results demonstrated that 666 collinearity blocks were detected in the soybean genome across 20 chromosomes, and 521 collinearity relationships existed in 231 of the 242 effective soybean oil-related QTLs.  This included 214 inclusion relationships and 307 intersecting relationships.  Among them, the collinearity among QTLs that are related to soybean oil content was shown on a maximum of seven chromosomes and minimum of one chromosome, with the majority of QTLs having collinearity on two chromosomes.  Using overlapping hotspot regions in the soybean oil QTLs with collinearity, we mined for novel oil content-related genes.  Overall, we identified 23 putatively functional genes associated with oil content in soybean and annotated them using a number of annotation databases.  Our findings provide a valuable framework for elucidating evolutionary relationships between soybean oil-related QTLs and lay a foundation for functional marker-assisted breeding relating to soybean oil content.
Keywords:  soybean oil QTLs        collinearity analysis       candidate genes  
Received: 22 August 2017   Accepted:
Fund: This study was financially supported by the National Key R&D Program of China (2016YFD0100500, 2016YFD0100300, 2016YFD0100201-21), the National Natural Science Foundation of China (31701449, 31471516, 31401465, 31400074, 31501332), the Natural Science Foundation of Heilongjiang Province, China (QC2017013), the Young Innovative Talent Training Plan of Undergraduate Colleges and Universities in Heilongjiang Province, China (UNPYSCT-2016144), the Special Financial Aid to Post-doctor Research Fellow in Heilongjiang, China (To Qi Zhaoming), the Heilongjiang Funds for Distinguished Young Scientists, China (JC2016004), the Outstanding Academic Leaders Projects of Harbin, China (2015RQXXJ018), the China Post Doctoral Project (2015M581419), the Dongnongxuezhe Project, China (to Chen Qingshan), and the Young Talent Project of Northeast Agricultural University, China (to Qi Zhaoming, 518062).
Corresponding Authors:  Correspondence CHEN Qing-shan, Tel/Fax: +86-451-55191945, E-mail:; QI Zhao-ming, E-mail:    
About author:  XU Ming-yue, E-mail:; LIU Zhang-xiong, E-mail:; * These authors contributed equally to this study.

Cite this article: 

XU Ming-yue, LIU Zhang-xiong, QIN Hong-tao, QI Hui-dong, WANG Zhong-yu, MAO Xin-rui, XIN Dawei, HU Zhen-bang, WU Xiao-xia, JIANG Hong-wei, QI Zhao-ming, CHEN Qing-shan. 2018. Identification of novel soybean oil content-related genes using QTLbased collinearity analysis from the collective soybean genome. Journal of Integrative Agriculture, 17(08): 1727-1735.

Ahn S, Tanksley S D. 1993. Comparative linkage maps of the rice and maize genomes. Proceedings of the National Academy of Sciences of the United States of America, 90, 7980–7984.
Bailey P C, McKibbin R S, Lenton J R, Holdsworth M J, Flintham J E, Gale M D. 1999. Genetic map locations for orthologous Vp1 genes in wheat and rice. Theoretical and Applied Genetics, 98, 281–284.
Ball C A, Cherry J M. 2001. Genome comparisons highlight similarity and diversity within the eukaryotic kingdoms, Current Opinion in Chemical Biology, 5, 86–89.
Boeglin W E, Itoh A, Zheng Y, Coffa G, Howe G A, Brash A R. 2008. Investigation of substrate binding and product stereochemistry issues in two linoleate 9-lipoxygenases. Lipids, 43, 979–987.
Boleda M D, Saubi N, Farrés J, Parés X. 1993. Physiological substrates for rat alcohol dehydrogenase classes: Aldehydes of lipid peroxidation, omega-hydroxyfatty acids, and retinoids. Archives of Biochemistry and Biophysics, 307, 85–90.
Burton J W. 1987. Quantitative genetics: Results relevant to soybean breeding. American Society of Agronomy, 16, 211–247.
Chen J, Liang C, Chen C, Zhang W, Sun S, Liao Y, Zhang X, Yang L, Song C, Wang M, Shi J, Huang Q, Liu G, Liu J, Zhou H, Zhou W, Yu Q, An N, Chen Y, Cai Q, et al. 2013. Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution. Nature Communications, 4, 67–88.
Coleman R A, Lewin T M, Van Horn C G, Gonzalez-Baro M R. 2002. Do long-chain acyl-CoA synthetases regulate fatty acid entry into synthetic versus degradative pathways? The Journal of Nutrition, 132, 2123–2126.
Gawronski P, Schnurbusch T. 2012. High-density mapping of the earliness per se-3Am (Eps-3Am) locus in diploid einkorn wheat and its relation to the syntenic regions in rice and Brachypodium distachyon L. Molecular Breeding, 30, 1097–1108.
Geetika S, Poonam S, Preeti A, Parul G, Gulshan K, Vishal A. 2016. Genome-wide characterization and expression profiling of TIFY gene family in pigeonpea (Cajanus cajan (L.) Mill sp.) under copper stress. Journal of Plant Biochemistry & Biotechnology, 25, 301–310.
Guillas I, Jiang J C, Vionnet C, Roubaty C, Uldry D, Chuard R, Wang J, Jazwinski S M, Conzelmann A. 2003. Human homologues of LAG1 reconstitute acyl-CoA-dependent ceramide synthesis in yeast. Journal of Biological Chemistry, 278, 37083–37091.
Hall J N, Schwartz R L. 1998. Effective Perl Programming: Writing Better Programs with Perl. Addison-Wesley Longman Publishing Co., Inc. Boston, MA, USA.
Jaillon O, Aury J M, Noel B, Policriti A, Clepet C. 2007. The grapevine genome sequence suggests ancestralhexaploidization in major angiosperm phyla. Nature, 449, 463–467.
Jiao Y, Li J, Tang H, Paterson A H. 2014. Integrated syntenic and phylogenomic analyses reveal an ancient genome duplication in monocots. The Plant Cell, 26, 2792–2802.
Katrolia P, Jia H, Yan Q, Song S, Jiang Z, Xu H. 2012. Characterization of a protease-resistant α-galactosidase from the thermophilic fungus Rhizomucor miehei and its application in removal of raffinose family oligosacch­arides. Bioresource Technology, 110, 578–586.
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones S J, Marra M A. 2009. Circos: An information aesthetic for comparative genomics. Genome Research, 19, 1639–1645.
Kurata N, Moore G, Nagamura Y, Foote T, Yano M. 1994. Conservation of genome structure between rice and wheat. Nature Biotechnology, 12, 276–278.
Lee R H, Hsu J H, Huang H J, Lo S F, Chen S C G. 2009. Alkaline alpha-galactosidase degrades thylakoid membranes in the chloroplast during leaf senescence in rice. New Phytologist, 184, 596–606.
Liscovitch M, Czarny M, Fiucci G, Tang X. 2000. Phospholipase D: Molecular and cell biology of a novel gene family. Biochemical Journal, 345, 401–415.
Lyons E, Pedersen B, Kane J, Alam M, Ming R, Tang H, Wang X, Bowers J, Paterson A, Lisch D, Freeling M. 2008. Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids. Plant Physiology, 148, 1772–1781.
Maceyka M, Sankala H, Hait NC, Le Stunff H, Liu H, Toman R, Collier C, Zhang M, Satin L S, Merrill Jr A H, Milstien S, Spiegel S. 2005. SphK1 and SphK2, sphingosine kinase isoenzymes with opposing functions in sphingolipid metabolism. Journal of Biological Chemistry, 280, 37118–37129.
Marone D, Russo M A, Laidò G, De Vita P, Papa R, Blanco A, Gadaleta A, Rubiales D, Mastrangelo A M. 2013. Genetic basis of qualitative and quantitative resistance to powdery mildew in wheat: From consensus regions to candidate genes. BMC Genomics, 14, 562.
Mason C H, Perreault W D. 1991. Collinearity, power, and interpretation of multiple regression analysis. Journal of Marketing Research, 28, 268–280.
McCouch S R. 2001. Genomics and synteny. Plant Physiology, 125, 152–155.
Nakamura Y, Koizumi R, Shui G, Shimojima M, Wenk M R, Ito T, Ohta H. 2009. Arabidopsis lipins mediate eukaryotic pathway of lipid metabolism and cope critically with phosphate starvation. Proceedings of the National Academy of Sciences of the United States of America, 106, 20978–20983.
Paterson A H, Lander E S, Hewitt J D, Peterson S, Lincoln S E, Tanksley S D. 1988. Resolution of quantitative traits into mendelian factors by using a complete linkage map of restriction fragment length polymorphisms. Nature, 335, 721–726.
Persson B, Kallberg Y, Bray J E, Bruford E, Dellaporta S L, Favia A D,Duarte R G, Jornvall H, Kavanagh K L, Kedishvili N. 2009. The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative. Chemico-Biological Interactions, 178, 94–98.
Pottorff M, Ehlers J D, Fatokun C, Roberts P A, Close T J. 2012. Leaf morphology in cowpea [Vigna unguiculata (L.) Walp]: QTL analysis, physical mapping and identifying a candidate gene using synteny with model legume species. BMC Genomics, 13, 234.
Sarma R N, Gill B S, Sasaki T, Galiba G, Sutka J. 1998. Comparative mapping of the wheat chromosome 5A Vrn-A1 region with rice and its relationship to QTL for flowering time. Theoretical & Applied Genetics, 97, 103–109.
Schlueter J A, Lin J Y, Schlueter S D, Vasylenko-Sanders I F, Deshpande S, Yi J, O’Bleness M, Roe B A, Nelson R T, Scheffler B E. 2007. Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing. BMC Genomics, 8, 330–345.
Schmutz J, Cannon S B, Schlueter J, Ma J, Mitros T, Nelson W, Hyten D L, Song Q, Thelen J J, Cheng J, Cheng D, Xu U, Hellsten G D, May Y, Yu T, Sakurai T, Umezawa M K, Bhattacharyya D, Sandhu B, Valliyodan E, et al. 2010. Genome sequence of the palaeopolyploid soybean. Nature, 463, 178–183.
Svastits-Dücsö L, Nguyen Q D, Lefler D D, Rezessy-Szabo J M. 2009. Effects of galactomannan as carbon source on production of α-galactosidase by Thermomyces lanuginosus: Fermentation, purification and partial characterization. Enzyme Microbial Technology, 45, 367–371.
Tang H, Bowers J E, Wang X, Ming R, Alam M, Paterson A H. 2008. Synteny and collinearity in plant genomes. Science, 320, 486–488.
Venkataraman K, Riebeling C, Bodennec J, Riezman H, Allegood J C, Sullards M C, Merrill A H, Futerman A H. 2002. Upstream of growth and differentiation factor 1 (uog1), a mammalian homolog of the yeast longevity assurance gene 1 (LAG1), regulates N-stearoyl-sphinganine (C18-(Dihydro) ceramide) synthesis in a fumonisin B1-independent manner in mammalian cells. Journal of Biological Chemistry, 277, 35642–35649.
Wang N A, Xiang Y, Fang L C, Wang Y J, Xin H P, Li S H. 2013. Patterns of gene duplication and their contribution to expansion of gene families in grapevine. Plant Molecular Biology Reporter, 31, 852–861.
Wang X. 2000. Multiple forms of phospholipase D in plants: The gene family, catalytic and regulatory properties, and cellular functions. Progress in Lipid Research, 39, 109–149.
Wang Y, Tang H, Debarry J D, Tan X, Li J, Wang X, Lee T H, Jin H, Marler B, Guo H, Kissinger J C, Paterson A H. 2012. MCScanX: A toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Research, 40, e49.
Wang Y, Yao J, Zhang Z F, Zheng Y L. 2006. The comparative analysis based on maize integrated QTL map and meta-analysis of plant height QTL. Chinese Science Bulletin, 51, 2219–2230.
Wilson R F. 2008. Soybean: Market driven research needs In: Stacey G, ed., Genetics and Genomics of Soybean. Springer-Verlag GmbH, Heidelberg, Germany.
Xu P, Zhang X, Wang X, Ji W, Zhou Y, Ji Y, Liu X, Wang W. 2014. Genome sequence and genetic diversity of the common carp, Cyprinus carpio. Nature Genetics, 46, 1212–1219.
Zubieta C, Koscheski P, Ross J R, Yang Y, Pichersky E, Noel J P. 2003. Structural basis for substrate recognition in the salicylic acid carboxyl methyltransferase family. The Plant Cell, 15, 1704–1716.
[1] ZHANG Hua, WU Hai-yan, TIAN Rui, KONG You-bin, CHU Jia-hao, XING Xin-zhu, DU Hui, JIN Yuan, LI Xi-huan, ZHANG Cai-ying. Genome-wide association and linkage mapping strategies reveal genetic loci and candidate genes of phosphorus utilization in soybean[J]. >Journal of Integrative Agriculture, 2022, 21(9): 2521-2537.
[2] WU Zhe, YANG Xuan, ZHAO Yu-xuan, JIA Li. Identifying candidate genes involved in trichome formation on carrot stems by transcriptome profiling and resequencing [J]. >Journal of Integrative Agriculture, 2022, 21(12): 3589-3599.
[3] JIA Jia, WANG Huan, CAI Zhan-dong, WEI Ru-qian, HUANG Jing-hua, XIA Qiu-ju, XIAO Xiao-hui, MA Qi-bin, NIAN Hai, CHENG Yan-bo. Identification and validation of stable and novel quantitative trait loci for pod shattering in soybean [Glycine max (L.) Merr.][J]. >Journal of Integrative Agriculture, 2022, 21(11): 3169-3184.
[4] DING Xiao-yu, XU Jin-song, HUANG He, QIAO Xing, SHEN Ming-zhen, CHENG Yong, ZHANG Xue-kun. Unraveling waterlogging tolerance-related traits with QTL analysis in reciprocal intervarietal introgression lines using genotyping by sequencing in rapeseed (Brassica napus L.)[J]. >Journal of Integrative Agriculture, 2020, 19(8): 1974-1983.
[5] XU Zhong, SUN Hao, ZHANG Zhe, Zhao Qing-bo, Babatunde Shittu Olasege, Li Qiu-meng, Yue Yang, Ma Pei-pei, Zhang Xiang-zhe, Wang Qi-shan, Pan Yu-chun .
Genome-wide detection of selective signatures in a Jinhua pig population
[J]. >Journal of Integrative Agriculture, 2020, 19(5): 1314-1322.
[6] XIA Ning, YAN Wen-bing, WANG Xiao-qi, SHAO Yu-peng, YANG Ming-ming, WANG Zhi-kun, ZHAN Yu-hang, TENG Wei-li, HAN Ying-peng, SHI Yan-guo. Genetic dissection of hexanol content in soybean seed through genome-wide association analysis[J]. >Journal of Integrative Agriculture, 2019, 18(6): 1222-1229.
[7] CHEN Bing-ru, WANG Chun-yu, WANG Ping, ZHU Zhen-xing, XU Ning, SHI Gui-shan, YU Miao, WANG Nai, LI Ji-hong, HOU Jia-ming, LI Shu-jie, ZHOU Yu-fei, GAO Shi-jie, LU Xiao-chun, HUANG Rui. Genome-wide association study for starch content and constitution in sorghum (Sorghum bicolor (L.) Moench)[J]. >Journal of Integrative Agriculture, 2019, 18(11): 2446-2456.
[8] DIAO Shu-qi, LUO Yuan-yu, MA Yun-long, DENG Xi, HE Ying-ting, GAO Ning, ZHANG Hao, LI Jia-qi, CHEN Zan-mou, ZHANG Zhe. Genome-wide detection of selective signatures in a Duroc pig population[J]. >Journal of Integrative Agriculture, 2018, 17(11): 2528-2535.
[9] GONG Qian-chun, YU Hong-xiao, MAO Xin-rui, QI Hui-dong, SHI Yan, XIANG Wei, CHEN Qing-shan,. Meta-analysis of soybean amino acid QTLs and candidate gene mining[J]. >Journal of Integrative Agriculture, 2018, 17(05): 1074-1084.
[10] ZHAO Jie, QIN Jing-jing, SONG Qian, SUN Chuan-qing, LIU Feng-xia. Combining QTL mapping and expression profile analysis to identify candidate genes of cold tolerance from Dongxiang common wild rice (Oryza rufipogon Griff.)[J]. >Journal of Integrative Agriculture, 2016, 15(9): 1933-1943.
[11] Lü Rui-hua, XU Yan-hao, Rodger Boyd, ZHANG Xiao-qi, Sue Broughton, Michael Jones, LI Cheng-dao, CHEN Yao-feng. Barley and Wheat Share the Same Gene Controlling the Short Basic Vegetative Period[J]. >Journal of Integrative Agriculture, 2013, 12(10): 1703-1711.
No Suggested Reading articles found!