Journal of Integrative Agriculture ›› 2018, Vol. 17 ›› Issue (05): 1074-1084.DOI: 10.1016/S2095-3119(17)61783-0
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收稿日期:2017-04-18出版日期:2018-05-20发布日期:2018-05-04
Meta-analysis of soybean amino acid QTLs and candidate gene mining
GONG Qian-chun*, YU Hong-xiao*, MAO Xin-rui, QI Hui-dong, SHI Yan, XIANG Wei, CHEN Qing-shan, QI Zhao-ming
- Key Laboratory of Soybean Biology, Ministry of Education/College of Agriculture, Northeast Agricultural University, Harbin 150030, P.R.China
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Received:2017-04-18Online:2018-05-20Published:2018-05-04 -
Contact:Correspondence CHEN Qing-shan, Tel/Fax: +86-451-55191945, E-mail: qshchen@126.com; QI Zhao-ming, E-mail: qizhaoming1860@126.com -
About author:GONG Qian-chun, E-mail: superqian@outlook.com; YU Hong-xiao, E-mail: 13303619805@163.com; * These authors contributed equally to this study. -
Supported by:This study was financially supported by the National Key R&D Program of China (2016YFD0100500, 2016YFD0100300, 2016YFD0100201-21), the “Challenge Cup” National College Student Curricular Academic Science and Technology Works Competition of Ministry of Education of China (to Gong Qianchun, guided by Qi Zhaoming), the National Natural Science Foundation of China (31701449, 31471516, 31401465, 31400074, 31501332), the China Post Doctoral Project (2015M581419), the Dongnongxuezhe Project (to Chen Qingshan), China, the Young Talent Project (to Qi Zhaoming) of Northeast Agriculture University, China (518062), the Heilongjiang Funds for Distinguished Young Scientists, China (JC2016004), and the Outstanding Academic Leaders Projects of Harbin, China (2015RQXXJ018).
引用本文
. [J]. Journal of Integrative Agriculture, 2018, 17(05): 1074-1084.
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.
| Arcade A, Labourdette A, Falque M, Mangin B, Chardon F, Charcosset A, Joets J. 2004. BioMercator: Integrating genetic maps and QTL towards discovery of candidate genes. Bioinformatics, 20, 2324–2326.Bolger M E, Weisshaar B, Scholz U, Stein N, Usadel B, Mayer K F. 2014. Plant genome sequencing-applications for crop improvement. Current Opinion in Biotechnology, 26, 31–37. Catoni E, Desimone M, Hilpert M, Wipf D, Kunze R, Schneider A, Flügge U, Schumacher K, Frommer W B. 2003. Expression pattern of a nuclear encoded mitochondrial arginine-ornithine translocator gene from Arabidopsis. BMC Plant Biology, 3, 1.Chardon F, Virlon B, Moreau L, Falque M, Joets J, Decousset L, Murigneux A, Charcosset A. 2004. Genetic architecture of flowering time in maize as inferred from quantitative trait loci meta-analysis and synteny conservation with the rice genome. Genetics, 168, 2169–2185. Chen N W, Sévignac M, Thareau V, Magdelenat G, David P, Ashfield T, Innes R W, Geffroy V. 2010. Specific resistances against Pseudomonas syringae effectors AvrB and AvrRpm1 have evolved differently in common bean (Phaseolus vulgaris), soybean (Glycine max), and Arabidopsis thaliana. New Phytologist, 187, 941–956.Danan S, Veyrieras J B, Lefebvre V. 2011a. Construction of a potato consensus map and QTL meta-analysis offer new insights into the genetic architecture of late blight resistance and plant maturity traits. BMC Plant Biology, 11, 16.Danan S, Veyrieras J B, Lefebvre V. 2011b. Genomic selection in tree breeding: Testing accuracy of prediction models including dominance effect. BMC Proceedings, 5, 1753–6561.Gao L F, Guo Y, Hao Z B, Qiu L J. 2013. Integration and “Overview” analysis of QTLs related to plant height in soybean. Hereditas, 35, 215–224.Glass G V. 1976. Primary, secondary, and meta-analysis of research 1. Educational Researcher, 5, 3–8.Goffinet B, Gerber S. 2000. Quantitative trait loci: A meta-analysis. Genetics, 155, 463–473.von Groll U, Berger D, Altmann T. 2002. The subtilisin-like serine protease SDD1 mediates cell-to-cell signaling during Arabidopsis stomatal development. The Plant Cell, 14, 1527–1539.Guo B, Sleper D A, Lu P, Shannon J G, Nguyen H T, Arelli P R. 2006. QTLs associated with resistance to soybean cyst nematode in soybean: Meta-analysis of QTL locations. Crop Science, 46, 595–602.Gutierrez-Gonzalez J J, Vuong T D, Zhong R, Yu O, Lee J D, Shannon G, Ellersieck M, Nguyen H T, Sleper D A. 2011. Major locus and other novel additive and epistatic loci involved in modulation of isoflavone concentration in soybean seeds. Theoretical and Applied Genetics, 123, 1375–1385.Gutierrez-Gonzalez J J, Wu X, Gillman J D, Lee J D, Zhong R, Yu O, Shannon G, Ellersieck M, Nguyen H T, Sleper D A. 2010. Intricate environment-modulated genetic networks control isoflavone accumulation in soybean seeds. BMC Plant Biology, 10, 105.Gutierrez-Gonzalez J J, Wu X, Zhang J, Lee J D, Ellersieck M, Shannon J G, Yu O, Nguyen H T, Sleper D A. 2009. Genetic control of soybean seed isoflavone content: Importance of statistical model and epistasis in complex traits. Theoretical and Applied Genetics, 119, 1069–1083.Hao Z, Li X, Liu X, Xie C, Li M, Zhang D, Zhang S. 2010. Meta-analysis of constitutive and adaptive QTL for drought tolerance in maize. Euphytica, 174, 165–177.Hoover T A, Roof W D, Foltermann K F, O’Donovan G A, Bencini D A, Wild J R. 1983. Nucleotide sequence of the structural gene (pyrB) that encodes the catalytic polypeptide of aspartate transcarbamoylase of Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America, 80, 2462–2466.Huang L L, Zhong K Z, Ma Q B, Nian H, Yang Y. 2011. Integrated QTLs map of phosphorus efficiency in soybean by Meta-analysis. Chinese Journal of Oil Crop Sciences, 33, 25–32. (in Chinese)Kassem M A, Meksem K, Iqbal M J, Njiti V N, Banz W J, Winters T A, Wood A, Lightfoot D A. 2004. Definition of soybean genomic regions that control seed phytoestrogen amounts. BioMed Research International, 2004, 52–60.Kwanyuen P, Burton J W. 2010. A modified amino acid analysis using PITC derivatization for soybeans with accurate determination of cysteine and half-cystine. Journal of the American Oil Chemists’ Society, 87, 127–132.Lewis M W, Leslie M E, Fulcher E H, Darnielle L, Healy P N, Youn J Y, Liljegren S J. 2010. The SERK1 receptor-like kinase regulates organ separation in Arabidopsis flowers. The Plant Journal, 62, 817–828.Li M W, Xin D, Gao Y, Li K P, Fan K, Muñoz N B, Yung W S, Lam H M. 2016. Using genomic information to improve soybean adaptability to climate change. Journal of Experimental Botany, 68, 1823–1834.Liu S, Luo L, Liu Z X, Guan R X, Qiu L J. 2011. Integration of QTLs related to soybean protein content and “qualification” of them by overview method. Soybean Science, 30, 1–7. (in Chinese)Medic J, Atkinson C, Hurburgh Jr C R. 2014. Current knowledge in soybean composition. Journal of the American Oil Chemists’ Society, 91, 363–384.Panthee D R, Kwanyuen P, Sams C E, West D R, Saxton A M, Pantalone V R. 2004. Quantitative trait loci for β-conglycinin (7S) and glycinin (11S) fractions of soybean storage protein. Journal of the American Oil Chemists’ Society, 81, 1005–1012.Panthee D R, Pantalone V R, Sams C E, Saxton A M, West D R, Orf J H, Killam A S. 2006a. Quantitative trait loci controlling sulfur containing amino acids, methionine and cysteine, in soybean seeds. Theoretical and Applied Genetics, 112, 546–553.Panthee D R, Pantalone V R, Saxton A M, West D R, Sams C E. 2006b. Genomic regions associated with amino acid composition in soybean. Molecular Breeding, 17, 79–89.Primomo V S, Poysa V, Ablett G R, Jackson C J, Gijzen M, Rajcan I. 2005. Mapping QTL for individual and total isoflavone content in soybean seeds. Crop Science, 45, 2454–2464.Qi Z M, Wu Q, Han X, Sun Y N, Du X Y, Liu C Y, Jiang H W, Hu G H, Chen Q S. 2011. Soybean oil content QTL mapping and integrating with meta-analysis method for mining genes. Euphytica, 179, 499–514.Qiu H M, Li Z, Yu Y, Ma X P, Zheng Y H, Meng F F, Hou Y L, Wang Y Q, Wang S M. 2015. Mining and analysis of genes related to sulfur containing amino acids in soybean and bioinformatic analysis based on meta-QTL. Chinese Journal of Oil Crop Sciences, 37, 141–147. (in Chinese)Qiu H M, Yang C M, Gao S Q, Hou Y L, Ma X P, Sun X M, Zheng H Y, Wang Y Q, Wang S M. 2014. Phenotype identification and cluster analysis of soybean in upper latitudes regions based on protein content and amino acid composition. Journal of Plant Genetic Resources, 15, 1202–1208. (in Chinese) Schmutz J I, Cannon S B, Schlueter J, Ma J, Mitros T, Nelson W, Hyten D L, Song Q, Thelen J J, Cheng J, Xu D, Hellsten U, May G D, Yu Y, Sakurai T, Umezawa T, Bhattacharyya M K, Sandhu D, Valliyodan B, Lindquist E, et al. 2010. Genome sequence of the palaeopolyploid soybean. Nature, 463, 178–183.Shah K, Vervoort J, de Vries S C. 2001. Role of threonines in the Arabidopsis thaliana somatic embryogenesis receptor kinase 1 activation loop in phosphorylation. Journal of Biological Chemistry, 276, 41263–41269.Smallwood C J. 2012. Detection of quantitative trait loci for marker-assisted selection of soybean isoflavone genistein. MSc thesis, University of Tennessee, Knoxville.Stock K F, Jönsson L, Ricard A, Mark T. 2016. Genomic applications in horse breeding. Animal Frontiers, 6, 45–52.Stombaugh S K, Orf J H, Jung H G, Chase K, Lark K G, Somers D A. 2004. Quantitative trait loci associated with cell wall polysaccharides in soybean seed. Crop Science, 44, 2101–2106.Sun Y N, Luan H H, Qi Z M, Shan D P, Liu C Y, Hu G H, Chen Q S. 2012a. Mapping and meta-analysis of height QTLs in soybean. Legume Genomics and Genetics, 3, 1–7.Sun Y N, Pan J B, Shi X L, Du X Y, Wu Q, Qi Z M, Jiang H W, Xin D W, Liu C Y, Hu G H, Chen Q S. 2012b. Multi-environment mapping and meta-analysis of 100-seed weight in soybean. Molecular Biology Reports, 39, 9435–9443.Thilakarathna M S, Raizada M N. 2017. A meta-analysis of the effectiveness of diverse rhizobia inoculants on soybean traits under field conditions. Soil Biology and Biochemistry, 105, 177–196.Thu N B A, Nguyen Q T, Hoang X L T, Thao N P, Tran L S P. 2014. Evaluation of drought tolerance of the Vietnamese soybean cultivars provides potential resources for soybean production and genetic engineering. BioMed Research International, 2014, 809736.Trijatmiko K R, Prasetiyono J, Thomson M J, Cruz C M V, Moeljopawiro S, Pereira A. 2014. Meta-analysis of quantitative trait loci for grain yield and component traits under reproductive-stage drought stress in an upland rice population. Molecular Breeding, 34, 283–295.Verret V, Gardarin A, Pelzer E, Médiène S, Makowski D, Valantin-Morison M. 2017. Can legume companion plants control weeds without decreasing crop yield? A meta-analysis. Field Crops Research, 204, 158–168.Wang J, Song W K, Zhang W B, Liu C Y, Hu G H, Chen Q S. 2009. Meta-analysis of insect-resistance QTLs in soybean. Hereditas, 31, 593–561.Wang J L, Liu C Y, Wang J, Qi Z M, Hui L I, Hu G H, Chen Q S. 2010. An integrated QTL Map of fungal disease resistance in soybean (Glycine max L. Merr): A method of meta-analysis for mining R genes. Agricultural Sciences in China, 9, 223–232.Wang J Y, Xiong Y C, Li F M, Siddique K H, Turner N C. 2017. Effects of drought stress on morphophysiological traits, biochemical characteristics, yield, and yield components in different ploidy wheat: A meta-analysis. Advances in Agronomy, 143, 139–173.Wang X, Jiang G L, Song Q, Cregan P B, Scott R A, Zhang J, Yen Y, Brown M. 2015. Quantitative trait locus analysis of seed sulfur-containing amino acids in two recombinant inbred line populations of soybean. Euphytica, 201, 293–305.Warrington C V, Abdel-Haleem H, Hyten D L, Cregan P B, Orf J H, Killam A S, Bajjalieh N, Li Z, Boerma H R. 2015. QTL for seed protein and amino acids in the Benning×Danbaekkong soybean population. Theoretical and Applied Genetics, 128, 839–850.Wu Q, Qi Z M, Liu C Y, Hu G H, Chen Q S. 2009. An integrated QTL map of growth stage in soybean [Glycine max (L.) Merr.]: Constructed through meta-analysis. Acta Agronomica Sinica, 35, 1418–1424. (in Chinese)Yang K, Moon J K, Jeong N, Chun H K, Kang S T, Back K, Jeong S C. 2011. Novel major quantitative trait loci regulating the content of isoflavone in soybean seeds. Genes & Genomics, 33, 685–692.Yellareddygari S K R, Pasche J S, Taylor R J, Gudmestad N C. 2016. Individual participant data meta-analysis of foliar fungicides applied for potato early blight management. Plant Disease, 100, 200–206.Yoshikawa T, Okumoto Y, Ogata D, Sayama T, Teraishi M, Terai M, Toda T, Yamada K, Yagasaki K, Yamada N, Tsukiyama T. 2010. Transgressive segregation of isoflavone contents under the control of four QTLs in a cross between distantly related soybean varieties. Breed Science, 60, 243–254.Zeng G, Li D, Han Y, Teng W, Wang J, Qiu L, Li W. 2009. Identification of QTL underlying isoflavone contents in soybean seeds among multiple environments. Theoretical and Applied Genetics, 118, 1455–1463. |
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