QTL Mapping and Epistatic Interaction Analysis for Oil Content in Cultivated Peanut

doi:10.7668/hbnxb.20191533

Abstract

Abstract: To explore the genetic basis that modulates oil content in peanut, a recombinant inbred line (RIL) population(181 individuals) was constructed by crossing two parents(Huayu 36 and 6-13) with different oil contents. The oil content of RIL population(F_2:7-F_2:8) demonstrated normal distribution and transgressive segregations were observed in three environments (E1, E2, E3). The broad-sense heritability was 0.55. QTL mapping was performed by composite interval mapping method(CIM-ADD) and a total of 5 QTLs were mapped on chromosome 6, 8, 15 and 17, with phenotypic variance explained(PVE) of 7.39%-17.67%. In the E1, two loci, qOC6 and qOC8.1 were detected with the PVE of 17.67% and 9.17%, respectively. In the E2, there were three QTLs, qOC8.2 (PVE=8.83%), qOC15 (PVE=16.53%) and qOC17 (PVE=7.39%), mapped on chromosome 8, 15 and 17. In the E3, only one QTL, qOC15 was identified with the PVE of 17.39%. Notably the major QTL, qOC15, was expressed in two environments, spanning a nearly 2.8 Mb genomic region with 6-13 allele contributing to the trait. Additionally, epistatic interaction was analyzed by inclusive composite interval mapping method (ICIM-EPI) and 21 pairs of epistatic QTLs were detected on chromosome 1, 3, 5, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19 and 20, with the PVE by epistatic effect of 1.24%-3.54%, and PVE by interaction effect between epistatic QTL and environment of 0-1.67%. Gene annotation was performed in the qOC15 region and resulted in 97 putative functional genes, which mostly impacts on cellular catalyst activity and metabolic process, 4 of which were predicted to be involved in lipid biosynthesis, metabolic and transport processes.These 5 additive QTLs and 21 pairs of epistatic QTLs provide a theoretical basis for both peanut quality improvement and cloning of associated genes.

Key words: Peanut, Recombinant inbred line, Oil content, Quantitative trait locus, Gene annotation

CLC Number:

S565.03

ZHANG Shengzhong, HU Xiaohui, MIAO Huarong, YANG Weiqiang, CUI Fenggao, QIU Junlan, CHEN Silong, ZHANG Jiancheng, CHEN Jing. QTL Mapping and Epistatic Interaction Analysis for Oil Content in Cultivated Peanut[J]. ACTA AGRICULTURAE BOREALI-SINICA, 2021, 36(1): 27-35. doi: 10.7668/hbnxb.20191533.

/ / Recommend / Download Citations

URL: http://www.hbnxb.net/EN/10.7668/hbnxb.20191533

http://www.hbnxb.net/EN/Y2021/V36/I1/27

References

[1] 廖伯寿,雷永,王圣玉,李栋,黄家权,姜慧芳,任小平. 花生重组近交系群体的遗传变异与高油种质的创新[J]. 作物学报,2008,34(6):999-1004. doi:10.3724/SP.J.1006.2008.00999.
Liao B S,Lei Y,Wang S Y,Li D,Huang J Q,Jiang H F,Ren X P. Genetic diversity of peanut RILs and enhancement for high oil genotypes[J]. Acta Agronomica Sinica,2008,34(6):999-1004.
[2] 姜慧芳,任小平. 我国栽培种花生资源农艺和品质性状的遗传多样性[J]. 中国油料作物学报,2006,28(4):421-426.doi:10.3321/j.issn:1007-9084.2006.04.009.
Jiang H F,Ren X P. Genetic diversity of peanut resource on morphological characters and seed chemical components in China[J]. Chinese Journal of Oil Crop Sciences,2006,28(4):421-426.
[3] Wang Y H,Liu S J,Ji S L,Zhang W W,Wang C M,Jiang L,Wan J M. Fine mapping and marker-assisted selection(MAS) of a low glutelin content gene in rice[J]. Cell Research,2005,15(8):622-630. doi:10.1038/sj.cr.7290332.
[4] Prasanna B M,Pixley K,Warburton M L,Xi C X. Molecular marker-assisted breeding options for maize improvement in Asia[J]. Molecular Breeding,2010,26(2):339-356. doi:10.1007/s11032-009-9387-3.
[5] Chu Y,Wu C L,Holbrook C C,Tillman B L,Person G,Ozias-Akins P. Marker-assisted selection to pyramid nematode resistance and the high oleic trait in peanut[J]. The Plant Genome,2011,4(2):110-117. doi:10.3835/plantgenome2011.01.0001.
[6] Varshney R K,Pandey M K,Janila P,Nigam S N,Sudini H,Gowda M V C,Sriswathi M,Radhakrishnan T,Manohar S S,Nagesh P. Marker-assisted introgression of a QTL region to improve rust resistance in three elite and popular varieties of peanut(Arachis hypogaea L.)[J]. Theoretical and Applied Genetics,2014,127(8):1771-1781. doi:10.1007/s00122-014-2338-3.
[7] 禹山林,杨庆利,潘丽娟,薄文娜. 花生种子含油量的遗传分析[J]. 植物遗传资源学报,2009,10(3):453-456.
Yu S L,Yang Q L,Pan L J,Bo W N. Genetic analysis for oil content of peanut seeds[J]. Journal of Plant Genetic Resources,2009,10(3):453-456.
[8] 陈四龙,李玉荣,程增书,廖伯寿,雷永,刘吉生. 花生含油量杂种优势表现及主基因+多基因遗传效应分析[J]. 中国农业科学,2009,42(9):3048-3057.doi:10.3864/j.issn.0578-1752.2009.09.005.
Chen S L,Li Y R,Cheng Z S,Liao B S,Lei Y,Liu J S. Heterosis and genetic analysis of oil content in peanut using mixed model of major gene and polygene[J]. Scientia Agricultura Sinica,2009,42(9):3048-3057.
[9] Sarvamangala C,Gowda M V C,Varshney R K. Identification of quantitative trait loci for protein content,oil content and oil quality for groundnut(Arachis hypogaea L.)[J]. Field Crops Research,2011,122(1):49-59. doi:10.1016/j.fcr.2011.02.010.
[10] Pandey M K,Wang M L,Qiao L X,Feng S P,Khera P,Wang H,Tonnis B,Barkley N A,Wang J P,Holbrook C C,Culbreath A K,Varshney R K,Guo B Z. Identification of QTLs associated with oil content and mapping FAD2 genes and their relative contribution to oil quality in peanut(Arachis hypogaea L.)[J]. BMC Genetics,2014,15(1):133. doi:10.1186/s12863-014-0133-4.
[11] Shasidhar Y,Vishwakarma M K,Pandey M K,Janila P,Variath M T,hasidhar Y,Vishwakarma M K,Pandey M K,Janila P,Variath M T,Manohar S S,Nigam S N,Guo B Z,Varshney R K. Molecular mapping of oil content and fatty acids using dense genetic maps in groundnut(Arachis hypogaea L.)[J]. Frontiers in Plant Science,2017,8:794. doi:10.3389/fpls.2017.00794.
[12] Wilson J N,Chopra R,Baring M R,Selvaraj M G,Simpson C E,Chagoya J,Burow M D. Advanced backcross quantitative trait loci(QTL) analysis of oil concentration and oil quality traits in peanut(Arachis hypogaea L.)[J]. Tropical Plant Biology,2017,10(1):1-17. doi:10.1007/s12042-016-9180-5.
[13] Liu N,Guo J B,Zhou X J,Wu B,Huang L,Luo H Y,Chen Y N,Chen W G,Lei Y,Huang Y,Liao B S,Jiang H F. High-resolution mapping of a major and consensus quantitative trait locus for oil content to a~0.8-Mb region on chromosome A08 in peanut(Arachis hypogaea L.)[J]. Theoretical and Applied Genetics,2020,133(1):37-49. doi:10.1007/s00122-019-03438-6.
[14] Selvaraj M G,Narayana M,Schubert A M,Ayers J L,Baring M R,Burow M D. Identification of QTLs for pod and kernel traits in cultivated peanut by bulked segregant analysis[J]. Electronic Journal of Biotechnology,2009,12(2):1-10. doi:10.2225/vol12-issue2-fulltext-13.
[15] 黄莉,赵新燕,张文华,樊志明,任小平,廖伯寿,姜慧芳,陈玉宁. 利用RIL群体和自然群体检测与花生含油量相关的SSR标记[J]. 作物学报,2011,37(11):1967-1974. doi:10.3724/SP.J.1006.2011.01967.
Huang L,Zhao X Y,Zhang W H Fan Z M,Ren X P,Liao B S,Jiang H F,Chen Y N. Identification of SSR markers linked to oil content in peanut(Arachis hypogaea L.) through RIL population and natural population[J]. Acta Agronomica Sinica,2011,37(11):1967-1974.doi:10.3724/SP.J.1006.2011.01967.
[16] Zhuang W J, Chen H, Yang M, Wang J P, Pandey M K, Zhang C, Chang W C, Zhang L S, Zhang X T, Tang R H, Garg V, Wang X J, Tang H B, Chow C N, Wang J P, Deng Y, Wang D P, Khan A W, Yang Q, Cai T C, Bajaj P, Wu K C, Guo B Z, Zhang X Y, Li J J, Liang F, Hu J, Liao B S, Liu S Y, Chitikineni A, Yan H S, Zheng Y X, Shan S H, Liu Q Z, Xie D Y, Wang Z Y, Khan S A, Ali N, Zhao C Z, Li X G, Luo Z L, Zhang S B, Zhuang R R, Peng Z, Wang S Y, Mamadou G, Zhuang Y H, Zhao Z F, Yu W C, Xiong F Q, Quan W P, Yuan M, Li Y, Zou H F, Xia H, Zha L, Fan J P, Yu J G, Xie W P, Yuan J Q, Chen K, Zhao S S, Chu W T, Chen Y T, Sun P C, Meng F B, Zhuo T, Zhao Y H, Li C J, He G H, Zhao Y L, Wang C C, Kavikishor P B, Pan R L, Paterson A H, Wang X Y, Ming R, Varshney R K. The genome of cultivated peanut provides insight into legume karyotypes,polyploid evolution and crop domestication[J]. Nature Genetics,2019,51(5):865-876. doi:10.1038/s41588-019-0402-2.
[17] Bertioli D J,Jenkins J,Clevenger J,Dudchenko O,Gao D Y,Seijo G,Leal-Bertioli S C M,Ren L H,Farmer A D,Pandey M K,Samoluk S S,Abernathy B,Agarwal G,Ball én-Taborda C,Cameron C,Campbell J,Chavarro C,Chitikineni A,Chu Y,Dash S,Baidouri M E,Guo B Z,Huang W,Kim K D,Korani W,Lanciano S,Lui C G,Mirouze M,Moretzsohn M C,Pham M,Shin J H,Shirasawa K,Sinharoy S,Sreedasyam A,Weeks N T,Zhang X Y,Zheng Z,Sun Z Q,Froenicke L,Aiden E L,Michelmore R,Varshney R K,Holbrook C C,Cannon E K S,Scheffler B E,Grimwood J,Ozias-Akins P,Cannon S B,Jackson S A,Schmutz J.The genome sequence of segmental allotetraploid peanut Arachis hypogaea[J]. Nature Genetics,2019,51(5):877-884. doi:10.1038/s41588-019-0405-z.
[18] Chen X P, Lu Q, Liu H, Zhang J N, Hong Y B, Lan H F, Li H F, Wang J P, Liu H Y, Li S X, Pandey M K, Zhang Z K, Zhou G Y, Yu J G, Zhang G Q, Yuan J Q, Li X Y, Wen S J, Meng F B, Yu S L, Wang X Y, Siddique K H M, Liu Z J, Paterson A H, Varshney R K, Liang X Q. Sequencing of cultivated peanut, Arachis hypogaea,yields insights into genome evolution and oil improvement[J]. Molecular Plant,2019,12(7):920-934. doi:10.1016/j.molp.2019.03.005.
[19] Meng L,Li H H,Zhang L Y,Wang J K. QTL IciMapping:Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations[J]. The Crop Journal,2015,3(3):269-283. doi:10.1016/j.cj.2015.01.001.
[20] Zhang S Z, Hu X H, Miao H R, Chu Y, Cui F G, Yang W Q, Wang C M, Shen Y, Xu T T, Zhao L B, Zhang J C, Chen J. QTL identification for seed weight and size based on a high-density SLAF-seq genetic map in peanut(Arachis hypogaea L.)[J]. BMC Plant Biology,2019,19:537. doi:10.1186/s12870-019-2164-5.
[21] Broman K W,Wu H,Sen S,Churchill G A. R/qtl:QTL mapping in experimental crosses[J]. Bioinformatics,2003,19(7):889-890. doi:10.1093/bioinformatics/btg112.
[22] Ashburner M,Ball C A,Blake J A,Botstein D,Butler H,Cherry J M,Davis A P,Dolinski K,Dwight S S,Eppig J T,Harris M A,Hill D P,Issel-Tarver L,Kasarskis A,Lewis S,Matese J C,Richardson J E,Ringwald M,Rubin G M,Sherlock G. Gene ontology:tool for the unification of biology[J]. Nature Genetics,2000,25(1):25-29. doi:10.1038/75556.
[23] Hu X H, Zhang S Z, Miao H R, Cui F G, Shen Y, Yang W Q, Xu T T, Chen N, Chi X Y, Zhang Z M, Chen J.High-density genetic map construction and identification of QTLs controlling oleic and linoleic acid in peanut using SLAF-seq and SSRs[J]. Scientific Reports,2018,8:5479.doi:10.1038/s41598-018-23873-7.
[24] Wang Z H, Huai D X, Zhang Z H, Cheng K, Kang Y P, Wan L Y, Yan L Y, Jiang H F, Lei Y, Liao B S. Development of a high-density genetic map based on specific length amplified fragment sequencing and its application in quantitative trait loci analysis for yield-related traits in cultivated peanut[J]. Frontiers in Plant Science,2018,9:827. doi:10.3389/fpls.2018.00827.
[25] Chu Y,Chee P,Culbreath A,Isleib T G,Holbrook C C,Ozias-Akins P. Major QTLs for resistance to early and late leaf spot diseases are identified on chromosomes 3 and 5 in peanut(Arachis hypogaea)[J]. Frontiers in Plant Science,2019,10:883. doi:10.3389/fpls.2019.00883.
[26] Liu H, Sun Z Q, Zhang X Y, Qin L, Qi F Y, Wang Z Y, Du P, Xu J, Zhang Z X, Han S Y, Li S J, Gao M, Zhang L N, Cheng Y J, Zheng Z, Huang B Y, Dong W Z.QTL mapping of web blotch resistance in peanut by high-throughput genome-wide sequencing[J]. BMC Plant Biology,2020,20:249. doi:10.1186/s12870-020-02455-8.
[27] 张胜忠,焦坤,胡晓辉,苗华荣,陈静. 花生百仁质量和含油量的遗传分析[J]. 花生学报,2018,47(4):7-12.doi:10.14001/j.issn.1002-4093.2018.04.002.
Zhang S Z,Jiao K,Hu X H,Miao H R,Chen J. Genetic analysis for seed mass and oil content of peanuts[J]. Journal of Peanut Science,2018,47(4):7-12.
[28] Zhao L F,Katavic V,Li F L,Haughn G W,Kunst L. Insertional mutant analysis reveals that long-chain acyl-CoA synthetase 1(LACS1),but not LACS8,functionally overlaps with LACS9 in Arabidopsis seed oil biosynthesis[J]. The Plant Journal,2010,64(6):1048-1058. doi:10.1111/j.1365-313X.2010.04396.x.
[29] Yasuno R,Von Wettstein-Knowles P,Wada H. Identification and molecular characterization of the β-ketoacyl-[acyl carrier protein]synthase component of the Arabidopsis mitochondrial fatty acid synthase[J]. Journal of Biological Chemistry,2004,279(9):8242-8251. doi:10.1074/jbc.M308894200.V
[30] Rylott E L,Eastmond P J,Gilday A D,Slocombe S P,Larson T R,Baker A,Graham I A. The Arabidopsis thaliana multifunctional protein gene(MFP2) of peroxisomal β-oxidation is essential for seedling establishment[J]. The Plant Journal,2006,45(6):930-941. doi:10.1111/j.1365-313X.2005.02650.x.
[31] Guo Z H,Ye Z W,Haslam R P,Michaelson L V,Napier J A,Chye M L. Arabidopsis cytosolic acyl-CoA-binding proteins function in determining seed oil composition[J]. The Plant Direct,2019,3(12):00182. doi:10.1002/pld3.182.
[32] DeBono A,Yeats T H,Rose J K C,Bird D,Jetter R,Kunst L,Samuels L. Arabidopsis LTPG is a glycosylphosphatidylinositol-anchored lipid transfer protein required for export of lipids to the plant surface[J]. Plant Cell,2009,21(4):1230-1238. doi:10.1105/tpc.108.064451.
[33] Hagiwara W E,Onishi K,Takamure O I,Sano Y. Transgressive segregation due to linked QTLs for grain characteristics of rice[J]. Euphytica,2006,150(1):27-35. doi:10.1007/s10681-006-9085-8.
[34] Balakrishnan D, Surapaneni M,Yadavalli V R,Addanki K R,Mesapogu S,Beerelli K,Neelamraju S. Detecting CSSLs and yield QTLs with additive,epistatic and QTL×environment interaction effects from Oryza sativa× O. nivara IRGC81832 cross[J]. Scientific Reports,2020,10:7766. doi:10.1038/s41598-020-64300-0.
[35] Li Z K,Luo L J,Mei H W,Wang Q Y,Tabien R,Zhong D B,Ying C S,Stansel J W,Khush G S,Paterson A H. Overdominant epistatic loci are the primary genetic basis of inbreeding depression and heterosis in rice. I. biomass and grain yield[J]. Genetics,2001,158:1755-1771. doi:10.1017/S0016672301005183.
[36] Carlborg Ö,Haley C S. Epistasis:too often neglected in complex trait studies?[J]. Nature Reviews Genetics,2004,5(8):618-625. doi:10.1038/nrg1407.
[37] Cho Y B,Jones S I,Vodkin L O. Mutations in Argonaute5 illuminate epistatic interactions of the K1 and I loci leading to saddle seed color patterns in Glycine max[J]. The Plant Cell,2017,29(4):708. doi:10.1105/tpc.17.00162.

Please choose a citation manager

Content to export