Scientia Agricultura Sinica ›› 2018, Vol. 51 ›› Issue (16): 3029-3039.doi: 10.3864/j.issn.0578-1752.2018.16.001

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Location and Mapping of the Determinate Growth Habit of Brassica napus by Bulked Segregant Analysis (BSA) Using Whole Genome Re-Sequencing

ZHANG YaoFeng, ZHANG DongQing, YU HuaSheng, LIN BaoGang, HUA ShuiJin, DING HouDong, FU Ying   

  1. Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021
  • Received:2018-01-18 Online:2018-08-16 Published:2018-08-16

RichHTML

24

PDF

409

Abstract: 【Objective】Mechanical harvesting has been one of the major goals of rapeseed breeding and genetic research worldwide. A natural and novel rapeseed mutant with determinate inflorescence (di1) was identified in this study. Genetic analysis, gene mapping, candidate gene prediction and gene cloning were used to elucidate the genetic control of determinate inflorescence.【Method】For genetic analysis, reciprocal crosses were performed between determinate inflorescence line FM8 and wild type FM7, and the inflorescence morphology was observed for F1 and F2 progenies. Two pools with 20 di1 F2 lines and 20 wild type lines were constructed. For gene mapping of determinate inflorescence, 20× and 10× depth of whole genome re-sequencing were conducted for the two pools and parental lines, respectively. The associated loci were aligned to the genome of A. thaliana for synteny blocks searching. Potential candidate genes for determinate inflorescence were predicted by annotation analyses of genes within the physical boundaries of the associated regions. Gene cloning was used to identify polymorphisms and screen candidate gene(s). 【Result】The di1 mutant showed a single fruiting body or a cluster of fruiting bodies at the top of the inflorescence axis, and the growth of inflorescence was hampered. The F1 progenies from the reciprocal crosses were indeterminate, and the trait segregation of indeterminate inflorescence and determinate inflorescence among F2 progenies fit the 13:3 segregation ratio, assuming that the determinate inflorescence was controlled by two pairs of recessive duplicate genes interacting with one pair of recessive epistatic inhibitor genes. Whole genome re-sequencing of two pools and two parental lines identified 30123 homozygous SNPs and 107636 homozygous InDels. Seven significantly associated loci were mapped on chromosomes of A08, A09, A10, C08 and C09. Of which, the locus on chromosome A10 not only exhibited the highest peak, but also showed homologous with the two loci on chromosome C09 by synteny analysis. Genes of TERMINAL FLOWER 1 (TFL1), FLOWERING LOCUS C (FLC), ATBZIP14 (FD), MULTICOPY SUPPRESSOR OF IRA1 4 (FVE) and SCHLAFMUTZE (SMZ) were predicted as potential candidate genes. Gene cloning identified coding region polymorphisms and protein polymorphisms for genes of TFL1, FVE and SMZ.【Conclusion】The determinate inflorescence of di1 mutant was controlled by two pairs of recessive duplicate genes interacting with one pair of recessive epistatic inhibitor genes. Seven loci were significantly associated with determinate inflorescence. Of which, the loci on chromosomes A10 and C09 were homologous. TFL1, FVE and SMZ showed coding region polymorphisms and protein polymorphisms, and were deduced to be candidate genes for determinate inflorescence.

Key words: Brassica napus, determinate inflorescence, gene mapping, associated regions, candidate genes

[1]    王汉中, 殷艳. 我国油料产业形势分析与发展对策建议. 中国油料作物学报, 2014, 36(3): 414-421.
WANG H Z, YIN Y. Analysis and strategy for oil crop industry in China. Chinese Journal of Oil Crop Sciences, 2014, 36(3): 414-421. (in Chinese)
[2]    张凤英. 被子植物花序的演化问题. 植物杂志, 1985, 3: 040.
ZHANG F Y. The evolution of the inflorescence of angiosperms. Plants, 1985, 3: 040 (in Chinese)
[3]    BANGA S S. Genetic manipulations for oilseeds improvement- conventional. Changing Global Vegetable Oils Scenario: Issues and Challenges Before India, 2007, 17: 34.
[4]    HUIJSER P, SCHMID M. The control of developmental phase transitions in plants. Development, 2011, 138(19): 4117-4129.
[5]    LONG J, BARTON M K. Initiation of axillary and floral meristems in Arabidopsis. Developmental biology, 2000, 218(2): 341-353.
[6]    HEPWORTH S R, KLENZ J E, HAUGHN G W. UFO in the Arabidopsis inflorescence apex is required for floral-meristem identity and bract suppression. Planta, 2006, 223(4): 769-778.
[7]    KWIATKOWSKA D. Flowering and apical meristem growth dynamics. Journal of Experimental Botany, 2008, 59(2): 187-201.
[8]    HEMPEL F D, FELDMAN L J. Specification of chimeric flowering shoots in wild-type Arabidopsis. The Plant Journal, 1995, 8(5): 725-731.
[9]    AMASINO R. Seasonal and developmental timing of flowering. The Plant Journal, 2010, 61(6): 1001-1013.
[10]   BRATZEL F, TURCK F. Molecular memories in the regulation of seasonal flowering: from competence to cessation. Genome biology, 2015, 16(1): 192.
[11]   SHANNON S, MEEKS-WAGNER D R. A mutation in the Arabidopsis TFL1 gene affects inflorescence meristem development. The Plant Cell, 1991, 3(9): 877-892.
[12]   BRADLEY D, CARPENTER R, COPSEY L, VINCENT C, ROTHSTEIN S, COEN E. Control of inflorescence architecture in Antirrhinum. Nature, 1996, 379(6568): 791-797.
[13]   DHANASEKAR P, REDDY K S. A novel mutation in TFL1 homolog affecting determinacy in cowpea (Vigna unguiculata). Molecular genetics and genomics, 2015, 290(1): 55-65.
[14]   KAUR H, BANGA S S. Discovery and mapping of Brassica juncea Sdt1 gene associated with determinate plant growth habit. Theoretical and applied genetics, 2015, 128(2): 235-245.
[15]   ZHANG H, MIAO H, LI C, WEI L, DUAN Y, MA Q, KONG J, XU  F, CHANG S. Ultra-dense SNP genetic map construction and identification of SiDt gene controlling the determinate growth habit in Sesamum indicum L.. Scientific reports, 2016, 6: 31556.
[16]   刘毅. 有限开花习性芝麻的发现及其杂交后代. 中国油料, 1990, 1: 88.
LIU Y. The discovery of a sesame with determinate flowering habit and its hybrid progenies. Oil Crops of China, 1990, 1: 88 (in Chinese)
[17]   BRADLEY D, RATCLIFFE O, VINCENT C, CARPENTER R, COEN E. Inflorescence commitment and architecture in Arabidopsis. Science, 1997, 275(5296): 80-83.
[18]   PNUELI L, GUTFINGER T, HAREVEN D, BEN-NAIM O, RON N, ADIR N, LIFSCHITZ E. Tomato SP-interacting proteins define a conserved signaling system that regulates shoot architecture and flowering. The Plant Cell, 2001, 13(12): 2687-2702.
[19]   AMAYA I, RATCLIFFE O J, BRADLEY D J. Expression of CENTRORADIALIS (CEN) and CEN-like genes in tobacco reveals a conserved mechanism controlling phase change in diverse species. The Plant Cell, 1999, 11(8): 1405-1417.
[20]   JENSEN C S, SALCHERT K, NIELSEN K K. A TERMINAL FLOWER1-like gene from perennial ryegrass involved in floral transition and axillary meristem identity. Plant Physiology, 2001, 125(3): 1517-1528.
[21]   FOUCHER F, MORIN J, COURTIADE J, CADIOUX S, ELLIS N, BANFIELD M J, RAMEAU C. DETERMINATE and LATE FLOWERING are two TERMINAL FLOWER1/CENTRORADIALIS homologs that control two distinct phases of flowering initiation and development in pea. The Plant Cell, 2003, 15(11): 2742-2754.
[22]   PILLITTERI L J, LOVATT C J, WALLING L L. Isolation and characterization of a TERMINAL FLOWER homolog and its correlation with juvenility in citrus. Plant Physiology, 2004, 135(3): 1540-1551.
[23]   ZHANG S, HU W, WANG L, LIN C, CONG B, SUN C, LUO D. TFL1/CEN-like genes control intercalary meristem activity and phase transition in rice. Plant Science, 2005, 168(6): 1393-1408.
[24]   KOTODA N, WADA M. MdTFL1, a TFL1-like gene of apple, retards the transition from the vegetative to reproductive phase in transgenic Arabidopsis. Plant Science, 2005, 168(1): 95-104.
[25]   Bansal P, Kaur P, Banga S K, Banga S S. Augmenting genetic diversity in Brassica juncea through its resynthesis using purposely selected diploid progenitors. International Journal of Plant Breeding, 2009, 3: 41-45.
[26]   Kaur H, Gupta S, Kumar N, Akhatar J, Banga S S. Progression of molecular and phenotypic diversification in resynthesized Brassica juncea (L.) gene pool with determinate inflorescence. Euphytica, 2014, 199(3): 325-338.
[27]   LI K, YAO Y, XIAO L, ZHAO Z, GUO S, FU Z, DU D. Fine mapping of the Brassica napus Bnsdt1 gene associated with determinate growth habit. Theoretical and Applied Genetics, 2018, 131(1): 193-208.
[28]   LI H, DURBIN R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 2009, 25(14): 1754-1760.
[29]   LI H, HANDSAKER B, WYSOKER A, FENNELL T, RUAN J, HOMER N, ABECASIS G M, DUEBIN R. The sequence alignment/ map format and SAMtools. Bioinformatics, 2009, 25(16): 2078-2079.
[30]   MCKENNA A, HANNA M, BANKS E, SIVACHENKO A, CIBULSKIS K, KERNYTSKY A, GARIMELLA K, ALTSHULER D, GABRIE S, DALY M, DEPRISTO M A. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome research, 2010, 20(9): 1297-1303.
[31]   WANG K, LI M, HAKONARSON H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic acids research, 2010, 38(16): e164.
[32]   TAKAGI H, ABE A, YOSHIDA K, KOSUGI S, NATSUME S, MITSUOKA C, UEMURA A, UTSUSHI H, TAMIRU M, TAKUNO S, INNAN H, CANO L M, KAMOUN S, TERAUCHI R. QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. The Plant Journal, 2013, 74(1): 174-183.
[33]   CONESA A, GÖTZ S, GARCÍA-GÓMEZ J M, TEROL J, TALÓN M, ROBLES M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 2005, 21(18): 3674-3676.
[34]   SEARLE I, HE Y, TURCK F, VINCENT C, FORNARAL F, KROBER S, AMASINO R A, COUPLAND G. The transcription factor FLC confers a flowering response to vernalization by repressing meristem competence and systemic signaling in Arabidopsis. Genes & development, 2006, 20(7): 898-912.
[35]   BLÁZQUEZ M A, AHN J H, WEIGEL D. A thermosensory pathway controlling flowering time in Arabidopsis thaliana. Nature genetics, 2003, 33(2): 168-171.
[36]   TAOKA K, OHKI I, TSUJI H, FURUITA K, HAYASHI K, YANASE T, YAMAGUCHI M, NAKASHIMA C, PURWESTRI Y A, TAMAKI S. 14-3-3 proteins act as intracellular receptors for rice Hd3a florigen. Nature, 2011, 476(7360): 332-335.
[37]   NAN H Y, CAO D, ZHANG D Y, LI Y, LU S J, TANG L L, YUAN X H, LIU B H, KONG F J. GmFT2a and GmFT5a redundantly and differentially regulate flowering through interaction with and upregulation of the bZIP transcription factor GmFDL19 in soybean. PLoS ONE, 2014, 9(5): e97669.
[38]   PURWESTRI Y A, OGAKI Y, TAMAKI S, TSUJI H, SHIMAMOTO K. The 14-3-3 protein GF14c acts as a negative regulator of flowering in rice by interacting with the florigen Hd3a. Plant and Cell Physiology, 2009, 50(3): 429-438.
[39]   WIGGE P A, KIM M C, JAEGER K E, BUSCH W, SCHMID M, LOHMANN J U, WEIGEL D. Integration of spatial and temporal information during floral induction in Arabidopsis. Science, 2005, 309(5737): 1056-1059.
[40]   JAEGER K E, PULLEN N, LAMZIN S, MORRIS R J, WIGGE P A. Interlocking feedback loops govern the dynamic behavior of the floral transition in Arabidopsis. The Plant Cell, 2013, 25(3): 820-833.
[41]   JUNG J H, SEO Y H, SEO P J, REYES J L, YUN J, CHUA N H, PARK C M. The GIGANTEA-regulated microRNA172 mediates photoperiodic flowering independent of CONSTANS in Arabidopsis. The Plant Cell, 2007, 19(9): 2736-2748.
[42]   HO W W H, WEIGEL D. Structural features determining flower promoting activity of Arabidopsis FLOWERING LOCUS T. The Plant Cell, 2014, 26(2): 552-564.
[43]   LI Q, FAN C M, ZHANG X M, WANG X, WU F Q, HU R B, FU Y F. Identification of a soybean MOTHER OF FT AND TFL1 homolog involved in regulation of seed germination. PLoS ONE, 2014, 9(6): e99462.
[44]   HANANO S, GOTO K. Arabidopsis TERMINAL FLOWER1 is involved in the regulation of flowering time and inflorescence development through transcriptional repression. The Plant Cell, 2011, 23(9): 3172-3184.
[45]   TAHERY Y, ABHUL-HAMID H, TAHERY E. Terminal Flower 1 (TFL1) homolog genes in dicot plants. World Applied Sciences Journal, 2011, 12(545): 551.
[46]   LIU F, QUESADA V, CREVILLE P, BAURLE I, SWIEZEWSKI S, DEAN C. The Arabidopsis RNA-Binding protein FCA requires a lysine-specific demethylase 1 homolog to downregulate FLC. Molecular Cell, 2007, 28: 398-407.
[47]   刘新庆, 郭蕊, 范晓宁, 王雪, 龙鸿. 拟南芥晚花突变体fve-1和fca-1营养生长时相转变. 热带农业科学, 2016, 36(6): 45-49.
LIU X Q, GUO R, FAN X N, WANG X, LONG H. Vegetative phase change in late-flowering mutants fve-1 and fca-1 in Arabidopsis thaliana. Chinese Journal of Tropical Agriculture, 2016, 36(6): 45-49 (in Chinese)
[48]   MATHIEU J, YANT L J, MURDTER F, KUTTNER F, SCHMID M. Repression of flowering by the miR172 target SMZ. PLOS Biology, 2009, 7(7): e1000148.
[1] DIAO WeiNan,YUAN PingLi,GONG ChengSheng,ZHAO ShengJie,ZHU HongJu,LU XuQiang,HE Nan,YANG DongDong,LIU WenGe. Genetic Analysis and Gene Mapping of Canary Yellow in Watermelon Flesh [J]. Scientia Agricultura Sinica, 2021, 54(18): 3945-3958.
[2] XU XinYang,SHEN Jia,ZHANG YueJian,LI GuoJing,NIU XiaoWei,SHOU WeiSong. Fine Mapping of an Immature Rind Color Gene GR in Melon [J]. Scientia Agricultura Sinica, 2021, 54(15): 3308-3319.
[3] ZHANG Shuo,ZHI Hui,TANG ChanJuan,LUO MingZhao,TANG Sha,JIA GuanQing,JIA YanChao,DIAO XianMin. Cytological Characters Analysis and Low-Resolution Mapping of Stripe-Leaf MutantA36-S in Foxtail Millet [J]. Scientia Agricultura Sinica, 2021, 54(14): 2952-2964.
[4] MA Jian, LI CongCong, HUANG YaTing, XIE YuLi, CHENG LingLing, WANG JianShe. Fine Mapping and Candidate Gene Analysis of Seed Coat Color Gene CmSC1 in Melon [J]. Scientia Agricultura Sinica, 2021, 54(10): 2167-2178.
[5] Jian MA,CongCong LI,JianShe WANG. Fine Mapping and Candidate Gene Analysis of a Short Internodes Gene Cmdm1 in Melon (Cucumis melo L.) [J]. Scientia Agricultura Sinica, 2020, 53(4): 802-810.
[6] LIANG HuiZhen,XU LanJie,DONG Wei,YU YongLiang,YANG HongQi,TAN ZhengWei,LI Lei,LIU XinMei. Mixed Inheritance Analysis and QTL Mapping for γ-Tocopherol Content in Soybean [J]. Scientia Agricultura Sinica, 2020, 53(11): 2149-2160.
[7] GONG ChengSheng, ZHAO ShengJie, LU XuQiang, HE Nan, ZHU HongJu, DOU JunLing, YUAN PingLi, LI BingBing, LIU WenGe. Chemical Compositions and Gene Mapping of Wax Powder on Watermelon Fruit Epidermis [J]. Scientia Agricultura Sinica, 2019, 52(9): 1587-1600.
[8] BAI TuanHui,LI Li,ZHENG XianBo,WANG MiaoMiao,SONG ShangWei,JIAO Jian,SONG ChunHui. Screening and Expression Analysis of Co Candidate Genes in Columnar Apple [J]. Scientia Agricultura Sinica, 2019, 52(23): 4350-4363.
[9] XIE Jia, ZHANG XiaoBo, TAO YiRan, XIONG YuZhen, ZHOU Qian, SUN Ying, YANG ZhengLin, ZHONG BingQiang, SANG XianChun. Identification and Gene Mapping of a Shorten Panicle and Seed Mutant sps1 in Rice (Oryza sativa L.) [J]. Scientia Agricultura Sinica, 2018, 51(9): 1617-1626.
[10] XUE HongLi, YANG JunJun, TANG Sha, ZHI Hui, WANG Rui, JIA GuanQing, QIAO ZhiJun, DIAO XianMin. Morphological Characterization and Gene Mapping of a Panicle Apical Abortion Mutant (sipaa1) in Foxtail Millet [J]. Scientia Agricultura Sinica, 2018, 51(9): 1627-1640.
[11] REN YiYing, CUI Cui, WANG Qian, TANG ZhangLin, XU XinFu, LIN Na, YIN JiaMing, LI JiaNa, ZHOU QingYuan. Genome-Wide Association Analysis of Silique Density on Racemes and Its Component Traits in Brassica napus L. [J]. Scientia Agricultura Sinica, 2018, 51(6): 1020-1033.
[12] TIAN ZhiTao, ZHAO YongGuo, LENKA Havlickova, HE Zhesi, ANDREA L Harper, IAN Bancroft, ZOU XiLing, ZHANG XueKun, LU GuangYuan. Dynamic and Associative Transcriptomic Analysis of Glucosinolate Content in Seeds and Silique Walls of Brassica napus [J]. Scientia Agricultura Sinica, 2018, 51(4): 635-651.
[13] CHEN XuePing, LIU ShiYao, YIN NengWen, JING LingYun, WEI LiJuan, LIN Na, XIAO Yang, XU XinFu, LI JiaNa, LIU LieZhao. Construction of a Near Infrared Model for Detecting Stem Fiber Component Content and Lignin Monomer G/S in Rapeseed [J]. Scientia Agricultura Sinica, 2018, 51(4): 688-696.
[14] YAN Jing, WANG XiaoLei, ZHANG YuChi, ZHANG QingLing, WANG Jian, QIANG Sheng, SONG XiaoLing . Fitness of Herbicide-Resistant BC3F4 between two herbicide-resistant transgenic Brassica napus and wild Brassica juncea [J]. Scientia Agricultura Sinica, 2018, 51(1): 105-118.
[15] ZHANG XiaoBo, XIE Jia, ZHANG XiaoQiong, TIAN WeiJiang, HE PeiLong, LIU SiCen, HE GuangHua, ZHONG BingQiang, SANG XianChun. Identification and Gene Mapping of a Dwarf and Curled Flag Leaf Mutant dcfl1 in Rice (Oryza sativa L.) [J]. Scientia Agricultura Sinica, 2017, 50(9): 1551-1558.
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
No Suggested Reading articles found!
京ICP备09089781号-30
Copyright 2018 © Editorial office of Scientia Agricultura Sinica
Tel: 86-010-82106279    E-mail: zgnykx@mail.caas.net.cn
Supported by Beijing Magtech Co.Ltd