Identification and Expression Analysis of the YABBY Gene Family in Sunflower

doi:10.13560/j.cnki.biotech.bull.1985.2024-0139

Abstract

Abstract:

【Objective】The identification of HaYABBY gene related to flower development in sunflower（Helianthus annuus L.）is conductive to exploring its biological function and regulatory mechanism in the floral development of sunflower, and to provide important molecular clues for sunflower variety breeding.【Method】Based on sunflower genome database and our transcriptome data, bioinformatics analysis was conducted to analyze the physicochemical properties, chromosome localization, phylogenetic relationship, gene structure, conserved motif, protein structure, promoter cis-action regulatory element, and tissue expression pattern, etc. RT-qPCR was used to analyze the differences of HaYABBY gene expression between WT sunflower and cb1（crazy broccoli 1）mutant with the defection of meristem determinacy and floral organ differentiation at st2-st8.【Result】Twelve members of YABBY family were identified, belonging to 4 subfamilies, and located in 8 chromosomes； meanwhile, the members in the same subfamily shared similar gene structure and conserved motifs. Results of tissue expression pattern showed that 8 members presented high expressions during flower development in sunflower, including HaYABBY1a, HaYABBY1c, HaYABBY3, HaYABBY4b, HaYABBY5a, HaYABBY5b, HaCRABS CLAWa, and HaCRABS CLAWb, among which HaYABBY3, HaYABBYY5a, and HaYABBYY5d expressed with up-regulation at the late stages of flower development in cb1 mutant; while the expression of HaYABBYY4b and HaCRABS CLAWa was strongly inhibited in cb1 mutants, corresponding to their expressions at early floral developmental in WT plants. The analysis of cis-regulatory elements showed that all the HaYABBY members contained multiple promoter cis-acting elements, some acting elements only existing in specific genes. Among them, endosperm expression elements were presented in HaCRABS CLAWa and HaYABBY4a. Auxin responders were in HaCRABS CLAWa, HaCRABS CLAWb, HaYABBY4a, HaYABBY4b and HaYABBY5c. Meristem expression elements existed in HaYABBY1a, HaYABBY1c, HaYABBY4b, HaYABBY5a, and HaYABBY5d. Gibberellin response elements were included in HaCRABS CLAWa, HaYABBY5b, HaYABBY5c, and HaYABBY5d. Seed-specific regulatory elements presented in HaYABBY5a, HaYABBY5c, and HaYABBY5d.【Conclusion】Five HaYABBY genes of HaYABBY3, HaYABBY4b, HaYABBY5a, HaYABBY5d and HaCRABS CLAW play important roles in the process of floral meristem transformation and floral organ formation in sunflower, and they might depend on the regulation of auxin, gibberellin and meristem expression related regulators during meristem transformation and floral organogenesis, and need the involvement of the auxin response factor ARFs, gibberellin response factor MYBs and flower organ development regulator MADS-boxes.

Key words: sunflower, YABBY gene family, flower development, floral meristem transformation, floral organogenesis, gene expression

WANG Qian, ZHOU Jia-yan, WANG Qian, DENG Yu-ping, ZHANG Min-hui, CHEN Jing, YANG Jun, ZOU Jian. Identification and Expression Analysis of the YABBY Gene Family in Sunflower[J]. Biotechnology Bulletin, 2024, 40(8): 199-211.

Figures/Tables 7

Table 1 Information of YABBY gene family members in sunflower

基因 Gene	基因编号 Gene ID	染色体分布Chromosome distribution			氨基酸数目 Number of amino acids	等电点 pI	分子量 Molecular weight/Da	亚细胞定位 Subcellular location
基因 Gene	基因编号 Gene ID	编号No.	开始位置Starting	结束位置Ending	氨基酸数目 Number of amino acids	等电点 pI	分子量 Molecular weight/Da	亚细胞定位 Subcellular location
HaYABBY 1a	HanXRQr2_Chr06g0245541	6	12 754 239	12 758 093	219	7.21	24 420.73	细胞核
HaYABBY 1b	HanXRQr2_Chr13g0613121	13	161 766 031	161 771 918	216	6.72	24 136.35	细胞核
HaYABBY 1c	HanXRQr2_Chr04g0185291	4	195 371 365	195 376 174	219	7.21	24 437.79	细胞核
HaCRABS CLAWa	HanXRQr2_Chr12g0549931	1	81 233 913	81 243 999	173	9.4	19 366.25	细胞核
HaCRABS CLAWb	HanXRQr2_Chr15g0688211	15	39 093 254	39 095 798	180	9.28	19 765.53	细胞核
HaYABBY 3	HanXRQr2_Chr13g0577751	13	57 727 478	57 739 518	225	9.16	24 724.41	细胞核
HaYABBY 4a	HanXRQr2_Chr17g0787111	17	15 387 218	15 388 714	197	4.98	21 878.58	细胞核
HaYABBY 4b	HanXRQr2_Chr06g0253091	6	30 699 177	3 700 575	236	6.4	26 603.38	细胞核
HaYABBY 4c	HanXRQr2_Chr03g0102331	3	78 930 712	78 931 672	99	7.82	10 936.49	细胞核
HaYABBY 5a	HanXRQr2_Chr17g0801501	17	53 868 011	53 872 537	227	8.55	25 164.39	细胞核
HaYABBY 5b	HanXRQr2_Chr10g0462601	10	175 418 675	175 424 195	200	9.74	22 555.59	细胞核
HaYABBY 5c	HanXRQr2_Chr12g0523971	12	5 127 939	5 135 711	186	9.67	21 053.74	细胞核
HaYABBY 5d	HanXRQr2_Chr06g0238981	6	1 174 948	1 181 807	229	8.5	25 139.60	细胞核

Fig. 1 Chromosome localization of YABBY genes in sunflower

Fig. 2 Phylogenetic tree analysis of YABBY gene family members in sunflower ★,●,▲ and ■indicate Arabidopsis, sunflower, Chrysanthemum morifolium and Lactuca sativa respectively

Fig. 3 Gene structure and conserved motifs for YABBY family members A: Mapping of conserved motifs for YABBY family members. B: Mapping of gene structure for YABBY family members. C: Amino acid sequence comparison of core conserved domain of YABBY family members

Fig. 4 Analysis of tissue expression pattern of YABBY gene in WT sunflower FPKM refers to transcriptional abundance of YABBY gene family. Tissues: YR: young root; YS: young stem; YL: young leaf; R: root; S: stem; L: leaf. Expression period: St2: flower primordium initiation stage; St3: flower organ formation stage; St4: meiosis stage; St5: pollen maturation stage; St6: florets opening stage; St7: fruit filling stage and St8 seed full stage. The lowercase letter indicates significant difference at P<0.05 level. The same below

Fig. 5 Differential expression analysis of YABBY gene in WT sunflower and cb1 mutant A: Phenotypic characteristics of WT sunflower and cb1 mutant inflorescence. B: Phenotypic characteristics of inflorescences in WT and cb1 mutant sunflower from St2-St8. C: Relative expression of YABBY gene in WT and cb1 during inflorescence development（st2-st8）. All data are mean ±SD（n=3）. *: Significant difference（P<0.05）; **: extremely significant difference（P<0.01）

Fig. 6 Cis-acting element analysis of promoter region in YABBY family members

References 50

[1]	Wellmer F, Riechmann JL. Gene networks controlling the initiation of flower development[J]. Trends Genet, 2010, 26(12): 519-527. doi: 10.1016/j.tig.2010.09.001 pmid: 20947199
[2]	Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, et al. DNA-binding specificities of plant transcription factors and their potential to define target genes[J]. Proc Natl Acad Sci USA, 2014, 111(6): 2367-2372. doi: 10.1073/pnas.1316278111 pmid: 24477691
[3]	Porto MS, Pinheiro MPN, Batista VGL, et al. Plant promoters: an approach of structure and function[J]. Mol Biotechnol, 2014, 56(1): 38-49. pmid: 24122284
[4]	Udvardi MK, Kakar K, Wandrey M, et al. Legume transcription factors: global regulators of plant development and response to the environment[J]. Plant Physiol, 2007, 144(2): 538-549. doi: 10.1104/pp.107.098061 pmid: 17556517
[5]	刁志娟. 水稻三个花器官发育关键基因和一个SUPERMAN-like基因的功能和表达分析[D]. 福州: 福建农林大学, 2011.
	Diao ZJ. Functional and expressional analysis of three pivotal genes for floral organ development and a SUPERMAN-like gene in rice(Oryza sativa L.)[D]. Fuzhou: Fujian Agriculture and Forestry University, 2011.
[6]	Nam J, DePamphilis CW, Ma H, et al. Antiquity and evolution of the MADS-box gene family controlling flower development in plants[J]. Mol Biol Evol, 2003, 20(9): 1435-1447.
[7]	Mantegazza O, Gregis V, Mendes MA, et al. Analysis of the Arabidopsis REM gene family predicts functions during flower development[J]. Ann Bot, 2014, 114(7): 1507-1515.
[8]	Costanzo E, Trehin C, Vandenbussche M. The role of WOX genes in flower development[J]. Ann Bot, 2014, 114(7): 1545-1553.
[9]	Viola IL, Gonzalez DH. TCP transcription factors in plant reproductive development: juggling multiple roles[J]. Biomolecules, 2023, 13(5): 750.
[10]	Yamada T, Yokota S, Hirayama Y, et al. Ancestral expression patterns and evolutionary diversification of YABBY genes in angiosperms[J]. Plant J, 2011, 67(1): 26-36.
[11]	Bartholmes C, Hidalgo O, Gleissberg S. Evolution of the YABBY gene family with emphasis on the basal eudicot Eschscholzia californica(Papaveraceae)[J]. Plant Biol, 2012, 14(1): 11-23.
[12]	Finet C, Floyd SK, Conway SJ, et al. Evolution of the YABBY gene family in seed plants[J]. Evol Dev, 2016, 18(2): 116-126.
[13]	Zhang TP, Li CY, Li DX, et al. Roles of YABBY transcription factors in the modulation of morphogenesis, development, and phytohormone and stress responses in plants[J]. J Plant Res, 2020, 133(6): 751-763. doi: 10.1007/s10265-020-01227-7 pmid: 33033876
[14]	Romanova MA, Maksimova AI, Pawlowski K, et al. YABBY genes in the development and evolution of land plants[J]. Int J Mol Sci, 2021, 22(8): 4139.
[15]	Siegfried KR, Eshed Y, Baum SF, et al. Members of the YABBY gene family specify abaxial cell fate in Arabidopsis[J]. Development, 1999, 126(18): 4117-4128. doi: 10.1242/dev.126.18.4117 pmid: 10457020
[16]	Sawa S, Watanabe K, Goto K, et al. FILAMENTOUS FLOWER, a meristem and organ identity gene of Arabidopsis, encodes a protein with a zinc finger and HMG-related domains[J]. Genes Dev, 1999, 13(9): 1079-1088.
[17]	Bowman JL. The YABBY gene family and abaxial cell fate[J]. Curr Opin Plant Biol, 2000, 3(1): 17-22. doi: 10.1016/s1369-5266(99)00035-7 pmid: 10679447
[18]	Lee JY, Baum SF, Oh SH, et al. Recruitment of CRABS CLAW to promote nectary development within the eudicot clade[J]. Development, 2005, 132(22): 5021-5032.
[19]	Yamada T, Ito M, Kato M. YABBY2-homologue expression in lateral organs of Amborella trichopoda(Amborellaceae)[J]. Int J Plant Sci, 2004, 165(6): 917-924.
[20]	Sawa S, Ito T, Shimura Y, et al. FILAMENTOUS FLOWER controls the formation and development of Arabidopsis inflorescences and floral meristems[J]. Plant Cell, 1999, 11(1): 69-86. pmid: 9878633
[21]	Bowman JL, Smyth DR. CRABS CLAW, a gene that regulates carpel and nectary development in Arabidopsis, encodes a novel protein with zinc finger and helix-loop-helix domains[J]. Development, 1999, 126(11): 2387-2396. doi: 10.1242/dev.126.11.2387 pmid: 10225998
[22]	Villanueva JM, Broadhvest J, Hauser BA, et al. INNER NO OUTER regulates abaxial- adaxial patterning in Arabidopsis ovules[J]. Genes Dev, 1999, 13(23): 3160-3169.
[23]	Eshed Y, Izhaki A, Baum SF, et al. Asymmetric leaf development and blade expansion in Arabidopsis are mediated by KANADI and YABBY activities[J]. Development, 2004, 131(12): 2997-3006.
[24]	Sarojam R, Sappl PG, Goldshmidt A, et al. Differentiating Arabidopsis shoots from leaves by combined YABBY activities[J]. Plant Cell, 2010, 22(7): 2113-2130.
[25]	Chen Q, Atkinson A, Otsuga D, et al. The Arabidopsis FILAMENTOUS FLOWER gene is required for flower formation[J]. Development, 1999, 126(12): 2715-2726. doi: 10.1242/dev.126.12.2715 pmid: 10331982
[26]	Lugassi N, Nakayama N, Bochnik R, et al. A novel allele of FILAMENTOUS FLOWER reveals new insights on the link between inflorescence and floral meristem organization and flower morphogenesis[J]. BMC Plant Biol, 2010, 10: 131. doi: 10.1186/1471-2229-10-131 pmid: 20584289
[27]	Fourquin C, Vinauger-Douard M, Fogliani B, et al. Evidence that CRABS CLAW and TOUSLED have conserved their roles in carpel development since the ancestor of the extant angiosperms[J]. Proc Natl Acad Sci U S A, 2005, 102(12): 4649-4654.
[28]	Yamaguchi T, Nagasawa N, Kawasaki S, et al. The YABBY gene DROOPING LEAF regulates carpel specification and midrib development in Oryza sativa[J]. Plant Cell, 2004, 16(2): 500-509. doi: 10.1105/tpc.018044 pmid: 14729915
[29]	Ishikawa M, Ohmori Y, Tanaka W, et al. The spatial expression patterns of DROOPING LEAF orthologs suggest a conserved function in grasses[J]. Genes Genet Syst, 2009, 84(2): 137-146. pmid: 19556707
[30]	Orashakova S, Lange M, Lange S, et al. The CRABS CLAW ortholog from California poppy(Eschscholzia californica, Papaveraceae), EcCRC, is involved in floral meristem termination, gynoecium differentiation and ovule initiation[J]. Plant J, 2009, 58(4): 682-693.
[31]	Balasubramanian S, Schneitz K. NOZZLE links proximal-distal and adaxial-abaxial pattern formation during ovule development in Arabidopsis thaliana[J]. Development, 2002, 129(18): 4291-4300. doi: 10.1242/dev.129.18.4291 pmid: 12183381
[32]	Meister RJ, Kotow LM, Gasser CS. SUPERMAN attenuates positive INNER NO OUTER autoregulation to maintain polar development of Arabidopsis ovule outer integuments[J]. Development, 2002, 129(18): 4281-4289. doi: 10.1242/dev.129.18.4281 pmid: 12183380
[33]	di Rienzo V, Imanifard Z, Mascio I, et al. Functional conservation of the grapevine candidate gene INNER NO OUTER for ovule development and seed formation[J]. Hortic Res, 2021, 8(1): 29.
[34]	Tanaka W, Toriba T, Ohmori Y, et al. The YABBY gene TONGARI-BOUSHI1 is involved in lateral organ development and maintenance of meristem organization in the rice spikelet[J]. Plant Cell, 2012, 24(1): 80-95.
[35]	Ali Buttar Z, Yang Y, Sharif R, et al. Genome wide identification, characterization, and expression analysis of YABBY-gene family in wheat (Triticum aestivum L.)[J]. Agronomy, 2020, 10(8): 1189.
[36]	Chen YY, Hsiao YY, Chang SB, et al. Genome-wide identification of YABBY genes in Orchidaceae and their expression patterns in Phalaenopsis orchid[J]. Genes, 2020, 11(9): 955.
[37]	Cong B, Barrero LS, Tanksley SD. Regulatory change in YABBY-like transcription factor led to evolution of extreme fruit size during tomato domestication[J]. Nat Genet, 2008, 40(6): 800-804. doi: 10.1038/ng.144 pmid: 18469814
[38]	Li Z, Zhang ZH, Yan PC, et al. RNA-Seq improves annotation of protein-coding genes in the cucumber genome[J]. BMC Genomics, 2011, 12: 540. doi: 10.1186/1471-2164-12-540 pmid: 22047402
[39]	Zhang X, Ding L, Song AP, et al. DWARF AND ROBUST PLANT regulates plant height via modulating gibberellin biosynthesis in chrysanthemum[J]. Plant Physiol, 2022, 190(4): 2484-2500. doi: 10.1093/plphys/kiac437 pmid: 36214637
[40]	Gross T, Broholm S, Becker A. CRABS CLAW acts as a bifunctional transcription factor in flower development[J]. Front Plant Sci, 2018, 9: 835. doi: 10.3389/fpls.2018.00835 pmid: 29973943
[41]	Yang ZE, Gong Q, Wang LL, et al. Genome-wide study of YABBY genes in upland cotton and their expression patterns under different stresses[J]. Front Genet, 2018, 9: 33.
[42]	Wils CR, Kaufmann K. Gene-regulatory networks controlling inflorescence and flower development in Arabidopsis thaliana[J]. Biochim Biophys Acta Gene Regul Mech, 2017, 1860(1): 95-105.
[43]	Lee DY, An G. Two AP2 family genes, SUPERNUMERARY BRACT(SNB)and OsINDETERMINATE SPIKELET 1(OsIDS1), synergistically control inflorescence architecture and floral meristem establishment in rice[J]. Plant J, 2012, 69(3): 445-461.
[44]	Melzer S, Lens F, Gennen J, et al. Flowering-time genes modulate meristem determinacy and growth form in Arabidopsis thaliana[J]. Nat Genet, 2008, 40(12): 1489-1492.
[45]	Jiu ST, Zhang YP, Han P, et al. Genome-wide identification and expression analysis of VviYABs family reveal its potential functions in the developmental switch and stresses response during grapevine development[J]. Front Genet, 2022, 12: 762221.
[46]	Mäkilä R, Wybouw B, Smetana O, et al. Gibberellins promote polar auxin transport to regulate stem cell fate decisions in cambium[J]. Nat Plants, 2023, 9(4): 631-644.
[47]	Freire-Rios A, Tanaka K, Crespo I, et al. Architecture of DNA elements mediating ARF transcription factor binding and auxin-responsive gene expression in Arabidopsis[J]. Proc Natl Acad Sci U S A, 2020, 117(39): 24557-24566.
[48]	Vaddepalli P, Scholz S, Schneitz K. Pattern formation during early floral development[J]. Curr Opin Genet Dev, 2015, 32: 16-23. doi: 10.1016/j.gde.2015.01.001 pmid: 25687790
[49]	Dai MQ, Hu YF, Zhao Y, et al. A WUSCHEL-LIKE HOMEOBOX gene represses a YABBY gene expression required for rice leaf development[J]. Plant Physiol, 2007, 144(1): 380-390.
[50]	Siefers N, Dang KK, Kumimoto RW, et al. Tissue-specific expression patterns of Arabidopsis NF-Y transcription factors suggest potential for extensive combinatorial complexity[J]. Plant Physiol, 2009, 149(2): 625-641.