SiYABBYs Involved in Rhamnoside Biosynthesis During the Flower Development of Setaria italica, Based on Metabolomics

doi:10.13560/j.cnki.biotech.bull.1985.2022-1463

Abstract

Abstract:

Flower organ is the premise and basis of reproductive development, and also plays a decisive role at the final stage of spikelet formation. YABBY transcription factors play an important role in the development of flower organs. In order to clarify the function of YABBY gene family and improve the yield of foxtail millet (Setaria italica), we studied the sequence characteristics and expression patterns of YABBY gene family members in the foxtail millet. We analyzed genome-wide identification of YABBY gene family in the foxtail millet, the physical and chemical properties, and tissue expression patterns of SiYABBYs gene. Also, we aligned YABBY sequences of the foxtail millet, Arabidopsis and rice（Oryza sativa）for functional prediction. The results showed that 8 YABBY family members in the foxtail millet, encoding 150-303 amino acids. And we found these SiYABBYs genes were specifically expressed in panicles at heading and pollination stages, which may be involved in the development of vegetative tissues and the formation of flower organs in the foxtail millet. The expressions of SiYABBYs were correlated with the metabolome data at heading and pollination stages of the foxtail millet. The results showed that SiYABBY1/SiYABBY5/SiYABBY7/SiYABBY8 were closely related to rhamnoside metabolic pathway. Also, the results indicated that rhamnoside accumulation in the panicles during the pollination might be related to the fertility and seed setting rate of the foxtail millet.

Key words: foxtail millet, YABBY family, metabolomics

HAN Hua-rui, YANG Yu-lu, MEN Yi-han, HAN Shang-ling, HAN Yuan-huai, HUO Yi-qiong, HOU Si-yu. SiYABBYs Involved in Rhamnoside Biosynthesis During the Flower Development of Setaria italica, Based on Metabolomics[J]. Biotechnology Bulletin, 2023, 39(6): 189-198.

Figures/Tables 5

References 36

[1]	韩尚玲, 霍轶琼, 等. 基于WGCNA发掘谷子穗部类黄酮合成途径调控关键基因[J]. 作物学报, 2022, 48(7): 1645-1657. doi: 10.3724/SP.J.1006.2022.14107
	Han SL, Huo YQ, et al. Identification of regulatory genes related to flavonoids synthesis by weighted gene correlation network analysis in the panicle of foxtail millet[J]. Acta Agron Sin, 2022, 48(7): 1645-1657.
[2]	Yang ZR, Zhang HS, Li XK, et al. A mini foxtail millet with an Arabidopsis-like life cycle as a C₄ model system[J]. Nat Plants, 2020, 6(9): 1167-1178. doi: 10.1038/s41477-020-0747-7
[3]	顾伟航. 水稻花器官发育分子调控机制的研究[D]. 上海: 上海交通大学, 2018.
	Gu WH. The molecular mechanisms of rice flower development[D]. Shanghai: Shanghai Jiao Tong University, 2018.
[4]	Zhu Y, Wagner D. Plant inflorescence architecture: the formation, activity, and fate of axillary meristems[J]. Cold Spring Harb Perspect Biol, 2020, 12(1): a034652. doi: 10.1101/cshperspect.a034652 URL
[5]	Feller A, Machemer K, Braun EL, et al. Evolutionary and comparative analysis of MYB and bHLH plant transcription factors[J]. Plant J, 2011, 66(1): 94-116. doi: 10.1111/tpj.2011.66.issue-1 URL
[6]	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. doi: 10.3390/ijms22084139 URL
[7]	Golz JF, Roccaro M, Kuzoff R, et al. GRAMINIFOLIA promotes growth and polarity of Antirrhinum leaves[J]. Development, 2004, 131(15): 3661-3670. doi: 10.1242/dev.01221 URL
[8]	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
[9]	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
[10]	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. doi: 10.1242/dev.02067 URL
[11]	Shchennikova AV, Slugina MA, Beletsky AV, et al. The YABBY genes of leaf and leaf-like organ polarity in leafless plant Monotropa hypopitys[J]. Int J Genomics, 2018, 2018: 7203469.
[12]	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. doi: 10.1101/gad.13.23.3160 URL
[13]	Yamaguchi T, Nagasawa N, et al. The YABBY gene DROOPING LEAF regulates carpel specification and midrib development in Oryza sativa[J]. Plant Cell, 2004, 16(2): 500-509. pmid: 14729915
[14]	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. doi: 10.1105/tpc.111.094797 URL
[15]	Jang S, Hur J, Kim SJ, et al. Ectopic expression of OsYAB1causes extra stamens and carpels in rice[J]. Plant Mol Biol, 2004, 56(1): 133-143. doi: 10.1007/s11103-004-2648-y URL
[16]	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. doi: 10.1104/pp.107.095737 URL
[17]	夏妙林, 唐冬英, 杨远柱, 等. 水稻OsYABBY6基因参与叶片发育的初步研究[J]. 生命科学研究, 2017, 21(1): 23-30.
	Xia ML, Tang DY, Yang YZ, et al. Preliminary study on the rice OsYABBY6 gene involving in the regulation of leaf development[J]. Life Sci Res, 2017, 21(1): 23-30.
[18]	Strable J, Wallace JG, Unger-Wallace E, et al. Maize YABBY genes drooping leaf1 and drooping leaf2 regulate plant architecture[J]. Plant Cell, 2017, 29(7): 1622-1641. doi: 10.1105/tpc.16.00477 URL
[19]	Juarez MT, Twigg RW, Timmermans MCP. Specification of adaxial cell fate during maize leaf development[J]. Development, 2004, 131(18): 4533-4544. doi: 10.1242/dev.01328 pmid: 15342478
[20]	赵翔宇, 谢洪涛, 陈祥彬, 等. 小麦TaYAB2基因的过量表达造成转基因拟南芥叶片近轴面特征趋向远轴面[J]. 作物学报, 2012, 38(11): 2042-2051. doi: 10.3724/SP.J.1006.2012.02042
	Zhao XY, Xie HT, Chen XB, et al. Ectopic expression of TaYAB2, a member of YABBY gene family in wheat, causes partial abaxialization of adaxial epidermises of leaves in Arabidopsis[J]. Acta Agron Sin, 2012, 38(11): 2042-2051. doi: 10.3724/SP.J.1006.2012.02042 URL
[21]	Guo J, Zhou X, Dai K, et al. Comprehensive analysis of YABBY gene family in foxtail millet(Setaria italica)and functional characterization of SiDL[J]. J Integr Agric, 2022, 21(10): 2876-2887. doi: 10.1016/j.jia.2022.07.052 URL
[22]	Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2^-ΔΔCT method[J]. Methods, 2001, 25(4): 402-408. doi: 10.1006/meth.2001.1262 pmid: 11846609
[23]	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. doi: 10.1111/tpj.2011.67.issue-1 URL
[24]	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
[25]	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
[26]	Ikeda T, Tanaka W, Mikami M, et al. Generation of artificial drooping leaf mutants by CRISPR-Cas9 technology in rice[J]. Genes Genet Syst, 2016, 90(4): 231-235. doi: 10.1266/ggs.15-00030 pmid: 26617267
[27]	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. doi: 10.1266/ggs.84.137 URL
[28]	Stahle MI, Kuehlich J, Staron L, et al. YABBYs and the transcriptional corepressors LEUNIG and LEUNIG_HOMOLOG maintain leaf polarity and meristem activity in Arabidopsis[J]. Plant Cell, 2009, 21(10): 3105-3118. doi: 10.1105/tpc.109.070458 URL
[29]	Dai MQ, Hu YF, Zhao Y, et al. Regulatory networks involving YABBY genes in rice shoot development[J]. Plant Signal Behav, 2007, 2(5): 399-400. doi: 10.4161/psb.2.5.4279 URL
[30]	Yang C, Ma YM, Li JX. The rice YABBY4 gene regulates plant growth and development through modulating the gibberellin pathway[J]. J Exp Bot, 2016, 67(18): 5545-5556. doi: 10.1093/jxb/erw319 URL
[31]	Dai MQ, Zhao Y, Ma Q, et al. The rice YABBY1 gene is involved in the feedback regulation of gibberellin metabolism[J]. Plant Physiol, 2007, 144(1): 121-133.
[32]	Yamada T, et al. Expression pattern of INNER NO OUTER homologue in Nymphaea(Water Lily Family, Nymphaeaceae)[J]. Dev Genes Evol, 2003, 213(10): 510-513. doi: 10.1007/s00427-003-0350-8 URL
[33]	Karioti A, Kitsaki CK, Zygouraki S, et al. Occurrence of flavonoids in Ophrys(Orchidaceae)flower parts[J]. Flora Morphol Distribution Funct Ecol Plants, 2008, 203(7): 602-609.
[34]	Zhou CH, Sun CD, Chen KS, et al. Flavonoids, phenolics, and antioxidant capacity in the flower of Eriobotrya japonica Lindl[J]. Int J Mol Sci, 2011, 12(5): 2935-2945. doi: 10.3390/ijms12052935 URL
[35]	Shen N, Wang T, Gan Q, et al. Plant flavonoids: classification, distribution, biosynthesis, and antioxidant activity[J]. Food Chem, 2022, 383: 132531. doi: 10.1016/j.foodchem.2022.132531 URL
[36]	Amalesh S, Gouranga D, Sanjoy KD. Roles of flavonoids in plants[J]. Int J Pharm Sci Tech, 2011, 6(1): 12-35.

亚族 Subfamily	在拟南芥中的功能 Function in Arabidopsis thaliana	在水稻中的功能 Function in rice	谷子中功能预测 Function prediction in foxtail millet
YAB3	AtFIL：调控花序和花分生组织的形成和发育 ATFIL: Regulates the formation and development of inflorescence and floral meristems	OsYABBY3：侧生器官的形成和分生组织的分化 OsYABBY3: Formation of lateral organs and differentiation of meristems	SiYABBY1/SiYABBY5/SiYABBY7：参与侧生器官的发育以及花器官和小穗的形成和发育 SiYABBY1/SiYABBY5/SiYABBY7: Participate in lateral organ development and the formation and development of flower organs and spikelet
	AtYAB3：参与营养组织的发育 AtYAB3: Participate in the development of nutritive tissues	OsYABBY4：调控维管组织的发育和叶片的极性 OsYABBY4: Regulates vascular tissue development and leaf polarity
		OsYABBY5：小穗发育 OsYABBY5: Spikelets development
INO	AtINO：调节外胚珠珠被的发育 AtINO: To regulate the development of the outer ovules	OsYABBY7	SiYABBY3：调节外胚珠和花器官的发育 SiYABBY3: Adjust the ovule and floral organ development
CRC	AtCRC：心皮发育的关键调节因子 AtCRC: Carpel development a key regulating factor	OsDL：调控心皮的形成 OsDL: Regulate the formation of carpels	SiYABBY8（SiDL）：导致开花延迟、叶片卷曲和种子变小以及参与心皮的形成 SiYABBY8（SiDL）: Cause delayed flowering, smaller hairy leaves and seeds, and participate in the formation of carpel
YAB2	AtYAB2：参与营养组织的发育 AtYAB2: Participate in the development of nutritive tissues	OsYABBY1：雄蕊和心皮的分生组织发育 OsYABBY1: Meristematic development of stamens and carpels	SiYABBY2/SiYABBY4/SiYABBY6：参与营养组织的发育和花器官的形成 SiYABBY2/SiYABBY4/SiYABBY6: Involved in the development of vegetative tissues and the formation of floral organs
		OsYABBY2
		OsYABBY6：调控水稻的株高和产量 OsYABBY6: Regulate the plant height and yield of rice

亚族 Subfamily	在拟南芥中的功能 Function in Arabidopsis thaliana	在水稻中的功能 Function in rice	谷子中功能预测 Function prediction in foxtail millet
YAB3	AtFIL：调控花序和花分生组织的形成和发育 ATFIL: Regulates the formation and development of inflorescence and floral meristems	OsYABBY3：侧生器官的形成和分生组织的分化 OsYABBY3: Formation of lateral organs and differentiation of meristems	SiYABBY1/SiYABBY5/SiYABBY7：参与侧生器官的发育以及花器官和小穗的形成和发育 SiYABBY1/SiYABBY5/SiYABBY7: Participate in lateral organ development and the formation and development of flower organs and spikelet
	AtYAB3：参与营养组织的发育 AtYAB3: Participate in the development of nutritive tissues	OsYABBY4：调控维管组织的发育和叶片的极性 OsYABBY4: Regulates vascular tissue development and leaf polarity
		OsYABBY5：小穗发育 OsYABBY5: Spikelets development
INO	AtINO：调节外胚珠珠被的发育 AtINO: To regulate the development of the outer ovules	OsYABBY7	SiYABBY3：调节外胚珠和花器官的发育 SiYABBY3: Adjust the ovule and floral organ development
CRC	AtCRC：心皮发育的关键调节因子 AtCRC: Carpel development a key regulating factor	OsDL：调控心皮的形成 OsDL: Regulate the formation of carpels	SiYABBY8（SiDL）：导致开花延迟、叶片卷曲和种子变小以及参与心皮的形成 SiYABBY8（SiDL）: Cause delayed flowering, smaller hairy leaves and seeds, and participate in the formation of carpel
YAB2	AtYAB2：参与营养组织的发育 AtYAB2: Participate in the development of nutritive tissues	OsYABBY1：雄蕊和心皮的分生组织发育 OsYABBY1: Meristematic development of stamens and carpels	SiYABBY2/SiYABBY4/SiYABBY6：参与营养组织的发育和花器官的形成 SiYABBY2/SiYABBY4/SiYABBY6: Involved in the development of vegetative tissues and the formation of floral organs
		OsYABBY2
		OsYABBY6：调控水稻的株高和产量 OsYABBY6: Regulate the plant height and yield of rice

转录因子 Transcription factor	结合基序 Motif ID	靶基因 Target gene	模板链 Strand	起始位置 Start	终止为止 End	P值 P-value	q值 q-value	匹配序列 Matched sequence
SiYABBY8	UN0396.1	Si1g24720	-	1 734	1 741	2.65e-05	1	TAATCATA
		Si1g07250	+	698	705	5.3e-05	1	TTATCATA
		Si1g24750	+	1 165	1 172	7.95e-05	1	TAATCATA
		Si7g05130	+	1 478	1 485	7.95e-05	1	TAATCATT
SiYABBY1 SiYABBY5 SiYABBY7	UN0415.1	Si8g14530	-	121	128	3.23e-05	0.529	AATAATAA
		Si9g17990	-	1 088	1 095	3.23e-05	0.529	AATAATAA
		Si7g30480	+	1 319	1 326	3.23e-05	0.529	AATAATAA
		Si9g30300	-	1 314	1 321	3.23e-05	0.529	AATAATAA
		Si7g01180	-	1 785	1 792	3.23e-05	0.529	AATAATAA
		Si7g01180	-	389	396	6.46e-05	0.529	AATAATTA
		Si6g16950	-	861	868	6.46e-05	0.529	AATAATTA
		Si6g16950	+	896	903	6.46e-05	0.529	AATAATTA
		Si7g30480	-	1 593	1 600	6.46e-05	0.529	AATAATTA
		Si9g04210	+	1 645	1 652	6.46e-05	0.529	AATAATTA
		Si9g04210	-	1 647	1 654	6.46e-05	0.529	AATAATTA
		Si7g01180	-	1 793	1 800	6.46e-05	0.529	AATAATTA
		Si7g05130	-	164	171	9.69e-05	0.56	AATATTAA
		Si9g52070	+	249	256	9.69e-05	0.56	AATATTAA
		Si7g01180	-	431	438	9.69e-05	0.56	AATATTAA
		Si9g30300	+	849	856	9.69e-05	0.56	AATATTAA
		Si7g30480	-	1 452	1 459	9.69e-05	0.56	AATATTAA
		Si5g36410	+	1 437	1 444	9.69e-05	0.466	AATATTAA

转录因子 Transcription factor	结合基序 Motif ID	靶基因 Target gene	模板链 Strand	起始位置 Start	终止为止 End	P值 P-value	q值 q-value	匹配序列 Matched sequence
SiYABBY8	UN0396.1	Si1g24720	-	1 734	1 741	2.65e-05	1	TAATCATA
		Si1g07250	+	698	705	5.3e-05	1	TTATCATA
		Si1g24750	+	1 165	1 172	7.95e-05	1	TAATCATA
		Si7g05130	+	1 478	1 485	7.95e-05	1	TAATCATT
SiYABBY1 SiYABBY5 SiYABBY7	UN0415.1	Si8g14530	-	121	128	3.23e-05	0.529	AATAATAA
		Si9g17990	-	1 088	1 095	3.23e-05	0.529	AATAATAA
		Si7g30480	+	1 319	1 326	3.23e-05	0.529	AATAATAA
		Si9g30300	-	1 314	1 321	3.23e-05	0.529	AATAATAA
		Si7g01180	-	1 785	1 792	3.23e-05	0.529	AATAATAA
		Si7g01180	-	389	396	6.46e-05	0.529	AATAATTA
		Si6g16950	-	861	868	6.46e-05	0.529	AATAATTA
		Si6g16950	+	896	903	6.46e-05	0.529	AATAATTA
		Si7g30480	-	1 593	1 600	6.46e-05	0.529	AATAATTA
		Si9g04210	+	1 645	1 652	6.46e-05	0.529	AATAATTA
		Si9g04210	-	1 647	1 654	6.46e-05	0.529	AATAATTA
		Si7g01180	-	1 793	1 800	6.46e-05	0.529	AATAATTA
		Si7g05130	-	164	171	9.69e-05	0.56	AATATTAA
		Si9g52070	+	249	256	9.69e-05	0.56	AATATTAA
		Si7g01180	-	431	438	9.69e-05	0.56	AATATTAA
		Si9g30300	+	849	856	9.69e-05	0.56	AATATTAA
		Si7g30480	-	1 452	1 459	9.69e-05	0.56	AATATTAA
		Si5g36410	+	1 437	1 444	9.69e-05	0.466	AATATTAA