Genome-wide identification and expression of DELLA protein gene family in Brassica napus

doi:10.7505/j.issn.1007-9084.2019.03.007

Abstract

Abstract:

DELLA protein is a key factor involved in GA regulatory pathways and plays an important role in regulating plant growth and development. In order to reveal the distribution and characteristics of DELLA protein family in Brassica napus, family members, sequence characteristics, evolutionary relationships and tissue expression were analyzed using bioinformatics. The results showed that there were 13 DELLA protein genes in Brassica napus, located in 8 chromosomes with 2 random sequences (chrC09_random and chrCnn_random); The phylogenetic tree analysis found that the family was clustered into 4 subfamilies. One subfamily contains 7 genes, and the second, third and fourth subfamilies each included 2 genes. The expression analysis of different tissues showed tissue-specific expression in each tissue, and BnaA10g17240D, BnaC09g40420D、BnaCnng68300D and BnaC05g47760D were relatively high in each tissue. Among the stems, BnaA06g34810D、BnaA09g18700D and BnaC09g52270D had the highest expression. This study provided a reference for studying the genes functionality in the future.

Key words: Brassica napus L. , DELLA gene family , gene expression

JIA Yong-peng, LI Kai-xiang, ZAN Ling-xiong, Yao Yan-mei, DU De-zhi* . Genome-wide identification and expression of DELLA protein gene family in Brassica napus[J]. 中国油料作物学报, 2019, 41(3): 360-.

References

[1] Daviere J M, Achard P. Gibberellin signaling in plants[J]. Development, 2013, 140(6): 1147-1151.
[2] Li W J, Zhang J X, Sun H Y, et al. FveRGA1, encoding a DELLA protein, negatively regulates runner production in Fragaria vesca[J]. Planta, 2018, 247(4): 941-951.
[3] 李威, 李国瑞, 黄凤兰, 等. DELLA家族蛋白研究进展[J]. 安徽农业科学, 2016, 44(32): 147-148.
[4] Zhao X Y, Zhu D F, Zhou B, et al. Over-expression of the AtGA2ox8 gene decreases the biomass accumulation and lignification in rapeseed (Brassica napus L.)[J]. J Zhejiang Univ Sci B, 2010, 11(7): 471-481.
[5] Peng J R, Richards D E, Hartley N M, et al. ‘Green revolution’ genes encode mutant gibberellin response modulators[J]. Nature, 1999, 400(6741): 256-261.
[6] Pearce S, Saville R, Vaughan S P, et al. Molecular characterization of Rht-1 dwarfing genes in hexaploid wheat[J]. Plant Physiol, 2011, 157(4): 1820-1831.
[7] Chen J H, Cheng T L, Wang P K, et al. Genome-wide bioinformatic analysis of DELLA-family proteins from plants[J]. Plant Omics, 2013, 6(3): 201-207.
[8] Davière J M, Achard P. A pivotal role of DELLAs in regulating multiple hormone signals[J]. Mol Plant, 2016, 9(1): 10-20.
[9] Tyler L. DELLA proteins and gibberellin-regulated seed germination and floral development in Arabidopsis[J]. Plant Physiol, 2004, 135(2): 1008-1019.
[10] 陈宇杰, 刘飞, 梁菲菲, 等. 蓖麻DELLA蛋白家族GAI基因克隆、表达及生物信息学分析[J]. 内蒙古民族大学学报:自然科学版, 2017, 32(4): 320-327.
[11] 张文颖, 王晨, 朱旭东, 等. 葡萄全基因组DELLA蛋白基因家族鉴定及其应答外源赤霉素调控葡萄果实发育的特征[J]. 中国农业科学, 2018, 51(16): 3130-3146.
[12] Gao Y, Chen J M, Zhao Y, et al. Molecular cloning and expression analysis of a RGA-like gene responsive to plant hormones in Brassica napus[J]. Mol Biol Rep, 2012, 39(2): 1957-1962.
[13] Sun T P. Gibberellin-GID1-DELLA: A pivotal regulatory module for plant growth and development[J]. Plant Physiol, 2010, 154(2): 567-570.
[14] Murase K, Hirano Y, Sun T P, et al. Gibberellin-induced DELLA recognition by the gibberellin receptor GID1[J]. Nature, 2008, 456(7221): 459-463.
[15] Fu X. Gibberellin-mediated proteasome-dependent degradation of the barley DELLA protein SLN1 repressor[J]. Plant Cell Online, 2002, 14(12): 3191-3200.
[16] Ueguchi-Tanaka M, Nakajima M, Katoh E, et al. Molecular interactions of a soluble gibberellin receptor, GID1, with a rice DELLA protein, SLR1, and gibberellin[J]. Plant Cell Online, 2007, 19(7): 2140-2155.
[17] Zhao B, Li H T, Li J J, et al. Brassica napus DS-3, encoding a DELLA protein, negatively regulates stem elongation through gibberellin signaling pathway[J]. Theor Appl Genet, 2017, 130(4): 727-741.
[18] Li H T, Wang B, Zhang Q H, et al. Genome-wide analysis of the auxin/indoleacetic acid (Aux/IAA) gene family in allotetraploid rapeseed (Brassica napus L.)[J]. BMC Plant Biol, 2017, 17: 204.
[19] Tamura K, Stecher G, Peterson D, et al. MEGA6: molecular evolutionary genetics analysis version 6.0[J]. Mol Biol Evol, 2013, 30(12): 2725-2729.
[20] 李晓康, 刘红芳, 刘婧琳, 等. 油菜miR156基因家族及其靶基因生物信息学分析及鉴定[J]. 中国油料作物学报, 2018, 40(2): 163-173.
[21] 李春金, 郭媛媛, 杨启航, 等. 甘蓝型油菜HMG基因家族的生物信息学分析[J]. 中国油料作物学报, 2018, 40(3): 318-325.
[22] Wang D P, Wan H L, Zhang S, et al. Γ-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates[J]. Biol Direct, 2009, 4(1): 20.
[23] Chalhoub B, Denoeud F, Liu S Y, et al. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome[J]. Science, 2014, 345(6199): 950-953.
[24] Wu D C, Yao J, Ho K S, et al. Limitations of alignment-free tools in total RNA-seq quantification[J]. BMC Genomics, 2018, 19(1): 1-14.
[25] 夏胜前, 张毅, 涂金星. 油菜重要性状功能基因研究进展[J]. 中国油料作物学报, 2018, 40(5): 656-663.
[26] Du H Y, Yang C, Ding G D, et al. Genome-wide identification and characterization of SPX domain-containing members and their responses to phosphate deficiency in Brassica napus[J]. Front Plant Sci, 2017, 8: 35.
[27] Chen H F, Zhang Q, He M L, et al. Molecular characterization of the genome-wide BOR transporter gene family and genetic analysis of BnaC04.BOR1;1c in Brassica napus[J]. BMC Plant Biol, 2018, 18: 193.
[28] Hajiebrahimi A, Owji H, Hemmati S. Genome-wide identification, functional prediction, and evolutionary analysis of the R2R3-MYB superfamily in Brassica napus[J]. Genome, 2017, 60(10): 797-814.