Cloning and Characterization Analysis of the BABY BOOM Gene in Gossypium hirsutum
SHU Li-Zhe1, GONG Ze-Yu2, LEI Zhong-Ping3, TANG Bao-Shan1, LU Bi-Xia1, SONG Yin1, HE Dao-Hua1,*
1 College of Agronomy, Northwest A&F University, Yangling 712100, China; 2 College of Innovation and Experiment, Northwest A&F University, Yangling 712100, China; 3 College of Life Sciences, Northwest A&F University, Yangling 712100, China
Abstract：BABY BOOM (BBM) proteins are plant-specific transcription factors belonging to APETALA2/ethylene-responsive factor (AP2/ERF) family that may play an important regulatory role in somatic embryogenesis. By means of homology-based cloning, GhBBMa (GenBank No. MW836956) and GhBBMd (GenBank No. MW836957) were obtained from upland cotton (Gossypium hirsutum) cultivar YZ-1. The resequencing and phenotypic data of three natural populations, and the genome sequence of cultivar ZM24 were collected to characterize BBM genes and corresponding proteins. Especially, the expression profiles were analyzed by RNA-seq dataset and qRT-PCR assay. GhBBMa and GhBBMd were located on chromosomes A08 and D08. The opening reading frame (ORF) of GhBBMa/d were both composed of 9 exons, correspondingly with 2 028 bp and 2 025 bp in coding sequence (CDS), encoding 675 and 674 amino acids, respectively. The GhBBMa/d proteins contained two AP2 domains and excluded signal peptide or transmembrane domains. The bioinformatics subcellular location indicated that GhBBM appeared to accumulate in the cytoplasm. The phylogenetic tree showed that the GhBBMs were closely related to that from Theobroma cacao, which both belonged to the Malvales. The resequencing data of the natural populations showed that the sequence polymorphisms of GhBBMa and GhBBMd were 1.222 and 1.422 SNP/kb, respectively. The linkage disequilibrium (LD) decay distances were over 5.54 kb and 12.76 kb for GhBBMa and GhBBMd, respectively, indicating that GhBBMd was subjected to more evolutional selective pressure than GhBBMa. Association mapping showed that GhBBMa and GhBBMd had significant phenotypic effects on traits such as micronaire values and so on. RNA-seq dataset showed that the expression level of GhBBMa and GhBBMd genes was high in roots and ovules, but was very low in other tissues. GhBBMd was more vigorously transcripted in embryogenic callus than that in non-embryogenic callus. qRT-PCR assays showed that GhBBMa and GhBBMd had the highest expression accumulation in 30 d embryogenic callus and -3 days post anthesis (DPA) ovules. In summary, GhBBMa and GhBBMd, were cloned with low sequence diversity in DNA and substantive phenotypic effects on several traits. Two genes exhibited divergent expression abundance at different stages of somatic embryogenesis. According to the integrated results from RNA-seq dataset and qRT-PCR assay, GhBBMa/d might function in triggering embryogenesis. This study will facilitate the explore of mechanism of GhBBM involved in somatic embryogenesis.
束立哲, 宫则宇, 雷忠萍, 唐保善, 卢碧霞, 宋银, 贺道华. 陆地棉BABY BOOM基因的克隆及特征分析[J]. 农业生物技术学报, 2021, 29(5): 885-899.
SHU Li-Zhe, GONG Ze-Yu, LEI Zhong-Ping, TANG Bao-Shan, LU Bi-Xia, SONG Yin, HE Dao-Hua. Cloning and Characterization Analysis of the BABY BOOM Gene in Gossypium hirsutum. 农业生物技术学报, 2021, 29(5): 885-899.
[1] 金双侠. 2006. 棉花遗传转化体系的优化及突变体的创制[D].博士学位论文, 华中农业大学, 导师: 张献龙, pp. 2-22. (Jin S X.2006. Optimization of agrobacterium-mediated transformation of cotton and the development of mutants[D]. Thesis for Ph.D., Huazhong Agricultural University, Supervisor: Zhang X L, pp. 2-22.) [2] 孙滨, 占小登, 曹立勇, 等. 2017.水稻AP2/ERF转录因子的研究进展[J].农业生物技术学报, 25(11): 1860-1869. (Sun B, Zhan X D, Cao L Y, et al.2017. Research progress of AP2/ERF transcription factor in rice (Oryza sativa)[J]. Journal of Agricultural Biotechnology, 25(11):1860-1869.) [3] 许智宏, 张宪省, 苏英华, 等. 2019. 植物细胞全能性和再生[J]. 中国科学: 生命科学, 49(10): 1282-1300. (Xu Z H, Zhang X S, Su Y H, et al.2019. Plant cell totipotency and regeneration[J]. Scientia Sinica Vitae, 49(10): 1282-1300.) [4] 张朝军, 李付广, 张玲. 2008. 植物体细胞胚胎发生机理的研究进展[J]. 棉花学报, 20(02): 141-147. (Zhang C J, Li F G, Zhang L.2008. Advance in research on plant somatic embryogenesis[J]. Cotton Science, 20(02): 141-147.) [5] 赵方东, 李麟坤, 何旭升, 等. 2017. 关键基因和相关激素在植物胚胎发生前后期的作用[J]. 生物技术通报, 33(12): 30-36. (Zhao F D, Li L K, He X S, et al.2017. Roles of key genes and relevant plant hormones in the early and late stages of plant embryogenesis[J]. Biotechnology Bulletin, 33(12): 30-36. [6] Beasley C A.1971. In Vitro culture of fertilized cotton ovules[J]. BioScience, 21(17): 906-907. [7] Boutilier K, Offringa R, Sharma V K, et al.2002. Ectopic expression of BABY BOOM triggers a conversion from vegetative to embryonic growth[J]. Plant Cell, 14(8): 1737-1749. [8] Bouchabké-Coussa O, Obellianne M, Linderme D, et al.2013. Wuschel overexpression promotes somatic embryogenesis and induces organogenesis in cotton (Gossypium hirsutum L.) tissues cultured in vitro[J]. Plant Cell Reports, 32(5): 675-686. [9] Chen Z J, Sreedasyam A, Ando A, et al.2020. Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement[J]. Nature Genetics, 52(5): 525-533. [10] Davidonis G H, Hamilton R H.1983. Plant regeneration from callus tissue of Gossypium hirsutum L.[J]. Plant Science Letters, 32(1-2): 89-93. [11] Deng W, Luo K, Li Z, et al.2009. A novel method for induction of plant regeneration via somatic embryogenesis[J]. Plant Science, 177(1): 43-48. [12] Fang L, Wang Q, Hu Y, et al.2017. Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits[J]. Nature Genetics, 49(7): 1089-1098. [13] Florez S L, Erwin R L, Maximova S N, et al.2015. Enhanced somatic embryogenesis in Theobroma cacao using the homologous BABY BOOM transcription factor[J]. BMC Plant Biology, 15(1): 121. [14] Guo F, Liu C, Xia H, et al.2013. Induced expression of AtLEC1 and AtLEC2 differentially promotes somatic embryogenesis in transgenic tobacco plants[J]. PLOS ONE, 8(8): e71714. [15] He D H, Lei Z P, Tang B S, et al.2015. Identification and analysis of the TIFY gene family in Gossypium raimondii[J]. Genetics and Molecular Research, 14(3):10119-10138. [16] Heidmann I, de Lange B, Lambalk J, et al.2011. Efficient sweet pepper transformation mediated by the BABY BOOM transcription factor[J]. Plant Cell Reports, 30(6): 1107-1115. [17] Horstman A, Li M, Heidmann I, et al.2017. The BABY BOOM transcription factor activates the LEC1-ABI3-FUS3-LEC2 network to induce somatic embryogenesis[J]. Plant Physiology, 175(2): 848-857. [18] Huang G, Wu Z, Percy R G, et al.2020. Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution[J]. Nature Genetics, 52(5): 516-524. [19] Laux T, Mayer K F, Berger J, et al.1996. The WUSCHEL gene is required for shoot and floral meristem integrity in Arabidopsis[J]. Development, 122(1): 87-96. [20] Li K P, Sun X M, Han H, et al.2014. Isolation, characterization and expression analysis of the BABY BOOM (BBM) gene from Larix kaempferi × L. olgensis during adventitious rooting[J]. Genes, 551(2): 111-118. [21] Livak K J, Schmittgen T D.2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2 (-Delta Delta C(T)) Method[J]. Methods, 25(4): 402-408. [22] Lowe K, Wu E, Wang N, et al.2016. Morphogenic regulators Baby boom and Wuschel improve monocot transformation[J]. Plant Cell, 28(9): 1998-2015. [23] Ma Z, He S, Wang X, et al.2018. Resequencing a core collection of upland cotton identifies genomic variation and loci influencing fiber quality and yield[J]. Nature Genetics, 50(6): 803-813. [24] Mahdavi-Darvari F, Noor N M, Ismanizan I.2015. Epigenetic regulation and gene markers as signals of early somatic embryogenesis[J]. Plant Cell, Tissue and Organ Culture, 120(2): 407-422. [25] Sakhanokho H F, Zipf A, Rajasekaran K, et al.2001. Induction of highly embryogenic calli and plant regeneration in upland (Gossypium hirsutum L.) and pima (Gossypium barbadense L.) cottons[J]. Corp Science, 41(4): 1235-1240. [26] Wang M, Tu L, Lin M, et al.2017. Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication[J]. Nature Genetics, 49(4): 579-587. [27] Wang M, Wang Q L, Zhang B H.2013. Evaluation and selection of reliable reference genes for gene expression under abiotic stress in cotton (Gossypium hirsutum L.)[J]. Gene, 530(1): 44-50. [28] Wen L, Li W, Parris S, et al.2020. Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative upland cotton line (Gossypium hirsutum L.)[J]. BMC Developmental Biology, 20(1): 25. [29] Yavuz C, Tillaboeva S, Bakhsh A.2020. Apprehending the potential of BABY BOOM transcription factors to mitigate cotton regeneration and transformation[J]. Journal of Cotton Research, 3(1), 29. [30] Yang Z, Ge X, Yang Z, et al.2019. Extensive intraspecific gene order and gene structural variations in upland cotton cultivars[J]. Nature Communications, 10(1): 2989. [31] Zhang Z Y, Zhao H, Li W, et al.2019. Genome-wide association study of callus induction variation to explore the callus formation mechanism of rice[J]. Journal of Integrative Plant Biology, 61(11): 1134-1150.
