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.
SHU Li-Zhe,GONG Ze-Yu,LEI Zhong-Ping, et al. Cloning and Characterization Analysis of the BABY BOOM Gene in Gossypium hirsutum[J]. 农业生物技术学报, 2021, 29(5): 885-899.
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