Identification of BABY BOOM and LEAFY COTYLEDON genes in sweet pepper (Capsicum annuum L.) genome by their partial gene sequences

Abstract

Haploid plant production via anther culture is a valuable tool to rapidly create pure lines for plant breeding programs. Some sweet pepper (Capsicum annuum L.) varieties produce embryogenic anther culture readily, while others do not respond at all. The switching of microspore developmental program from gametophyte- to sporophyte-type is regulated by transcription factors like BABY BOOM (BBM) and LEAFY COTYLEDON (LEC). Genes encoding these transcription factors have not been found in sweet pepper yet. The sequences of BBM and LEC from other plants, annotated in National Center for Biotechnology Information (NCBI), were used to design degenerative primers for conservative regions in these genes and to amplify BBM- and LEC-like sequences from genomic DNA of sweet pepper by PCR. The PCR products were cloned and sequenced. Sequence comparison revealed high similarity between the isolated sequences and those annotated in NCBI for BBM and LEC1. The obtained sequences were subjected to bioinformatics analyses to determine the exon–intron structure. Exons were translated in protein products in silico. The protein blast of the pepper BBM in the NCBI database revealed presence of an AP2-type functional domain, which is typical for the BBM family. The pepper LEC sequence was found to carry CBFD-NFYB-HMF motif, typical for the LEAFY COTYLEDON gene product family. RT-PCR confirmed high levels of expression of the BBM and LEC genes at the early stages of direct embryos development in anther culture. Expression of the two genes was not detected either in mature pepper plants or in non-embryogenic anthers. The two genes were detected in genomes of 14 pepper varieties, some of which do not respond with formation of direct embryos. We assume that differences in responses between varieties should be attributed not to presence/absence of two genes, but to their interaction with other genes’ products and different factor like micro-RNAs involved in the regulation of their expression.