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Herrania species: A potential genetic resource for cocoa breeding revealed by a comparative bioinformatic study among close species

Abstract:

Herrania umbratica, a native species of South America, is used as a wild cacao source parallelly with Theobroma cacao. Despite its importance, its genomic information are not well presented and available. The gene models and proteins of H. umbratica with T. cacao, three Malvaceae species and three model plants were compared. H. umbratica shared the most proteins and genes with T. cacao, with more than 96% of similarity. The next close species to H. umbratica was Durio zibethinus followed by Gossypium raimondii and Corchorus capsularis. Species-specific genes of H. umbratica like Glu S. griseus protease inhibitor, WRKY34, disease resistance protein At4g27190, RPP13, and CEP are involved in disease response, stress adaptation, and growth and development. Five copies of theobromine synthase genes were revealed for H. umbratica and 10 for T. cacao. By blastn, blastp and blastx respectively, 2,179 gene models, 2,488 proteins and 2,722 gene models distributed in 58 transcription factors families were disclosed for H. umbratica. C2H2 with 739 members, WD40-like with 404, and MYB-HB-like with 311 were the top transcription factors. Simple sequence repeat species-specific markers were one deca-nucleotide unit (TTATTAAATG)3 and five nona-nucleotide units including (AAAAACAAA)3, (CAACAGCAG)3, (GACGATGAC)3, (GACGATGAC)3, and (TGGCGGTGG)3. This study disclosed that H. umbratica is a natural wild genetic resource for cacao breeding and can be used as a reliable gene pool to ameliorate cacao vegetation form, production, disease resistance, and stress adaptation.