Genome-wide identification and analysis of the MADS-box gene family and its potential role in fruit ripening in black raspberry (Rubus occidentalis L.)

Article type: Research Article

Authors: Wu, Yaqiong^a | Zhang, Chunhong^a | Wu, Wenlong^a | Li, Weilin^{b; *} | Lyu, Lianfei^{a; *}

Affiliations: [a] Research Center for Pomology, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China | [b] Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China

Correspondence: [*] Corresponding author: Weilin Li, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China. Tel.: +86 25 8542 8531; E-mail: wlli@njfu.edu.cn. and Lianfei Lyu, Research Center for Pomology, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Qian Hu Hou Cun No.1, Nanjing, 210014, China. Tel.: +86 25 8434 7093; E-mail: njbglq@163.com.

Abstract: BACKGROUND:Black raspberry is a vital fruit crop with a high antioxidant function. MADS-box genes play an important role in the regulation of fruit development in angiosperms. OBJECTIVE:To understand the regulatory role of the MADS-box family, a total of 80 MADS-box genes were identified and analyzed. METHODS:The MADS-box genes in the black raspberry genome were analyzed using bioinformatics methods. Through an analysis of the promoter elements, the possible functions of different members of the family were predicted. The spatiotemporal expression patterns of members of the MADS-box family during black raspberry fruit development and ripening were systematically analyzed. RESULTS:The genes were classified into type I (Mα: 33; Mβ: 6; Mγ: 10) and type II (MIKC*: 2; MIKCC: 29) genes. We also obtained a complete overview of the RoMADS-box gene family through phylogenetic, gene structure, conserved motif, and cis element analyses. The relative expression analysis showed different expression patterns, and most RoMADS-box genes were more highly expressed in fruit than in other tissues of black raspberry. CONCLUSIONS:This finding indicates that the MADS-box gene family is involved in the regulation of fruit ripening processes in black raspberry.

Keywords: Gene family analysis, gene structure, conserved motif, cis element, expression pattern

DOI: 10.3233/JBR-200679

Journal: Journal of Berry Research, vol. 11, no. 2, pp. 301-315, 2021