Genome-wide identification and characterization of the Lateral Organ Boundaries Domain (LBD) gene family in nine Rosaceae species and expression pattern in Prunus mume

Weichao Liu; Xiaoyu Guo; Tangchun Zheng; Xue Li; Sagheer Ahmad; Jia Wang; Qixiang Zhang; Tangren Cheng

doi:10.48130/opr-0024-0005

Ornamental Plant Research (Jan 2024)

Genome-wide identification and characterization of the Lateral Organ Boundaries Domain (LBD) gene family in nine Rosaceae species and expression pattern in Prunus mume

Weichao Liu,
Xiaoyu Guo,
Tangchun Zheng,
Xue Li,
Sagheer Ahmad,
Jia Wang,
Qixiang Zhang,
Tangren Cheng

Affiliations

Weichao Liu: Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
Xiaoyu Guo: Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
Tangchun Zheng: Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
Xue Li: Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
Sagheer Ahmad: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Jia Wang: Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
Qixiang Zhang: Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
Tangren Cheng: Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China

DOI: https://doi.org/10.48130/opr-0024-0005
Journal volume & issue: Vol. 4, no. 1
pp. 1 – 14

Abstract

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Transcription factors (TFs) encoded by the lateral organ boundaries domain (LBD) gene family are known to control many plant-specific developmental processes. However, the comparative analysis of the LBD gene family in Rosaceae species and its expression pattern in mei remains unclear. Here, we identified a total of 406 LBDs in nine Rosaceae species, including 39 in black raspberry (Rubus occidentalis), 34 in strawberry (Fragaria vesca), 39 in Chinese rose (Rosa chinensis), 42 in peach (Prunus persica), 41 in apricot (Prunus armeniaca), 41 in mei (Prunus mume var. tortuosa), 60 in pear (Pyrus communis), 41 in hawthorn (Crataegus pinnatifida) and 69 in apple (Malus domestica), respectively. The LBDs of nine Rosaceae species were classified into seven major subclasses. The chromosome localization, collinearity analysis, and gene duplication relationship revealed that segment duplication was the main driving force for the amplification of LBDs in the Rosoideae and Amygdaloideae. Ka/Ks analysis suggested most of the LBD gene pairs might be under purification selection. GO and cis-acting elements analysis showed that LBDs may play important roles in many biological processes and could respond to hormones and stresses. RNA-seq data showed that PmLBD17/19/41 genes contained both low-temperature and MeJA response elements and played a significant variation across different geographic locations and periods. PmLBD30, the ortholog of EgLBD29, exhibited an up-regulation followed by a decrease, which is hypothesized to possibly play a role in the formation of a weeping trait in mei. Our studies offer important data about the development of the LBD family in Rosaceae and the subsequent validation of LBDs' functional genes in P. mume.

Published in Ornamental Plant Research

ISSN: 2769-2094 (Online)
Publisher: Maximum Academic Press
Country of publisher: China
LCC subjects: Science: Botany: Plant ecology; Technology: Environmental technology. Sanitary engineering: Environmental effects of industries and plants
Website: https://www.maxapress.com/opr

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