Genome-wide identification, characterization, and genetic diversity of CCR gene family in Dalbergia odorifera

Yue Wang; Jieru Xu; Wenxiu Zhao; Jia Li; Jinhui Chen

doi:10.3389/fpls.2022.1064262

Genome-wide identification, characterization, and genetic diversity of CCR gene family in Dalbergia odorifera

Front Plant Sci. 2022 Dec 19:13:1064262. doi: 10.3389/fpls.2022.1064262. eCollection 2022.

Authors

Yue Wang^{1

2}, Jieru Xu^{1

2}, Wenxiu Zhao^{1

2}, Jia Li^{1

2}, Jinhui Chen^{1

2

3}

Affiliations

¹ Hainan Yazhou Bay Seed Laboratory, School of Forestry, Sanya Nanfan Research Institute of Hainan University, Sanya, China.
² Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China.
³ Research Institute of Forestry, Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, China.

Abstract

Introduction: Lignin is a complex aromatic polymer plays major biological roles in maintaining the structure of plants and in defending them against biotic and abiotic stresses. Cinnamoyl-CoA reductase (CCR) is the first enzyme in the lignin-specific biosynthetic pathway, catalyzing the conversion of hydroxycinnamoyl-CoA into hydroxy cinnamaldehyde. Dalbergia odorifera T. Chen is a rare rosewood species for furniture, crafts and medicine. However, the CCR family genes in D. odorifera have not been identified, and their function in lignin biosynthesis remain uncertain.

Methods and results: Here, a total of 24 genes, with their complete domains were identified. Detailed sequence characterization and multiple sequence alignment revealed that the DoCCR protein sequences were relatively conserved. They were divided into three subfamilies and were unevenly distributed on 10 chromosomes. Phylogenetic analysis showed that seven DoCCRs were grouped together with functionally characterized CCRs of dicotyledons involved in developmental lignification. Synteny analysis showed that segmental and tandem duplications were crucial in the expansion of CCR family in D. odorifera, and purifying selection emerged as the main force driving these genes evolution. Cis-acting elements in the putative promoter regions of DoCCRs were mainly associated with stress, light, hormones, and growth/development. Further, analysis of expression profiles from the RNA-seq data showed distinct expression patterns of DoCCRs among different tissues and organs, as well as in response to stem wounding. Additionally, 74 simple sequence repeats (SSRs) were identified within 19 DoCCRs, located in the intron or untranslated regions (UTRs), and mononucleotide predominated. A pair of primers with high polymorphism and good interspecific generality was successfully developed from these SSRs, and 7 alleles were amplified in 105 wild D. odorifera trees from 17 areas covering its whole native distribution.

Discussion: Overall, this study provides a basis for further functional dissection of CCR gene families, as well as breeding improvement for wood properties and stress resistance in D. odorifera.

Keywords: Dalbergia odorifera; cinnamoyl-CoA reductase; forest breeding; genetic diversity; simple sequence repeat.