AUTHOR=Wang Yue , Xu Jieru , Zhao Wenxiu , Li Jia , Chen Jinhui 

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

JOURNAL=Frontiers in Plant Science

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.1064262

DOI=10.3389/fpls.2022.1064262

ISSN=1664-462X

ABSTRACT=<sec><title>Introduction</title><p>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. <italic>Dalbergia odorifera</italic> T. Chen is a rare rosewood species for furniture, crafts and medicine. However, the <italic>CCR</italic> family genes in <italic>D. odorifera</italic> have not been identified, and their function in lignin biosynthesis remain uncertain.</p></sec><sec><title>Methods and Results</title><p>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 <italic>CCR</italic> family in <italic>D. odorifera</italic>, and purifying selection emerged as the main force driving these genes evolution. Cis-acting elements in the putative promoter regions of <italic>DoCCRs</italic> 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 <italic>DoCCRs</italic> among different tissues and organs, as well as in response to stem wounding. Additionally, 74 simple sequence repeats (SSRs) were identified within 19 <italic>DoCCRs</italic>, 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 <italic>D. odorifera</italic> trees from 17 areas covering its whole native distribution.</p></sec><sec><title>Discussion</title><p>Overall, this study provides a basis for further functional dissection of <italic>CCR</italic> gene families, as well as breeding improvement for wood properties and stress resistance in <italic>D. odorifera</italic>.</p></sec>