Genome-wide identification and characterization of the lateral organ boundaries domain gene family in Brassica rapa var . rapa

Qin Yu; Simin Hu; Jiancan Du; Yongping Yang; Xudong Sun

doi:10.1016/j.pld.2019.11.004

Genome-wide identification and characterization of the lateral organ boundaries domain gene family in Brassica rapa var . rapa

Plant Divers. 2019 Dec 19;42(1):52-60. doi: 10.1016/j.pld.2019.11.004. eCollection 2020 Feb.

Authors

Qin Yu^{1

2

3

4}, Simin Hu^{1

2

3

4}, Jiancan Du^{1

2

3

4}, Yongping Yang^{1

2

3}, Xudong Sun^{1

2

3}

Affiliations

¹ Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China.
² Plant Germplasm and Genomics Center, The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
³ Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
⁴ University of the Chinese Academy of Sciences, Beijing 100049, China.

Abstract

The Lateral Organ Boundaries Domain (LBD) genes encode highly conserved plant-specific LOB domain proteins which regulate growth and development in various species. However, members of the LBD gene family have yet to be identified in Brassica rapa var. rapa. In the present study, fifty-nine LBD genes were identified and distributed on 10 chromosomes. The BrrLBD proteins are predicted to encode hydrophobic polypeptides between 118 and 394 amino acids in length and with molecular weights ranging from 13.31 to 44.24 kDa; the theoretical pI for these proteins varies from 4.83 to 9.68. There were 17 paralogous gene pairs in the BrrLBD family, suggesting that the amplification of the BrrLBD gene family involved large-scale gene duplication events. Members of the BrrLBD family were divided into 7 subclades (class I a to e, class II a and b). Analysis of gene structure and conserved domains revealed that most BrrLBD genes of the same subclade had similar gene structures and protein motifs. The expression profiles of 59 BrrLBD genes were determined through Quantitative Real-time fluorescent PCR (qRT-PCR). Most BrrLBD genes in the same subclade had similar gene expression profiles. However, the expression patterns of 7 genes differed from their duplicates, indicating that although the gene function of most BrrLBD genes has been conserved, some BrrLBD genes may have undergone evolutionary change.

Keywords: Brassica rapa var. rapa; Expression profiles; LBD; LBD gene sequence analysis; Transcription factors.