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Title: Comparative analysis of the genetic variability within the Q-type C2H2 zinc-finger transcription factors in the economically important cabbage, canola and Chinese cabbage genomes

item Lawrence, Susan
item Novak, Nicole

Submitted to: Hereditas
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/22/2018
Publication Date: 9/21/2018
Citation: Lawrence, S.D., Novak, N.G. 2018. Comparative analysis of the genetic variability within the Q-type C2H2 zinc-finger transcription factors in the economically important cabbage, canola and Chinese cabbage genomes. Hereditas. 155:29.

Interpretive Summary: Crop plants are threatened in survival and yield by drought, excess salt (salinity) in soils, and insect pest attack. Plants that can survive these threats, and produce good yields, are crucial to the success of American agriculture. Scientists have determined that a family of regulatory genes known as the Q-type-2-zinc fingered C2H2 transcription factors (Q-type C2H2 TFs) can play a crucial role in enhancing tolerance to such stresses. Identifying and characterizing new genes in this family can augment breeding programs by identifying new genes that lead to plants with increased tolerance to stress. This study investigated all the Q-type C2H2 TFs in three different species, including varieties such as cabbage, broccoli, canola and Chinese cabbage, with the goal to detect and characterize the crops’ diversity for these genes. This resulted in the identification of 146 genes. Discovery of these genes will be important to scientists and plant breeders interested in producing new stress tolerant varieties of these valuable vegetable and oil crops.

Technical Abstract: Brassica oleracea, B. rapa and B. napus encompass many economically important vegetable and oil crops; such as cabbage, broccoli, canola and Chinese cabbage. The sequencing of reference genomes for these three species allows an opportunity for gene discovery with an eye towards discerning the natural variability available for future breeding. The Q-type C2H2 zinc-finger protein (ZFP) transcription factors (TF) contain zinc finger motifs with a conserved QALGGH as part of the motif and play a critical role in the plants response to abiotic and biotic stress. They contain two zinc-fingers per protein, which bind to the promoter of genes, and negatively regulate transcription via the ethylene-responsive element binding factor-associated amphiphilic repression (EAR) motif. This work identifies a total of 146 Q-type C2H2-ZFPs from these 3 species. There are 37 found in Brassica oleracea, 35 in Brassica rapa and a total of 74 in Brassica napus. Brassica oleracea and B. rapa are diploid and split into different species about 3.7 million years ago (mya). Brassica napus is polyploid and formed by fusion of the diploids about 7500 years ago. It is clear that the level of sequence similarity and arrangement of these genes on their chromosomes have mostly remained intact in Brassica napus, when compared to the chromosomes inherited from either B. rapa or B. oleracea. In contrast, the difference between the protein sequences of the orthologs of B. rapa and B. oleracea is greater and their organization on the chromosomes is much more divergent. In general, the 146 proteins are highly conserved within the known motifs and differences within subgroups of ZFPs were defined. Alignment of these proteins gives a snapshot of the variability within these proteins that may be available to future Brassica breeding programs.