S01 - Session O4 - The trifoliate orange (Poncirus trifoliata) genome and its repertoire of disease resistance and cold tolerance-related genes for genetic improvement of citrus

Authors: Zhanao Deng *, Ze Peng, Jessen V. Bredeson, Shengqiang Shu, Guohong Albert Wu, Nidhi Rawat, Dongliang Du, Soraj Parajuli, Qibin Yu, Qian You, Daniel Rokhsar, Fred Gmitter

Trifoliate orange is a deciduous close relative of evergreen Citrus and has important traits for citrus production and breeding, including resistance/tolerance to citrus greening disease (Huanglongbing, HLB), citrus tristeza virus (CTV), citrus nematodes (CN), and cold. A high-quality, chromosome-scale reference genome was assembled de novo for the trifoliate orange accession DPI 50-7. The 264.9 Mb assembly contains nine chromosomal pseudomolecules and 25,538 protein-coding genes, covering 97.2% of the estimated gene space. The genome was annotated with 348 nucleotide binding-site (NBS)-containing genes, including 51 genes belonging to the NBS-LRR class, 77 to the CC-NBS-LRR class, and eight to the TIR-NBS-LRR class. Seven NBS genes are located within the Ctv region that confers dominant qualitative resistance to CTV. Fifteen NBS genes (2 NBS, 2 CC-NBS, 10 CC-NBS-LRR and 1 NBS-LRR) are located within a 1-Mb genomic region at the major quantitative trait locus Tyr1 for resistance to CN. The 14 QTL intervals that were previously associated with HLB tolerance, are located in seven genomic regions on trifoliate orange chromosomes 6, 7, 8 and 9. These regions contain 20 genes known to be responsive to HLB. The transcription factor WRKY70 that was upregulated in HLB-diseased sweet orange, is positively selected in trifoliate orange. One of these genomic regions on chromosome 6 contained one CC-NBS gene, and one genomic region on chromosome 9 that explained major phenotypic variance for HLB tolerance contained 10 NBS genes (3 NBS, 1 CC-NBS and 6 TIR-NBS). Trifoliate orange has tolerance to extreme cold temperatures, able to survive -26°C. Sixty-nine and 119 trifoliate orange genes are homologous to Arabidopsis cold signaling pathway genes and 'first-wave' transcription factor genes or CBF regulon genes, respectively. Among them, LOW-TEMPERATURE-INDUCED 65 ( LTI65 ), COR413 - PM1 , and hybrid proline-rich protein ( PRP ) were positively selected in trifoliate orange and other cold-tolerant citrus. These genes may play critically important roles in trifoliate orange's cold tolerance.