CgABR1‐CgFAD negatively regulates the fruit neck length in citrus

Summary Pummelo ( Citrus maxima ) is a fundamental species of Citrus which contributes to most of the cultivated citrus, including sweet orange, lemon and etc. The fruit neck is a structural feature of pummelo, and a long fruit neck reduces the edible rate of the fruit. In this study, we assembled a telomere‐to‐telomere (T2T) gap‐free reference genome for the typical short fruit neck cultivar, ‘Pingshan’ pummelo, and a chromosome‐level genome for the typical long fruit neck cultivar, ‘Shatian’ pummelo. Here, we used a segment population derived from a cross between a long fruit neck cultivar (‘Guanxi’ pummelo) and a short fruit neck (‘Pingshan’ pummelo) cultivar to map the determinant controlling the fruit neck length. We identified a strong peak on chromosome 1 within the 27.5–30.5 Mb physical region and found a 52 bp deletion linked with the fruit neck length. Moreover, by combining RNA sequencing data of the fruit neck development and variation analysis, we identified two genes, one encodes ethylene‐responsive transcription factor ( CgABR1 ) and the other encodes FAD‐dependent urate hydroxylase ( CgFAD ). Genetic transformation confirmed that overexpression of CgABR1 and CgFAD can inhibit fruit neck length. DNA affinity purification sequencing, electrophoretic mobility shift assays and dual‐LUC reporter assays demonstrated that CgABR1 can activate the expression of CgFAD by directly binding to its promoter. In summary, we assembled a T2T gap‐free genome for pummelo and identified the key genes for fruit neck length in citrus, offering an important resource and new genes for citrus genetic improvement and breeding programs.