Skip to main content
ARS Home » Pacific West Area » Riverside, California » National Clonal Germplasm Repository for Citrus » Research » Publications at this Location » Publication #390868
Research Project: Conservation, Management and Distribution of Citrus and Date Genetic Resources and Associated Information

Location: National Clonal Germplasm Repository for Citrus

Title: Pangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in citric fruits

Author
item HUANG, YUE - Huazhong Agricultural University
item HE, JIAXIAN - Huazhong Agricultural University
item XU, YUANTAO - Huazhong Agricultural University
item ZHENG, WEIKANG - Huazhong Agricultural University
item WANG, SHAOHUA - Yunnan Academy Of Agriculture Sciences
item CHEN, PENG - Hunan Academy Of Agricultural Sciences
item ZHENG, B - Hunan Academy Of Agricultural Sciences
item YANG, S - Hunan Academy Of Agricultural Sciences
item JIANG, XIAOLIN - Huazhong Agricultural University
item LIU, ZISHUANG - Huazhong Agricultural University
item WANG, LUN - Huazhong Agricultural University
item WANG, XIA - Huazhong Agricultural University
item LIU, SHENJUN - Huazhong Agricultural University
item LU, ZHIHAO - Huazhong Agricultural University
item LIU, ZHIANG - Huazhong Agricultural University
item YU, HUIWEN - Huazhong Agricultural University
item ZHANG, YIN - Huazhong Agricultural University
item YUE, JIANQIANG - Yunnan Academy Of Agriculture Sciences
item GAO, J - Yunnan Academy Of Agriculture Sciences
item ZHOU, XIANYAN - Yunnan Academy Of Agriculture Sciences
item LONG, CHUNRUI - Yunnan Academy Of Agriculture Sciences
item ZENG, XIULI - Qinghai University
item GUO, YONG-JIE - Kunming Institute Of Botany
item ZHANG, WEN-FU - Chinese Academy Of Sciences
item XIE, ZONGZHOU - Huazhong Agricultural University
item LI, CHUNLONG - Huazhong Agricultural University
item MA, ZHAOCHENG - Huazhong Agricultural University
item JIAO, WENBIAO - Huazhong Agricultural University
item ZHANG, FEI - Huazhong Agricultural University
item LARKIN, ROBERT - Huazhong Agricultural University
item Krueger, Robert
item SMITH, MALCOLM - Department Of Agriculture And Fisheries
item MING, RAY - University Of Illinois
item DENG, X - Huazhong Agricultural University
item XU, QIANG - Huazhong Agricultural University

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/28/2023
Publication Date: 10/2/2023
Citation: Huang, Y., He, J., Xu, Y., Zheng, W., Wang, S., Chen, P., Zheng, B., Yang, S., Jiang, X., Liu, Z., Wang, L., Wang, X., Liu, S., Lu, Z., Liu, Z., Yu, H., Zhang, Y., Yue, J., Gao, J., Zhou, X., Long, C., Zeng, X., Guo, Y., Zhang, W., Xie, Z., Li, C., Ma, Z., Jiao, W., Zhang, F., Larkin, R.M., Krueger, R., Smith, M., Ming, R., Deng, X., Xu, Q. 2023. Pangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in citric fruits. Nature Genetics. 55:1964-1975. https://doi.org/10.1038/s41588-023-01516-6.
DOI: https://doi.org/10.1038/s41588-023-01516-6

Interpretive Summary: The flavor of citrus fruits is determined by sugars, acids, and secondary compounds. In this study, 302 citrus accessions acquired from global resources were sequenced, in addition to 16 species in the orange subfamily (Aurantioideae) of the Rutaceae. Genome size variation and gene expression was influenced by long terminal repeat sequences. In citrus fruits, citric acid is a major determinant of acidity and naringin (a secondary compound) is a major determinant of bitterness. Both were present in high concentrations in wild Citrus, at lower concentrations in cultivated citrus, and were barely detectable in related non-Citrus genera. This study also identified regulators of the genes associated with the production of citric acid and naringin.

Technical Abstract: Citrus fruits contain abundant metabolites that contribute to diversified tastes, with acidity and bitterness being major factors. Here, we compiled genome sequences of 302 worldwide accessions, and de novo assembled the genomes of 16 species in the orange subfamily. We constructed a pan-genome and identified solo LTRs as considerable contributors to genome size variation and expression levels of their neighboring genes. We revealed that citric acid and naringin, which determine fruit acidity and bitterness, were barely detectable in Citrus -related genera, but were at high levels in wild Citrus and to reduced levels in cultivated Citrus . We identified the MYB-domain transcription factor PH4 as a regulator of both naringin and citric acid accumulation in citrus fruits, and mutations of PH4 and their target genes associated with the evolution of fruit taste. This study provides insights into the evolution of orange subfamily and the regulatory mechanisms behind fruit taste.