New gene identified that dramatically boosts papaya productivity
image: The papaya cultivar Zihui with high quality and high yield. A. The whole plant morphology of ‘Zihui’ papaya. B. ‘Zihui’ has yellow flowers. C. inflorescence and flower quantity. D. Mature papaya fruit. E. The inner cavity and flesh thickness of papaya fruit, (left) common papaya cultivar, (right) ‘Zihui’ papaya. F. The fruit shoulder of ‘Zihui’ papaya. Image link: https://academic.oup.com/view-large/figure/511947455/uhaf045f1.tif?login=false
Credit: Horticulture Research
Papaya is a key tropical fruit crop valued for its nutrition, versatility, and global economic importance. However, domestication has narrowed its genetic diversity, limiting improvement in important agronomic traits such as disease resistance, fruit quality, and yield. Traditional breeding has been further challenged by limited knowledge of the genomic variation within cultivated and wild germplasm. Recent advances in sequencing and pangenome analysis now allow breeders to more precisely characterize gene presence/absence variation and selection signatures. Due to these genetic bottlenecks and trait complexity, there is a need to systematically dissect the genomic diversity and yield-related variations in papaya to guide future breeding efforts.
Researchers from the Guangdong Academy of Agricultural Sciences and collaborating institutions have published (DOI: 10.1093/hr/uhaf045) a comprehensive genomic study of papaya in Horticulture Research on February 17, 2025. The team assembled a chromosome-level genome of the high-yield cultivar ‘Zihui’ and analyzed 201 papaya accessions to reveal domestication history and identify yield-related genes. Their study highlights Cp_zihui06549 and Cp_zihui06768 as key contributors to increased fruit production, providing valuable insights for breeding high-yield papaya varieties.
The researchers generated a 344.17 Mb genome assembly for the ‘Zihui’ cultivar and identified 22,250 protein-coding genes, including 283 genes specific to this variety. Population resequencing of 201 accessions revealed four major papaya groups and highlighted genomic regions under strong domestication selection. A genome-wide association study identified significant SNPs in promoter regions of Cp_zihui06549 and Cp_zihui06768, correlating strongly with increased fruit number and total yield. Functional assays confirmed that overexpression of Cp_zihui06549 in tomato more than doubled the number of fruits per plant, with minimal change in individual fruit size, thereby substantially boosting total productivity. Additionally, the team constructed the first pan-genome of papaya, identifying 1,543 nonreference genes and revealing gene loss events affecting terpene synthase pathways that may have reduced disease resistance during domestication. Together, these results provide a detailed map of genetic variation shaping yield traits and highlight specific gene targets for trait improvement.
"Our findings offer a new understanding of how domestication has shaped papaya productivity at the genomic level," said the study’s corresponding authors. "The identification and validation of Cp_zihui06549 as a positive regulator of fruit yield is especially exciting. It not only clarifies the biological basis underlying high-yield phenotypes, but also provides a practical gene target for future crop improvement strategies."
This study provides actionable genetic targets for breeding high-yield papaya varieties and establishes a foundation for molecular-assisted selection. By linking gene-level variation with agronomic performance, breeders can efficiently introduce beneficial alleles such as Cp_zihui06549 into existing cultivars. The pan-genome also highlights lost resistance-related genes, guiding efforts to restore or reintroduce disease resilience traits. Beyond papaya, the integrated genomic strategy used here can be applied to other fruit crops with narrow genetic bases, accelerating the development of resilient, high-yielding cultivars optimized for future climate and production demands.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhaf045
Funding information
This work was supported by the ‘Young and Middle-aged Academic Leaders’ Training Fund Project of Guangdong Academy of Agricultural Sciences (Grant no. R2023PY-JX005), the Guangdong Basic and Applied Basic Research Foundation (Grant no. 2022A1515010697), the Cultivation Project of Fruit Tree Research Institute, Guangdong Academy of Agricultural Sciences (Grant no. 23107), and the Guangzhou Science and Technology Planning Project (Grant no. 2023B03J1369).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.