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ARS Home » Pacific West Area » Hilo, Hawaii » Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center » Tropical Plant Genetic Resources and Disease Research » Research » Publications at this Location » Publication #423170
Research Project: Conservation, Management, and Genetic Improvement of Tropical and Subtropical Fruit, Nut, and Beverage Crop Germplasm for the Pacific Region

Location: Tropical Plant Genetic Resources and Disease Research

Title: Recreating viable YYh genotype uncovers the role of CpYYL underlying YY lethality in papaya

Author
item YUE, JINGJING - Fujian Agriculture And Forest University
item LIU, JUAN - Wuhan Botanical Garden
item ZANG, QIUXIA - Fujian Agricultural & Forestry University
item WAI, CHING MAN - Michigan State University
item DENG, BAN - Fujian Agricultural & Forestry University
item TONG, YIHAN - Fujian Agricultural & Forestry University
item ZUO, LIPING - Fujian Agricultural & Forestry University
item XIANG, TAO - Fujian Agricultural & Forestry University
item XIE, WANGYANG - Fujian Agricultural & Forestry University
item ZHAO, XIAOBING - Fujian Agricultural & Forestry University
item LAI, JUAN - Fujian Agricultural & Forestry University
item LIAO, JINGJIN - Fujian Agricultural & Forestry University
item LAI, QINGQING - Fujian Agricultural & Forestry University
item XU, LIANGWEI - Fujian Agricultural & Forestry University
item ZHU, YATING - Fujian Agricultural & Forestry University
item HE, JUAN - Fujian Agricultural & Forestry University
item ZHANG, MINGJING - Fujian Agricultural & Forestry University
item NIE, SUYUE - Fujian Agricultural & Forestry University
item LIN, ZENG - Fujian Agricultural & Forestry University
item LIANG, YANQING - Fujian Agricultural & Forestry University
item JIANG, SHAOLIAN - Fujian Agricultural & Forestry University
item CHEN, XI - Fujian Agricultural & Forestry University
item WANG, BOWEI - Fujian Agriculture And Forest University
item HUANG, YONGJI - Minjiang University
item XU, YI - Guangxi University
item NGUYEN, JULIE - University Of Illinois
item MA, YAYING - Fujian Agricultural & Forestry University
item FUMIA, NATHAN - Hawaii Agriculture Research Center
item JONES, TYLER - Hawaii Agriculture Research Center
item QUESADA-ROJAS, PATRICIA - Universidad De Costa Rica
item MORA-NEWCOMER, ERIC - Universidad De Costa Rica
item ZHANG, JISEN - Fujian Agricultural & Forestry University
item Yu, Qingyi
item WANG, MING-LI - Hawaii Agriculture Research Center
item MING, RAY - University Of Illinois

Submitted to: Nature Communications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/12/2026
Publication Date: 1/24/2026
Citation: Yue, J., Liu, J., Zeng, Q., Wai, C.M., Deng, B., Tong, Y., Zuo, L., Xiang, T., Xie, W., Zhao, X., Lai, J., Liao, J., Lai, Q., Xu, L., Zhu, Y., He, J., Zhang, M., Nie, S., Lin, Z., Liang, Y., Jiang, S., Chen, X., Wang, B., Huang, Y., Xu, Y., Nguyen-Edquilang, J., Ma, Y., Fumia, N., Jones, T., Quesada-Rojas, P., Mora-Newcomer, E., Zhang, J., Yu, Q., Wang, M., Ming, R. 2026. Recreating viable YYh genotype uncovers the role of CpYYL underlying YY lethality in papaya. 17,1999.Nature Communications. https://doi.org/10.1038/s41467-026-68627-6.
DOI: https://doi.org/10.1038/s41467-026-68627-6

Interpretive Summary: One of the major problems for papaya production is the segregation of sex types. Classical genetic analyses led to the hypothesis of five factors in the sex determination region, Mp, male peduncle; l, zygotic lethal (YY lethality); sa, suppressor of the androecium; sg, suppressor of the gynoecium; and C, hypothetical factor for recombination suppression in the sex determining region. In this study, we identified two of the four genes, Mp and l, and named them CpMp-h and CpYYL, respectively. Loss of CpYYL function impaired starch and sucrose metabolism in papaya embryo, causing embryo abortion. The zygotic lethal function of CpYYL was confirmed by genetic transformation and comparative genomic analysis. We identified a retrotransposon insertion in the promoter region of CpMp in hermaphrodite allele. The retrotransposon insertion in the promotor of CpMp-h caused higher methylation in CpMp-h, leading to the reversion of long male peduncles to short hermaphrodite peduncles. Viable YYh and YhYh genotypes created in this study provided an unprecedented and rapid approach to solve the most pressing issue in papaya improvement - breeding hermaphrodite cultivars with no segregation of sex types.

Technical Abstract: Papaya is a trioecious species with XX females, XY males, and XYh hermaphrodites. Any combination of Y and Yh chromosomes is lethal. The gene underlying YY lethality is pivotal in the transition from stage 2 to stage 3 in sex chromosome evolution. Here, we identify and functionally validate the YY lethality gene in papaya, CpYYL. Loss of CpYYL function accelerates glycolysis and reduces sucrose accumulation in embryo, causing embryo abortion. CpYYL interacts with CpAKRP and overexpression of both genes partially rescues seed abortion in the heterozygous emb506 and akrp mutants, indicating conserved role in plastid differentiation and embryo development. Viable YYh and YhYh plants are generated through genetic engineering and crossing, although both genotypes show high seedling mortality. Crossing YYh male with XX female papaya shows 1:1 ratio of male to hermaphrodite plants without recombination between MSY and HSY. Identification of CpYYL fills a critical gap in papaya sex chromosome evolution, and provides new resources for genomic and epigenetic studies.