科技科学

Uncovering the mechanism of female restitution in sugarcane hybrids

Nature作者：Sihui Zhu2026年8月5日正文已收录本站

Data availability

The genome assemblies and corresponding gene annotation results, raw sequencing datasets of US56-14-4, 10-9201, 10-9208 and the other six F1 hybrids have been deposited at the Genome Sequence Archive (GSA) database71 in the National Genomics Data Center, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences and China National Center for Bioinformation (CNCB), under accession numbers PRJCA032574 (CRA020620 and CRA022922). The LA Purple genome is available from CNCB Genome Warehouse under accession GWHHOJF00000000.1. The raw sequencing fastq data of LA Purple are available from CNCB BioProject accession PRJCA039904.

Code availability

The code of an algorithm KLASSIFY that classify chimeric reads and identify breakpoints is available on GitHub https://github.com/tanghaibao/klassify (including full simulation and evaluation scripts with exact parameters, random seeds and example commands) and the code is archived on Zenodo at https://doi.org/10.5281/zenodo.20838810 (v0.1.6)72.

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Acknowledgements

We thank A. Paterson for restructuring and revising the manuscript.

Funding

This project was supported by the National Key Research and Development Program of China (2023YFD1200700, 2023YFD1200701) to R.M., (2024YFF1000800) to H. Tang and R.M., and the National Natural Science Foundation of China (W2531027) to R.M.

Author information

Author notes

  1. These authors contributed equally: Sihui Zhu, Haibao Tang

Authors and Affiliations

  1. Center for Genomics and Biotechnology, National Engineering Research Center of Sugarcane, Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Provincial Key Laboratory of Haixia Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China

    Sihui Zhu, Haibao Tang, Jing Zhou, Lingmin Cai, Wen Wang, Yanhong Zhou, Haoming Mao, Liping Zuo, Yutong Zheng, Yixing Zhang, Zhaoqian Ji, Huanhuan Tao, Jianling Pan, Yating Xu, Huiru Chen & Ray Ming

  2. Hawaii Agriculture Research Center, Kunia, HI, USA

    Tyler Jones, Nathan Fumia & Chifumi Nagai

Authors

  1. Sihui Zhu
  2. Haibao Tang
  3. Tyler Jones
  4. Nathan Fumia
  5. Jing Zhou
  6. Lingmin Cai
  7. Wen Wang
  8. Yanhong Zhou
  9. Haoming Mao
  10. Liping Zuo
  11. Yutong Zheng
  12. Yixing Zhang
  13. Zhaoqian Ji
  14. Huanhuan Tao
  15. Jianling Pan
  16. Yating Xu
  17. Huiru Chen
  18. Chifumi Nagai
  19. Ray Ming

Contributions

R.M. conceived the project and coordinated research activities. R.M. and C.N. designed the crosses and C.N. and T.J. performed the hybridization experiments. C.N., T.J. and N.F. conducted field trials and maintained plant materials. J.Z. and S.Z. collected the plant materials for sequencing. S.Z. assembled and annotated all the genomes. H. Tang developed the new tool to identify recombination breakpoints. Y. Zhou counted the chromosome number of the F1. Y. Zhang assisted with genomic analyses. R.M., H. Tang, S.Z., H.M., W.W., L.C., L.Z., Y. Zheng, Z.J., J.P., H. Tao, Y.X. and H.C. manually checked the chromosomal breakpoints results. S.Z. conducted the comparative genomic analyses between the F1 and parents. R.M., S.Z. and H. Tang wrote the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Ray Ming.

Ethics declarations

Competing interests

The authors declare no competing interests.

Peer review

Peer review information

Nature thanks André Marques who co-reviewed with Meng Zhang; and the other, anonymous reviewers for their contribution to the peer review of this work. Peer reviewer reports are available.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data figures and tables

Extended Data Fig. 1 SDR-mediated recombinant chromosome formation.

Assuming the second division restitution occurred in LA Purple, for a pair of homologous chromosomes, Chr1A and Chr1B, after normal first division and abnormal second division, the products would include a new recombinant chromosome and a non-recombinant chromosome identical to LA Purple. In the sequencing data of offspring, reads supporting both chromosomal structures around the crossover point are excepted. For example, two types of reads span the Chr1A breakpoint: one is recombinant reads, and other one is non-recombinant reads. Since no intact Chr1B exists in the offspring, only one type of reads can be aligned back to the Chr1B breakpoint. We define the breakpoints of Chr1A and Chr1B as “Type II” and “Type I” points, respectively. The Type I and Type II will always appear in pairs, and the number of pairs reflects the crossover events.

Extended Data Fig. 2 An actual IGV screenshot display of breakpoint in 9208 So-subgenome.

The breakpoint in So (S. officinarum) gametes, where it contains a Type I breakpoint paired with a Type II breakpoint between SoChr01B and SoChr01F.

Extended Data Fig. 3 The distribution of Type I and Type II breakpoints on Chr01 revealed by re-sequencing data of 8 F1s with female parent LA Purple as control.

The panel from top to bottom shows the depth profiles of LA Purple (So) Chr01A-H chromosomes using HiFi datasets from LA Purple and 8 F1 individuals. The blue and red vertical bars mark the location of Type I and Type II breakpoints identified by KLASSIFY, respectively. Type II breakpoints are exclusive to the So genome, while Type I can be observed in both So and Ss genomes. The gray hatched regions indicate the predicted centromeres.

Extended Data Fig. 4 An actual IGV screenshot display of breakpoint in 9208 Ss-subgenome.

The example breakpoint in Ss (S. spontaneum) gametes, where it contains a Type I breakpoint paired with another Type I breakpoint between SsChr04D and SsChr04G.

Extended Data Fig. 5 The distribution of Type I breakpoints on Chr01 revealed by re-sequencing data of 8 F1s with male parent US56-14-4 as control.

The top panel shows Chr01A-I chromosomes of US56-14-4 (Ss). Clear 0: 1: 2 and 0: 0.5: 1 depth ratio pattern are observed in the two sets of parental chromosomes, indicating distinct chromosomal composition in the gametes produced by female and male parents. The blue vertical bars mark the location of identified type I breakpoints, respectively. The type II breakpoints only appear in So chromosome. The gray regions indicate the predicted centromeres. Chr01E in US56-14-4 is a collapsed chromosome with a 2x of average depth. The regions of 0.5x depth in Ss-subgenome of F1s can be attributed to the collapsed chromosomal fragments as described in Table S2 and Fig. S6.

Extended Data Table 1 Reads binning of eight F1 individuals using parent-specific k-mers from LA Purple and US56-14-4

Full size table

Extended Data Table 2 Number of Type I and Type II breakpoints in eight F1 genomes derived from LA Purple × US56-14-4 cross

Full size table

Supplementary information

Supplementary Information (download DOCX )

This file contains Supplementary Notes, Supplementary Figs. 1-15 and Supplementary Fig. 25, and Supplementary References.

Reporting Summary (download PDF )

Supplementary Fig. 16 (download PDF )

Distribution of genomic features across the 80 chromosomes of US56-14-4. Centromeric and telomeric regions were predicted by quartet. The density of DNA transposons, LINEs, SINEs, and satellites elements were calculated using a window size of 500 kb, and visualized using Rectchr v1.34 (https://github.com/hewm2008/RectChr).

Supplementary Fig. 17 (download PDF )

Distribution of genomic features across the 79 S. officinarum-derived chromosomes of 10-9208. The density of DNA transposons, LINEs, SINEs, and Gypsy, Copia elements are calculated using window size of 500-kb.

Supplementary Fig. 18 (download PDF )

Distribution of genomic features across the 39 S. spontaneum-derived chromosomes of 10-9208. The density of DNA transposons, LINEs, SINEs, and Gypsy, Copia elements are calculated using window size of 500-kb.

Supplementary Fig. 19 (download PDF )

Distribution of genomic features across the 77 S. officinarum-derived chromosomes of 10-9201. The density of DNA transposons, LINEs, SINEs, and Gypsy, Copia elements are calculated using window size of 500-kb.

Supplementary Fig. 20 (download PDF )

Distribution of genomic features across the 40 S. spontaneum-derived chromosomes of 10-9201. The density of DNA transposons, LINEs, SINEs, and Gypsy, Copia elements are calculated using window size of 500-kb.

Supplementary Fig. 21 (download PDF )

The schematic diagrams of all the S. officinarum-derived chromosomes of 10-9208 reveal the recombination relationships of maternal chromosomes, conforming to the role of SDR in gametogenesis in LA Purple. In the subplots (a), (c), (e), (g), (i), (k), (m), (o), and (q), the upper-left panel shows the 8 homologous chromosomes of LA Purple, whereas the bottom-left panel depicts the resultant chromosomes resulting from parental chromosomes recombination, along with the chromosomes not involved in fragments exchange. The vertical axis (from bottom to top) denotes the start and end coordinates of linear genomic sequences. The offspring chromosome IDs, labelled at the top of each ideogram, are named based on the composition and order of parental fragments, which was inferred from the DNA alignment results. Two parallel black lines next to the chromosome ideogram denote twice the average sequencing depth, while a single black line indicates the average depth. The subplots (b), (d), (f), (h), (j), (l), (n), (p) and (r) described the sequencing coverage of LA Purple genome using the HiFi reads of 10-9208.

Supplementary Fig. 22 (download PDF )

The schematic diagrams of all the S. officinarum-derived chromosomes of 10-9201 reveal the recombination relationships of maternal chromosomes. In every subplot, the top panel illustrates the 8 parental homologous chromosomes, whereas the bottom panel depicts the resultant chromosomes resulting from parental chromosomes recombination, along with the chromosomes not involved in fragments exchange. The vertical axis (from bottom to top) denotes the start and end coordinates of linear genomic sequences. The offspring chromosome IDs, labelled at the top of each ideogram, are named based on the composition and order of parental fragments, which was inferred from the DNA alignment results. Two parallel black lines next to the chromosome ideogram denote twice the average sequencing depth, while a single black line indicates the average depth. The asterisk indicates that the breakpoints can be supported by both the KLASSIFY algorithm and collinearity-based method.

Supplementary Fig. 23 (download PDF )

The schematic diagrams of all the S. spontaneum-derived chromosomes of 10-9208 reveal the recombination relationships of paternal chromosomes. In every subplot, the top panel represents 10 parental homologous chromosomes, while the bottom panel depicts the crossover region resulting from two parental chromosomes recombination and the chromosomes not involved in fragments exchange. The direction from bottom to top is the starting and ending points of linear sequences in the genome. The chromosome ID of offspring were named at the top of each chromosome ideogram based on the composition and order of parental fragments. The right panel shows the sequencing depth profile of US56-14-4 using binned S. spontaneum-derived HiFi reads of 10-9208. The dash lines mark the collapsed regions in the US56-14-4 assembly. The reads were randomly assigned to one of the two identical regions by aligner tools (minimap2 used in this study), thereby resulting in a sequencing depth half of the whole-genome average. But only one of the two copies was truly passed down to F1s, just like the other regions marked by solid lines.

Supplementary Fig. 24 (download PDF )

The schematic diagrams of all the S. spontaneum-derived chromosomes of 10-9201 reveal the recombination relationships of paternal chromosomes. In every subplot, the top panel represents 10 parental homologous chromosomes, while the bottom panel depicts the crossover region resulting from two parental chromosomes recombination and the chromosomes not involved in fragments exchange. The direction from bottom to top is the starting and ending points of linear sequences in the genome. The chromosome ID of offspring were named at the top of each chromosome ideogram based on the composition and order of parental fragments. The right panel shows the sequencing depth profile of US56-14-4 using binned S. spontaneum-derived HiFi reads of 10-9201. The dash lines mark the collapsed regions in the US56-14-4 assembly. The reads were randomly assigned to one of the two identical regions by aligner tools (minimap2 used in this study), thereby resulting in a sequencing depth half of the whole-genome average. But only one of the two copies was truly passed down to F1, just like the other regions marked by solid lines.

Supplementary Fig. 26 (download PDF )

Sequencing depth and breakpoints distribution plot of eight F1s on the two parental genomes (LA Purple and US56-14-4). The HiFi reads of 8 F1s were mapped to the merged parental genome using minimap25. Subplots (a) - (i) show 9 groups of S. officinarum chromosomes, while the rest are S. spontaneum chromosomes. We can see clear 0: 1: 2 and 0: 0.5: 1 depth patterns in two sets of parental data, which implies the gametes produced by the female and male parents are different. The blue and red vertical bars mark the location of identified type I and type II breakpoints, respectively. The type II breakpoints only appear in S. officinarum chromosomes. The gray hatched regions indicate the predicted centromeres.

Supplementary Fig. 27 (download PDF )

A complete demonstration of a Type II breakpoint. Fine-scale ‘zoom-in’ breakpoint sequences of this example region. The sequences with yellow and blue-coloured ID are intercepted from SoChr01B and SoChr01F flanking the breakpoints; the purple and green ones are recombinant and non-recombinant reads respectively; the brown one is intercepted from recombinant chromosome SoChr01FB in offspring 10-9208. The asterisks below each alignment denote sequence conservation. The area marked in grey between two polymorphic sites delineates the crossover boundary. Since no sequence variation exists between two parental chromosomes in this interval, DNA breakage and crossover event can occur at any coordinate. Upstream of the left boundary, all the reads match SoChr01B; downstream of the right boundary, the recombinant reads switch to match SoChr01F, while the non-recombinant reads remain consistent with SoChr01B.

Supplementary Tables (download XLSX )

This file contains Supplementary Tables 1-20.

Peer Review File (download PDF )

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Zhu, S., Tang, H., Jones, T. et al. Uncovering the mechanism of female restitution in sugarcane hybrids. Nature (2026). https://doi.org/10.1038/s41586-026-10863-3

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