GAMETE maps the genetic architecture of chromatin accessibility in rice pollen at single-nucleus resolution.
5 affiliations
- 1National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
- 2Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430000, China.
- 3College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430000, China.
- 4National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China. [email protected].
- 5Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430000, China. [email protected].
Abstract
Background
Dissecting the genetic basis of cell-type-specific gene regulation during gametogenesis remains a major challenge. Population-level studies mask cellular heterogeneity, while the extreme data sparsity of single-cell profiling precludes robust genetic mapping.Results
We present GAMETE (Genetic Architecture Mapping of Epigenetic Traits at single-nucleus resolution), an integrated framework combining MPS-ATAC-seq, a high-throughput single-nucleus ATAC-seq method, with robust computational approaches for genotype inference and genetic mapping from sparse single-nucleus data. Applying GAMETE to hybrid rice pollen, we simultaneously profile chromatin accessibility and infer the genotypes of 4,887 individual haploid nuclei, revealing distinct chromatin landscapes across pollen cell types. This uncovers an unexpected elevation of chromatin accessibility at gypsy retrotransposons in microspores preceding their silencing in sperm cells, exposing a surveillance gap that may contribute to genome expansion. The synchronized profiling enables us to construct a single-cell recombination map, map segregation distortion loci and trace their developmental origins, and identify 16,113 chromatin accessibility QTLs (caQTLs), 48.6% of which exhibit pronounced cell-type specificity. Analysis of introgression lines supports a cell-type-specific trans-acting caQTL regulating the pollen-essential gene DTM1.Conclusions
This work establishes GAMETE as a broadly applicable framework for dissecting the genetic architecture of chromatin accessibility during gametogenesis without the need for subsequent generations.
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BibTeX
@article{liu2026gamete,
title = {{GAMETE maps the genetic architecture of chromatin accessibility in rice pollen at single-nucleus resolution.}},
author = {Yinmeng Liu and Chunjiao Xia and Junjie Li and Jiacheng Li and Haichuan Yang and Zhanxiang Zong and Luchang Ming and Junjiao Yang and Hantong Lian and Meng Luo and Tao Zhu and Xiaogang He and Yongzhong Xing and Sibin Yu and Yidan Ouyang and Weibo Xie},
journal = {Genome biology},
year = {2026},
month = aug,
doi = {10.1186/s13059-026-04226-4},
url = {https://europepmc.org/article/MED/42972586},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - GAMETE maps the genetic architecture of chromatin accessibility in rice pollen at single-nucleus resolution.
AU - Yinmeng Liu
AU - Chunjiao Xia
AU - Junjie Li
AU - Jiacheng Li
AU - Haichuan Yang
AU - Zhanxiang Zong
AU - Luchang Ming
AU - Junjiao Yang
AU - Hantong Lian
AU - Meng Luo
AU - Tao Zhu
AU - Xiaogang He
AU - Yongzhong Xing
AU - Sibin Yu
AU - Yidan Ouyang
AU - Weibo Xie
PY - 2026
DA - 2026/08/04
JO - Genome biology
DO - 10.1186/s13059-026-04226-4
UR - https://europepmc.org/article/MED/42972586
AB - Background Dissecting the genetic basis of cell-type-specific gene regulation during gametogenesis remains a major challenge. Population-level studies mask cellular heterogeneity, while the extreme data sparsity of single-cell profiling precludes robust genetic mapping.Results We present GAMETE (Genetic Architecture Mapping of Epigenetic Traits at single-nucleus resolution), an integrated framework combining MPS-ATAC-seq, a high-throughput single-nucleus ATAC-seq method, with robust computational approaches for genotype inference and genetic mapping from sparse single-nucleus data. Applying GAMETE to hybrid rice pollen, we simultaneously profile chromatin accessibility and infer the genotypes of 4,887 individual haploid nuclei, revealing distinct chromatin landscapes across pollen cell types. This uncovers an unexpected elevation of chromatin accessibility at gypsy retrotransposons in microspores preceding their silencing in sperm cells, exposing a surveillance gap that may contribute to genome expansion. The synchronized profiling enables us to construct a single-cell recombination map, map segregation distortion loci and trace their developmental origins, and identify 16,113 chromatin accessibility QTLs (caQTLs), 48.6% of which exhibit pronounced cell-type specificity. Analysis of introgression lines supports a cell-type-specific trans-acting caQTL regulating the pollen-essential gene DTM1.Conclusions This work establishes GAMETE as a broadly applicable framework for dissecting the genetic architecture of chromatin accessibility during gametogenesis without the need for subsequent generations.
SN - 1474-7596
SN - 1474-760X
ER -