{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,29]],"date-time":"2026-08-29T05:18:28Z","timestamp":1787980708837,"version":"build-2784847793"},"reference-count":59,"publisher":"MDPI AG","issue":"17","license":[{"start":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T00:00:00Z","timestamp":1787788800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Key Research and Development Program of China","award":["2022YFD1200703"],"award-info":[{"award-number":["2022YFD1200703"]}]},{"DOI":"10.13039\/501100007162","name":"2024 East, West and North Guangdong Talent Development Assistance Program","doi-asserted-by":"publisher","award":["CARS-01-07"],"award-info":[{"award-number":["CARS-01-07"]}],"id":[{"id":"10.13039\/501100007162","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004493","name":"International Atomic Energy Agency Coordinated Research Project","doi-asserted-by":"publisher","award":["D24015"],"award-info":[{"award-number":["D24015"]}],"id":[{"id":"10.13039\/501100004493","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Plants"],"abstract":"<jats:p>Global food security is facing challenges from population growth to diminishing arable land. Space mutation breeding holds promise for overcoming the variation limitations in conventional breeding; however, the mutagenic effects of the deep-space environment on rice and the transgenerational inheritance patterns of induced variations remain unclear. In this study, rice seeds carried by the Chang\u2019e-5 spacecraft were used as materials. Whole-genome sequencing and whole-genome bisulfite sequencing were performed on the first (SP1) and second generations (SP2) of space-mutagenized plants after their return to Earth. The results showed that the number of genomic variants in the SP2 generation increased significantly compared with SP1, and SNPs, homozygous sites, and variants in coding regions were more heritable. The genome-wide methylation level was elevated in the SP2 generation, and among differentially methylated cytosines, those in the CG context exhibited the highest heritability. Furthermore, large-scale screening for nitrogen efficiency, tolerance to PEG-induced stress, and germination-stage cold resistant mutants was conducted in the SP2 generation, and phenotypic validation was performed in the third generation (SP3). By integrating multi-omics analyses of representative mutants to mine candidate genes, a number of heritable elite mutants were obtained, and seven candidate genes for key traits were identified. This study systematically elucidates the transgenerational inheritance patterns of deep-space-induced variation in rice. The multi-trait mutants obtained provide valuable germplasm resources for gene cloning and breeding applications in rice.<\/jats:p>","DOI":"10.3390\/plants15172614","type":"journal-article","created":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T08:02:27Z","timestamp":1787817747000},"page":"2614","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genetic Analysis of Genomic and Methylomic Variation and Identification of Multi-Trait Mutants in Rice Carried on Chang\u2019e-5"],"prefix":"10.3390","volume":"15","author":[{"given":"Kai","family":"Sun","sequence":"first","affiliation":[{"name":"National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinrui","family":"Li","sequence":"additional","affiliation":[{"name":"National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China"},{"name":"College of Agriculture, South China Agricultural University, Guangzhou 510642, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhe","family":"Zhao","sequence":"additional","affiliation":[{"name":"National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China"},{"name":"College of Agriculture, South China Agricultural University, Guangzhou 510642, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shiyi","family":"Chen","sequence":"additional","affiliation":[{"name":"National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China"},{"name":"College of Agriculture, South China Agricultural University, Guangzhou 510642, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuanyuan","family":"Guo","sequence":"additional","affiliation":[{"name":"National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China"},{"name":"College of Agriculture, South China Agricultural University, Guangzhou 510642, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ying","family":"Ling","sequence":"additional","affiliation":[{"name":"National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China"},{"name":"College of Agriculture, South China Agricultural University, Guangzhou 510642, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongfen","family":"Wang","sequence":"additional","affiliation":[{"name":"National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China"},{"name":"College of Agriculture, South China Agricultural University, Guangzhou 510642, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhikai","family":"Han","sequence":"additional","affiliation":[{"name":"National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China"},{"name":"College of Agriculture, South China Agricultural University, Guangzhou 510642, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zengtong","family":"Luo","sequence":"additional","affiliation":[{"name":"National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China"},{"name":"College of Agriculture, South China Agricultural University, Guangzhou 510642, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wuming","family":"Xiao","sequence":"additional","affiliation":[{"name":"National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China"},{"name":"College of Agriculture, South China Agricultural University, Guangzhou 510642, China"},{"name":"Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, South China Agricultural University, Guangzhou 510642, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiafeng","family":"Wang","sequence":"additional","affiliation":[{"name":"National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China"},{"name":"College of Agriculture, South China Agricultural University, Guangzhou 510642, China"},{"name":"Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, South China Agricultural University, Guangzhou 510642, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guili","family":"Yang","sequence":"additional","affiliation":[{"name":"National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China"},{"name":"College of Agriculture, South China Agricultural University, Guangzhou 510642, China"},{"name":"Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, South China Agricultural University, Guangzhou 510642, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongzhu","family":"Liu","sequence":"additional","affiliation":[{"name":"National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China"},{"name":"College of Agriculture, South China Agricultural University, Guangzhou 510642, China"},{"name":"Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, South China Agricultural University, Guangzhou 510642, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tao","family":"Guo","sequence":"additional","affiliation":[{"name":"National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China"},{"name":"College of Agriculture, South China Agricultural University, Guangzhou 510642, China"},{"name":"Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, South China Agricultural University, Guangzhou 510642, China"},{"name":"Guangdong Zhaohua Aerospace Breeding Innovation Research Institute, Heyuan 517000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chun","family":"Chen","sequence":"additional","affiliation":[{"name":"National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China"},{"name":"College of Agriculture, South China Agricultural University, Guangzhou 510642, China"},{"name":"Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, South China Agricultural University, Guangzhou 510642, China"},{"name":"Guangdong Zhaohua Aerospace Breeding Innovation Research Institute, Heyuan 517000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,27]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"756","DOI":"10.1016\/j.oneear.2022.06.008","article-title":"Research priorities for global food security under extreme events","volume":"5","author":"Mehrabi","year":"2022","journal-title":"One Earth"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"3777","DOI":"10.1111\/pce.15299","article-title":"Enhancing food production through modern agricultural technology","volume":"49","author":"Yu","year":"2026","journal-title":"Plant Cell Environ."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"101172","DOI":"10.1016\/j.xplc.2024.101172","article-title":"Breeding herbicide-resistant rice using CRISPR-Cas gene editing and other technologies","volume":"6","author":"Luo","year":"2025","journal-title":"Plant 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