Feilong Guo, Changbin Yin, Tian Li, Sitong Liu, Jiayu Dong, Hao Jiang, Yu Fang, Jun Wei, Yi Han, Yu Li, Hong Cao, Yuting Ning, Galal Khamis, Xin Deng, Ke Wang, Jirui Wang, Cuijun Zhang, Fei Lu, Yongxiu Liu
{"title":"小麦种子大小和种子休眠相关等位基因的选择拮抗作用","authors":"Feilong Guo, Changbin Yin, Tian Li, Sitong Liu, Jiayu Dong, Hao Jiang, Yu Fang, Jun Wei, Yi Han, Yu Li, Hong Cao, Yuting Ning, Galal Khamis, Xin Deng, Ke Wang, Jirui Wang, Cuijun Zhang, Fei Lu, Yongxiu Liu","doi":"10.1186/s13059-025-03770-9","DOIUrl":null,"url":null,"abstract":"Seed dormancy and size are two crucial traits influencing crop yield, and they have undergone strong selection during cereal domestication and improvement. However, the genetic basis underlying the antagonistic effects between seed dormancy and seed size remains poorly understood. Based on genome-wide association study, we perform a comprehensive comparative analysis of 545 global wheat accessions to dissect the genetic architecture of these two traits during wheat improvement. We detect a strong negative correlation between the accumulation of favorable alleles for seed dormancy and the accumulation of favorable alleles for seed size. At the wheat genome level, a set of SNPs harboring antagonistic alleles explain up to 26.56% and 47.21% of the phenotypic variation for seed dormancy and seed size, respectively. In contrast, a set of SNPs with synergistic alleles account for only 0.54% and 1.12% of the variation in both traits. During wheat breeding improvement, favorable alleles associated with increased seed size are preferentially selected, resulting in a compromise in seed dormancy. Under different climate conditions, the frequencies of haplotypes of the pleiotropic genes with antagonistic effects and synergistic loci collectively shape wheat diversity through balancing seed dormancy and seed size. Our findings reveal the genetic architecture underlying the observed weakening of seed dormancy as seed size increases during wheat improvement, enabling further genome-informed cultivar breeding to balance and improve seed dormancy and seed size traits.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"57 1","pages":""},"PeriodicalIF":10.1000,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Antagonistic effects of selection on alleles associated with seed size and seed dormancy in wheat\",\"authors\":\"Feilong Guo, Changbin Yin, Tian Li, Sitong Liu, Jiayu Dong, Hao Jiang, Yu Fang, Jun Wei, Yi Han, Yu Li, Hong Cao, Yuting Ning, Galal Khamis, Xin Deng, Ke Wang, Jirui Wang, Cuijun Zhang, Fei Lu, Yongxiu Liu\",\"doi\":\"10.1186/s13059-025-03770-9\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Seed dormancy and size are two crucial traits influencing crop yield, and they have undergone strong selection during cereal domestication and improvement. However, the genetic basis underlying the antagonistic effects between seed dormancy and seed size remains poorly understood. Based on genome-wide association study, we perform a comprehensive comparative analysis of 545 global wheat accessions to dissect the genetic architecture of these two traits during wheat improvement. We detect a strong negative correlation between the accumulation of favorable alleles for seed dormancy and the accumulation of favorable alleles for seed size. At the wheat genome level, a set of SNPs harboring antagonistic alleles explain up to 26.56% and 47.21% of the phenotypic variation for seed dormancy and seed size, respectively. In contrast, a set of SNPs with synergistic alleles account for only 0.54% and 1.12% of the variation in both traits. During wheat breeding improvement, favorable alleles associated with increased seed size are preferentially selected, resulting in a compromise in seed dormancy. Under different climate conditions, the frequencies of haplotypes of the pleiotropic genes with antagonistic effects and synergistic loci collectively shape wheat diversity through balancing seed dormancy and seed size. Our findings reveal the genetic architecture underlying the observed weakening of seed dormancy as seed size increases during wheat improvement, enabling further genome-informed cultivar breeding to balance and improve seed dormancy and seed size traits.\",\"PeriodicalId\":12611,\"journal\":{\"name\":\"Genome Biology\",\"volume\":\"57 1\",\"pages\":\"\"},\"PeriodicalIF\":10.1000,\"publicationDate\":\"2025-09-25\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Genome Biology\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1186/s13059-025-03770-9\",\"RegionNum\":1,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"BIOTECHNOLOGY & APPLIED MICROBIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genome Biology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1186/s13059-025-03770-9","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}
Antagonistic effects of selection on alleles associated with seed size and seed dormancy in wheat
Seed dormancy and size are two crucial traits influencing crop yield, and they have undergone strong selection during cereal domestication and improvement. However, the genetic basis underlying the antagonistic effects between seed dormancy and seed size remains poorly understood. Based on genome-wide association study, we perform a comprehensive comparative analysis of 545 global wheat accessions to dissect the genetic architecture of these two traits during wheat improvement. We detect a strong negative correlation between the accumulation of favorable alleles for seed dormancy and the accumulation of favorable alleles for seed size. At the wheat genome level, a set of SNPs harboring antagonistic alleles explain up to 26.56% and 47.21% of the phenotypic variation for seed dormancy and seed size, respectively. In contrast, a set of SNPs with synergistic alleles account for only 0.54% and 1.12% of the variation in both traits. During wheat breeding improvement, favorable alleles associated with increased seed size are preferentially selected, resulting in a compromise in seed dormancy. Under different climate conditions, the frequencies of haplotypes of the pleiotropic genes with antagonistic effects and synergistic loci collectively shape wheat diversity through balancing seed dormancy and seed size. Our findings reveal the genetic architecture underlying the observed weakening of seed dormancy as seed size increases during wheat improvement, enabling further genome-informed cultivar breeding to balance and improve seed dormancy and seed size traits.
Genome BiologyBiochemistry, Genetics and Molecular Biology-Genetics
CiteScore
21.00
自引率
3.30%
发文量
241
审稿时长
2 months
期刊介绍:
Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens.
With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category.
Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.