Genome‐wide analysis of genomic imprinting in the endosperm and allelic variation in flax

• Published in: The Plant journal : for cell and molecular biology Vol. 107; no. 6; pp. 1697 - 1710
• Main Authors: Jiang, Haixia, Guo, Dongliang, Ye, Jiali, Gao, Yanfang, Liu, Huiqing, Wang, Yue, Xue, Min, Yan, Qingcheng, Chen, Jiaxun, Duan, Lepeng, Li, Gongze, Li, Xiao, Xie, Liqiong
• Format: Journal Article
• Language: English
• Published: England Blackwell Publishing Ltd 01.09.2021
• Subjects: Alleles; Crosses, Genetic; Cultivars; Domestication; Endosperm; Endosperm - genetics; Epigenetics; Flax; Flax - genetics; flax endosperm; Flowering; Gene Expression Regulation, Plant; Gene sequencing; Genes; Genes, Plant; Genome, Plant; Genome-Wide Association Study; Genomic analysis; Genomic Imprinting; Heredity; intraspecific variation; Linum usitatissimum; Multigene Family; Nucleotides; Plant species; Plants (botany); Positive selection; Reproducibility of Results; seed size; Seeds - genetics; Sequence Analysis, RNA; Single-nucleotide polymorphism; Subgroups; Variation; positive selection; genomic imprinting; flax endosperm; intraspecific variation; seed size
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/tpj.15411

Summary Genomic imprinting is an epigenetic phenomenon that causes biased expression of maternally and paternally inherited alleles. In flowering plants, genomic imprinting predominantly occurs in the triploid endosperm and plays a vital role in seed development. In this study, we identified 248 candidate imprinted genes including 114 maternally expressed imprinted genes (MEGs) and 134 paternally expressed imprinted genes (PEGs) in flax (Linum usitatissimum L.) endosperm using deep RNA sequencing. These imprinted genes were neither clustered in specific chromosomal regions nor well conserved among flax and other plant species. MEGs tended to be expressed specifically in the endosperm, whereas the expression of PEGs was not tissue‐specific. Imprinted single nucleotide polymorphisms differentiated 200 flax cultivars into the oil flax, oil‐fiber dual purpose flax and fiber flax subgroups, suggesting that genomic imprinting contributed to intraspecific variation in flax. The nucleotide diversity of imprinted genes in the oil flax subgroup was significantly higher than that in the fiber flax subgroup, indicating that some imprinted genes underwent positive selection during flax domestication from oil flax to fiber flax. Moreover, imprinted genes that underwent positive selection were related to flax functions. Thirteen imprinted genes related to flax seed size and weight were identified using a candidate gene‐based association study. Therefore, our study provides information for further exploration of the function and genomic variation of imprinted genes in the flax population. Significance Statement Genomic imprinting predominantly occurs in the endosperm and plays a vital role in seed development. We performed genome‐wide screening and a comprehensive analysis of genomic imprinting in the flax endosperm. Population‐level analysis of imprinted genes revealed that genomic imprinting contributed to intraspecific variation. Imprinted genes underwent positive selection and were related to flax domestication functions. We identified 13 imprinted genes related to flax seed size. Thus, our study provides some insight into the functioning and genomic variation with imprinting in the flax population.