Multi-omics analyses help to analyze the variation produced by in vitro culture

Citrus is an important, economically valuable horticultural crop characterized by nucellar polyembryony that prevents the production of hybrid offspring. Citrus is thus propagated mainly by asexual means such as grafting and cuttings. Sweet orange (Citrus sinensis), one of the most popular citrus cultivars worldwide, was produced from multiple crosses between mandarin (Citrus reticulata) and pummelo (Citrus grandis), resulting in a genome with high heterozygosity. Citrus genetic improvement and breeding programs rely heavily on somatic mutations. Therefore, studying somaclonal variation patterns in citrus has great potential value for producing useful cultivars. Although the use of callus induction for clonal propagation has been reported previously, this experimental system has not been widely exploited to uncover dynamic somaclonal variation during cell dedifferentiation and later developmental reprogramming.

Recently, scientists from the Huazhong Agricultural University performed a comprehensive investigation of the genomes, methylomes, and transcriptomes of newly induced calli and sweet orange calli maintained in in vitro culture for 30 years. These multi-omics analyses offer a detailed view of genomic and epigenomic dynamics during dedifferentiation and in vitro culture. The variation observed for polyploids in response to in vitro culture was also compared, revealing different patterns of subgenome dominance between in vitro and in vivo polyploids, as well as the effects of somaclonal variation on somatic embryogenesis during in vitro culture.

“We propose that changes in TE (transposable element) activity, dynamic DNA methylation, and the reprogramming of gene expression may ultimately affect the ability of somatic embryogenesis during in vitro culture. Our study may guide researchers to select the appropriate duration of in vitro culture to avoid or gain additional variation as a function of the desired goals”, Prof Xu said. These results provide the foundation to harness in vitro variation and offer a deeper understanding of the variation introduced by tissue culture during germplasm conservation, somatic embryogenesis, gene editing, and breeding programs.

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Reference

Authors

Xia Wang, Lili Ke, Shuting Wang, Jialing Fu, Jidi Xu, Yujin Hao, Chunying Kang, Wenwu Guo, Xiuxin Deng and Qiang Xu

Affiliations

Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, No. 1, Shizishan Street, Wuhan 430070, China

About Qiang Xu

Dr. Qiang Xu is a professor at Huazhong Agricultural University and Vice Dean of the College of Horticulture and Forestry. Prof. Xu has been supported by the National Outstanding Youth Science Fund (2020–2025) and also by the Leading Talent of the National Ten Thousand Talents Plan, and the National Outstanding Youth Science Fund (2013–2015). He is mainly engaged in fruit tree genomics and molecular breeding research. Prof. Xu led his team to make a breakthrough in citrus genome research, cloned genes for citrus “polyembryonic” apomixis, fruit quality regulation, canker resistance, and Huanglong disease resistance. Based on genomic information, Prof. Xu’s team domesticate wild citrus from scratch to create new, high-quality, and efficient varieties. Papers by Prof. Xu have been published in internationally influential journals such as Nature Genetics, Nature Plants, and Molecular Plant.