Genome-wide unbalanced expression bias and expression level dominance toward Brassica oleracea in artificially synthesized intergeneric hybrids of Raphanobrassica

Libin Zhang,Jiangsheng Wu,Hongsheng He,Jianjie He,Maoteng Li

doi:10.1038/s41438-021-00672-2

Abstract

Raphanobrassica (RrRrCrCr, 2n = 4x = 36), which is generated by distant hybridization between the maternal parent Raphanus sativus (RsRs, 2n = 2x = 18) and the paternal parent Brassica oleracea (C°C°, 2n = 2x = 18), displays intermediate silique phenotypes compared to diploid progenitors. However, the hybrid shares much more similarities in silique phenotypes with those of B. oleracea than those of R. sativus. Strikingly, the silique of Raphanobrassica is obviously split into two parts. To investigate the gene expression patterns behind these phenomena, transcriptome analysis was performed on the upper, middle, and lower sections of pods (RCsiu, RCsim, and RCsil), seeds in the upper and lower sections of siliques (RCseu and RCsel) from Raphanobrassica, whole pods (Rsi and Csi) and all seeds in the siliques (Rse and Cse) from R. sativus and B. oleracea. Transcriptome shock was observed in all five aforementioned tissues of Raphanobrassica. Genome-wide unbalanced biased expression and expression level dominance were also discovered, and both of them were toward B. oleracea in Raphanobrassica, which is consistent with the observed phenotypes. The present results reveal the global gene expression patterns of different sections of siliques of Raphanobrassica, pods, and seeds of B. oleracea and R. sativus, unraveling the tight correlation between global gene expression patterns and phenotypes of the hybrid and its parents.

Highlights

Hybridization provides a way of interspecific or intergeneric genome transfer for incorporating preferable traits from the parents to the progeny
We aimed to explore the global gene expression patterns of Raphanobrassica and its parents, determine the relationships between the gene expression and the silique phenotypes in which the hybrid shows intermediate traits compared to its diploid progenitors and shares many more similarities with B. oleracea
The main reason for Expression level dominance (ELD) is that numerous homoeologs or RrRr homoeologs were downregulated compared to those in the diploid progenitors, with 547 (367 + 180, 84.0%), 1 026 (656 + 370, 83.7%), 917 (559 + 358, 79.9%) and 1 026 (670 + 356, 95.8%) homoeolog pairs detected in RCsiu, RCsim, RCsil, and RCseu, respectively (Fig. 5b). These results reveal that the expression level dominance in RCsiu, RCsim, RCsil, and RCseu is toward CC, and the main reason for ELD is due to the downregulated expression of both RrRr and CrCr homoeologs or the downregulated expression of RrRr homoeologs

Summary

Introduction

Hybridization provides a way of interspecific or intergeneric genome transfer for incorporating preferable traits from the parents to the progeny. Allopolyploid hybrids generated from interspecific or intergeneric hybridization have provided abundant genetic resources for molecular biology research and crop breeding. Many crops, such as wheat[1], cotton[2], rapeseed[3], and Chinese cabbage[4], are derived from hybridization between different species. MiRNA expression patterns were explored between B. napus, B. rapa, and their F1 hybrids[21]. The genomic instability and the difficulty of the production of distant hybrids impede a better understanding of global expression patterns and/or regulatory mechanisms of gene expression during hybridization

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Conclusion