Journal
SCIENCE CHINA-LIFE SCIENCES
Volume 64, Issue 9, Pages 1491-1501Publisher
SCIENCE PRESS
DOI: 10.1007/s11427-020-1749-9
Keywords
homoeologous recombination; recombinant transcripts; triploid; innate immunity
Categories
Funding
- National Natural Science Foundation of China [31702334, 31730098, U19A2040, 31430088]
- Key Research and Development Program of Hunan Province [2018NK2072, 2017NK1031]
- Earmarked Fund for China Agriculture Research System [CARS-45]
- 111 Project [D20007]
- High-Level Talent Agglomeration Program of Hunan, China [2019RS1044]
- Cooperative Innovation Center of Engineering and New Products for Developmental Biology of Hunan Province [20134486]
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The study identified 140 homoeologous recombinations between two triploids and detected transcriptions of homoeologous recombinant genes. By comparing expressed recombinant reads to total expressed reads, the potential relationship between homoeologous recombinations related to innate immunity and adaptation of the triploids and allotetraploids was revealed.
Homoeologous recombination (HR), the exchange of homoeologous chromosomes, contributes to subgenome adaptation to diverse environments by producing various phenotypes. However, the potential relevance of HR and innate immunity is rarely described in triploid cyprinid fish species. In our study, two allotriploid genotypes (R2C and RC2), whose innate immunity was stronger than their inbred parents (Carassius auratus red var. and Cyprinus carpio L.), were obtained from backcrossing between male allotetraploids of C. auratus red var.xC. carpio L. and females of their two inbred parents, respectively. The work detected 140 HRs shared between the two triploids at the genomic level. Further, transcriptions of 54 homoeologous recombinant genes (HRGs) in R2C and 65 HRGs in RC2 were detected using both Illumina and PacBio data. Finally, by comparing expressed recombinant reads to total expressed reads in each of the genes, a range of 0.1%-10% was observed in most of the 99-193 HRGs, of which six recombinant genes were classified as response to stimulus. These results not only provide a novel way to predict HRs in allopolyploids based on cross prediction at both genomic and transcriptional levels, but also insight into the potential relationship between HRs related to innate immunity and adaptation of the triploids and allotetraploids.
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