Combined genomic and transcriptomic analysis reveals the contribution of tandem duplication genes to low-temperature adaptation in perennial ryegrass

Perennial ryegrass (Lolium perenne L.) is an agronomically important cool-season grass species that is widely used as forage for ruminant animal production and cultivated in temperate regions for the establishment of lawns. However, the underlying genetic mechanism of the response of L. perenne to low temperature is still unclear. In the present study, we performed a comprehensive study and identified 3,770 tandem duplication genes (TDGs) in L. perenne, and evolutionary analysis revealed that L. perenne might have undergone a duplication event approximately 7.69 Mya. GO and KEGG pathway functional analyses revealed that these TDGs were mainly enriched in photosynthesis, hormone-mediated signaling pathways and responses to various stresses, suggesting that TDGs contribute to the environmental adaptability of L. perenne. In addition, the expression profile analysis revealed that the expression levels of TDGs were highly conserved and significantly lower than those of all genes in different tissues, while the frequency of differentially expressed genes (DEGs) from TDGs was much higher than that of DEGs from all genes in response to low-temperature stress. Finally, in-depth analysis of the important and expanded gene family indicated that the members of the ELIP subfamily could rapidly respond to low temperature and persistently maintain higher expression levels during all low temperature stress time points, suggesting that ELIPs most likely mediate low temperature responses and help to facilitate adaptation to low temperature in L. perenne. Our results provide evidence for the genetic underpinning of low-temperature adaptation and valuable resources for practical application and genetic improvement for stress resistance in L. perenne.

Automated summary

In this study, we conducted a comprehensive analysis of L. perenne and identified 3,770 tandem duplication genes (TDGs). Evolutionary analysis revealed a duplication event in L. perenne approximately 7.69 million years ago. Functional analysis showed that these TDGs were mainly enriched in photosynthesis, hormone-mediated signaling pathways, and stress responses, indicating their contribution to environmental adaptability. Expression profile analysis demonstrated that TDGs had highly conserved expression levels and were significantly lower compared to all genes in different tissues, but had a higher frequency of differentially expressed genes (DEGs) in response to low-temperature stress. Furthermore, analysis of an important gene family revealed that ELIPs were likely responsible for low temperature responses and adaptation in L. perenne. This study provides evidence for the genetic basis of low-temperature adaptation and valuable resources for stress resistance improvement in L. perenne.