Recently, cotton functional genomics group from Chinese Academy of Agricultural Science, Institute of Cotton Research (CAAS, ICR) has constructed the graphical cotton transposon-related variome, revealing the crucial role of transposon activities in modern cotton cultivation. The related research was published on Journal of Advanced Research entitled as “Cotton transposon-related variome reveals roles of transposon-relatedvariations in modern cotton cultivation”.

The cotton transposon activity is the important source of genomic innovation. In cotton, research about the transposon focused on the genomic expansion and divergence. However, knowledge about the role of cotton transposon in modern cotton cultivation remains unknown.

The research constructed a graphical cotton transposon-related variome containing 35980 transposon activities. The researchers built a concolutional neural network model named as SLMH to predict the extent of methylation level of transposon activities. The results showed that recently inserted transposons had low methylation level, indicating human domestication could change epigenomic features of transposon activities. The genomic and transcriptomic data of 167 upland cotton accessions were aligned to the graphical transposon-related variome, and a framework including association analysis, t-test, eQTL identification and Mendel randomization analysis was proposed to investigate relationship between transposon activities and phenotypic variation. With this framework, researchers detected a gene, GhSPL4 , related to the cotton fiber elongation, indicating the framework could reduce the type Ierror and type II error simultaneously by multi-omic data supporting. The transposon activities related to the geographical adaptation have been detected by cross-entropy algorithm. This cotton transposon-related variome provided convenient data resource for modern cotton cultivation.

This research is funded by China Agriculture Research System (NO.CARS-15-06). NaturalScience Foundation of Henan Province (232300421041 and222300420382). Central Public-interest Scientific Institution BasalResearch Fund (No. 1610162022016) and Agricultural Science andTechnology Innovation Program of Chinese Academy of Agricultural Science. The phD student Liu Shang, associated professor Cheng Hailiang and assisted professor Zhang Youping are the first co-authors. The professor Song Guoli and Liu Ji are corresponding authors. The article is available on:

https://doi.org/10.1016/j.jare.2024.05.019

The construction and utilization of cotton transposon-related variome

By Liu Shang 

(LiuShang19941115@Outlook.com)