| Transposable element is a piece of DNA sequence that can move to a new location in the genome,and are divided into RNA transposons and DNA transposons according to whether RNA is needed during the transposon.Transposable element can regulate gene expression by inserting into near genes,acting as or deriving cis regulatory elements,generating non-coding RNA and so on.In recent years,with the development of sequencing technology,the study of transposable element has also made a lot of progress in plant populations.Cotton fiber is the main source of natural textile fibers in the world and occupies an important position in the textile industry.Modern cotton is dominated by tetraploid upland cotton,which has undergone multiplication,evolution and domestication,and is a model system for studying evolution and domestication.Currently,there are very few studies on transposable element’s function from the population level in cotton.This study collected a total of 1034 published resequencing data on tetraploid upland cotton accessions,constructed a polymorphism map of transposable elements,and found that it may play a role in cotton domestication of important traits.The specific results are as follows:(1)The transposable element polymorphism map of upland cotton(Gossypium hirsutum)population was constructed,and the characteristics of non-reference transposable element insertions polymorphism(TIP)were fully analyzed.It is found that long terminal repeat retrotransposon is the main component of non-reference TIPs,and the proportion of DNA transposon is no more than 10%.Non-reference TIPs have no insertion preference for the centromeric region,but the distribution density at both ends of the chromosome is significantly reduced.It is known that the gene density in this region is high,so it is speculated that non-reference TIPs are strictly controlled by the genome.In the genome,non-reference TIPs are mainly distributed in the intergenic region(75%),and in the genome functional region,the distribution proportion of DNA transposons is higher than that of RNA transposons(52% and 17%).In the population,non-reference TIPs with distribution frequency less than 0.05 accounted for 99% of the total,and most non-reference TIPs existed only in a few accessions.(2)The amplification time of non-reference TIPs was shorter than that of reference transposons,and the outbreak time of non-reference TIPs in wild cotton was earlier than that in cultivated cotton.The reference transposons has an obvious amplification in 0-2 million years,and the amplification time can be traced back to 14 million years ago.More than 97% of non-reference TIPs were amplified within 2 million years,and there was an obvious amplification peak in 0-1 million years.In the wild cotton population(Ghlandrace),the number of non-reference TIPs amplified the most in 0.2-0.3 million years(12.3%),while in the cultivated cotton(Ghlmp USO and Ghlmp CHN),the non-reference TIPs had a large outbreak in 0-0.1 million years(44.1% and 46.4%).(3)Non-reference TIPs in different frequencies and subgroups are selected differently by the genome.It was found that in different functional regions of the genome,the proportion of high-frequency non-reference TIPs was significantly higher than that of low-frequency non-reference TIPs,but these two kinds of transposons tended to insert into the same kind of genes.The proportion of non-reference TIPs in the Dt subgenome was significantly higher than that in the At subgenome.(4)A large number of transposons were lost and inserted during the domestication of upland cotton.Through the domestication selection analysis of Ghlandrace and Ghlmp USO,Ghlmp USO and Ghlmp CHN,Ghlandrace and cultivar,it is found that during the domestication process,the original population lost a large number of nonreference TIPs and some genes,at the same time,new non-reference TIPs and genes were obtained,and the proportion of non-reference TIPs conserved among populations in their total number is very small(less than 10%).Among the genes with non-reference TIPs insertion,the number of genes located in the Dt subgenome is more than that in the At subgenome.Gene Ontology(GO)enrichment analysis of the detected domesticated genes showed that these genes were mainly enriched in reproductive process,cell cycle process,seed development and other pathways.We also found that in the domestication selection regions,some non-reference TIPs were inserted near the quantitative trait loci(QTL)significantly related to fiber traits,including fiber length,strength and so on(< 1 kb).Based on our analysis results,we established a polymorphism map of nonreference TIPs in tetraploid upland cotton,and preliminarily explored the role of nonreference TIPs in the process of domestication.The impact of transposable elements on gene function needs to be further studied. |
