Interpopulation differences of retroduplication variations (RDVs) in rice retrogenes and their phenotypic correlations

Haiyue Zeng; Xingyu Chen; Hongbo Li; Jun Zhang; Zhaoyuan Wei; Yi Wang

doi:10.1016/j.csbj.2020.12.046

Interpopulation differences of retroduplication variations (RDVs) in rice retrogenes and their phenotypic correlations

Comput Struct Biotechnol J. 2021 Jan 5:19:600-611. doi: 10.1016/j.csbj.2020.12.046. eCollection 2021.

Authors

Haiyue Zeng^{1

2

3}, Xingyu Chen³, Hongbo Li⁴, Jun Zhang⁵, Zhaoyuan Wei^{1

2}, Yi Wang^{1

2}

Affiliations

¹ State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China.
² Biological Science Research Center, Southwest University, Chongqing 400715, China.
³ Shennong Class, Southwest University, Chongqing 400715, China.
⁴ College of Electronic and Information Engineering, Southwest University, Chongqing 400715.
⁵ College of Computer & Information Science, Southwest University, Chongqing 400715, China.

Abstract

Retroduplication variation (RDV), a type of retrocopy polymorphism, is considered to have essential biological significance, but its effect on gene function and species phenotype is still poorly understood. To this end, we analyzed the retrocopies and RDVs in 3,010 rice genomes. We calculated the RDV frequencies in the genome of each rice population; detected the mutated, ancestral and expressed retrogenes in rice genomes; and analyzed their RDV influence on rice phenotypic traits. Collectively, 73 RDVs were identified, and 14 RDVs in ancestral retrogenes can significantly affect rice phenotypes. Our research reveals that RDV plays an important role in rice migration, domestication and evolution. We think that RDV is a good molecular breeding marker candidate. To our knowledge, this is the first study on the relationship between retrogene function, expression, RDV and species phenotype.

Keywords: BP, Biological process; CC, Cellular component; FPKM, Fragments per kilobase per million mapped reads; GO, Gene ontology; Indel, Insertion-deletion; MF, Molecular function; MST, monosaccharide transporter; ORF, Open reading frame; RDV; RDV, Retroduplication variation; Retrocopy; Retrogene; Retroposition; Rice.