Zeng Haiyue, Chen Xingyu, Li Hongbo, Zhang Jun, Wei Zhaoyuan, Wang Yi
State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China.
Biological Science Research Center, Southwest University, Chongqing 400715, China.
Comput Struct Biotechnol J. 2021 Jan 5;19:600-611. doi: 10.1016/j.csbj.2020.12.046. eCollection 2021.
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.
反向复制变异（RDV）是一种反转录多态性，被认为具有重要的生物学意义，但其对基因功能和物种表型的影响仍知之甚少。为此，我们分析了3010个水稻基因组中的反转录基因和RDV。我们计算了每个水稻群体基因组中的RDV频率；检测了水稻基因组中发生突变的、祖先的和表达的反转录基因；并分析了它们的RDV对水稻表型性状的影响。总共鉴定出73个RDV，其中祖先反转录基因中的14个RDV可显著影响水稻表型。我们的研究表明，RDV在水稻迁移、驯化和进化中起重要作用。我们认为RDV是一个很好的分子育种标记候选物。据我们所知，这是关于反转录基因功能、表达、RDV与物种表型之间关系的首次研究。
