The Copy Number Variation of OsMTD1 Regulates Rice Plant Architecture.

Qing Liu,Wenzhen Ku,Wanhuang Lin,Langtao Xiao,Xue-Feng Yao,Jianhua Tong,Yunhua Zhu,Ruozhong Wang,Chun-Ming Liu,Chao Huang,Yi Su,Keqin Peng,Yuxing Mo,Jinke Xu,Zhigang Huang,Shitou Xia

doi:10.3389/fpls.2020.620282

Abstract

Copy number variation (CNV) may have phenotypic effects by altering the expression level of the gene(s) or regulatory element(s) contained. It is believed that CNVs play pivotal roles in controlling plant architecture and other traits in plant. However, the effects of CNV contributing to special traits remain largely unknown. Here we report a CNV involved in rice architecture by modulating tiller number and leaf angle. In the genome of Oryza sativa ssp. japonica cv. Nipponbare, we found a locus Loc_Os08g34249 is derived from a 13,002-bp tandem duplication in the nearby region of OsMTD1, a gene regulating tillering in rice. Further survey of 230 rice cultivars showed that the duplication occurred in only 13 japonica rice cultivars. Phenotypic investigation indicated that this CNV region may contribute to tiller number. Moreover, we revealed that OsMTD1 not only influences rice tiller number and leaf angle, but also represses pri-miR156f transcription in the CNV region. Intriguingly, this CNV performs function through both the dosage and position effects on OsMTD1 and pri-miR156f. Thus, our work identified a CNV and revealed a molecular regulatory basis for its effects on plant architecture, implying this CNV may possess importance and application potential in molecular breeding in rice.

Highlights

Genomic rearrangements include duplications, deletions, and inversions of unique genomic segments at specific regions, as well as translocations, marker chromosomes, isochromosomes, and other complex rearrangements (Lupski, 1998; Feuk et al, 2006; Weckselblatt and Rudd, 2015)
Nipponbare, we found that another locus, Loc_Os08g34249, is identical in DNA sequence to OsMTD1, a gene previously reported responsible for tillering in rice
As OsMTD1-located Copy number variation (CNV) covering approximately 13,000-bp DNA sequence is an evolutionarily recent duplication in some japonica cultivars after highly selective breeding programs, it is not surprising that OsMTD1-located CNV contributes to one or more currently advantageous traits in rice

Summary

Introduction

Deletions, and inversions of unique genomic segments at specific regions, as well as translocations, marker chromosomes, isochromosomes, and other complex rearrangements (Lupski, 1998; Feuk et al, 2006; Weckselblatt and Rudd, 2015). These rearrangements are not random events, but instead the reflection of higher-order architectural features of the genome (Lee and Lupski, 2006; Zmien’ko et al, 2014).

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Results

Conclusion