Genome Resequencing for Autotetraploid Rice and Its Closest Relatives Reveals Abundant Variation and High Potential in Rice Breeding

Author:

Zhang Yachun12,Du Anping1ORCID,Tong Liqi2,Yan Gui2,Lu Longxiang13,Yin Yanni2,Fu Xingyue13,Yang Huixin13,Li Hui1,Huang Weizao1,Cai Detian2,Song Zhaojian2,Zhang Xianhua2,He Yuchi2,Tu Shengbin13

Affiliation:

1. Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China

2. State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China

3. University of Chinese Academy of Sciences, Beijing 100049, China

Abstract

Polyploid rice and its reverted diploid show rich phenotypic variation and strong heterosis, showing great breeding value. However, the genomic differences among tetraploids, counterpart common diploids, tetraploid-revertant diploids, and hybrid descendants are unclear. In this work, we bred a new excellent two-line hybrid rice variety, Y Liang You Duo Hui 14 (HTRM12), using Haitian tetraploid self-reverted diploid (HTRM2). Furthermore, we comparatively analyzed the important agronomic traits and genome-wide variations of those closest relatives, Haitian diploid (HT2), Haitian tetraploid (HT4), HTRM2, and HTRM12 in detail, based on multiple phenotypic investigations, genome resequencing, and bioinformatics analysis. The results of agronomic traits analysis and genome-wide variation analysis of single nucleotide polymorphism (SNP), insertion–deletion (InDel), and copy number variation (CNV) show that HT4 and HTRM2 had abundant phenotypic and genomic variations compared to HT2. HTRM2 can inherit important traits and variations from HT4. This implies that tetraploid self-reverted diploid has high potential in creating excellent breeding materials and in breeding breakthrough hybrid rice varieties. Our study verifies the feasibility that polyploid rice could be used as a mutation carrier for creating variations and provides genomic information, new breeding materials, and a new way of application for tetraploid rice breeding.

Funder

Alliance of International Science Organizations

Sichuan Science and Technology Program

Bureau of International Cooperation, Chinese Academy of Science

Chinese National Natural Science Foundation

Wuhan Science and Technology Major Project “Development and application of polyploid rice”

Technology Innovation Guidance Project of Science and Technology Department of Jiangxi Province

Open Project Program of Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Province

State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China

2022 Sanya Science and Technology innovation project

Publisher

MDPI AG

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