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Genome Resequencing for Autotetraploid Rice and Its Closest Relatives Reveals Abundant Variation and High Potential in Rice Breeding
Sunday, 2025/01/12 | 07:09:07

Yachun ZhangAnping DuLiqi TongGui YanLongxiang LuYanni YinXingyue FuHuixin YangHui LiWeizao HuangDetian CaiZhaojian SongXianhua ZhangYuchi He Shengbin Tu

Int J Mol Sci.; 2024 Aug 19; 25(16):9012. doi: 10.3390/ijms25169012.

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.

 

See https://pubmed.ncbi.nlm.nih.gov/39201698/

 

Figure 1. The field performance of hybrid rice HTRM12. (A,B) the field performance of HTRM12 population in production trial at maturity stage (A) and grain filling stage (B); (C) the plant phenotype of HTRM12 at grain filling stage; (D) the panicles phenotype of HTRM12 at grain filling stage; (E) the caryopses and brown grains phenotype of HTRM12 at maturity stage; (FI) comparison of the yield and yield constitution factors between HTRM12 and control variety FLY4; (J) comparison of the panicle length between HTRM12 and control variety FLY4; (K) comparison of the plant height between HTRM12 and control variety FLY4; (LO) comparison of total spikelet number per panicle, seed setting rate, heading date, and whole growth period between HTRM12 and control variety FLY4. Data collected from different regional trial sites were used for plotting, and values were shown as means ± SD (n = 18 trial sites). Student’s t-test was used for difference significance analysis (two-tailed). Specially for (K), the Welch’s t-test (two-tailed) was used for difference significance analysis. For (HJ), the Mann–Whiney U test (two-tailed) was used for difference significance analysis. ns presents no significant difference; *** presents p < 0.001; **** presents p < 0.0001.

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