Identification, Analysis, and Confirmation of Seed Storability-Related Loci in Dongxiang Wild Rice ( Oryza rufipogon Griff.)

Dongxiang wild rice ( Griff.) (DXWR) has strong seed storability and identifying its elite gene resources may facilitate genetic improvements in rice seed storability. In this study, we developed two backcross inbred lines (BILs) populations, with DXWR as a common donor parent and two rice varieties...

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Published in:Genes 2021-11, Vol.12 (11), p.1831
Main Authors: Zhao, Minmin, Hu, Biaolin, Fan, Yuanwei, Ding, Gumu, Yang, Wanling, Chen, Yong, Chen, Yanhong, Xie, Jiankun, Zhang, Fantao
Format: Article
Language:English
Subjects:
Aging
Biotechnology industry
Chromosome 4
Chromosome 9
Frameshift mutation
Genes, Plant
Genetic engineering
Genomes
Germination
Humidity
Inbreeding
Mutation
Oryza - genetics
Oryza - physiology
Oryza rufipogon
Plant Breeding
Polymorphism, Single Nucleotide
Population
Quantitative Trait Loci
Rice
Seeds
Seeds - genetics
Seeds - physiology
Whole genome sequencing
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Summary:Dongxiang wild rice ( Griff.) (DXWR) has strong seed storability and identifying its elite gene resources may facilitate genetic improvements in rice seed storability. In this study, we developed two backcross inbred lines (BILs) populations, with DXWR as a common donor parent and two rice varieties (F6 and R974) as recipient parents. Bulked segregant analysis via whole genome sequencing (BSA-seq) was used to identify seed storability-related loci in the DXWR and F6 population. Two main genomic regions containing 18,550,000-20,870,000 bp on chromosome 4 and 7,860,000-9,780,000 bp on chromosome 9 were identified as candidate loci of DXWR seed storability; these overlapped partially with seed storability-related quantitative trait loci (QTLs) discovered in previous studies, suggesting that these loci may provide important regions for isolating the responsible genes. In total, 448 annotated genes were predicted within the identified regions, of which 274 and 82 had nonsynonymous and frameshift mutations, respectively. We detected extensive metabolic activities and cellular processes during seed storability and confirmed the effects of the seed storability-related candidate loci using four BILs from DXWR and R974. These results may facilitate the cloning of DXWR seed storability-related genes, thereby elucidating rice seed storability and its improvement potential.
ISSN:2073-4425
2073-4425
DOI:10.3390/genes12111831