Dataset Information

Identification and genetic analysis of qCL1.2, a novel allele of the "green revolution" gene SD1 from wild rice (Oryza rufipogon) that enhances plant height.

ABSTRACT:

Background

The exploitation of novel alleles from wild rice that were lost during rice cultivation could be very important for rice breeding and evolutionary studies. Plant height (PH) was a target of artificial selection during rice domestication and is still a target of modern breeding. The "green revolution" gene semi-dwarf 1 (SD1) were well documented and used in the past decades, allele from wild rice could provide new insights into the functions and evolution of this gene.

Results

We identified a PH-related quantitative trait locus, qCL1.2,from wild riceusing a set of chromosome segment substitution lines. qCL1.2encodesa novel allele of SD1 gene. The wild allele of SD1 is a dominant locus that can significantly promote rice internode length by regulating the expression levels of genes involved in gibberellin biosynthesis and signal transduction. Nucleotide diversity and haplotype network analyses of the SD1 gene were performed using 2822 rice landraces. Two previously reported functional nucleotide polymorphisms clearly differentiated japonica and indica rice; however, they were not associated with PH selection. Other new functional nucleotide polymorphisms in the coding, but not promoter, regions were involved in PH selection during rice domestication. Our study increasesunderstanding of the rice SD1 gene and provides additional evidence of this gene's selection during rice domestication.

Conclusions

Our findings provide evidence thatSD1 gene from wild rice enhances plant height and new functional nucleotide polymorphisms of this gene were artificially selected during cultivated rice differentiation.

SUBMITTER: Zhang L

PROVIDER: S-EPMC7291570 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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Publications

Identification and genetic analysis of qCL1.2, a novel allele of the "green revolution" gene SD1 from wild rice (Oryza rufipogon) that enhances plant height.

Zhang Lizhen L Huang Jingfen J Wang Yanyan Y Xu Rui R Yang Ziyi Z Zhao Zhigang Z Liu Shijia S Tian Yunlu Y Zheng Xiaoming X Li Fei F Wang Junrui J Song Yue Y Li Jiaqi J Cui Yongxia Y Zhang Li-Fang LF Cheng Yunlian Y Lan Jinhao J Qiao Weihua W Yang Qingwen Q

BMC genetics 20200611 1

<h4>Background</h4>The exploitation of novel alleles from wild rice that were lost during rice cultivation could be very important for rice breeding and evolutionary studies. Plant height (PH) was a target of artificial selection during rice domestication and is still a target of modern breeding. The "green revolution" gene semi-dwarf 1 (SD1) were well documented and used in the past decades, allele from wild rice could provide new insights into the functions and evolution of this gene.<h4>Resul ...[more]

PMID: 32527215

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Project description:BackgroundMicroRNAs (miRNAs) is a class of non-coding RNAs involved in post- transcriptional control of gene expression, via degradation and/or translational inhibition. Six-hundred sixty-one rice miRNAs are known that are important in plant development. However, flowering-related miRNAs have not been characterized in Oryza rufipogon Griff. It was approved by supervision department of Guangdong wild rice protection. We analyzed flowering-related miRNAs in O. rufipogon using high-throughput sequencing (deep sequencing) to understand the changes that occurred during rice domestication, and to elucidate their functions in flowering.ResultsThree O. rufipogon sRNA libraries, two vegetative stage (CWR-V1 and CWR-V2) and one flowering stage (CWR-F2) were sequenced using Illumina deep sequencing. A total of 20,156,098, 21,531,511 and 20,995,942 high quality sRNA reads were obtained from CWR-V1, CWR-V2 and CWR-F2, respectively, of which 3,448,185, 4,265,048 and 2,833,527 reads matched known miRNAs. We identified 512 known rice miRNAs in 214 miRNA families and predicted 290 new miRNAs. Targeted functional annotation, GO and KEGG pathway analyses predicted that 187 miRNAs regulate expression of flowering-related genes. Differential expression analysis of flowering-related miRNAs showed that: expression of 95 miRNAs varied significantly between the libraries, 66 are flowering-related miRNAs, such as oru-miR97, oru-miR117, oru-miR135, oru-miR137, et al. 17 are early-flowering -related miRNAs, including osa-miR160f, osa-miR164d, osa-miR167d, osa-miR169a, osa-miR172b, oru-miR4, et al., induced during the floral transition. Real-time PCR revealed the same expression patterns as deep sequencing. miRNAs targets were confirmed for cleavage by 5'-RACE in vivo, and were negatively regulated by miRNAs.ConclusionsThis is the first investigation of flowering miRNAs in wild rice. The result indicates that variation in miRNAs occurred during rice domestication and lays a foundation for further study of phase change and flowering in O. rufipogon. Complicated regulatory networks mediated by multiple miRNAs regulate the expression of flowering genes that control the induction of flowering.

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Dataset Information

Identification and genetic analysis of qCL1.2, a novel allele of the "green revolution" gene SD1 from wild rice (Oryza rufipogon) that enhances plant height.

Background

Results

Conclusions

Publications

Identification and genetic analysis of qCL1.2, a novel allele of the "green revolution" gene SD1 from wild rice (Oryza rufipogon) that enhances plant height.

Similar Datasets

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