Regain flood adaptation in rice through a 14-3-3 protein OsGF14h

Sun, Jian; Zhang, Guangchen; Cui, Zhibo; Kong, Ximan; Gui, Rui; Han, Yaling; Li, Zhuan; Lang, Hong; Hua, Yimin; Zhang, Xuemin; Xu, Quan; Tang, Liang; Xu, Zhengjin; Ma, Dianrong; Chen, Wenfu

doi:10.1038/s41467-022-33320-x

Cited by 41 publications

(32 citation statements)

References 66 publications

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“…To adapt to various growth environments, rice germplasm resources retain a lot of elite genes. The seed hull gene Bh4 37 , the awn development gene An-1 8 , and plant architecture gene PROG1 14 were cloned from wild rice, and the hypoxia tolerant germination gene GF14h was recently cloned from weed rice and rice natural populations 38,39 . Whereas for rice dormancy gene cloning is rare 21,40 .…”

Section: Discussionmentioning

confidence: 99%

Novel quantitative trait locus qSDR3.1 represses Oryza sativa. L seed dormancy

Guo

Tang

Wang

et al. 2022

Preprint

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Preharvest sprouting (PHS), a deleterious phenotype that occurs frequently in rice growing regions with high temperature and precipitation, negatively affects yield, quality, and processing. Seed dormancy can prevent PHS. We report discovery of qSDR3.1, a new quantitative trait locus (QTL) for seed dormancy in rice. knockout lines of qSDR3.1 exhibited significant reduction in PHS. The qSDR3.1 locus negatively regulated seed dormancy by directly inhibiting the transcriptional activity of ABSCISIC ACID INSENSITIVE5 (ABI5). Haplotype analysis showed that qSDR3.1 was divided into five haplotypes and three amino acid (aa) types. The 102nd (aa102) and 105th (aa105) amino acids of qSDR3.1 were the key amino acids responsible for the differences in dormancy between Xian and Geng. Genetic diversity analysis revealed that qSDR3.1 was artificially selected during domestication. We proposed a two-line model for the process of rice dormancy domestication from wild rice to Xian and Geng, and we provide new candidate genes and germplasm for genetic improvement of rice seed dormancy.

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Section: Discussionmentioning

confidence: 99%

Novel quantitative trait locus qSDR3.1 represses Oryza sativa. L seed dormancy

Guo

Tang

Wang

et al. 2022

Preprint

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“…The genotype of the GWAS panel for the heading date has been effectively used to study the genetic basis of agronomic traits in weedy rice ( Sun et al., 2022 ). All raw reads were screened for high quality with Q20 quality scores >95% and Guanine and cytosine (GC) content <50%.…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

“…In order to further reveal the domestication and evolution relationship of Hd1 in different rice ecotypes, we used the sequencing data of 1,293 accessions to perform haplotype network analysis including five ecotypes, temperate japonica, tropical japonica, japonica intermediate, weedy rice, and wild rice [Oryza rufipogon (Or-IIIa)]. The sequence data of wild rice and weedy rice were from Sun et al (2022), and the sequence of the japonica population was obtained from the database http:// ricevarmap.ncpgr.cn/. The haplotype network was built based on 14 SNP variations of the Hd1 Coding sequence (CDS) region with Or-IIIa as an outgroup by using the "Median Joining Network" approach implemented in Popart software (Version 1.7).…”

Section: Haplotype Network Analysismentioning

confidence: 99%

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Genetic basis of the early heading of high-latitude weedy rice

Gui

Liang

et al. 2022

Front. Plant Sci.

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Japonica rice (Oryza sativa L.) is an important staple food in high-latitude regions and is widely distributed in northern China, Japan, Korea, and Europe. However, the genetic diversity of japonica rice is relatively narrow and poorly adapted. Weedy rice (Oryza sativa f. spontanea) is a semi-domesticated rice. Its headings are earlier than the accompanied japonica rice, making it a potential new genetic resource, which can make up for the defects of wild rice that are difficult to be directly applied to japonica rice improvement caused by reproductive isolation. In this study, we applied a natural population consisting of weedy rice, japonica landrace, and japonica cultivar to conduct a genome-wide association study (GWAS) of the heading date and found four loci that could explain the natural variation of the heading date in this population. At the same time, we developed recombinant inbred lines (RILs) crossed by the early-heading weedy rice WR04-6 and its accompanied japonica cultivar ShenNong 265 (SN265) to carry out a QTL mapping analysis of the heading date and mapped four quantitative trait locus (QTLs) and three epistatic effect gene pairs. The major locus on chromosome 6 overlapped with the GWAS result. Further analysis found that two genes, Hd1 and OsCCT22, on chromosome 6 (Locus 2 and Locus 3) may be the key points of the early-heading character of weedy rice. As minor effect genes, Dth7 and Hd16 also have genetic contributions to the early heading of weedy rice. In the process of developing the RIL population, we introduced fragments of Locus 2 and Locus 3 from the weedy rice into super-high-yielding japonica rice, which successfully promoted its heading date by at least 10 days and expanded the rice suitable cultivation area northward by about 400 km. This study successfully revealed the genetic basis of the early heading of weedy rice and provided a new idea for the genetic improvement of cultivated rice by weedy rice.

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“…By interacting with two transcription factors, OsHOX3 and OsVP1, the gene inhibits the activity of the ABA receptor OsPYL5 in a hypoxic environment, reduces the sensitivity of ABA, and also activates the biosynthesis of gibberellin (GA), ultimately causing strong germination and emergence of weedy rice seeds. However, in modern genetic improvement, the lost of 4 bases of OsGF14h in cultivated japonica rice caused the the weakening of its function, so germination and emergence were limited under hypoxia conditions (Sun et al, 2022).…”

Section: Improving Ag Tolerance By Pyramiding Breedingmentioning

confidence: 99%

High-density genetic mapping identified QTLs for anaerobic germination tolerance in rice

Liang

Du²,

Pang³

et al. 2022

Front. Plant Sci.

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The tolerance of rice anaerobic germination (AG) is the main limiting factor for direct seeding application, yet the genetics mechanism is still in its infancy. In the study, recombinant inbred lines population of TD70 Japonica cultivar and Kasalath Indica cultivar, was employed to construct a high-density genetic map by whole genome re-sequencing. As a result, a genetic map containing 12,328 bin-markers was constructed and a total of 50 QTLs were then detected for CL(coleoptile length), CD (coleoptile diameter), CSA (coleoptile surface area) and CV (coleoptile volume) related traits in the two stages of anaerobic treatment using complete interval mapping method (inclusive composite interval mapping, ICIM). Among the four traits associated with coleoptile, coleoptile volume had the largest number of QTLs (17), followed by coleoptile diameter (16), and coleoptile length had 5 QTLs. These QTLs could explain phenotypic contribution rates ranging from 0.34% to 11.17% and LOD values ranging from 2.52 to 11.57. Combined with transcriptome analysis, 31 candidate genes were identified. Furthermore, 12 stable QTLs were used to detect the aggregation effect analysis. Besides, It was found that individuals with more aggregation synergistic alleles had higher phenotypic values in different environments. Totally, high-density genetic map, QTL mapping and aggregation effect analysis of different loci related to the anaerobic germination of rice seeds were conducted to lay a foundation for the fine mapping of related genes in subsequent assisted breeding.

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Regain flood adaptation in rice through a 14-3-3 protein OsGF14h

Cited by 41 publications

References 66 publications

Novel quantitative trait locus qSDR3.1 represses Oryza sativa. L seed dormancy

Novel quantitative trait locus qSDR3.1 represses Oryza sativa. L seed dormancy

Genetic basis of the early heading of high-latitude weedy rice

High-density genetic mapping identified QTLs for anaerobic germination tolerance in rice

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