Genome-wide analyses reveal the role of noncoding variation in complex traits during rice domestication

Zheng, Xiaoming; Chen, J.; Pang, Hongbo; Liu, S.; Gao, Qian; Wang, J. R.; Qiao, Weihua; Wang, H.; Liu, J.; Olsen, Kenneth M.; Yang, Qing

doi:10.1126/sciadv.aax3619

Cited by 40 publications

(39 citation statements)

References 41 publications

(77 reference statements)

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“…Zheng et al 2019);(2) 98.76% of the interval sequences between these transcribed regions were less than 5 kb in length, which is consistent with the distribution characteristics of intergenic pre-miRNAs(Zheng et al 2019); and (3) the sequences of these transcribed regions shared high similarity with 37.2% of the ncRNAs deposited in the Ensembl ncRNA database. These results also highlight the significance of RNA-Seq in identifying the boundaries between sense-antisense gene pairs and quantitatively characterizing transcriptomes at a high resolution.…”

supporting

confidence: 74%

“…During rice domestication, artificial selection has been reported to have a major impact on rice gene expression (Zheng et al 2019). According to previous studies on domesticated plants, the 5' regulatory regions of many genes evolved under the pressure of artificial selection and that the 5' regulatory regions of DEGs evolved faster those of non-DEGs .…”

Section: Discussionmentioning

confidence: 99%

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Comparative analysis of the transcriptomes of two rice subspecies reveals differentially expressed genes associated with phenotypic differences and reproductive isolation

Pang

Wang

Chen

et al. 2019

Preprint

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Background: Rice has been used as a model plant to study adaptation, genome evolution and reproductive isolation among species and the genetics and evolution of complex traits. Two subspecies of cultivated rice, Oryza sativa ssp. indica and O. sativa ssp. japonica, with reproductive isolation and differences in morphology and phenotypic differences, were established during the process of rice domestication. Results: To understand how domestication has changed the transcriptomes of the two rice subspecies and given rise to the phenotypic differences, we obtained approximately 700 Gb RNA-Seq data from 26 indica and 25 japonica plants, and identified 97,005 transcribed fragments and 7702 novel transcriptionally active regions. We also identified 1857 (4.58% in all genes) differentially expressed genes (DEGs) between indica and japonica rice. According to previous population genetic analyses, these DEGs may associate with the phenotypic differences between the two subspecies. Functional annotation of these DEGs indicates that they are involved in cell wall biosynthesis and reproductive processes. Furthermore, compared with the non-DEGs, the DEGs from both subspecies had more 5′ flanking regions with low polymorphism to divergence ratios, indicating a stronger positive selection pressure on the regulation of the DEGs.Conclusion: This study improves our understanding of the rice genome by comparatively analyzing the transcriptomes of indica and japonica rice and identifies DEGs that may be responsible for the reproductive isolation and phenotypic differences between the two rice subspecies.

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supporting

confidence: 74%

Section: Discussionmentioning

confidence: 99%

Comparative analysis of the transcriptomes of two rice subspecies reveals differentially expressed genes associated with phenotypic differences and reproductive isolation

Pang

Wang

Chen

et al. 2019

Preprint

Self Cite

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“…PCR amplifications were performed with a 5700 thermocycler (PE Applied Biosystems, USA 41 . Based on solid foundation on study of O. rufipogon diversity, we selected the markers without null alleles for analysis 12,14,[42][43][44][45] .We used POPGENE 1.31 46 and GENEPOP 3.4 47 to calculate the genetic diversity parameters: the mean number of alleles per locus (A), the effective number of alleles (A E ), the Shannon-Weaver information index (I), the observed heterozygosity (H O ), and the expected heterozygosity (H E ) 48,49 . Deviation from Hardy-Weinberg equilibrium and population differentiation were assessed at each locus across all populations using F statistics, including the fixation index within populations (F IS ), the fixation index across all populations (F IT ) and the gene differentiation index (F ST ) 50 .…”

Section: Groupmentioning

confidence: 99%

Conservation recommendations for Oryza rufipogon Griff. in China based on genetic diversity analysis

Wang

Shi

et al. 2020

Sci Rep

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Over the past 30 years, human disturbance and habitat fragmentation have severely endangered the survival of common wild rice (Oryza rufipogon Griff.) in China. A better understanding of the genetic structure of O. rufipogon populations will therefore be useful for the development of conservation strategies. We examined the diversity and genetic structure of natural O. rufipogon populations at the national, provincial, and local levels using simple sequence repeat (SSR) markers. Twenty representative populations from sites across China showed high levels of genetic variability, and approximately 44% of the total genetic variation was among populations. At the local level, we studied fourteen populations in Guangxi Province and four populations in Jiangxi Province. Populations from similar ecosystems showed less genetic differentiation, and local environmental conditions rather than geographic distance appeared to have influenced gene flow during population genetic evolution. We identified a triangular area, including northern Hainan, southern Guangdong, and southwestern Guangxi, as the genetic diversity center of O. rufipogon in China, and we proposed that this area should be given priority during the development of ex situ and in situ conservation strategies. Populations from less common ecosystem types should also be given priority for in situ conservation. Common wild rice (Oryza rufipogon Griff.) is the putative progenitor of Asian cultivated rice, one of the most important food crops in the world. It is also an important source of germplasm for rice improvement 1-3. Ding Ying found wild rice (O. rufipogon) in Guangzhou in 1926, and the wild × cultivated cross Zhong Shan No. 1 was widely planted in South China for more than 50 years. In 1970, Yuan Longping and his assistant discovered wild rice with male sterility in Hainan and used it to breed high yielding "three-line" hybrid rice varieties 4,5. The increased yield of this hybrid rice saved thousands of lives in China and around the world. In recent years, wild rice has been used to introduce genes that confer agriculturally beneficial traits into cultivated species, and it holds great potential for future rice breeding efforts. Before the 1970s, O. rufipogon was found in 113 counties of eight provinces in southern China, including Guangdong, Guangxi, Hainan, Yunnan, Hunan, Jiangxi, Fujian, and Taiwan, although the populations in Taiwan disappeared in 1978 6,7. Since the 1980s, many wild rice habitats have been converted to agricultural or industrial use because of the rapid development of the rural economy and the population expansion in rural China. Consequently, areas of wild rice cultivation have dramatically decreased. Our recent work indicates that approximately 70% of the O. rufipogon populations have disappeared, and all large populations (growth area > 33 hm 2) have either disappeared or decreased dramatically (unpublished data). The threatened status of wild rice has attracted increasing attention in China, and there is a desire to collect samples...

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“…The primary barrier in lncRNA studies is the ability to distinguish functional lncRNA candidates from the background, which is full of transcriptional noise. Functional lncRNA screenings have been carried out in multiple published studies with different screening strategies, including the reverse genetics strategy, which uses CRISPRi technology [49,50]; comparative genomics and transcriptome-based prediction across species, wild species, and cultivars [39,51]; and mapping based on epigenetic recombination lines [43,52]. The reported practices on functional lncRNA screening are hindered by limitations.…”

Section: The Lncrna Function Is High Likely Speci C To the Species Ormentioning

confidence: 99%

“…Some lncRNAs are affected by positive selection in domesticated species, such as BRAFP in mammals [3]. The expression of lncRNAs is also altered during domestication in rice [4]. Therefore, lncRNAs actively take part in the evolution of species just as coding genes do.…”

Section: Introductionmentioning

confidence: 99%

The Functional Examination of Conserved and Non-conserved lncRNA in Allotetraploid Gossypium hirsutum

Guan¹,

Wang²,

Han³

et al. 2020

Preprint

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Background The relationship between the lncRNA conservation level and its function is controversial. One of the technique barrier to address this question is how to define the conserved non-coding genes across species.Results We developed an evolutionary model using diploid and allotetraploid cotton species to identify 80% of the non-coding transcripts unique to the allotetraploid cotton in comparison with its diploid ancestors. This led us to define conserved lncRNA and non-conserved lncRNA based on their conservation throughout polyploid evolution. LncRNA expression was preferentially associated with the flanking protein-coding genes, indicating a regulatory role in cis in response to environmental stimuli. However, the conserved and non-conserved lncRNAs showed no difference in their levels of association with the expression of the flanking protein-coding genes. The 111 selected highly expressed conserved and non-conserved lncRNA candidates were subjected to a virus-induced gene silencing operation that was integrated with abiotic stress treatments. From the low-throughput, functional screening pilot test, we obtained candidate lncRNAs related to plant height, tolerance to drought and other abiotic stresses. Conclusions The conservation level of the lncRNAs may impact on their expression patterns and functions as individual case rather than in genome wide.

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Genome-wide analyses reveal the role of noncoding variation in complex traits during rice domestication

Cited by 40 publications

References 41 publications

Comparative analysis of the transcriptomes of two rice subspecies reveals differentially expressed genes associated with phenotypic differences and reproductive isolation

Comparative analysis of the transcriptomes of two rice subspecies reveals differentially expressed genes associated with phenotypic differences and reproductive isolation

Conservation recommendations for Oryza rufipogon Griff. in China based on genetic diversity analysis

The Functional Examination of Conserved and Non-conserved lncRNA in Allotetraploid Gossypium hirsutum

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