Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa)
Abstract Background Cultivated rice consists of two subspecies, Indica and Japonica, that exhibit well-characterized differences at the morphological and genetic levels. However, the differences between these subspecies at the transcriptome level remains largely unexamined. Here, we provide a compre...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2020-06-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12864-020-06786-6 |
| _version_ | 1818459795819069440 |
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| author | Malachy T. Campbell Qian Du Kan Liu Sandeep Sharma Chi Zhang Harkamal Walia |
| author_facet | Malachy T. Campbell Qian Du Kan Liu Sandeep Sharma Chi Zhang Harkamal Walia |
| author_sort | Malachy T. Campbell |
| collection | DOAJ |
| description | Abstract Background Cultivated rice consists of two subspecies, Indica and Japonica, that exhibit well-characterized differences at the morphological and genetic levels. However, the differences between these subspecies at the transcriptome level remains largely unexamined. Here, we provide a comprehensive characterization of transcriptome divergence and cis-regulatory variation within rice using transcriptome data from 91 accessions from a rice diversity panel (RDP1). Results The transcriptomes of the two subspecies of rice are highly divergent. Japonica have significantly lower expression and genetic diversity relative to Indica, which is likely a consequence of a population bottleneck during Japonica domestication. We leveraged high-density genotypic data and transcript levels to identify cis-regulatory variants that may explain the genetic divergence between the subspecies. We identified significantly more eQTL that were specific to the Indica subspecies compared to Japonica, suggesting that the observed differences in expression and genetic variability also extends to cis-regulatory variation. Conclusions Using RNA sequencing data for 91diverse rice accessions and high-density genotypic data, we show that the two species are highly divergent with respect to gene expression levels, as well as the genetic regulation of expression. The data generated by this study provide, to date, the largest collection of genome-wide transcriptional levels for rice, and provides a community resource to accelerate functional genomic studies in rice. |
| first_indexed | 2024-12-14T23:20:02Z |
| format | Article |
| id | doaj.art-de2d1ff3e2b44853b0e68b8bcaaefa31 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-14T23:20:02Z |
| publishDate | 2020-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-de2d1ff3e2b44853b0e68b8bcaaefa312022-12-21T22:44:00ZengBMCBMC Genomics1471-21642020-06-0121111610.1186/s12864-020-06786-6Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa)Malachy T. Campbell0Qian Du1Kan Liu2Sandeep Sharma3Chi Zhang4Harkamal Walia5Department of Agronomy and Horticulture, University of Nebraska LincolnSchool of Biological Sciences, University of Nebraska LincolnSchool of Biological Sciences, University of Nebraska LincolnDepartment of Agronomy and Horticulture, University of Nebraska LincolnSchool of Biological Sciences, University of Nebraska LincolnDepartment of Agronomy and Horticulture, University of Nebraska LincolnAbstract Background Cultivated rice consists of two subspecies, Indica and Japonica, that exhibit well-characterized differences at the morphological and genetic levels. However, the differences between these subspecies at the transcriptome level remains largely unexamined. Here, we provide a comprehensive characterization of transcriptome divergence and cis-regulatory variation within rice using transcriptome data from 91 accessions from a rice diversity panel (RDP1). Results The transcriptomes of the two subspecies of rice are highly divergent. Japonica have significantly lower expression and genetic diversity relative to Indica, which is likely a consequence of a population bottleneck during Japonica domestication. We leveraged high-density genotypic data and transcript levels to identify cis-regulatory variants that may explain the genetic divergence between the subspecies. We identified significantly more eQTL that were specific to the Indica subspecies compared to Japonica, suggesting that the observed differences in expression and genetic variability also extends to cis-regulatory variation. Conclusions Using RNA sequencing data for 91diverse rice accessions and high-density genotypic data, we show that the two species are highly divergent with respect to gene expression levels, as well as the genetic regulation of expression. The data generated by this study provide, to date, the largest collection of genome-wide transcriptional levels for rice, and provides a community resource to accelerate functional genomic studies in rice.http://link.springer.com/article/10.1186/s12864-020-06786-6RNA sequencingOryza sativaPopulation geneticsRegulatory variationExpression quantitative trait lociGene expression |
| spellingShingle | Malachy T. Campbell Qian Du Kan Liu Sandeep Sharma Chi Zhang Harkamal Walia Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa) BMC Genomics RNA sequencing Oryza sativa Population genetics Regulatory variation Expression quantitative trait loci Gene expression |
| title | Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa) |
| title_full | Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa) |
| title_fullStr | Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa) |
| title_full_unstemmed | Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa) |
| title_short | Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa) |
| title_sort | characterization of the transcriptional divergence between the subspecies of cultivated rice oryza sativa |
| topic | RNA sequencing Oryza sativa Population genetics Regulatory variation Expression quantitative trait loci Gene expression |
| url | http://link.springer.com/article/10.1186/s12864-020-06786-6 |
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