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Li G, Jiang D, Wang J, Liao Y, Zhang T, Zhang H, Dai X, Ren H, Chen C, Zheng Y. A High-Continuity Genome Assembly of Chinese Flowering Cabbage ( Brassica rapa var. parachinensis) Provides New Insights into Brassica Genome Structure Evolution. PLANTS (BASEL, SWITZERLAND) 2023; 12:2498. [PMID: 37447059 DOI: 10.3390/plants12132498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/19/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023]
Abstract
Chinese flowering cabbage (Brassica rapa var. parachinensis) is a popular and widely cultivated leaf vegetable crop in Asia. Here, we performed a high quality de novo assembly of the 384 Mb genome of 10 chromosomes of a typical cultivar of Chinese flowering cabbage with an integrated approach using PacBio, Illumina, and Hi-C technology. We modeled 47,598 protein-coding genes in this analysis and annotated 52% (205.9/384) of its genome as repetitive sequences including 17% in DNA transposons and 22% in long terminal retrotransposons (LTRs). Phylogenetic analysis reveals the genome of the Chinese flowering cabbage has a closer evolutionary relationship with the AA diploid progenitor of the allotetraploid species, Brassica juncea. Comparative genomic analysis of Brassica species with different subgenome types (A, B and C) reveals that the pericentromeric regions on chromosome 5 and 6 of the AA genome have been significantly expanded compared to the orthologous genomic regions in the BB and CC genomes, largely driven by LTR-retrotransposon amplification. Furthermore, we identified a large number of structural variations (SVs) within the B. rapa lines that could impact coding genes, suggesting the functional significance of SVs on Brassica genome evolution. Overall, our high-quality genome assembly of the Chinese flowering cabbage provides a valuable genetic resource for deciphering the genome evolution of Brassica species and it can potentially serve as the reference genome guiding the molecular breeding practice of B. rapa crops.
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Affiliation(s)
- Guangguang Li
- Guangzhou Academy of Agricultural Sciences, Guangzhou 510335, China
| | - Ding Jiang
- Guangzhou Academy of Agricultural Sciences, Guangzhou 510335, China
| | - Juntao Wang
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Yi Liao
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Ting Zhang
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Hua Zhang
- Guangzhou Academy of Agricultural Sciences, Guangzhou 510335, China
| | - Xiuchun Dai
- Guangzhou Academy of Agricultural Sciences, Guangzhou 510335, China
| | - Hailong Ren
- Guangzhou Academy of Agricultural Sciences, Guangzhou 510335, China
| | - Changming Chen
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Yansong Zheng
- Guangzhou Academy of Agricultural Sciences, Guangzhou 510335, China
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Chang L, Hu M, Ning J, He W, Gao J, Ndjiondjop MN, Fu Y, Liu F, Sun H, Gu P, Sun C, Zhu Z. The genetic control of glabrous glume during African rice domestication. J Genet Genomics 2022; 49:427-436. [DOI: 10.1016/j.jgg.2022.02.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/08/2022] [Accepted: 02/08/2022] [Indexed: 11/27/2022]
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Huang L, Liu H, Wu J, Zhao R, Li Y, Melaku G, Zhang S, Huang G, Bao Y, Ning M, Chen B, Gong Y, Hu Q, Zhang J, Zhang Y. Evolution of Plant Architecture in Oryza Driven by the PROG1 Locus. FRONTIERS IN PLANT SCIENCE 2020; 11:876. [PMID: 32655603 PMCID: PMC7325765 DOI: 10.3389/fpls.2020.00876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 05/28/2020] [Indexed: 05/20/2023]
Abstract
The genetic control of plant architecture in crops is critical for agriculture and understanding morphological evolution. This study showed that an open reading frame (ORF) of the rice domestication gene PROG1 appeared 3.4-3.9 million years ago (Mya). Subsequently, it acquired a novel protein-coding gene function in the genome of O. rufipogon (~0.3-0.4 Mya). This extremely young gene and its paralogous C2H2 genes located nearby define the prostrate architecture of O. rufipogon and, thus, are of adaptive significance for wild rice in swamp and water areas. However, selection for dense planting and high yield during rice domestication silenced the PROG1 gene and caused the loss of the RPAD locus containing functional C2H2 paralogs; hence, domesticated lines exhibit an erect plant architecture. Analysis of the stepwise origination process of PROG1 and its evolutionary genetics revealed that this zinc-finger coding gene may have rapidly evolved under positive selection and promoted the transition from non- or semi-prostrate growth to prostrate growth. A transgenic assay showed that PROG1 from O. rufipogon exerts a stronger function compared with PROG1 sequences from other Oryza species. However, the analysis of the expression levels of PROG1 in different Oryza species suggests that the transcriptional regulation of PROG1 has played an important role in its evolution. This study provides the first strong case showing how a fundamental morphological trait evolved in Oryza species driven by a gene locus.
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Affiliation(s)
- Liyu Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, China
- *Correspondence: Liyu Huang,
| | - Hui Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Junjie Wu
- College of Agriculture and Biology Science, Dali University, Dali, China
| | - Ruoping Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | | | - Getachew Melaku
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, China
- Agricultural Biotechnology Directorate of the Ethiopian Biotechnology Institute, Addis Ababa, Ethiopia
| | - Shilai Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, China
| | - Guangfu Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, China
| | - Yachong Bao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, China
| | - Min Ning
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, China
| | - Benjia Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, China
| | - Yurui Gong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, China
| | - Qingyi Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, China
| | - Jing Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, China
| | - Yesheng Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- BGI-Baoshan, Baoshan, China
- Yesheng Zhang,
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Large-scale identification and functional analysis of NLR genes in blast resistance in the Tetep rice genome sequence. Proc Natl Acad Sci U S A 2019; 116:18479-18487. [PMID: 31451649 DOI: 10.1073/pnas.1910229116] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Tetep is a rice cultivar known for broad-spectrum resistance to blast, a devastating fungal disease. The molecular basis for its broad-spectrum resistance is still poorly understood. Is it because Tetep has many more NLR genes than other cultivars? Or does Tetep possess multiple major NLR genes that can individually confer broad-spectrum resistance to blast? Moreover, are there many interacting NLR pairs in the Tetep genome? We sequenced its genome, obtained a high-quality assembly, and annotated 455 nucleotide-binding site leucine-rich repeat (NLR) genes. We cloned and tested 219 NLR genes as transgenes in 2 susceptible cultivars using 5 to 12 diversified pathogen strains; in many cases, fewer than 12 strains were successfully cultured for testing. Ninety cloned NLRs showed resistance to 1 or more pathogen strains and each strain was recognized by multiple NLRs. However, few NLRs showed resistance to >6 strains, so multiple NLRs are apparently required for Tetep's broad-spectrum resistance to blast. This was further supported by the pedigree analyses, which suggested a correlation between resistance and the number of Tetep-derived NLRs. In developing a method to identify NLR pairs each of which functions as a unit, we found that >20% of the NLRs in the Tetep and 3 other rice genomes are paired. Finally, we designed an extensive set of molecular markers for rapidly introducing clustered and paired NLRs in the Tetep genome for breeding new resistant cultivars. This study increased our understanding of the genetic basis of broad-spectrum blast resistance in rice.
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