Common wheat （Triticum aestivum L.） is one of the most important crops, and intra-specific wheat hybrids have obvious heterosis in yield and protein quality. Therefore, utilization of hybrid wheat varieties offers a...Common wheat （Triticum aestivum L.） is one of the most important crops, and intra-specific wheat hybrids have obvious heterosis in yield and protein quality. Therefore, utilization of hybrid wheat varieties offers an effective way to increase yield and nutrition. Cytoplasmic male sterility （CMS） systems are a useful genetic tool for hybrid crop breeding, and are ideal models for studying the genetic interaction and cooperative function of mitochondrial and nuclear genomes in plants （Schnable and Wise, 1998; Hanson and Bentolila, 2004）.展开更多
Oryza rufipogon Griff.is a wild progenitor of the Asian cultivated rice Oryza sativa.To better understand the genomic diversity of the wild rice,high-quality reference genomes of O.rufipogon populations are needed,whi...Oryza rufipogon Griff.is a wild progenitor of the Asian cultivated rice Oryza sativa.To better understand the genomic diversity of the wild rice,high-quality reference genomes of O.rufipogon populations are needed,which also facilitate utilization of the wild genetic resources in rice breeding.In this study,we generated a chromosome-level genome assembly of O.rufipogon using a combination of short-read sequencing,single-molecule sequencing,BioNano and Hi-C platforms.The genome sequence(399.8 Mb)was assembled into 46 scaffolds on the 12 chromosomes,with contig N50 and scaffold N50 of 13.2 Mb and 20.3 Mb,respectively.The genome contains 36,520 protein-coding genes,and 49.37% of the genome consists of repetitive elements.The genome has strong synteny with those of the O.sativa subspecies indica and japonica,but containing some large structural variations.Evolutionary analysis unveiled the polyphyletic origins of O.sativa,in which the japonica and indica genome formations involved different divergent O.rufipogon(including O.nivara)lineages,accompanied by introgression of genomic regions between japonica and indica.This high-quality reference genome provides insight on the genome evolution of the wild rice and the origins of the O.sativa subspecies,and valuable information for basic research and rice breeding.展开更多
Accurate quantitative reverse transcription PCR(q RT-PCR)requires reliable reference genes whose expression does not vary in different tissues and developmental stages.However,few reliable reference genes are availabl...Accurate quantitative reverse transcription PCR(q RT-PCR)requires reliable reference genes whose expression does not vary in different tissues and developmental stages.However,few reliable reference genes are available for q RT-PCR in rice(Oryza sativa).Here,we established an effective strategy for identifying novel reference genes(NRGs)for reliable normalization of q RT-PCR data in various rice organs and developmental stages.We selected candidate NRGs using the Information Commons for Rice Database and confirmed their expression in Rice Expression Profile Database(Rice XPro)data.Genes with low variation(<2.5 cycle quantification)across tissues and developmental stages,and little fluctuation in expression in heatmaps from Rice XPro data were considered stable NRGs.To validate this strategy,we selected 11 candidate NRGs and calculated their expression stability in different spatio-temporal conditions using five programs,and compared these genes with five established reference genes(ERGs).Only one of the ERGs(UBQ5)was reliable and 10 of the candidate NRGs were more stable than the four remaining ERGs.Therefore,public transcriptomic databases are useful for identifying NRGs.We selected two NRGs,UFC1(Homolog of UFM1-Conjugating Enzyme 1)and Fha B(Homolog of Adhesin Fha B)for q RT-PCR analysis in rice;their homologs might be suitable for other monocot plants.展开更多
基金supported by the National Natural Science Foundation of China(No.30971844)the Fundamental Research Funds of Northwest A & F University(No. QN2011003)+1 种基金China Postdoctoral Science Foundation to Wang Junwei(No.20070410835)the Tang Zhong-Ying Breeding Funding Project of Northwest A & F University
文摘Common wheat （Triticum aestivum L.） is one of the most important crops, and intra-specific wheat hybrids have obvious heterosis in yield and protein quality. Therefore, utilization of hybrid wheat varieties offers an effective way to increase yield and nutrition. Cytoplasmic male sterility （CMS） systems are a useful genetic tool for hybrid crop breeding, and are ideal models for studying the genetic interaction and cooperative function of mitochondrial and nuclear genomes in plants （Schnable and Wise, 1998; Hanson and Bentolila, 2004）.
基金supported by the Key Research Program of Guangzhou Science Technology and Innovation Commission(201904020030)the Major Program of Guangdong Basic and Applied Basic Research(2019B030302006)the National Natural Science Foundation of China(31701051)。
文摘Oryza rufipogon Griff.is a wild progenitor of the Asian cultivated rice Oryza sativa.To better understand the genomic diversity of the wild rice,high-quality reference genomes of O.rufipogon populations are needed,which also facilitate utilization of the wild genetic resources in rice breeding.In this study,we generated a chromosome-level genome assembly of O.rufipogon using a combination of short-read sequencing,single-molecule sequencing,BioNano and Hi-C platforms.The genome sequence(399.8 Mb)was assembled into 46 scaffolds on the 12 chromosomes,with contig N50 and scaffold N50 of 13.2 Mb and 20.3 Mb,respectively.The genome contains 36,520 protein-coding genes,and 49.37% of the genome consists of repetitive elements.The genome has strong synteny with those of the O.sativa subspecies indica and japonica,but containing some large structural variations.Evolutionary analysis unveiled the polyphyletic origins of O.sativa,in which the japonica and indica genome formations involved different divergent O.rufipogon(including O.nivara)lineages,accompanied by introgression of genomic regions between japonica and indica.This high-quality reference genome provides insight on the genome evolution of the wild rice and the origins of the O.sativa subspecies,and valuable information for basic research and rice breeding.
基金supported by grants from the National Key Research and Development Program of China(2016YFD0100601)the National Natural Science Foundation of China(31772104,31771739,31600977)
文摘Accurate quantitative reverse transcription PCR(q RT-PCR)requires reliable reference genes whose expression does not vary in different tissues and developmental stages.However,few reliable reference genes are available for q RT-PCR in rice(Oryza sativa).Here,we established an effective strategy for identifying novel reference genes(NRGs)for reliable normalization of q RT-PCR data in various rice organs and developmental stages.We selected candidate NRGs using the Information Commons for Rice Database and confirmed their expression in Rice Expression Profile Database(Rice XPro)data.Genes with low variation(<2.5 cycle quantification)across tissues and developmental stages,and little fluctuation in expression in heatmaps from Rice XPro data were considered stable NRGs.To validate this strategy,we selected 11 candidate NRGs and calculated their expression stability in different spatio-temporal conditions using five programs,and compared these genes with five established reference genes(ERGs).Only one of the ERGs(UBQ5)was reliable and 10 of the candidate NRGs were more stable than the four remaining ERGs.Therefore,public transcriptomic databases are useful for identifying NRGs.We selected two NRGs,UFC1(Homolog of UFM1-Conjugating Enzyme 1)and Fha B(Homolog of Adhesin Fha B)for q RT-PCR analysis in rice;their homologs might be suitable for other monocot plants.
