Dear Editor,Traditionally,the consumption of milled rice(starchy endosperm) as a staple food mainly provides calories for human society,and the lack of many important nutrients in such processed grains has led to maln...Dear Editor,Traditionally,the consumption of milled rice(starchy endosperm) as a staple food mainly provides calories for human society,and the lack of many important nutrients in such processed grains has led to malnutrition in rice-consuming regions worldwide(United Nations System Standing Committee on Nutrition,2004).展开更多
The rice disease resistance （R） gene Xa3/Xa26 （having also been named Xa3 and Xa26） against Xanthomonas oryzae pv. oryzae （Xoo）, which causes bacterial blight disease, belongs to a multiple gene family clustered...The rice disease resistance （R） gene Xa3/Xa26 （having also been named Xa3 and Xa26） against Xanthomonas oryzae pv. oryzae （Xoo）, which causes bacterial blight disease, belongs to a multiple gene family clustered in chromosome 11 and is from an AA genome rice cultivar （Oryza sativa L.）. This family encodes leucine-rich repeat （LRR） receptor kinase- type proteins, Here, we show that the orthologs （alleles） of Xa3/Xa26, Xa3/Xa26-2, and Xa3/Xa26-3, from wild Oryza spe- cies O. officinalis （CC genome） and O. minuta （BBCC genome）, respectively, were also R genes against Xoo. Xa3/Xa26-2 and Xa3/Xa26-3 conferred resistance to 16 of the 18 Xoo strains examined. Comparative sequence analysis of the Xa3/Xa26 families in the two wild Oryza species showed that Xa3/Xa26-3 appeared to have originated from the CC genome of O. minuta. The predicted proteins encoded by Xa3/Xa26, Xa3/Xa26-2, and Xa3/Xa26-3 share 91-99% sequence identity and 94-99% sequence similarity. Transgenic plants carrying a single copy of Xa3/Xa26, Xa3/Xa26-2, or Xa3PXa26-3, in the same genetic background, showed a similar resistance spectrum to a set of Xoo strains, although plants carrying Xa3/Xa26-2 or Xa3/Xa26-3 showed lower resistance levels than the plants carrying Xa3/Xa26. These results suggest that the Xa3/Xa26 locus predates the speciation of A and C genome, which is approximately 7.5 million years ago. Thus, the resistance spec- ificity of this locus has been conserved for a long time.展开更多
We constructed a physical map of O. sativa ssp. japonica cv. ZH11 and compared it and its random sample sequences with the Nipponbare RefSeq derived from the same subspecies. This comparison showed that the two japoni...We constructed a physical map of O. sativa ssp. japonica cv. ZH11 and compared it and its random sample sequences with the Nipponbare RefSeq derived from the same subspecies. This comparison showed that the two japonica genomes were highly syntenic but revealed substantial differences in terms of structural variations, rates of substitutions and indels, and transposable element content. For example, contractions/expansions as large as 450 kb and repeat sequences that were present in high copy numbers only in ZH11 were detected. In tri-alignment regions using the indica variety 93-11 sequence as an outgroup, we found that： （1） the substitution rates of the two japonica-indica inter- subspecies comparison combinations were close but almost a magnitude higher than the substitution rate between the japonica rice varieties ZH11 and Nipponbare; （2） of the substitutions found between ZH11 and Nipponbare, 47.2% occurred in ZH11 and 52.6% in Nipponbare; （3） of the indels found between ZH11 and Nipponbare, the indels that occurred in ZH11 were 15.8 times of those in Nipponbare. Of the indels that occurred in ZH11, 75.67% were insertions and 24.33% deletions. Of the indels that occurred in Nipponbare, 48.23% were insertions and 51.77% were deletions. The ZH11 com- parative map covered four Nipponbare physical gaps, detected assembly errors in the Nipponbare sequence, and was integrated with the FSTs of a large ZH11 T-DNA insertion mutant library. ZH11 BAC clones can be browsed, searched, and obtained at our website, http：//GResource.hzau.edu.cn.展开更多
Dear Editor,Asian rice(Oryza sativa)is the staple food for half the world and is a model crop that has been extensively studied.It contributes20%of calories to the human diet(Stein et al.,2018).With the increase in g...Dear Editor,Asian rice(Oryza sativa)is the staple food for half the world and is a model crop that has been extensively studied.It contributes20%of calories to the human diet(Stein et al.,2018).With the increase in global population and rapid changes in climate,rice breeders need to develop new and sustainable cultivars with higher yields,healthier grains,and reduced environmental footprints(Wing et al.,2018).Since the first gold-standard reference genome of rice variety Nipponbare was published(International Rice Genome Sequencing Project,2005),an increasing number of rice accessions have been sequenced,assembled,and annotated with global efforts.Nowadays,a single reference genome is obviously insufficient to perform the genetic difference analysis for rice accessions.Therefore,the pan-genome has been proposed as a solution,which allows the discovery of more presence-absence variants compared with single-reference genome-based studies(Zhao et al.,2018).Over the past years,several databases,such as RAP-db(https://rapdb.dna.affrc.go.jp),RGAP(http://rice.uga.edu),and Gramene(https://www.gramene.org),have long-term served rice genomic research by providing information based on one or a series of individual reference genomes.To integrate and utilize the genomic information of multiple accessions,we performed comparative analyses and established the user-friendly Rice Gene Index(RGI;https://riceome.hzau.edu.cn)platform.RGI is the first gene-based pan-genome database for rice.展开更多
基金supported by the National Key R&D Program of China (2024YFF1000600)the National Natural Science Foundation of China (31821005,32261143466)+3 种基金the Hubei Fund to Support High Quality Development of Seed Industry (HBZY2023B001-08)the Science and Technology Major Program of Hubei Province (2021ABA011)the Hubei Provincial Natural Science Foundation of China (2023AFA043)the Earmarked Fund for China Agriculture Research System (CARS-01)。
文摘Dear Editor,Traditionally,the consumption of milled rice(starchy endosperm) as a staple food mainly provides calories for human society,and the lack of many important nutrients in such processed grains has led to malnutrition in rice-consuming regions worldwide(United Nations System Standing Committee on Nutrition,2004).
基金This work was supported by grants from the National Program on the Development of Basic Research in China，the National Natural Science Foundation of China
文摘The rice disease resistance （R） gene Xa3/Xa26 （having also been named Xa3 and Xa26） against Xanthomonas oryzae pv. oryzae （Xoo）, which causes bacterial blight disease, belongs to a multiple gene family clustered in chromosome 11 and is from an AA genome rice cultivar （Oryza sativa L.）. This family encodes leucine-rich repeat （LRR） receptor kinase- type proteins, Here, we show that the orthologs （alleles） of Xa3/Xa26, Xa3/Xa26-2, and Xa3/Xa26-3, from wild Oryza spe- cies O. officinalis （CC genome） and O. minuta （BBCC genome）, respectively, were also R genes against Xoo. Xa3/Xa26-2 and Xa3/Xa26-3 conferred resistance to 16 of the 18 Xoo strains examined. Comparative sequence analysis of the Xa3/Xa26 families in the two wild Oryza species showed that Xa3/Xa26-3 appeared to have originated from the CC genome of O. minuta. The predicted proteins encoded by Xa3/Xa26, Xa3/Xa26-2, and Xa3/Xa26-3 share 91-99% sequence identity and 94-99% sequence similarity. Transgenic plants carrying a single copy of Xa3/Xa26, Xa3/Xa26-2, or Xa3PXa26-3, in the same genetic background, showed a similar resistance spectrum to a set of Xoo strains, although plants carrying Xa3/Xa26-2 or Xa3/Xa26-3 showed lower resistance levels than the plants carrying Xa3/Xa26. These results suggest that the Xa3/Xa26 locus predates the speciation of A and C genome, which is approximately 7.5 million years ago. Thus, the resistance spec- ificity of this locus has been conserved for a long time.
基金This work was supported by a grant from the National Natural Science Foundation of China for International Collaboration，the 111 Project
文摘We constructed a physical map of O. sativa ssp. japonica cv. ZH11 and compared it and its random sample sequences with the Nipponbare RefSeq derived from the same subspecies. This comparison showed that the two japonica genomes were highly syntenic but revealed substantial differences in terms of structural variations, rates of substitutions and indels, and transposable element content. For example, contractions/expansions as large as 450 kb and repeat sequences that were present in high copy numbers only in ZH11 were detected. In tri-alignment regions using the indica variety 93-11 sequence as an outgroup, we found that： （1） the substitution rates of the two japonica-indica inter- subspecies comparison combinations were close but almost a magnitude higher than the substitution rate between the japonica rice varieties ZH11 and Nipponbare; （2） of the substitutions found between ZH11 and Nipponbare, 47.2% occurred in ZH11 and 52.6% in Nipponbare; （3） of the indels found between ZH11 and Nipponbare, the indels that occurred in ZH11 were 15.8 times of those in Nipponbare. Of the indels that occurred in ZH11, 75.67% were insertions and 24.33% deletions. Of the indels that occurred in Nipponbare, 48.23% were insertions and 51.77% were deletions. The ZH11 com- parative map covered four Nipponbare physical gaps, detected assembly errors in the Nipponbare sequence, and was integrated with the FSTs of a large ZH11 T-DNA insertion mutant library. ZH11 BAC clones can be browsed, searched, and obtained at our website, http：//GResource.hzau.edu.cn.
基金supported by Fundamental Research Funds for the Central Universities(2662020SKPY010)the Major Project of Hubei Hongshan Laboratory(2022HSZD031)Huazhong Agricultural University’s Start-up Fund to J.Z.
文摘Dear Editor,Asian rice(Oryza sativa)is the staple food for half the world and is a model crop that has been extensively studied.It contributes20%of calories to the human diet(Stein et al.,2018).With the increase in global population and rapid changes in climate,rice breeders need to develop new and sustainable cultivars with higher yields,healthier grains,and reduced environmental footprints(Wing et al.,2018).Since the first gold-standard reference genome of rice variety Nipponbare was published(International Rice Genome Sequencing Project,2005),an increasing number of rice accessions have been sequenced,assembled,and annotated with global efforts.Nowadays,a single reference genome is obviously insufficient to perform the genetic difference analysis for rice accessions.Therefore,the pan-genome has been proposed as a solution,which allows the discovery of more presence-absence variants compared with single-reference genome-based studies(Zhao et al.,2018).Over the past years,several databases,such as RAP-db(https://rapdb.dna.affrc.go.jp),RGAP(http://rice.uga.edu),and Gramene(https://www.gramene.org),have long-term served rice genomic research by providing information based on one or a series of individual reference genomes.To integrate and utilize the genomic information of multiple accessions,we performed comparative analyses and established the user-friendly Rice Gene Index(RGI;https://riceome.hzau.edu.cn)platform.RGI is the first gene-based pan-genome database for rice.
