Asian cultivated rice is one of the most important cereal crops globally,feeding approximately 50%of the world's population.Increasing rice nitrogen use efficiency(NUE)is crucial for achieving high yields with low...Asian cultivated rice is one of the most important cereal crops globally,feeding approximately 50%of the world's population.Increasing rice nitrogen use efficiency(NUE)is crucial for achieving high yields with low nitrogen inputs(Xu et al.,2012;Hu et al.,2023).However,modern cultivars are typically bred for high yields through excessive nitrogen fertilizer use,leading to the loss of beneficial alleles associated with high NUE during the breeding process(Wang and Peng,2017;Hu et al.,2023).Genetic improvement for high NUE should be a key strategy in breeding“Green Super Rice”(GSR)(Yu et al.,2021)and water-saving and drought-resistance rice(WDR)(Luo,2010;Xia et al.,2022)for sustainable agriculture.Asian cultivated rice is highly diverse and harbors vital genetic variants essential for adaptation to different environments(Wing et al.,2018).展开更多
Dissecting the mechanism of drought resistance(DR)and designing drought-resistant rice varieties are promising strategies to address the challenge of climate change.Here,we selected a typical droughtavoidant(DA)variet...Dissecting the mechanism of drought resistance(DR)and designing drought-resistant rice varieties are promising strategies to address the challenge of climate change.Here,we selected a typical droughtavoidant(DA)variety,IRAT109,and a drought-tolerant(DT)variety,Hanhui15,as parents to develop a stable recombinant inbred line(RIL)population(F8,1262 lines).The de novo assembled genomes of both parents were released.By resequencing of the RIL population,a set of 1189216 reliable SNPs were obtained and used to construct a dense genetic map.Using above-and belowground phenomic platforms and multimodal cameras,we captured 139040 image-based traits(i-traits)of whole-plant phenotypes in response to drought stress throughout the entire rice growth period and identified 32586 drought-responsive quantitative trait loci(QTLs),including 2097 unique QTLs.QTLs associated with panicle i-traits occurred more than 600 times on the middle of chromosome 8,and QTLs associated with leaf i-traits occurred more than 800 times on the 50 end of chromosome 3,indicating the potential effects of these QTLs on plant phenotypes.We selected three candidate genes(OsMADS50,OsGhd8,OsSAUR11)related to leaf,panicle,and root traits,respectively,and verified their functions in DR.OsMADS50 was found to negatively regulate DR by modulating leaf dehydration,grain size,and downward root growth.A total of 18 and 21 composite QTLs significantly related to grain weight and plant biomass were also screened from 597 lines in the RIL population under drought conditions in field experiments,and the composite QTL regions showed substantial overlap(76.9%)with known DR gene regions.Based on three candidate DR genes,we proposed a haplotype design suitable for different environments and breeding objectives.This study provides a valuable reference for multimodal and time-series phenomic analyses,deciphers the genetic mechanisms of DA and DT rice varieties,and offers a molecular navigation map for breeding of DR varieties.展开更多
基金supported by Joint Funds of National Natural Science Foundation of China(U24A20399)Natural Science Foundation of Shanghai(23JC1403500,22ZR1455300)+2 种基金Specific university discipline construction project(2023B10564002,2023B10564004)Shanghai Agricultural Science and Technology Innovation Program(2024-02-08-00-12-F00028)Earmarked Fund for China Agriculture Research System(CARS-01).
文摘Asian cultivated rice is one of the most important cereal crops globally,feeding approximately 50%of the world's population.Increasing rice nitrogen use efficiency(NUE)is crucial for achieving high yields with low nitrogen inputs(Xu et al.,2012;Hu et al.,2023).However,modern cultivars are typically bred for high yields through excessive nitrogen fertilizer use,leading to the loss of beneficial alleles associated with high NUE during the breeding process(Wang and Peng,2017;Hu et al.,2023).Genetic improvement for high NUE should be a key strategy in breeding“Green Super Rice”(GSR)(Yu et al.,2021)and water-saving and drought-resistance rice(WDR)(Luo,2010;Xia et al.,2022)for sustainable agriculture.Asian cultivated rice is highly diverse and harbors vital genetic variants essential for adaptation to different environments(Wing et al.,2018).
基金supported by the National Natural Science Foundation of China(32172098 and U21A20205)the Natural Science Foundation of Shanghai(23ZR1455900 and 22ZR1455200).
文摘Dissecting the mechanism of drought resistance(DR)and designing drought-resistant rice varieties are promising strategies to address the challenge of climate change.Here,we selected a typical droughtavoidant(DA)variety,IRAT109,and a drought-tolerant(DT)variety,Hanhui15,as parents to develop a stable recombinant inbred line(RIL)population(F8,1262 lines).The de novo assembled genomes of both parents were released.By resequencing of the RIL population,a set of 1189216 reliable SNPs were obtained and used to construct a dense genetic map.Using above-and belowground phenomic platforms and multimodal cameras,we captured 139040 image-based traits(i-traits)of whole-plant phenotypes in response to drought stress throughout the entire rice growth period and identified 32586 drought-responsive quantitative trait loci(QTLs),including 2097 unique QTLs.QTLs associated with panicle i-traits occurred more than 600 times on the middle of chromosome 8,and QTLs associated with leaf i-traits occurred more than 800 times on the 50 end of chromosome 3,indicating the potential effects of these QTLs on plant phenotypes.We selected three candidate genes(OsMADS50,OsGhd8,OsSAUR11)related to leaf,panicle,and root traits,respectively,and verified their functions in DR.OsMADS50 was found to negatively regulate DR by modulating leaf dehydration,grain size,and downward root growth.A total of 18 and 21 composite QTLs significantly related to grain weight and plant biomass were also screened from 597 lines in the RIL population under drought conditions in field experiments,and the composite QTL regions showed substantial overlap(76.9%)with known DR gene regions.Based on three candidate DR genes,we proposed a haplotype design suitable for different environments and breeding objectives.This study provides a valuable reference for multimodal and time-series phenomic analyses,deciphers the genetic mechanisms of DA and DT rice varieties,and offers a molecular navigation map for breeding of DR varieties.
