High-throughput single nucleotide polymorphism(SNP) arrays have emerged as essential genotyping tools,significantly accelerating breeding programs and advancing basic research.In this study,a high-throughput 10K SNP g...High-throughput single nucleotide polymorphism(SNP) arrays have emerged as essential genotyping tools,significantly accelerating breeding programs and advancing basic research.In this study,a high-throughput 10K SNP genotyping array for wax gourd was developed using genotyping by target sequencing(GBTS),featuring 10,722 SNPs evenly distributed across all 12 chromosomes,including 278 functional loci associated with key economic traits.To demonstrate its utility,genetic distances among 19 elite inbred lines were calculated from SNP data and correlated with heterosis for single fruit weight.The results revealed that greater genetic distance was associated with higher middle parent heterosis(MPH) for single fruit weight.Furthermore,56 commercial wax gourd cultivars collected from eight regions were selected and genotyped.Population structure analysis,phylogenetic analysis,and principal component analysis(PCA) collectively indicated that these cultivars fall into two major groups.Group I,comprising black or dark green skinned wax gourds,exhibited lower genetic diversity than Group II,which includes green or light green skinned varieties,reflecting shorter genetic distances within Group I.Finally,60 polymorphic SNPs were used to construct DNA fingerprints for distinguishing the 56 cultivars.As the first high-throughput genotyping platform for wax gourd,this SNP array provides an effective and powerful tool for genetic analysis.展开更多
Single nucleotide polymorphism(SNP)genotyping arrays provide an optimal high-throughput platform for genetic research and molecular breeding programs in both animals and plants.In this study,a highquality and custom-d...Single nucleotide polymorphism(SNP)genotyping arrays provide an optimal high-throughput platform for genetic research and molecular breeding programs in both animals and plants.In this study,a highquality and custom-designed Rice3K56 SNP array was developed with the resequencing data of 3024 rice accessions worldwide,which was then tested extensively in 192 representative rice samples.Printed on the Gene Titan chips of Affymetrix Axiom each containing 56,606 SNP markers,the Rice3K56 array has a high genotyping reliability(99.6%),high and uniform genome coverage(an average of 6.7-kb between adjacent SNPs),abundant polymorphic information and easy automation,compared with previously developed rice SNP arrays.When applied in rice varietal differentiation,population diversity analysis,gene mapping of 13 complex traits by a genome-wide association study analysis(GWAS),and genome selection experiments in a recombinant inbred line and a multi-parent advanced generation inter-cross populations,these properties of the Rice3K56 array were well demonstrated for its power and great potential to be a highly efficient tool for rice genetic research and genomic breeding.展开更多
[Objectives]This study was conducted to select suitable mixed seed coating agents for improving the quality of"grey-matter"hybrid rice seeds.[Methods]Three different mixed seed coating agents(A,B,C)were used...[Objectives]This study was conducted to select suitable mixed seed coating agents for improving the quality of"grey-matter"hybrid rice seeds.[Methods]Three different mixed seed coating agents(A,B,C)were used to coat the seeds of two varieties(Taiyou 390 and Zhenliangyou 8612)of hybrid rice with different"grey-matter"content(5%,15%,25%),and the results were investigated and compared.[Results]The combinations of treatment B(seed coating agent A+Linong)and treatment C(Manshijin+seed coating agent A)could significantly improve indexes including seed germination potential,germination rate,seed vigor,seedling height,fibrous roots and fresh weight of the two varieties with a"grey-matter"content greater than 15%,but had no significant effects on main root length,dry weight,leaf number and tiller number,and the effects of treatment B was better than those of treatment C.That is to say,mixed seed coating agent B(seed coating agent A+Linong)was suitable for use as a seed coating agent to improve the quality of"grey-matter"seeds.[Conclusions]This study provides a reference plan for the safe use of mixed seed batches with"grey-matter"deterioration.展开更多
Alternative splicing(AS)is a crucial post-transcriptional mechanism in plants,significantly contributing to the diversification of biological processes and adaptive responses.Distinct splice isoforms are generated by ...Alternative splicing(AS)is a crucial post-transcriptional mechanism in plants,significantly contributing to the diversification of biological processes and adaptive responses.Distinct splice isoforms are generated by exon skipping(ES),intron retention(IR)and other mechanisms,enabling plants to adapt to a range of biotic stresses,including those posed by bacteria,fungi and viruses.Advances in bioinformatics have greatly improved the detection and characterization of AS events,revealing their critical roles in plant immunity.This review highlights the involvement of AS in regulating RNA interference(RNAi),hormone signaling pathways,and immune responses such as pattern-triggered immunity(PTI)and effector-triggered immunity(ETI).In addition,pathogens exploit AS to produce effectors that subvert plant immunity.Beyond its role in natural immunity,AS also holds promise for pesticide development,offering opportunities to enhance plant disease resistance by targeting pest-associated or immunity-related genes.Future research on AS under biotic stress is expected to uncover novel regulatory mechanisms and provide new strategies for crop improvement and sustainable agriculture.展开更多
基金supported by the Science and Technology Talent Support Project of Hunan Province,China (2022TJ-N15)the Hunan Agricultural Science and Technology Innovation Fund,China (2024CX90 and 2024CX65)the Science and Technology Innovation Program of Hunan Province,China (2021NK1006)。
文摘High-throughput single nucleotide polymorphism(SNP) arrays have emerged as essential genotyping tools,significantly accelerating breeding programs and advancing basic research.In this study,a high-throughput 10K SNP genotyping array for wax gourd was developed using genotyping by target sequencing(GBTS),featuring 10,722 SNPs evenly distributed across all 12 chromosomes,including 278 functional loci associated with key economic traits.To demonstrate its utility,genetic distances among 19 elite inbred lines were calculated from SNP data and correlated with heterosis for single fruit weight.The results revealed that greater genetic distance was associated with higher middle parent heterosis(MPH) for single fruit weight.Furthermore,56 commercial wax gourd cultivars collected from eight regions were selected and genotyped.Population structure analysis,phylogenetic analysis,and principal component analysis(PCA) collectively indicated that these cultivars fall into two major groups.Group I,comprising black or dark green skinned wax gourds,exhibited lower genetic diversity than Group II,which includes green or light green skinned varieties,reflecting shorter genetic distances within Group I.Finally,60 polymorphic SNPs were used to construct DNA fingerprints for distinguishing the 56 cultivars.As the first high-throughput genotyping platform for wax gourd,this SNP array provides an effective and powerful tool for genetic analysis.
基金supported by the National Natural Science Foundation of China(31971927 and U21A20214)the Science and Technology Major Project of Anhui Province(2021d06050002)+4 种基金the Improved Varieties Joint Research(Rice)Project of Anhui Province(the 14th five-year plan)the National Key Research and Development Program of China(2020YFE0202300)the CAAS Innovative Team Awardthe Hainan Provincial Joint Project of Sanya Yazhou Bay Science and Technology City(B21HJ0215,B21HJ0223,and B21HJ0508)Nanfan Special Project,CAAS(YBXM04)。
文摘Single nucleotide polymorphism(SNP)genotyping arrays provide an optimal high-throughput platform for genetic research and molecular breeding programs in both animals and plants.In this study,a highquality and custom-designed Rice3K56 SNP array was developed with the resequencing data of 3024 rice accessions worldwide,which was then tested extensively in 192 representative rice samples.Printed on the Gene Titan chips of Affymetrix Axiom each containing 56,606 SNP markers,the Rice3K56 array has a high genotyping reliability(99.6%),high and uniform genome coverage(an average of 6.7-kb between adjacent SNPs),abundant polymorphic information and easy automation,compared with previously developed rice SNP arrays.When applied in rice varietal differentiation,population diversity analysis,gene mapping of 13 complex traits by a genome-wide association study analysis(GWAS),and genome selection experiments in a recombinant inbred line and a multi-parent advanced generation inter-cross populations,these properties of the Rice3K56 array were well demonstrated for its power and great potential to be a highly efficient tool for rice genetic research and genomic breeding.
基金Supported by Changsha Science and Technology Major Project(kh2201219)Special Project of the Central Government Guiding Local Science and Technology Development(2023ZYC010)。
文摘[Objectives]This study was conducted to select suitable mixed seed coating agents for improving the quality of"grey-matter"hybrid rice seeds.[Methods]Three different mixed seed coating agents(A,B,C)were used to coat the seeds of two varieties(Taiyou 390 and Zhenliangyou 8612)of hybrid rice with different"grey-matter"content(5%,15%,25%),and the results were investigated and compared.[Results]The combinations of treatment B(seed coating agent A+Linong)and treatment C(Manshijin+seed coating agent A)could significantly improve indexes including seed germination potential,germination rate,seed vigor,seedling height,fibrous roots and fresh weight of the two varieties with a"grey-matter"content greater than 15%,but had no significant effects on main root length,dry weight,leaf number and tiller number,and the effects of treatment B was better than those of treatment C.That is to say,mixed seed coating agent B(seed coating agent A+Linong)was suitable for use as a seed coating agent to improve the quality of"grey-matter"seeds.[Conclusions]This study provides a reference plan for the safe use of mixed seed batches with"grey-matter"deterioration.
基金funded by the National Key Research and Development Program of China(2021YFD1400500)National Natural Science Foundation of China(U23A6006,32272555)Ningbo Natural Science Foundation(2023Z124).
文摘Alternative splicing(AS)is a crucial post-transcriptional mechanism in plants,significantly contributing to the diversification of biological processes and adaptive responses.Distinct splice isoforms are generated by exon skipping(ES),intron retention(IR)and other mechanisms,enabling plants to adapt to a range of biotic stresses,including those posed by bacteria,fungi and viruses.Advances in bioinformatics have greatly improved the detection and characterization of AS events,revealing their critical roles in plant immunity.This review highlights the involvement of AS in regulating RNA interference(RNAi),hormone signaling pathways,and immune responses such as pattern-triggered immunity(PTI)and effector-triggered immunity(ETI).In addition,pathogens exploit AS to produce effectors that subvert plant immunity.Beyond its role in natural immunity,AS also holds promise for pesticide development,offering opportunities to enhance plant disease resistance by targeting pest-associated or immunity-related genes.Future research on AS under biotic stress is expected to uncover novel regulatory mechanisms and provide new strategies for crop improvement and sustainable agriculture.
