Heterosis is a well-known phenomenon widely applied in agriculture.Recent studies have suggested that differential gene and protein expression between hybrids and their parents play important roles in heterosis.Altern...Heterosis is a well-known phenomenon widely applied in agriculture.Recent studies have suggested that differential gene and protein expression between hybrids and their parents play important roles in heterosis.Alternative splicing(AS)is an essential posttranscriptional mechanism that can greatly affect the transcriptome and proteome diversity in plants.However,genome-wide AS divergence in hybrids compared to their parents and its potential contribution to heterosis have not been comprehensively investigated.We report the direct profiling of the AS landscape using RNA sequencing data from immature ears of the maize hybrid ZD808 and its parents NG5 and CL11.Our results revealed a large number of significant differential AS(DAS)events in ZD808 relative to its parents,which can be further classified into parental-dominant and novel DAS patterns.Parental-dominant,especially NG5-dominant,events were prevalent in the hybrid,accounting for 42%of all analyzed DAS events.Functional enrichment analysis revealed that the NG5-dominant AS events were involved mainly in regulating the expression of genes associated with carbon/nitrogen metabolism and cell division processes and contributed greatly to maize ear heterosis.Among ZD808,CL11,and NG5,32.5%of DAS contained or lacked binding sites of at least one annotated maize microRNA(miRNA)and may be involved in miRNA-mediated posttranscriptional regulation.Cis regulation was the predominant contributor to AS variation and participates in many important biological processes associated with immature ear development.This study provides a comprehensive view of genome-wide alternative splicing variation in a maize hybrid.展开更多
Evolution of resistance to Cry proteins in multiple pest insects has been threatening the sustainable use of Bacillus thuringiensis(Bt)-transgenic crops.Better understanding about the mechanism of resistance to Cry pr...Evolution of resistance to Cry proteins in multiple pest insects has been threatening the sustainable use of Bacillus thuringiensis(Bt)-transgenic crops.Better understanding about the mechanism of resistance to Cry proteins in insects is needed.Our preliminary study reported that the transcription of HaABCC3 was significantly decreased in a near-isogenic line(LFC2)of a Cry1Ac-resistant strain(LF60)of the global pest Helicoverpa armigera.However,the causality between HaABCC3 downregulation and resistance to Cry1Ac remains to be verified,and the regulatory mechanism underlying the HaABCC3 downregulation is still unclear.In this study,our data showed that both HaABCC3 and HaABCC3 downregulation were genetically linked to resistance to Cry1Ac in LF60.However,no InDels were observed in the coding sequence of HaABCC3 from LF60.Furthermore,F_(1) offspring from the cross of LF60 and a HaABCC2/3-knockout mutant exhibited moderate resistance to Cry1Ac toxin;this indicated that the high resistance to CrylAc toxin in LF60 may have resulted from multiple genetic factors,including HaABCC2 missplicing and HaABCC3 downregulation.Results from luciferase reporter assays showed that promoter activity of HaABCC3 in LF60 was significantly lower than that in the susceptible strain,which indicated that HaABCC3 downregulation was likely mediated by promoter variation.Consistently,multiple variations of the GATA-or FoxA-binding sites in the promoter region of HaABCC3 were identified.Collectively,all results in this study suggested that the downregulation of HaABCC3 observed in the H.armigera LF60 strain,which is resistant to CrylAc,may be mediated by a cis-regulatory mechanism.展开更多
During the past 3000 years,cattle on the Qinghai-Xizang Plateau have developed adaptive phenotypes under the selective pressure of hypoxia,ultraviolet(UV)radiation,and extreme cold.The genetic mechanism underlying thi...During the past 3000 years,cattle on the Qinghai-Xizang Plateau have developed adaptive phenotypes under the selective pressure of hypoxia,ultraviolet(UV)radiation,and extreme cold.The genetic mechanism underlying this rapid adaptation is not yet well understood.Here,we present whole-genome resequencing data for 258 cattle from 32 cattle breeds/populations,including 89 Tibetan cattle representing eight populations distributed at altitudes ranging from 3400 m to 4300 m.Our genomic analysis revealed that Tibetan cattle exhibited a continuous phylogeographic cline from the East Asian taurine to the South Asian indicine ancestries.We found that recently selected genes in Tibetan cattle were related to body size(HMGA2 and NCAPG)and energy expenditure(DUOXA2).We identified signals of sympatric introgression from yak into Tibetan cattle at different altitudes,covering 0.64%–3.26%of their genomes,which included introgressed genes responsible for hypoxia response(EGLN1),cold adaptation(LRP11),DNA damage repair(LATS1),and UV radiation resistance(GNPAT).We observed that introgressed yak alleles were associated with noncoding variants,including those in present EGLN1.In Tibetan cattle,three yak introgressed SNPs in the EGLN1 promoter region reduced the expression of EGLN1,suggesting that these genomic variants enhance hypoxia tolerance.Taken together,our results indicated complex adaptation processes in Tibetan cattle,where recently selected genes and introgressed yak alleles jointly facilitated rapid adaptation to high-altitude environments.展开更多
基金This project was supported by the National Key Research and Development Program of China(2016YFD0101002 and 2017YFD0101201)the National Natural Science Foundation of China(31500984)+1 种基金the Agricultural Science and Technology Innovation Program of CAASthe National Engineering Laboratory of Crop Molecular Breeding.
文摘Heterosis is a well-known phenomenon widely applied in agriculture.Recent studies have suggested that differential gene and protein expression between hybrids and their parents play important roles in heterosis.Alternative splicing(AS)is an essential posttranscriptional mechanism that can greatly affect the transcriptome and proteome diversity in plants.However,genome-wide AS divergence in hybrids compared to their parents and its potential contribution to heterosis have not been comprehensively investigated.We report the direct profiling of the AS landscape using RNA sequencing data from immature ears of the maize hybrid ZD808 and its parents NG5 and CL11.Our results revealed a large number of significant differential AS(DAS)events in ZD808 relative to its parents,which can be further classified into parental-dominant and novel DAS patterns.Parental-dominant,especially NG5-dominant,events were prevalent in the hybrid,accounting for 42%of all analyzed DAS events.Functional enrichment analysis revealed that the NG5-dominant AS events were involved mainly in regulating the expression of genes associated with carbon/nitrogen metabolism and cell division processes and contributed greatly to maize ear heterosis.Among ZD808,CL11,and NG5,32.5%of DAS contained or lacked binding sites of at least one annotated maize microRNA(miRNA)and may be involved in miRNA-mediated posttranscriptional regulation.Cis regulation was the predominant contributor to AS variation and participates in many important biological processes associated with immature ear development.This study provides a comprehensive view of genome-wide alternative splicing variation in a maize hybrid.
基金supported by Shenzhen Natural Science Foundation(grant numberJCYJ20200109150629266)Shenzhen Science and Technology Program(grant number KQTD20180411143628272).
文摘Evolution of resistance to Cry proteins in multiple pest insects has been threatening the sustainable use of Bacillus thuringiensis(Bt)-transgenic crops.Better understanding about the mechanism of resistance to Cry proteins in insects is needed.Our preliminary study reported that the transcription of HaABCC3 was significantly decreased in a near-isogenic line(LFC2)of a Cry1Ac-resistant strain(LF60)of the global pest Helicoverpa armigera.However,the causality between HaABCC3 downregulation and resistance to Cry1Ac remains to be verified,and the regulatory mechanism underlying the HaABCC3 downregulation is still unclear.In this study,our data showed that both HaABCC3 and HaABCC3 downregulation were genetically linked to resistance to Cry1Ac in LF60.However,no InDels were observed in the coding sequence of HaABCC3 from LF60.Furthermore,F_(1) offspring from the cross of LF60 and a HaABCC2/3-knockout mutant exhibited moderate resistance to Cry1Ac toxin;this indicated that the high resistance to CrylAc toxin in LF60 may have resulted from multiple genetic factors,including HaABCC2 missplicing and HaABCC3 downregulation.Results from luciferase reporter assays showed that promoter activity of HaABCC3 in LF60 was significantly lower than that in the susceptible strain,which indicated that HaABCC3 downregulation was likely mediated by promoter variation.Consistently,multiple variations of the GATA-or FoxA-binding sites in the promoter region of HaABCC3 were identified.Collectively,all results in this study suggested that the downregulation of HaABCC3 observed in the H.armigera LF60 strain,which is resistant to CrylAc,may be mediated by a cis-regulatory mechanism.
基金supported by the National Key R&D Program of China(2021YFD1200400 and 2021YFF1001000)the National Natural Science Foundation of China(32102523,32372854,31861143014,32260823,and 32172706)+5 种基金the Key Research and Development Program of Xizang Autonomous Region of China(XZ202301ZY0008N)the Yunnan Expert Workstations(202305AF150156),the China Agriculture Research System of MOF and MARA(CARS-37)the Postdoctoral Fellowship Program of CPSF(GZC20232149)the Program of Yunling Scholar and Yunling Cattle Special Program of Yunnan Joint Laboratory of Seeds and Seeding Industry(202205AR070001)the Construction of Yunling Cattle Technology Innovation Center and Industrialization of Achievements(2019ZG007)Finally,we thank the High-Performance Computing(HPC)Center of Northwest A&F University(NWAFU)and Hefei Advanced Computing Center for providing computing resources.
文摘During the past 3000 years,cattle on the Qinghai-Xizang Plateau have developed adaptive phenotypes under the selective pressure of hypoxia,ultraviolet(UV)radiation,and extreme cold.The genetic mechanism underlying this rapid adaptation is not yet well understood.Here,we present whole-genome resequencing data for 258 cattle from 32 cattle breeds/populations,including 89 Tibetan cattle representing eight populations distributed at altitudes ranging from 3400 m to 4300 m.Our genomic analysis revealed that Tibetan cattle exhibited a continuous phylogeographic cline from the East Asian taurine to the South Asian indicine ancestries.We found that recently selected genes in Tibetan cattle were related to body size(HMGA2 and NCAPG)and energy expenditure(DUOXA2).We identified signals of sympatric introgression from yak into Tibetan cattle at different altitudes,covering 0.64%–3.26%of their genomes,which included introgressed genes responsible for hypoxia response(EGLN1),cold adaptation(LRP11),DNA damage repair(LATS1),and UV radiation resistance(GNPAT).We observed that introgressed yak alleles were associated with noncoding variants,including those in present EGLN1.In Tibetan cattle,three yak introgressed SNPs in the EGLN1 promoter region reduced the expression of EGLN1,suggesting that these genomic variants enhance hypoxia tolerance.Taken together,our results indicated complex adaptation processes in Tibetan cattle,where recently selected genes and introgressed yak alleles jointly facilitated rapid adaptation to high-altitude environments.
