Seed number per silique(SNPS)is one of seed yield components in rapeseed,but its genetic mechanism remains elusive.Here a double haploid(DH)population derived from a hybrid between female 6Q006with 35–40 SNPS and mal...Seed number per silique(SNPS)is one of seed yield components in rapeseed,but its genetic mechanism remains elusive.Here a double haploid(DH)population derived from a hybrid between female 6Q006with 35–40 SNPS and male 6W26 with 10–15 SNPS was investigated for SNPS in the year 2017,2018,2019 and 2021,and genotyped with Brassica 60K Illumina Infinium SNP array.An overlapping major QTL(qSNPS.C09)explaining 51.50%of phenotypic variance on average was narrowed to a 0.90 Mb region from 44.87 Mb to 45.77 Mb on chromosome C09 by BSA-seq.Subsequently,two DEGs in this interval were detected between extreme individuals in DH and F_2populations by transcriptome sequencing at7 and 14 days after pollination siliques.Of which,BnaC09g45400D encoded an adenine phosphoribosyltransferase 5(APT5)has a 48-bp InDel variation in the promoter of two parents.Candidate gene association analysis showed that this InDel variation was associated with SNPS in a nature population of rapeseed,where 54 accessions carrying the same haplotype as parent 6Q006 had higher SNPS than103 accessions carrying the same haplotype as parent 6W26.Collectively,the findings are helpful for rapeseed molecular breeding of SNPS,and provide new insight into the genetic and molecular mechanism of SNPS in rapeseed.展开更多
Silique length influences seed yield in oilseed rape.It shows extensive variation in germplasm resources,and identifying the underlying genes and regulatory mechanisms would advance breeding for the trait.In the prese...Silique length influences seed yield in oilseed rape.It shows extensive variation in germplasm resources,and identifying the underlying genes and regulatory mechanisms would advance breeding for the trait.In the present study,a genome-wide association study(GWAS)using 331 core accessions planted in 10 environments revealed 13 loci associated with silique length on chromosomes A01,A04,A07,A09,and C03,explaining 6.2%–19.2%of phenotypic variance.Physiological analysis showed that silique length variation was attributable to differences in silique growth rate and/or duration before four weeks after flowering,with levels of endogenous phytohormones(auxin,ethylene,and GA24,GA12,and GA44)playing an important role.Cytological analysis showed that silique length variation was due mainly to differences in cell number followed by cell size.Transcriptomic analysis of two pools of silique walls with opposite length extremes revealed 3248 differentially expressed genes(DEGs).These DEGs were enriched in several pathways(such as cell wall,cell division,and hormone metabolism)associated with cell proliferation and expansion and silique development.Integrating GWAS,RNA-seq,and functional annotation results revealed 15 candidate genes for the major associated locus q SL.A09-3.Of these,Bna A9.ARF18 and Bna A9.CYP78 A9 were validated by haplotype analysis followed by candidate gene association.Sequence variation in the coding region of Bna A9.ARF18 and expression of Bna A9.CYP78 A9 in silique walls were strongly associated with silique length.Our results provide an explanation for the natural variation of silique length in oilseed rape germplasm and offer useful information for its improvement.展开更多
High-throughput phenotyping of growth kinetics and organ size in the model plant Arabidopsis thaliana requires rapid and precise methods for trait estimation.To address this need,we developed the Arabidopsis Phenotypi...High-throughput phenotyping of growth kinetics and organ size in the model plant Arabidopsis thaliana requires rapid and precise methods for trait estimation.To address this need,we developed the Arabidopsis Phenotypic Trait Estimation System,APTES,an open-access,high-throughput program that uses computer vision and deep learning to extract 64 leaf traits and 64 silique traits from photographs.The enhanced segmentation model Cascade Mask Region-based Convolutional Neural Network(Mask R-CNN)achieved precision(measure of positive prediction accuracy),recall(sensitivity in detection),and F1 score values(harmonic mean of precision and recall)of 0.965,0.958,and 0.961,respectively,for individual leaf segmentation.These metrics demonstrated a consistent improvement of approximately 1 percentage point over the baseline model.For silique segmentation,our enhanced DetectoRS model for silique segmentation attained precision,recall,and F1 scores of 0.954,0.930,and 0.942,respectively.Notably,precision increased by 1%,while the F1 score improved by 2 percentage points.Trait parameters were automatically calculated with coefficient of determination values for leaf and silique traits ranging from 0.776 to 0.976 and mean absolute percentage error values from 1.89%to 7.90%.We phenotyped 166 Arabidopsis accessions,using APTES,and subjected the resulting values to a genome-wide association study(GWAS),revealing 1,042 single-nucleotide polymorphisms(SNPs)as being significantly associated with 18 leaf and silique traits,and one significant SNP on chromosome 3 linked to silique number.Furthermore,we validated APTES across other public Arabidopsis databases and other plant species,with segmentation results demonstrating its applicability across diverse datasets.In conclusion,APTES is a valuable automated tool for leaf and silique segmentation and trait estimation,which should offer benefits to the broader plant science community.展开更多
Ovule initiation is a key step that strongly influences ovule number and seed yield.Notably,mutants with enhanced brassinosteroid(BR)and cytokinin(CK)signaling produce more ovules and have a higher seed number per sil...Ovule initiation is a key step that strongly influences ovule number and seed yield.Notably,mutants with enhanced brassinosteroid(BR)and cytokinin(CK)signaling produce more ovules and have a higher seed number per silique(SNS)than wild-type plants.Here,we crossed BR-and CKrelated mutants to test whether these phytohormones function together in ovule initiation.We determined that simultaneously enhancing BR and CK contents led to higher ovule and seed numbers than enhancing BR or CK separately,and BR and CK enhanced each other.Further,the BR-response transcription factor BZR1 directly interacted with the CK-response transcription factor ARABIDOPSIS RESPONSE REGULATOR1(ARR1).Treatments with BR or BR plus CK strengthened this interaction and subsequent ARR1 targeting and induction of downstream genes to promote ovule initiation.Enhanced CK signaling partially rescued the reduced SNS phenotype of BR-deficient/insensitive mutants whereas enhanced BR signaling failed to rescue the low SNS of CK-deficient mutants,suggesting that BR regulates ovule initiation and SNS through CK-mediated and-independent pathways.Our study thus reveals that interaction between BR and CK promotes ovule initiation and increases seed number,providing important clues for increasing the seed yield of dicot crops.展开更多
基金supported by the National Basic Research Program of China(2015CB150201)the Natural Science Foundation of Chongqing(cstc2019jcyj-bshX0055,cstc2019jcyj-zdxmX0012cstc2020jcyj-msxmX0461)。
文摘Seed number per silique(SNPS)is one of seed yield components in rapeseed,but its genetic mechanism remains elusive.Here a double haploid(DH)population derived from a hybrid between female 6Q006with 35–40 SNPS and male 6W26 with 10–15 SNPS was investigated for SNPS in the year 2017,2018,2019 and 2021,and genotyped with Brassica 60K Illumina Infinium SNP array.An overlapping major QTL(qSNPS.C09)explaining 51.50%of phenotypic variance on average was narrowed to a 0.90 Mb region from 44.87 Mb to 45.77 Mb on chromosome C09 by BSA-seq.Subsequently,two DEGs in this interval were detected between extreme individuals in DH and F_2populations by transcriptome sequencing at7 and 14 days after pollination siliques.Of which,BnaC09g45400D encoded an adenine phosphoribosyltransferase 5(APT5)has a 48-bp InDel variation in the promoter of two parents.Candidate gene association analysis showed that this InDel variation was associated with SNPS in a nature population of rapeseed,where 54 accessions carrying the same haplotype as parent 6Q006 had higher SNPS than103 accessions carrying the same haplotype as parent 6W26.Collectively,the findings are helpful for rapeseed molecular breeding of SNPS,and provide new insight into the genetic and molecular mechanism of SNPS in rapeseed.
基金the Technical Innovation Project of Hubei Province(2018ABA087)National Natural Science Foundation of China(31771840)+2 种基金the China Agriculture Research System of MOF and MARA(CARS-13)the Agricultural Science and Technology Innovation Program(CAAS-ASTIP-2013-OCRI)Fundamental Research Funds for Central Non-Profit Institute of Crop Sciences CAAS(Y2020YJ09)。
文摘Silique length influences seed yield in oilseed rape.It shows extensive variation in germplasm resources,and identifying the underlying genes and regulatory mechanisms would advance breeding for the trait.In the present study,a genome-wide association study(GWAS)using 331 core accessions planted in 10 environments revealed 13 loci associated with silique length on chromosomes A01,A04,A07,A09,and C03,explaining 6.2%–19.2%of phenotypic variance.Physiological analysis showed that silique length variation was attributable to differences in silique growth rate and/or duration before four weeks after flowering,with levels of endogenous phytohormones(auxin,ethylene,and GA24,GA12,and GA44)playing an important role.Cytological analysis showed that silique length variation was due mainly to differences in cell number followed by cell size.Transcriptomic analysis of two pools of silique walls with opposite length extremes revealed 3248 differentially expressed genes(DEGs).These DEGs were enriched in several pathways(such as cell wall,cell division,and hormone metabolism)associated with cell proliferation and expansion and silique development.Integrating GWAS,RNA-seq,and functional annotation results revealed 15 candidate genes for the major associated locus q SL.A09-3.Of these,Bna A9.ARF18 and Bna A9.CYP78 A9 were validated by haplotype analysis followed by candidate gene association.Sequence variation in the coding region of Bna A9.ARF18 and expression of Bna A9.CYP78 A9 in silique walls were strongly associated with silique length.Our results provide an explanation for the natural variation of silique length in oilseed rape germplasm and offer useful information for its improvement.
基金supported by grants from the National Key Research and Development Program of China(2023YFF1000100,2022YFD2002304)the National Natural Science Foundation of China(U21A20205,32270281,32300281)+6 种基金the Key Agricultural Core Technology Research Project in Hubei Province(HBNYHXGG2023-9)the Natural Science Foundation of Henan Province(232300421028,222300420107)Fundamental Research Funds for the Central Universities(2662024ZKPY003)the Henan Provincial Science and Technology R&D Program Joint Fund(242301420130)the China-UK Joint Phenomics Consortium(BB/R02118X/1)a National Capability Grant in Plant Phenotyping(BBS/E/W/0012844A)the European Plant Phenotyping Network(Grant Agreement No.731013).
文摘High-throughput phenotyping of growth kinetics and organ size in the model plant Arabidopsis thaliana requires rapid and precise methods for trait estimation.To address this need,we developed the Arabidopsis Phenotypic Trait Estimation System,APTES,an open-access,high-throughput program that uses computer vision and deep learning to extract 64 leaf traits and 64 silique traits from photographs.The enhanced segmentation model Cascade Mask Region-based Convolutional Neural Network(Mask R-CNN)achieved precision(measure of positive prediction accuracy),recall(sensitivity in detection),and F1 score values(harmonic mean of precision and recall)of 0.965,0.958,and 0.961,respectively,for individual leaf segmentation.These metrics demonstrated a consistent improvement of approximately 1 percentage point over the baseline model.For silique segmentation,our enhanced DetectoRS model for silique segmentation attained precision,recall,and F1 scores of 0.954,0.930,and 0.942,respectively.Notably,precision increased by 1%,while the F1 score improved by 2 percentage points.Trait parameters were automatically calculated with coefficient of determination values for leaf and silique traits ranging from 0.776 to 0.976 and mean absolute percentage error values from 1.89%to 7.90%.We phenotyped 166 Arabidopsis accessions,using APTES,and subjected the resulting values to a genome-wide association study(GWAS),revealing 1,042 single-nucleotide polymorphisms(SNPs)as being significantly associated with 18 leaf and silique traits,and one significant SNP on chromosome 3 linked to silique number.Furthermore,we validated APTES across other public Arabidopsis databases and other plant species,with segmentation results demonstrating its applicability across diverse datasets.In conclusion,APTES is a valuable automated tool for leaf and silique segmentation and trait estimation,which should offer benefits to the broader plant science community.
基金funded by the National Natural Science Foundation of China(31771591,32070342,and 31761163003)Project MDS-JF-2020-8 supported by the Shanghai Jiao Tong University JiRLMDS Joint Research Fund+2 种基金the Agri-X Interdisciplinary Fund of Shanghai Jiao Tong University(Agri-X20200204 and Agri-X2017006)the Bio-X Interdisciplinary Fund of Shanghai Jiao Tong University(20CX-04)the Scientific and Technological Innovation Funds of Shanghai Jiao Tong University(19×160020009)。
文摘Ovule initiation is a key step that strongly influences ovule number and seed yield.Notably,mutants with enhanced brassinosteroid(BR)and cytokinin(CK)signaling produce more ovules and have a higher seed number per silique(SNS)than wild-type plants.Here,we crossed BR-and CKrelated mutants to test whether these phytohormones function together in ovule initiation.We determined that simultaneously enhancing BR and CK contents led to higher ovule and seed numbers than enhancing BR or CK separately,and BR and CK enhanced each other.Further,the BR-response transcription factor BZR1 directly interacted with the CK-response transcription factor ARABIDOPSIS RESPONSE REGULATOR1(ARR1).Treatments with BR or BR plus CK strengthened this interaction and subsequent ARR1 targeting and induction of downstream genes to promote ovule initiation.Enhanced CK signaling partially rescued the reduced SNS phenotype of BR-deficient/insensitive mutants whereas enhanced BR signaling failed to rescue the low SNS of CK-deficient mutants,suggesting that BR regulates ovule initiation and SNS through CK-mediated and-independent pathways.Our study thus reveals that interaction between BR and CK promotes ovule initiation and increases seed number,providing important clues for increasing the seed yield of dicot crops.
