Besides the natural selection, the crops cultivated today have experienced two episodes of strong artifi cial selection, domestic and modern breeding. Domestication led to giant genetic structure differentiation
Background Cotton is a significant crop for fiber production;however,seed shape-related traits have been less investigated in comparison to fiber quality.Comprehending the genetic foundation of traits associated with ...Background Cotton is a significant crop for fiber production;however,seed shape-related traits have been less investigated in comparison to fiber quality.Comprehending the genetic foundation of traits associated with seed shape is crucial for improving the seed and fiber quality in cotton.Results A total of 238 cotton accessions were evaluated in four different environments over a period of two years.Traits including thousand grain weight(TGW),aspect ratio(AR),seed length,seed width,diameter,and roundness demonstrated high heritability and significant genetic variation,as indicated by phenotypic analysis.The association analysis involved 145 simple sequence repeats(SSR)markers and identified 50 loci significantly associated with six traits related to seed shape.The markers MON_DPL0504aa and BNL2535ba were identified as influencing multiple traits,including aspect ratio and thousand grain weight.Notably,markers such as HAU2588a and MUSS422aa had considerable influence on seed diameter and roundness.The identified markers represented an average phenotypic variance between 3.92%for seed length and 16.54%for TGW.Conclusions The research finds key loci for seed shape-related traits in cotton,providing significant potential for marker-assisted breeding.These findings establish a framework for breeding initiatives focused on enhancing seed quality,hence advancing the cotton production.展开更多
Grass pea(Lathyrus sativus L.)is an imperative food crop cultured in dryland agricultural ecology.It is a vital source of dietary protein to millions of populaces living in low-income countries in South-East Asia and ...Grass pea(Lathyrus sativus L.)is an imperative food crop cultured in dryland agricultural ecology.It is a vital source of dietary protein to millions of populaces living in low-income countries in South-East Asia and Africa.This study highlights the improvement of genomic properties and their application in marker-trait relationships for 17 yield-related characters in 400 grass pea genotypes from China and Bangladesh.These characters were assessed via 56 polymorphic markers using general linear model(GLM)(P+G+Q)and mixed linear model(MLM)(P+G+Q+K)in the tassel software based on the linkage disequilibrium and population structure analysis.Population structure analysis showed two major groups and one admixed group in the populace.Statistically significant loci pairs of linkage disequilibrium(LD)mean value(D′)was 0.479.A total of 99 and 61 marker-trait associations in GLM and MLM models allied to the 17 traits were accepted at a 5%level of significance.Among these markers,21 markers were associated with more than one trait;12 marker-trait associations passed the Bonferroni correction threshold.Both models found six markers C41936,C39067,C34100,C47146,C47638,and C43047 significantly associated with days to maturity,flower color,plant height,and seed per pod were detected in the Hebei and Liaoyang location(p≤0.01),and the interpretation rate(R^(2)value)11.2%to 43.6%.Conferring to the consequences,the association analysis methodology may operative system for quantitative,qualitative,and biochemical traits related to gene position mapping and support breeders in improving novel approaches for advancing the grass pea quality.展开更多
Correction:J Cotton Res 7,20(2024)https://doi.org/10.1186/s42397-024-00180-3 Following publication of the original article(Shui et al.2024),the author found 5 errors in the published article.1.One of the author’s nam...Correction:J Cotton Res 7,20(2024)https://doi.org/10.1186/s42397-024-00180-3 Following publication of the original article(Shui et al.2024),the author found 5 errors in the published article.1.One of the author’s name has been corrected from Gou Chunping to Guo Chunping.2.The reference(Zhao SQ.2016)in Table 2 has been updated to:Zhao SQ.Analysis on the major gene and multigene mixed inheritance and QTL mapping for early maturity traits in upland cotton.Chin Acad Agric Sci.2016.https://doi.org/10.3969/j.issn.201600501.(in Chinese with English abstract).3.In’Results’part,’Phenotype analysis of 238 cotton boll abscission among cotton accessions’paragraph,the phenotype analysis of AR1 ranging from 19.27%–63.79%,which was wrongly written as 19.27%-63.97%.4.The‘2018KRL’is modified to‘2018KEL’in Table 1.展开更多
Pythium stalk rot(PSR)is a destructive disease of maize,severely affecting yield and grain quality.The identification of quantitative trait loci(QTL)or genes for resistance to PSR forms the basis of diseaseresistant h...Pythium stalk rot(PSR)is a destructive disease of maize,severely affecting yield and grain quality.The identification of quantitative trait loci(QTL)or genes for resistance to PSR forms the basis of diseaseresistant hybrids breeding.In this study,a major QTL,Resistance to Pythium stalk rot 1(RPSR1),was identified from a set of recombinant inbred lines derived from MS71 and POP.Using a recombinant progeny testing strategy,RPSR1 was fine-mapped in a 472 kb interval.Through candidate gene expression,gene knock-down and knock-out studies,a leucine-rich repeat receptor-like kinase gene,PEP RECEPTOR 2(ZmPEPR2),was assigned as a PSR resistance gene.These results provide insights into the genetic architecture of resistance to PSR in maize,which should facilitate breeding maize for resistance to stalk rot.展开更多
Epigenetics-mediated breeding(epibreeding)involves engineering crop traits and stress responses through the targeted manipulation of key epigenetic features to enhance agricultural productivity.While conventional bree...Epigenetics-mediated breeding(epibreeding)involves engineering crop traits and stress responses through the targeted manipulation of key epigenetic features to enhance agricultural productivity.While conventional breeding methods raise concerns about reduced genetic diversity,epibreeding propels crop improvement through epigenetic variations that regulate gene expression,ultimately impacting crop yield.Epigenetic regulation in crops encompasses various modes,including histone modification,DNA modification,RNA modification,non-coding RNA,and chromatin remodeling.This review summarizes the epigenetic mechanisms underlying major agronomic traits in maize and identifies candidate epigenetic landmarks in the maize breeding process.We propose a valuable strategy for improving maize yield through epibreeding,combining CRISPR/Cas-based epigenome editing technology and Synthetic Epigenetics(SynEpi).Finally,we discuss the challenges and opportunities associated with maize trait improvement through epibreeding.展开更多
Peel color is an important appearance quality of melons that significantly affects consumer preferences.In this study,a near-isogenic line NIL-G(dark green peel)was generated from B8(grey-green peel)and B15(white peel...Peel color is an important appearance quality of melons that significantly affects consumer preferences.In this study,a near-isogenic line NIL-G(dark green peel)was generated from B8(grey-green peel)and B15(white peel).The F_2 population constructed by crossing NIL-G and B15 was used to study the inheritance pattern of peel color,and bulked-segregant analysis sequencing(BSA-seq)was employed to identify the interval in which the target gene was located.Genetic analysis showed that a dominant gene controls the dark green peel trait at maturity.BSAseq and molecular markers were used to localize the candidate gene in a 263.7 kb interval of chromosome 4,which contained the CmAPRR2 gene with known functions.Moreover,allelic sequence analysis revealed four SNP variations of the CmAPRR2 gene in B15,of which SNP.G614331A was located at the junction of the 6th exon and 6th intron.The G-to-A mutation caused alternative splicing of the transcript of CmAPRR2 in B15,generating two transcripts(CmAPRR2-A and CmAPRR2-B)with premature termination codons.Furthermore,the Kompetitive Allele Specific PCR(KASP)marker,APRR2-G/A,was developed based on this SNP and shown to co-segregate with the peel color phenotype in the F_(2) population.Compared to white-peel B15,the expression level of CmAPRR2 in dark green peel NIL-G was higher at each growth stage.Therefore,CmAPRR2 may be the key gene controlling the fruit color of melons.This study identified a novel allelic variant of CmAPRR2 that leads to white peel formation in mature melons.We also provides a theoretical basis for further research on the gene regulatory mechanism of melon peel colors,which promotes using molecular marker-assisted selection to modify melon peel colors in the future.展开更多
BACKGROUND An increasing number of studies to date have found preoperative magnetic resonance imaging(MRI)features valuable in predicting the prognosis of rectal cancer(RC).However,research is still lacking on the cor...BACKGROUND An increasing number of studies to date have found preoperative magnetic resonance imaging(MRI)features valuable in predicting the prognosis of rectal cancer(RC).However,research is still lacking on the correlation between preoperative MRI features and the risk of recurrence after radical resection of RC,urgently necessitating further in-depth exploration.AIM To investigate the correlation between preoperative MRI parameters and the risk of recurrence after radical resection of RC to provide an effective tool for predicting postoperative recurrence.METHODS The data of 90 patients who were diagnosed with RC by surgical pathology and underwent radical surgical resection at the Second Affiliated Hospital of Bengbu Medical University between May 2020 and December 2023 were collected through retrospective analysis.General demographic data,MRI data,and tumor markers levels were collected.According to the reviewed data of patients six months after surgery,the clinicians comprehensively assessed the recurrence risk and divided the patients into high recurrence risk(37 cases)and low recurrence risk(53 cases)groups.Independent sample t-test andχ2 test were used to analyze differences between the two groups.A logistic regression model was used to explore the risk factors of the high recurrence risk group,and a clinical prediction model was constructed.The clinical prediction model is presented in the form of a nomogram.The receiver operating characteristic curve,Hosmer-Lemeshow goodness of fit test,calibration curve,and decision curve analysis were used to evaluate the efficacy of the clinical prediction model.RESULTS The detection of positive extramural vascular invasion through preoperative MRI[odds ratio(OR)=4.29,P=0.045],along with elevated carcinoembryonic antigen(OR=1.08,P=0.041),carbohydrate antigen 125(OR=1.19,P=0.034),and carbohydrate antigen 199(OR=1.27,P<0.001)levels,are independent risk factors for increased postoperative recurrence risk in patients with RC.Furthermore,there was a correlation between magnetic resonance based T staging,magnetic resonance based N staging,and circumferential resection margin results determined by MRI and the postoperative recurrence risk.Additionally,when extramural vascular invasion was integrated with tumor markers,the resulting clinical prediction model more effectively identified patients at high risk for postoperative recurrence,thereby providing robust support for clinical decision-making.CONCLUSION The results of this study indicate that preoperative MRI detection is of great importance for predicting the risk of postoperative recurrence in patients with RC.Monitoring these markers helps clinicians identify patients at high risk,allowing for more aggressive treatment and monitoring strategies to improve patient outcomes.展开更多
One of agriculture’s major challenges is the low efficiency of phosphate(Pi)use,which leads to increased costs,harmful environmental impacts,and the depletion of phosphorus(P)resources.The TaPHT1;6 gene,which encodes...One of agriculture’s major challenges is the low efficiency of phosphate(Pi)use,which leads to increased costs,harmful environmental impacts,and the depletion of phosphorus(P)resources.The TaPHT1;6 gene,which encodes a high-affinity Pi transporter(PHT),plays a crucial role in Pi absorption and transport.In this study,the promoter and coding regions of three TaPHT1;6 gene copies on chromosomes 5A,5B,and 5D were individually amplified and sequenced from 167 common wheat(Triticum aestivum L.)cultivars.Sequence analysis revealed 16 allelic variation sites within the promoters of TaPHT1;6-5B among these cultivars,forming three distinct haplotypes:Hap1,Hap2,and Hap3.Field trials were conducted over two years to compare wheat genotypes with these haplotypes,focusing on assessing plant dry weight,grain yield,P content,Pi fertilizer absorption efficiency,and Pi fertilizer utilization efficiency.Results indicated that Hap3 represented the favored Pi-efficient haplotype.Dual-luciferase reporter assay demonstrated that the Hap3 promoter,carrying the identified allelic variation sites,exhibited higher gene-driven capability,leading to increased expression levels of the TaPHT1;6-5B gene.We developed a distributed cleaved amplified polymorphic site marker(dCAPS-571)to distinguish Hap3 from the other two haplotypes based on these allelic variation sites,presenting an opportunity for breeding Pi-efficient wheat cultivars.This study successfully identified polymorphic sites on TaPHT1;6-5B associated with Pi efficiency and developed a functional molecular marker to facilitate future breeding endeavors.展开更多
文摘Besides the natural selection, the crops cultivated today have experienced two episodes of strong artifi cial selection, domestic and modern breeding. Domestication led to giant genetic structure differentiation
基金supported by the Fund for BTNYGG(NYHXGG,2023AA102)the National Natural Science Foundation of China(32260510)+3 种基金the Key Project for Science,Technology Development of Shihezi city,Xinjiang Production and Construction Crops(2022NY01)Shihezi University high-level talent research project(RCZK202337)Science and Technology Major Project of the Department of Science and Technology of Xinjiang Uygur Autonomous region(2022A03004-1)the Key Programs for Science and Technology Development in Agricultural Field of Xinjiang Production and Construction Corps。
文摘Background Cotton is a significant crop for fiber production;however,seed shape-related traits have been less investigated in comparison to fiber quality.Comprehending the genetic foundation of traits associated with seed shape is crucial for improving the seed and fiber quality in cotton.Results A total of 238 cotton accessions were evaluated in four different environments over a period of two years.Traits including thousand grain weight(TGW),aspect ratio(AR),seed length,seed width,diameter,and roundness demonstrated high heritability and significant genetic variation,as indicated by phenotypic analysis.The association analysis involved 145 simple sequence repeats(SSR)markers and identified 50 loci significantly associated with six traits related to seed shape.The markers MON_DPL0504aa and BNL2535ba were identified as influencing multiple traits,including aspect ratio and thousand grain weight.Notably,markers such as HAU2588a and MUSS422aa had considerable influence on seed diameter and roundness.The identified markers represented an average phenotypic variance between 3.92%for seed length and 16.54%for TGW.Conclusions The research finds key loci for seed shape-related traits in cotton,providing significant potential for marker-assisted breeding.These findings establish a framework for breeding initiatives focused on enhancing seed quality,hence advancing the cotton production.
基金the financial support from the Protection and Utilization of Crop Germplasm Resources project from the Ministry of Agriculture and Rural Affairs of China(2019NWB036-07)China Agriculture Research System of MOF and MARA-Food Legumes(CARS-08)+2 种基金National Infrastructure for Crop Germplasm Resources Project from the Ministry of Science and Technology of China(NICGR2019)Agricultural Science and Technology Innovation Program(ASTIP)in CAAS and Bangladesh-Second Phase of the National Agricultural Technology Program-Phase II Project,Bangladesh Agricultural Research Council(BARC),Bangladesh(P149553)supported by Researchers Supporting Project Number(RSP2025R7),King Saud University,Riyadh,Saudi Arabia.
文摘Grass pea(Lathyrus sativus L.)is an imperative food crop cultured in dryland agricultural ecology.It is a vital source of dietary protein to millions of populaces living in low-income countries in South-East Asia and Africa.This study highlights the improvement of genomic properties and their application in marker-trait relationships for 17 yield-related characters in 400 grass pea genotypes from China and Bangladesh.These characters were assessed via 56 polymorphic markers using general linear model(GLM)(P+G+Q)and mixed linear model(MLM)(P+G+Q+K)in the tassel software based on the linkage disequilibrium and population structure analysis.Population structure analysis showed two major groups and one admixed group in the populace.Statistically significant loci pairs of linkage disequilibrium(LD)mean value(D′)was 0.479.A total of 99 and 61 marker-trait associations in GLM and MLM models allied to the 17 traits were accepted at a 5%level of significance.Among these markers,21 markers were associated with more than one trait;12 marker-trait associations passed the Bonferroni correction threshold.Both models found six markers C41936,C39067,C34100,C47146,C47638,and C43047 significantly associated with days to maturity,flower color,plant height,and seed per pod were detected in the Hebei and Liaoyang location(p≤0.01),and the interpretation rate(R^(2)value)11.2%to 43.6%.Conferring to the consequences,the association analysis methodology may operative system for quantitative,qualitative,and biochemical traits related to gene position mapping and support breeders in improving novel approaches for advancing the grass pea quality.
文摘Correction:J Cotton Res 7,20(2024)https://doi.org/10.1186/s42397-024-00180-3 Following publication of the original article(Shui et al.2024),the author found 5 errors in the published article.1.One of the author’s name has been corrected from Gou Chunping to Guo Chunping.2.The reference(Zhao SQ.2016)in Table 2 has been updated to:Zhao SQ.Analysis on the major gene and multigene mixed inheritance and QTL mapping for early maturity traits in upland cotton.Chin Acad Agric Sci.2016.https://doi.org/10.3969/j.issn.201600501.(in Chinese with English abstract).3.In’Results’part,’Phenotype analysis of 238 cotton boll abscission among cotton accessions’paragraph,the phenotype analysis of AR1 ranging from 19.27%–63.79%,which was wrongly written as 19.27%-63.97%.4.The‘2018KRL’is modified to‘2018KEL’in Table 1.
基金supported by National Natural Science Foundation of China(32302371 to Junbin Chen)the National Key Research and Development Program,Ministry of Science and Technology of China(2022YFD1201802 to Wangsheng Zhu)Research Program from State Key Laboratory of Maize Biobreeding(SKLMB2424 to Wangsheng Zhu).
文摘Pythium stalk rot(PSR)is a destructive disease of maize,severely affecting yield and grain quality.The identification of quantitative trait loci(QTL)or genes for resistance to PSR forms the basis of diseaseresistant hybrids breeding.In this study,a major QTL,Resistance to Pythium stalk rot 1(RPSR1),was identified from a set of recombinant inbred lines derived from MS71 and POP.Using a recombinant progeny testing strategy,RPSR1 was fine-mapped in a 472 kb interval.Through candidate gene expression,gene knock-down and knock-out studies,a leucine-rich repeat receptor-like kinase gene,PEP RECEPTOR 2(ZmPEPR2),was assigned as a PSR resistance gene.These results provide insights into the genetic architecture of resistance to PSR in maize,which should facilitate breeding maize for resistance to stalk rot.
基金supported by funding from the National Key R&D Program of China(2023ZD0407304)the Sci-Tech Innovation 2030 Agenda(2022ZD0115703)Fundamental Research Funds for Central Non-Profit of Chinese Academy of Agricultural Sciences(Y2023PT20).
文摘Epigenetics-mediated breeding(epibreeding)involves engineering crop traits and stress responses through the targeted manipulation of key epigenetic features to enhance agricultural productivity.While conventional breeding methods raise concerns about reduced genetic diversity,epibreeding propels crop improvement through epigenetic variations that regulate gene expression,ultimately impacting crop yield.Epigenetic regulation in crops encompasses various modes,including histone modification,DNA modification,RNA modification,non-coding RNA,and chromatin remodeling.This review summarizes the epigenetic mechanisms underlying major agronomic traits in maize and identifies candidate epigenetic landmarks in the maize breeding process.We propose a valuable strategy for improving maize yield through epibreeding,combining CRISPR/Cas-based epigenome editing technology and Synthetic Epigenetics(SynEpi).Finally,we discuss the challenges and opportunities associated with maize trait improvement through epibreeding.
基金supported by the Innovation and Development Program of Beijing Vegetable Research Center,China(KYCX202301)the Construction of Cucurbits Collaboration and Innovation Center,China(XTCX202301)+3 种基金the Youth Research Fund of Beijing Academy of Agriculture and Forestry Sciences,China(QNJJ202426)the National Natural Science Foundation of China(U21A20229 and 32102397)the Scientific Research Foundation of the Higher Education Institutions for Distinguished Young Scholars in Anhui Province,China(2022AH020037)and the Key Research and Development Projects of Anhui Province,China(2023z04020019)。
文摘Peel color is an important appearance quality of melons that significantly affects consumer preferences.In this study,a near-isogenic line NIL-G(dark green peel)was generated from B8(grey-green peel)and B15(white peel).The F_2 population constructed by crossing NIL-G and B15 was used to study the inheritance pattern of peel color,and bulked-segregant analysis sequencing(BSA-seq)was employed to identify the interval in which the target gene was located.Genetic analysis showed that a dominant gene controls the dark green peel trait at maturity.BSAseq and molecular markers were used to localize the candidate gene in a 263.7 kb interval of chromosome 4,which contained the CmAPRR2 gene with known functions.Moreover,allelic sequence analysis revealed four SNP variations of the CmAPRR2 gene in B15,of which SNP.G614331A was located at the junction of the 6th exon and 6th intron.The G-to-A mutation caused alternative splicing of the transcript of CmAPRR2 in B15,generating two transcripts(CmAPRR2-A and CmAPRR2-B)with premature termination codons.Furthermore,the Kompetitive Allele Specific PCR(KASP)marker,APRR2-G/A,was developed based on this SNP and shown to co-segregate with the peel color phenotype in the F_(2) population.Compared to white-peel B15,the expression level of CmAPRR2 in dark green peel NIL-G was higher at each growth stage.Therefore,CmAPRR2 may be the key gene controlling the fruit color of melons.This study identified a novel allelic variant of CmAPRR2 that leads to white peel formation in mature melons.We also provides a theoretical basis for further research on the gene regulatory mechanism of melon peel colors,which promotes using molecular marker-assisted selection to modify melon peel colors in the future.
文摘BACKGROUND An increasing number of studies to date have found preoperative magnetic resonance imaging(MRI)features valuable in predicting the prognosis of rectal cancer(RC).However,research is still lacking on the correlation between preoperative MRI features and the risk of recurrence after radical resection of RC,urgently necessitating further in-depth exploration.AIM To investigate the correlation between preoperative MRI parameters and the risk of recurrence after radical resection of RC to provide an effective tool for predicting postoperative recurrence.METHODS The data of 90 patients who were diagnosed with RC by surgical pathology and underwent radical surgical resection at the Second Affiliated Hospital of Bengbu Medical University between May 2020 and December 2023 were collected through retrospective analysis.General demographic data,MRI data,and tumor markers levels were collected.According to the reviewed data of patients six months after surgery,the clinicians comprehensively assessed the recurrence risk and divided the patients into high recurrence risk(37 cases)and low recurrence risk(53 cases)groups.Independent sample t-test andχ2 test were used to analyze differences between the two groups.A logistic regression model was used to explore the risk factors of the high recurrence risk group,and a clinical prediction model was constructed.The clinical prediction model is presented in the form of a nomogram.The receiver operating characteristic curve,Hosmer-Lemeshow goodness of fit test,calibration curve,and decision curve analysis were used to evaluate the efficacy of the clinical prediction model.RESULTS The detection of positive extramural vascular invasion through preoperative MRI[odds ratio(OR)=4.29,P=0.045],along with elevated carcinoembryonic antigen(OR=1.08,P=0.041),carbohydrate antigen 125(OR=1.19,P=0.034),and carbohydrate antigen 199(OR=1.27,P<0.001)levels,are independent risk factors for increased postoperative recurrence risk in patients with RC.Furthermore,there was a correlation between magnetic resonance based T staging,magnetic resonance based N staging,and circumferential resection margin results determined by MRI and the postoperative recurrence risk.Additionally,when extramural vascular invasion was integrated with tumor markers,the resulting clinical prediction model more effectively identified patients at high risk for postoperative recurrence,thereby providing robust support for clinical decision-making.CONCLUSION The results of this study indicate that preoperative MRI detection is of great importance for predicting the risk of postoperative recurrence in patients with RC.Monitoring these markers helps clinicians identify patients at high risk,allowing for more aggressive treatment and monitoring strategies to improve patient outcomes.
基金supported by the Shennong Laboratory Project of Henan Province,China(SN01-2022-01)the China Postdoctoral Science Foundation(2023M731006)the Project of Science and Technology of Henan Province,China(232102111104)。
文摘One of agriculture’s major challenges is the low efficiency of phosphate(Pi)use,which leads to increased costs,harmful environmental impacts,and the depletion of phosphorus(P)resources.The TaPHT1;6 gene,which encodes a high-affinity Pi transporter(PHT),plays a crucial role in Pi absorption and transport.In this study,the promoter and coding regions of three TaPHT1;6 gene copies on chromosomes 5A,5B,and 5D were individually amplified and sequenced from 167 common wheat(Triticum aestivum L.)cultivars.Sequence analysis revealed 16 allelic variation sites within the promoters of TaPHT1;6-5B among these cultivars,forming three distinct haplotypes:Hap1,Hap2,and Hap3.Field trials were conducted over two years to compare wheat genotypes with these haplotypes,focusing on assessing plant dry weight,grain yield,P content,Pi fertilizer absorption efficiency,and Pi fertilizer utilization efficiency.Results indicated that Hap3 represented the favored Pi-efficient haplotype.Dual-luciferase reporter assay demonstrated that the Hap3 promoter,carrying the identified allelic variation sites,exhibited higher gene-driven capability,leading to increased expression levels of the TaPHT1;6-5B gene.We developed a distributed cleaved amplified polymorphic site marker(dCAPS-571)to distinguish Hap3 from the other two haplotypes based on these allelic variation sites,presenting an opportunity for breeding Pi-efficient wheat cultivars.This study successfully identified polymorphic sites on TaPHT1;6-5B associated with Pi efficiency and developed a functional molecular marker to facilitate future breeding endeavors.
