Watermelon is a highly cultivated fruit crop renowned for its quality properties of fruit flesh.Among various quality factors,fruit flesh firmness is a crucial quality parameter influencing the fruit texture,shelf lif...Watermelon is a highly cultivated fruit crop renowned for its quality properties of fruit flesh.Among various quality factors,fruit flesh firmness is a crucial quality parameter influencing the fruit texture,shelf life and its commercial value.The auxin/indole-3-acetic acid(Aux/IAA)plays a significant role in fruit development and ripening of non-climacteric fruits.However,the regulatory mechanism of Aux/IAA in controlling fruit flesh firmness and ripening in watermelon remains unknown.In this study,we employed an integrative approach combining genome-wide association study(GWAS)and bulked segregant RNA-Seq analysis(BSR-Seq)to identify an overlapping candidate region between 12776310 and 12968331 bp on chromosome 6,underlying an auxin-responsive gene(Aux/IAA)associated with flesh firmness in watermelon.Transcriptome analysis,followed by real-time quantitative reverse transcription PCR(qRT-PCR),confirmed that the expression of Aux/IAA was consistently higher in fruits with high flesh firmness.The sequence alignment revealed a single base mutation in the coding region of Aux/IAA.Furthermore,the concomitant Kompetitive/Competitive allele-specific PCR(KASP)genotyping data sets for F2 population and germplasm accessions identified Aux/IAA as a strong candidate gene associated with flesh firmness.Aux/IAA was enriched in the plant hormone signal transduction pathway,involving cell enlargement and leading to low flesh firmness.We determined the higher accumulation of abscisic acid(ABA)in fruits with low flesh firmness than hard flesh.Moreover,overexpression of Aux/IAA induced higher flesh firmness with an increased number of fruit flesh cells while reducing ABA content and flesh cell sizes.Additionally,the allelic variation in Aux/IAA for soft flesh firmness was found to exist in Citrullus mucosospermus and gradually fixed into Citrullus lanatus during domestication,indicating that soft flesh firmness was a domesticated trait.These findings significantly enhanced our understanding of watermelon fruit flesh firmness and consequently the watermelon fruit quality.展开更多
The organoleptic qualities of watermelon fruit are defined by the sugar and organic acid contents,which undergo considerable variations during development and maturation.The molecular mechanisms underlying these varia...The organoleptic qualities of watermelon fruit are defined by the sugar and organic acid contents,which undergo considerable variations during development and maturation.The molecular mechanisms underlying these variations remain unclear.In this study,we used transcriptome profiles to investigate the coexpression patterns of gene networks associated with sugar and organic acid metabolism.We identified 3 gene networks/modules containing 2443 genes highly correlated with sugars and organic acids.Within these modules,based on intramodular significance and Reverse Transcription Quantitative polymerase chain reaction(RT-qPCR),we identified 7 genes involved in the metabolism of sugars and organic acids.Among these genes,Cla97C01G000640,Cla97C05G087120 and Cla97C01G018840(r^(2)=0.83 with glucose content)were identified as sugar transporters(SWEET,EDR6 and STP)and Cla97C03G064990(r^(2)=0.92 with sucrose content)was identified as a sucrose synthase from information available for other crops.Similarly,Cla97C07G128420,Cla97C03G068240 and Cla97C01G008870,having strong correlations with malic(r^(2)=0.75)and citric acid(r^(2)=0.85),were annotated as malate and citrate transporters(ALMT7,CS,and ICDH).The expression profiles of these 7 genes in diverse watermelon genotypes revealed consistent patterns of expression variation in various types of watermelon.These findings add significantly to our existing knowledge of sugar and organic acid metabolism in watermelon.展开更多
Leaf is a vital organ of plants that plays an essential role in photosynthesis and respiration.As an important agronomic trait in leaf development,leaf shape is classified into lobed,entire(no-lobed),and serrated in m...Leaf is a vital organ of plants that plays an essential role in photosynthesis and respiration.As an important agronomic trait in leaf development,leaf shape is classified into lobed,entire(no-lobed),and serrated in most crops.In this study,two-lobed leaf watermelon inbred lines WT2 and WCZ,and a no-lobed leaf watermelon inbred line WT20 were used to create two F_(2)populations.Segregation analysis suggested that lobed leaves were dominant over the no-lobed leaves,and it was controlled by a signal gene.A locus on watermelon chromosome 4 controlling watermelon lobed/no-lobed leaves was identified through BSA-seq strategy combined with linkage analysis.The candidate gene was fine-mapped to a 61.5 kb region between 21,224,481 and 21,285,957 bp on watermelon chromosome 4 using two F_(2)populations.Four functional genes were annotated in the candidate region,while sequences blast showed that there was a single-base deletion(A/-)only in the exon of Cla018360,which resulted in premature termination of translation in the no-lobed leaf lines.Function prediction showed that Cla018360 encodes an HD-Zip protein that has been reported to regulate the development of leaf shape.The single-base deletion also occurred in the HD-Zip domain.We inferred that the Cla018360 gene is the candidate gene for regulating the development of lobed/no-lobed leaves in watermelon.Gene expression analysis showed that Cla018360 was highly expressed in young leaves.Phylogenetic analysis showed that Cla018360 had a close genetic relationship with AtHB51,which had been reported to regulate the formation of leaf shape in Arabidopsis.Furthermore,transcriptome analysis showed that a total of 333 differentially expressed genes were identified between WT2 and WT20,of which 115 and 218 genes were upregulated and downregulated in no-lobed leaved watermelon WT20.This study not only provides a good entry point for studying leaf development but also provides foundational insights into breeding for special plant architecture in watermelon.展开更多
Cotton(Gossypium)stands as a crucial economic crop,serving as the primary source of naturalfiber for the textile sector.However,the evolutionary mechanisms driving speciation within the Gossypium genus remain unresolv...Cotton(Gossypium)stands as a crucial economic crop,serving as the primary source of naturalfiber for the textile sector.However,the evolutionary mechanisms driving speciation within the Gossypium genus remain unresolved.In this investigation,we leveraged 25 Gossypium genomes and introduced four novel assem-blies—G.harknessii,G.gossypioides,G.trilobum,and G.klotzschianum(Gklo)—to delve into the speciation history of this genus.Notably,we encountered intricate phylogenies potentially stemming from introgres-sion.These complexities are further compounded by incomplete lineage sorting(ILS),a factor likely to have been instrumental in shaping the swift diversification of cotton.Our focus subsequently shifted to the rapid radiation episode during a concise period in Gossypium evolution.For a recently diverged lineage comprising G.davidsonii,Gklo,and G.raimondii,we constructed afinely detailed ILS map.Intriguingly,this analysis revealed the non-random distribution of ILS regions across the reference Gklo genome.Moreover,we identified signs of robust natural selection influencing specific ILS regions.Noteworthy variations per-taining to speciation emerged between the closely related sister species Gklo and G.davidsonii.Approxi-mately 15.74%of speciation structural variation genes and 12.04%of speciation-associated genes were esti-mated to intersect with ILS signatures.Thesefindings enrich our understanding of the role of ILS in adaptive radiation,shedding fresh light on the intricate speciation history of the Gossypium genus.展开更多
基金the Agricultural Science and Technology Innovation Program(Grant No.CAAS-ASTIP-2021-ZFRI)China Agriculture Research System of MOF and MARA(Grant No.CARS-25-03)+3 种基金National Nature Science Foundation of China(Grant Nos.31672178 and 31471893)the Natural Science Foundation of Henan Province(Grant No.212300410312)the scientific and technological research in Henan Province(Grant No.202102110398)the key project of the Action of“Rejuvenating Mongolia with Science and Technology”(Grant No.NMKJXM202114).
文摘Watermelon is a highly cultivated fruit crop renowned for its quality properties of fruit flesh.Among various quality factors,fruit flesh firmness is a crucial quality parameter influencing the fruit texture,shelf life and its commercial value.The auxin/indole-3-acetic acid(Aux/IAA)plays a significant role in fruit development and ripening of non-climacteric fruits.However,the regulatory mechanism of Aux/IAA in controlling fruit flesh firmness and ripening in watermelon remains unknown.In this study,we employed an integrative approach combining genome-wide association study(GWAS)and bulked segregant RNA-Seq analysis(BSR-Seq)to identify an overlapping candidate region between 12776310 and 12968331 bp on chromosome 6,underlying an auxin-responsive gene(Aux/IAA)associated with flesh firmness in watermelon.Transcriptome analysis,followed by real-time quantitative reverse transcription PCR(qRT-PCR),confirmed that the expression of Aux/IAA was consistently higher in fruits with high flesh firmness.The sequence alignment revealed a single base mutation in the coding region of Aux/IAA.Furthermore,the concomitant Kompetitive/Competitive allele-specific PCR(KASP)genotyping data sets for F2 population and germplasm accessions identified Aux/IAA as a strong candidate gene associated with flesh firmness.Aux/IAA was enriched in the plant hormone signal transduction pathway,involving cell enlargement and leading to low flesh firmness.We determined the higher accumulation of abscisic acid(ABA)in fruits with low flesh firmness than hard flesh.Moreover,overexpression of Aux/IAA induced higher flesh firmness with an increased number of fruit flesh cells while reducing ABA content and flesh cell sizes.Additionally,the allelic variation in Aux/IAA for soft flesh firmness was found to exist in Citrullus mucosospermus and gradually fixed into Citrullus lanatus during domestication,indicating that soft flesh firmness was a domesticated trait.These findings significantly enhanced our understanding of watermelon fruit flesh firmness and consequently the watermelon fruit quality.
基金supported by the Agricultural Science and Technology Innovation Program(CAAS-ASTIP-2016-ZFRI)National Key R&D Program of China(2018YFD0100704)the China Agriculture Research System(CARS-25-03)+1 种基金National Natural Science Foundation of China[31672178&31471893]Scientific and Technological Project of Henan Province(202102110197).
文摘The organoleptic qualities of watermelon fruit are defined by the sugar and organic acid contents,which undergo considerable variations during development and maturation.The molecular mechanisms underlying these variations remain unclear.In this study,we used transcriptome profiles to investigate the coexpression patterns of gene networks associated with sugar and organic acid metabolism.We identified 3 gene networks/modules containing 2443 genes highly correlated with sugars and organic acids.Within these modules,based on intramodular significance and Reverse Transcription Quantitative polymerase chain reaction(RT-qPCR),we identified 7 genes involved in the metabolism of sugars and organic acids.Among these genes,Cla97C01G000640,Cla97C05G087120 and Cla97C01G018840(r^(2)=0.83 with glucose content)were identified as sugar transporters(SWEET,EDR6 and STP)and Cla97C03G064990(r^(2)=0.92 with sucrose content)was identified as a sucrose synthase from information available for other crops.Similarly,Cla97C07G128420,Cla97C03G068240 and Cla97C01G008870,having strong correlations with malic(r^(2)=0.75)and citric acid(r^(2)=0.85),were annotated as malate and citrate transporters(ALMT7,CS,and ICDH).The expression profiles of these 7 genes in diverse watermelon genotypes revealed consistent patterns of expression variation in various types of watermelon.These findings add significantly to our existing knowledge of sugar and organic acid metabolism in watermelon.
基金This research was supported by the National Natural Science Foundation of China(32102389,32172602)the Zhongyuan Youth Talent Support Program(ZYQR201912161)+3 种基金the Program for Science&Technology Innovation Talents in Universities of Henan Province(21HASTIT038)the Funding of Joint Research on Agricultural Varietie Improvement of Henan Province(2022010503)the Major Science and Technology Project of Henan Province(221100110400)the Science and Technology Innovation Fund of Henan Agricultural University(KJCX2021A14).
文摘Leaf is a vital organ of plants that plays an essential role in photosynthesis and respiration.As an important agronomic trait in leaf development,leaf shape is classified into lobed,entire(no-lobed),and serrated in most crops.In this study,two-lobed leaf watermelon inbred lines WT2 and WCZ,and a no-lobed leaf watermelon inbred line WT20 were used to create two F_(2)populations.Segregation analysis suggested that lobed leaves were dominant over the no-lobed leaves,and it was controlled by a signal gene.A locus on watermelon chromosome 4 controlling watermelon lobed/no-lobed leaves was identified through BSA-seq strategy combined with linkage analysis.The candidate gene was fine-mapped to a 61.5 kb region between 21,224,481 and 21,285,957 bp on watermelon chromosome 4 using two F_(2)populations.Four functional genes were annotated in the candidate region,while sequences blast showed that there was a single-base deletion(A/-)only in the exon of Cla018360,which resulted in premature termination of translation in the no-lobed leaf lines.Function prediction showed that Cla018360 encodes an HD-Zip protein that has been reported to regulate the development of leaf shape.The single-base deletion also occurred in the HD-Zip domain.We inferred that the Cla018360 gene is the candidate gene for regulating the development of lobed/no-lobed leaves in watermelon.Gene expression analysis showed that Cla018360 was highly expressed in young leaves.Phylogenetic analysis showed that Cla018360 had a close genetic relationship with AtHB51,which had been reported to regulate the formation of leaf shape in Arabidopsis.Furthermore,transcriptome analysis showed that a total of 333 differentially expressed genes were identified between WT2 and WT20,of which 115 and 218 genes were upregulated and downregulated in no-lobed leaved watermelon WT20.This study not only provides a good entry point for studying leaf development but also provides foundational insights into breeding for special plant architecture in watermelon.
基金the National Natural Science Foundation of China (32272090,32171994,and 32072023)the Central Plains Science and Technology Innovation Leader Project (214200510029 and 2022C01NY001)+1 种基金the Project of Sanya Yazhou Bay Science and Technology City (SCKY-JYRC-2022-88)the National Key R&D Program of China (2021YFE0101200)for financial support.
文摘Cotton(Gossypium)stands as a crucial economic crop,serving as the primary source of naturalfiber for the textile sector.However,the evolutionary mechanisms driving speciation within the Gossypium genus remain unresolved.In this investigation,we leveraged 25 Gossypium genomes and introduced four novel assem-blies—G.harknessii,G.gossypioides,G.trilobum,and G.klotzschianum(Gklo)—to delve into the speciation history of this genus.Notably,we encountered intricate phylogenies potentially stemming from introgres-sion.These complexities are further compounded by incomplete lineage sorting(ILS),a factor likely to have been instrumental in shaping the swift diversification of cotton.Our focus subsequently shifted to the rapid radiation episode during a concise period in Gossypium evolution.For a recently diverged lineage comprising G.davidsonii,Gklo,and G.raimondii,we constructed afinely detailed ILS map.Intriguingly,this analysis revealed the non-random distribution of ILS regions across the reference Gklo genome.Moreover,we identified signs of robust natural selection influencing specific ILS regions.Noteworthy variations per-taining to speciation emerged between the closely related sister species Gklo and G.davidsonii.Approxi-mately 15.74%of speciation structural variation genes and 12.04%of speciation-associated genes were esti-mated to intersect with ILS signatures.Thesefindings enrich our understanding of the role of ILS in adaptive radiation,shedding fresh light on the intricate speciation history of the Gossypium genus.