Currently, domestic production of vegetable soybean (aka “edamame”) lags well behind consumer demand, with approximately 70% of U.S.-consumed edamame imported each year. A major barrier for growth of the U.S. edamam...Currently, domestic production of vegetable soybean (aka “edamame”) lags well behind consumer demand, with approximately 70% of U.S.-consumed edamame imported each year. A major barrier for growth of the U.S. edamame industry is an overall lack of varieties with adequate consumer acceptability and adaption to the U.S. climate and environment. In this study, we evaluated eleven vegetable soybean genotypes (including one commercial check) for differences in yield, pod size, and resistance to local insect, bacterial, and fungal pressures in order to identify genotypes with the greatest potential for use in commercial edamame production. Although there were variations in average pod length (42.1 - 53.6 mm), width (10.9 - 12.7 mm), and thickness (6.29 - 7.34 mm) among the genotypes, only pod length showed statistical significance. In addition, genotype significantly affected fresh pod yield. The prevalence of specific insect pests varied by location and year and included soybean aphid, potato leafhopper, Mexican bean beetle, as well as a complex of stink bugs and lepidopteran larvae. For each of these insect pests, significant differences were observed. Some plant diseases observed on the edamame genotypes included: downy mildew, bacterial pustule, Fusarium pod rot, Cercospora blight and purple seed stain, and damping off. In 2018, in Whitethorne, VA, soybean downy mildew was quite prevalent and disease symptoms varied considerably. Overall, genotypes V16-0524 and R15-10280 showed particularly favorable yield, and resilience to native pests compared to the commercial check, UA-Kirksey. The genotypes V16-0524 and R15-10280 showed strong potential to increase the availability of varieties that can be used for commercial edamame production in the Mid-Atlantic region.展开更多
Inflorescence type and remontancy are two valuable traits in bigleaf hydrangea(Hydrangea macrophylla L.)and both are recessively inherited.Molecular marker-assisted selection(MAS)can greatly reduce the time necessary ...Inflorescence type and remontancy are two valuable traits in bigleaf hydrangea(Hydrangea macrophylla L.)and both are recessively inherited.Molecular marker-assisted selection(MAS)can greatly reduce the time necessary to breed cultivars with desired traits.In this study,a genome-wide association study(GWAS)using 5803 single-nucleotide polymorphisms(SNPs)was performed using a panel of 82 bigleaf hydrangea cultivars.One SNP locus(Hy_CAPS_Inflo)associated with inflorescence type was identified with general linear model(GLM)and mixed linear model(MLM)methods that explained 65.5%and 36.1%of the phenotypic variations,respectively.Twenty-three SNPs associated with remontancy were detected in GLM whereas no SNP was detected in MLM.The SNP locus(Hy_CAPS_Inflo)was converted to a cleaved amplified polymorphic sequence(CAPS)marker that showed absolute identification accuracy(100%)of inflorescence type in a validation panel consisting of eighteen H.macrophylla cultivars.The SNP was investigated in 341 F1 progenies using genotyping by sequencing(GBS)and co-segregated with inflorescence type(χ^(2)=0.12;P=0.73).The SNP was subsequently used for breeding selection using kompetitive allele specific PCR(KASP)technology.Future directions for the use of genomics and MAS in hydrangea breeding improvement are discussed.The results presented in this study provide insights for further research on understanding genetic mechanisms behind inflorescence type and remontancy in H.macrophylla.The CAPS and KASP markers developed here will be immediately useful for applying MAS to accelerate breeding improvement in hydrangea.展开更多
The term“undruggable”is to describe molecules that are not targetable or at least hard to target pharmacologically.Unfortunately,some targets with potent oncogenic activity fall into this category,and currently litt...The term“undruggable”is to describe molecules that are not targetable or at least hard to target pharmacologically.Unfortunately,some targets with potent oncogenic activity fall into this category,and currently little is known about how to solve this problem,which largely hampered drug research on human cancers.Ras,as one of the most common oncogenes,was previously considered“undruggable”,but in recent years,a few small molecules like Sotorasib(AMG-510)have emerged and proved their targeted anti-cancer effects.Further,myc,as one of the most studied oncogenes,and tp53,being the most common tumor suppressor genes,are both considered“undruggable”.Many attempts have been made to target these“undruggable”targets,but little progress has been made yet.This article summarizes the current progress of direct and indirect targeting approaches for ras,myc,two oncogenes,and tp53,a tumor suppressor gene.These are potential therapeutic targets but are considered“undruggable”.We conclude with some emerging research approaches like proteolysis targeting chimeras(PROTACs),cancer vaccines,and artificial intelligence(AI)-based drug discovery,which might provide new cues for cancer intervention.Therefore,this review sets out to clarify the current status of targeted anti-cancer drug research,and the insights gained from this review may be of assistance to learn from experience and find new ideas in developing new chemicals that directly target such“undruggable”molecules.展开更多
The Hydrangea genus belongs to the Hydrangeaceae family,in the Cornales order of flowering plants,which early diverged among the Asterids,and includes several species that are commonly used ornamental plants.Of them,H...The Hydrangea genus belongs to the Hydrangeaceae family,in the Cornales order of flowering plants,which early diverged among the Asterids,and includes several species that are commonly used ornamental plants.Of them,Hydrangea macrophylla is one of the most valuable species in the nursery trade,yet few genomic resources are available for this crop or closely related Asterid species.Two high-quality haplotype-resolved reference genomes of hydrangea cultivars‘Veitchii’and‘Endless Summer’[highest quality at 2.22 gigabase pairs(Gb),396 contigs,N5022.8 megabase pairs(Mb)]were assembled and scaffolded into the expected 18 pseudochromosomes.Utilizing the newly developed high-quality reference genomes along with high-quality genomes of other related flowering plants,nuclear data were found to support a single divergence point in the Asterids clade where both the Cornales and Ericales diverged from the euasterids.Genetic mapping with an F1 hybrid population demonstrated the power of linkage mapping combined with the new genomic resources to identify the gene for inflorescence shape,CYP78A5 located on chromosome 4,and a novel gene,BAM3 located on chromosome 17,for causing double flower.Resources developed in this study will not only help to accelerate hydrangea genetic improvement but also contribute to understanding the largest group of flowering plants,the Asterids.展开更多
Heat stress(HS)poses a significant challenge to tomato production due to disruption of the reproductive organs,especially the male gametophytes.This study reports HS-induced proteome changes in meiotic pollen mother c...Heat stress(HS)poses a significant challenge to tomato production due to disruption of the reproductive organs,especially the male gametophytes.This study reports HS-induced proteome changes in meiotic pollen mother cells during early stages of anther development.Tomato(Solanum lycopersicum L.×S.habrochaites)'Maxifort'were grown in a heated polytunnel in Nashville,Tennessee,USA.Plants at flowering stage were subjected to heat treatment at 40±2℃ for 4 hr(11:00−15:00 HR);and the non-heat-treated control was at 30±2℃(day/night)at the same period of time for 10 d.The size of the flower buds containing meiotic pollen mother cells was determined based on the histology of DAPI stained cross section of anthers.Flower buds were embedded in optimal cutting temperature solutions(OCT)and then cut into sections of 20μm thickness.Sections containing meiotic pollen mother cells were collected using laser capture microdissection(LCM).A protein extraction procedure was optimized for the LCM collected pollen samples which yielded 25−30μg protein from 150,000−200,000 pollen cells.The heatinduced proteomes of meiotic pollen mother cells were quantified using tandem mass tag(TMT)quantitative proteomics analysis.Among the 6,343 quantified proteins,254 differentially expressed proteins(DEPs)showed significant differences in abundance level from heat treated to non-heat-treated control conditions.The heat-up-regulated-DEPs(96 proteins)include heat shock proteins,calreticulin and exocytosis(synaptobrevin)which are involved in protein folding/refolding/targeting/removal and secretion of aggregated and damaged proteins/peptides.The heat-down-regulated-DEPs(158 proteins)were involved in pathways of ubiquitin-mediated protein degradation,antioxidant mechanism,and metabolic processes of carbohydrates and lipids.Proteins affecting apoptotic programmed cell death and pollen mother cell meiotic activity were significantly changed under HS.The identified proteins and the affected biological processes could represent the major heat tolerance mechanisms during early developmental stages of male gametophyte when exposed to daily periods of above 40°C HS condition.展开更多
In today＇s data centers supporting Internet-scale computing and input/output （I/0） services, increasingly more network-intensive applications are deployed on the network as a service. To this end, it is critical fo...In today＇s data centers supporting Internet-scale computing and input/output （I/0） services, increasingly more network-intensive applications are deployed on the network as a service. To this end, it is critical for the applications to quickly retrieve requests from the network and send their responses to the network. To facilitate this network func- tion, operating system usually provides an event notification mechanism so that the applications （or the library） know if the network is ready to supply data for them to read or to receive data for them to write. As a widely used and repre- sentative notification mechanism, epoll in Linux provides a scalable and high-performance implementation by allowing applications to specifically indicate which connections and what events on them need to be watched. As epoll has been used in some major systems, includ- ing key-value （KV） systems, such as Redis and Memcached, and web server systems such as NGINX, we have identified a substantial performance issue in its use. For the sake of efficiency, applications usually use epoll＇s system calls to inform the kernel exactly of what events they are interested in and always keep the information up-to-date. However, in a system with demanding network traffic, such a rigid main- tenance of the information is not necessary and the excess number of system calls for this purpose can substantially de- grade the system＇s performance. In this paper, we use Redis as an example to explore the issue. We propose a strategy of informing the kernel of the interest events in a manner adaptive to the current network load, so that the epoll system calls can be reduced and the events can be efficiently deliv- ered. We have implemented an event-polling library, named as FlexPoll, purely in user-level without modifying any ker- nel code. Our evaluation on Redis shows that the query through- put can be improved by up to 46.9% on micro-benchmarks, and even up to 67.8% on workloads emulating real-world ac- cess patterns. FlexPoll is a generic mechanism thus it can be adopted by other applications in a straightforward manner, such as NG1NX and Memcached.展开更多
Mung bean is an economically important legume crop species that is used as a food,consumed as a vegetable,and used as an ingredient and even as a medicine.To explore the genomic diversity of mung bean,we assembled a h...Mung bean is an economically important legume crop species that is used as a food,consumed as a vegetable,and used as an ingredient and even as a medicine.To explore the genomic diversity of mung bean,we assembled a high-quality reference genome(Vrad_JL7)that was479.35 Mb in size,with a contig N50 length of 10.34 Mb.A total of 40,125 protein-coding genes were annotated,representing96.9%of the genetic region.We also sequenced 217 accessions,mainly landraces and cultivars from China,and identified 2,229,343 high-quality single-nucleotide polymorphisms(SNPs).Population structure revealed that the Chinese accessions diverged into two groups and were distinct from non-Chinese lines.Genetic diversity analysis based on genomic data from 750 accessions in 23 countries supported the hypothesis that mung bean was first domesticated in south Asia and introduced to east Asia probably through the Silk Road.We constructed the first pan-genome of mung bean germplasm and assembled 287.73 Mb of non-reference sequences.Among the genes,83.1%were core genes and 16.9%were variable.Presence/absence variation(PAV)events of nine genes involved in the regulation of the photoperiodic flowering pathway were identified as being under selection during the adaptation process to promote early flowering in the spring.Genomewide association studies(GWASs)revealed 2,912 SNPs and 259 gene PAV events associated with 33 agronomic traits,including a SNP in the coding region of the SWEET10 homolog(jg24043)involved in crude starch content and a PAV event in a large fragment containing 11 genes for color-related traits.This high-quality reference genome and pan-genome will provide insights into mung bean breeding.展开更多
The species Vigna unguiculata L.(Walp),commonly known as cowpea,is a multi-purpose legume that has been selected into three subspecies that are divided into grain,fodder and pod(yardlong bean)types.However,genetic bas...The species Vigna unguiculata L.(Walp),commonly known as cowpea,is a multi-purpose legume that has been selected into three subspecies that are divided into grain,fodder and pod(yardlong bean)types.However,genetic bases for distinctions are not well understood.The purpose of this study was to apply genotyping-by-sequencing(GBS)and current reference genome for V.unguiculata to distinguish three subspecies and identify signatures of divergence.The collection of 130 accessions included 128 cultivated from:1)ssp.cylindrica,fodder type;2)ssp.sesquipedalis,pod vegetable type;and 3)ssp.unguiculata,grain type.Two wilds genotypes from spp.dekindtiana and spp.pubescens,were used to anchor phylogeny.A total of 11,083 highly informative single nucleotide polymorphisms(SNPs)were discovered.Wild accessions showed distinct genetic fingerprints and were separated from cultivated subspecies.Principal component analysis showed closer relationship between ssp.unguiculata and ssp.cylindrica compared to ssp.sesquipedalis.Relative differentiation of cultivated subspecies(with Fixation Index,FST)indicated the existence of discrete signatures of selection.This work clarifies the population structure,phylogeny,and domestication of cultivated cowpeas.Furthermore,significant genetic differences between grain and pod vegetable types can provide valuable information for future breeding in three cowpea groups.展开更多
文摘Currently, domestic production of vegetable soybean (aka “edamame”) lags well behind consumer demand, with approximately 70% of U.S.-consumed edamame imported each year. A major barrier for growth of the U.S. edamame industry is an overall lack of varieties with adequate consumer acceptability and adaption to the U.S. climate and environment. In this study, we evaluated eleven vegetable soybean genotypes (including one commercial check) for differences in yield, pod size, and resistance to local insect, bacterial, and fungal pressures in order to identify genotypes with the greatest potential for use in commercial edamame production. Although there were variations in average pod length (42.1 - 53.6 mm), width (10.9 - 12.7 mm), and thickness (6.29 - 7.34 mm) among the genotypes, only pod length showed statistical significance. In addition, genotype significantly affected fresh pod yield. The prevalence of specific insect pests varied by location and year and included soybean aphid, potato leafhopper, Mexican bean beetle, as well as a complex of stink bugs and lepidopteran larvae. For each of these insect pests, significant differences were observed. Some plant diseases observed on the edamame genotypes included: downy mildew, bacterial pustule, Fusarium pod rot, Cercospora blight and purple seed stain, and damping off. In 2018, in Whitethorne, VA, soybean downy mildew was quite prevalent and disease symptoms varied considerably. Overall, genotypes V16-0524 and R15-10280 showed particularly favorable yield, and resilience to native pests compared to the commercial check, UA-Kirksey. The genotypes V16-0524 and R15-10280 showed strong potential to increase the availability of varieties that can be used for commercial edamame production in the Mid-Atlantic region.
文摘Inflorescence type and remontancy are two valuable traits in bigleaf hydrangea(Hydrangea macrophylla L.)and both are recessively inherited.Molecular marker-assisted selection(MAS)can greatly reduce the time necessary to breed cultivars with desired traits.In this study,a genome-wide association study(GWAS)using 5803 single-nucleotide polymorphisms(SNPs)was performed using a panel of 82 bigleaf hydrangea cultivars.One SNP locus(Hy_CAPS_Inflo)associated with inflorescence type was identified with general linear model(GLM)and mixed linear model(MLM)methods that explained 65.5%and 36.1%of the phenotypic variations,respectively.Twenty-three SNPs associated with remontancy were detected in GLM whereas no SNP was detected in MLM.The SNP locus(Hy_CAPS_Inflo)was converted to a cleaved amplified polymorphic sequence(CAPS)marker that showed absolute identification accuracy(100%)of inflorescence type in a validation panel consisting of eighteen H.macrophylla cultivars.The SNP was investigated in 341 F1 progenies using genotyping by sequencing(GBS)and co-segregated with inflorescence type(χ^(2)=0.12;P=0.73).The SNP was subsequently used for breeding selection using kompetitive allele specific PCR(KASP)technology.Future directions for the use of genomics and MAS in hydrangea breeding improvement are discussed.The results presented in this study provide insights for further research on understanding genetic mechanisms behind inflorescence type and remontancy in H.macrophylla.The CAPS and KASP markers developed here will be immediately useful for applying MAS to accelerate breeding improvement in hydrangea.
基金supported by Grants from the National Natural Science Foundation of China(81902784)the CAMS Innovation Fund for Medical Sciences(CIFMS,2019-I2M-5-004)+2 种基金the Fund of Sichuan Provincial Department of Science and Technology(2022YFSY0058)the Research Funding(RCDWJS 2020-20)the Research and Development Program(RD-02-202002)from West China School/Hospital of Stomatology Sichuan University.
文摘The term“undruggable”is to describe molecules that are not targetable or at least hard to target pharmacologically.Unfortunately,some targets with potent oncogenic activity fall into this category,and currently little is known about how to solve this problem,which largely hampered drug research on human cancers.Ras,as one of the most common oncogenes,was previously considered“undruggable”,but in recent years,a few small molecules like Sotorasib(AMG-510)have emerged and proved their targeted anti-cancer effects.Further,myc,as one of the most studied oncogenes,and tp53,being the most common tumor suppressor genes,are both considered“undruggable”.Many attempts have been made to target these“undruggable”targets,but little progress has been made yet.This article summarizes the current progress of direct and indirect targeting approaches for ras,myc,two oncogenes,and tp53,a tumor suppressor gene.These are potential therapeutic targets but are considered“undruggable”.We conclude with some emerging research approaches like proteolysis targeting chimeras(PROTACs),cancer vaccines,and artificial intelligence(AI)-based drug discovery,which might provide new cues for cancer intervention.Therefore,this review sets out to clarify the current status of targeted anti-cancer drug research,and the insights gained from this review may be of assistance to learn from experience and find new ideas in developing new chemicals that directly target such“undruggable”molecules.
基金The research presented in this article was supported in part by funds from the Floral and Nursery Research Initiative administered through the United States Department of Agriculture,Agricultural Research Service(USDA-ARS).Theworkwas supported by USDA-ARS CRIS project numbers 6066-21310-005-00D and 8020-21000-072-000-DThe authors would like to thank Carrie Witcher for assistance with pollen collection and microscopy and Dr Jerry Jenkins from the HudsonAlpha Institute for Biotechnology for his technical advice on scaffolding.BenjaminMoore and Joseph Davis maintained the plants used in this experiment.This research used resources provided by the SCINet project of the USDA Agricultural Research Service,ARS project numbers 0500-00093-001-00-D and 5030-21000-069-00D.The mention of trade names of commercial products in the publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture.
文摘The Hydrangea genus belongs to the Hydrangeaceae family,in the Cornales order of flowering plants,which early diverged among the Asterids,and includes several species that are commonly used ornamental plants.Of them,Hydrangea macrophylla is one of the most valuable species in the nursery trade,yet few genomic resources are available for this crop or closely related Asterid species.Two high-quality haplotype-resolved reference genomes of hydrangea cultivars‘Veitchii’and‘Endless Summer’[highest quality at 2.22 gigabase pairs(Gb),396 contigs,N5022.8 megabase pairs(Mb)]were assembled and scaffolded into the expected 18 pseudochromosomes.Utilizing the newly developed high-quality reference genomes along with high-quality genomes of other related flowering plants,nuclear data were found to support a single divergence point in the Asterids clade where both the Cornales and Ericales diverged from the euasterids.Genetic mapping with an F1 hybrid population demonstrated the power of linkage mapping combined with the new genomic resources to identify the gene for inflorescence shape,CYP78A5 located on chromosome 4,and a novel gene,BAM3 located on chromosome 17,for causing double flower.Resources developed in this study will not only help to accelerate hydrangea genetic improvement but also contribute to understanding the largest group of flowering plants,the Asterids.
基金supported by 1890 Institution Teaching,Research and Extension Capacity Building Grants (CBG)Program,Award No.2018-38821-27737,2014-02868the Evans-Allen Research Funds from USDA-NIFA,and USDA-ARS CRIS Project 1907-21000-036/037-00D.
文摘Heat stress(HS)poses a significant challenge to tomato production due to disruption of the reproductive organs,especially the male gametophytes.This study reports HS-induced proteome changes in meiotic pollen mother cells during early stages of anther development.Tomato(Solanum lycopersicum L.×S.habrochaites)'Maxifort'were grown in a heated polytunnel in Nashville,Tennessee,USA.Plants at flowering stage were subjected to heat treatment at 40±2℃ for 4 hr(11:00−15:00 HR);and the non-heat-treated control was at 30±2℃(day/night)at the same period of time for 10 d.The size of the flower buds containing meiotic pollen mother cells was determined based on the histology of DAPI stained cross section of anthers.Flower buds were embedded in optimal cutting temperature solutions(OCT)and then cut into sections of 20μm thickness.Sections containing meiotic pollen mother cells were collected using laser capture microdissection(LCM).A protein extraction procedure was optimized for the LCM collected pollen samples which yielded 25−30μg protein from 150,000−200,000 pollen cells.The heatinduced proteomes of meiotic pollen mother cells were quantified using tandem mass tag(TMT)quantitative proteomics analysis.Among the 6,343 quantified proteins,254 differentially expressed proteins(DEPs)showed significant differences in abundance level from heat treated to non-heat-treated control conditions.The heat-up-regulated-DEPs(96 proteins)include heat shock proteins,calreticulin and exocytosis(synaptobrevin)which are involved in protein folding/refolding/targeting/removal and secretion of aggregated and damaged proteins/peptides.The heat-down-regulated-DEPs(158 proteins)were involved in pathways of ubiquitin-mediated protein degradation,antioxidant mechanism,and metabolic processes of carbohydrates and lipids.Proteins affecting apoptotic programmed cell death and pollen mother cell meiotic activity were significantly changed under HS.The identified proteins and the affected biological processes could represent the major heat tolerance mechanisms during early developmental stages of male gametophyte when exposed to daily periods of above 40°C HS condition.
基金This work was supported by National High Tech- nology Research and Development Program of China （863） （2011AA01A204）, and the National Natural Science Foundation of China （Grant No. 61272167）.
文摘In today＇s data centers supporting Internet-scale computing and input/output （I/0） services, increasingly more network-intensive applications are deployed on the network as a service. To this end, it is critical for the applications to quickly retrieve requests from the network and send their responses to the network. To facilitate this network func- tion, operating system usually provides an event notification mechanism so that the applications （or the library） know if the network is ready to supply data for them to read or to receive data for them to write. As a widely used and repre- sentative notification mechanism, epoll in Linux provides a scalable and high-performance implementation by allowing applications to specifically indicate which connections and what events on them need to be watched. As epoll has been used in some major systems, includ- ing key-value （KV） systems, such as Redis and Memcached, and web server systems such as NGINX, we have identified a substantial performance issue in its use. For the sake of efficiency, applications usually use epoll＇s system calls to inform the kernel exactly of what events they are interested in and always keep the information up-to-date. However, in a system with demanding network traffic, such a rigid main- tenance of the information is not necessary and the excess number of system calls for this purpose can substantially de- grade the system＇s performance. In this paper, we use Redis as an example to explore the issue. We propose a strategy of informing the kernel of the interest events in a manner adaptive to the current network load, so that the epoll system calls can be reduced and the events can be efficiently deliv- ered. We have implemented an event-polling library, named as FlexPoll, purely in user-level without modifying any ker- nel code. Our evaluation on Redis shows that the query through- put can be improved by up to 46.9% on micro-benchmarks, and even up to 67.8% on workloads emulating real-world ac- cess patterns. FlexPoll is a generic mechanism thus it can be adopted by other applications in a straightforward manner, such as NG1NX and Memcached.
基金supported by the National Key R&D Program of China(2019YFD1000700/2019YFD1000702)the China Agricultural Research System(CARS-08-G3)+2 种基金the Key Research and Development Program of Hebei(21326305D)the Hebei Agriculture Research System(HBCT2018070203)the Hebei Talent Project.
文摘Mung bean is an economically important legume crop species that is used as a food,consumed as a vegetable,and used as an ingredient and even as a medicine.To explore the genomic diversity of mung bean,we assembled a high-quality reference genome(Vrad_JL7)that was479.35 Mb in size,with a contig N50 length of 10.34 Mb.A total of 40,125 protein-coding genes were annotated,representing96.9%of the genetic region.We also sequenced 217 accessions,mainly landraces and cultivars from China,and identified 2,229,343 high-quality single-nucleotide polymorphisms(SNPs).Population structure revealed that the Chinese accessions diverged into two groups and were distinct from non-Chinese lines.Genetic diversity analysis based on genomic data from 750 accessions in 23 countries supported the hypothesis that mung bean was first domesticated in south Asia and introduced to east Asia probably through the Silk Road.We constructed the first pan-genome of mung bean germplasm and assembled 287.73 Mb of non-reference sequences.Among the genes,83.1%were core genes and 16.9%were variable.Presence/absence variation(PAV)events of nine genes involved in the regulation of the photoperiodic flowering pathway were identified as being under selection during the adaptation process to promote early flowering in the spring.Genomewide association studies(GWASs)revealed 2,912 SNPs and 259 gene PAV events associated with 33 agronomic traits,including a SNP in the coding region of the SWEET10 homolog(jg24043)involved in crude starch content and a PAV event in a large fragment containing 11 genes for color-related traits.This high-quality reference genome and pan-genome will provide insights into mung bean breeding.
基金The sources of funding included Evans Allen project TENX-07 to Tennessee State University from the National Institute of Food and Agriculture(NIFA)of United States Department of Agriculture(USDA)for M.S and Ph.D.student assistantship for XW,as well as research funds for MWBChina Scholarship Council(CSC)scholarship for funding of XW student establishmenta grant from Evolutionary Genomics(currently Thirsty Crops Inc.)sponsored by Bill and Melinda Gates Foundation for legume genome wide association studies.
文摘The species Vigna unguiculata L.(Walp),commonly known as cowpea,is a multi-purpose legume that has been selected into three subspecies that are divided into grain,fodder and pod(yardlong bean)types.However,genetic bases for distinctions are not well understood.The purpose of this study was to apply genotyping-by-sequencing(GBS)and current reference genome for V.unguiculata to distinguish three subspecies and identify signatures of divergence.The collection of 130 accessions included 128 cultivated from:1)ssp.cylindrica,fodder type;2)ssp.sesquipedalis,pod vegetable type;and 3)ssp.unguiculata,grain type.Two wilds genotypes from spp.dekindtiana and spp.pubescens,were used to anchor phylogeny.A total of 11,083 highly informative single nucleotide polymorphisms(SNPs)were discovered.Wild accessions showed distinct genetic fingerprints and were separated from cultivated subspecies.Principal component analysis showed closer relationship between ssp.unguiculata and ssp.cylindrica compared to ssp.sesquipedalis.Relative differentiation of cultivated subspecies(with Fixation Index,FST)indicated the existence of discrete signatures of selection.This work clarifies the population structure,phylogeny,and domestication of cultivated cowpeas.Furthermore,significant genetic differences between grain and pod vegetable types can provide valuable information for future breeding in three cowpea groups.
