Bulked-segregant analysis by deep sequencing(BSA-seq) is a widely used method for mapping QTL(quantitative trait loci) due to its simplicity, speed, cost-effectiveness, and efficiency. However, the ability of BSA-seq ...Bulked-segregant analysis by deep sequencing(BSA-seq) is a widely used method for mapping QTL(quantitative trait loci) due to its simplicity, speed, cost-effectiveness, and efficiency. However, the ability of BSA-seq to detect QTL is often limited by inappropriate experimental designs, as evidenced by numerous practical studies. Most BSA-seq studies have utilized small to medium-sized populations, with F2populations being the most common choice. Nevertheless, theoretical studies have shown that using a large population with an appropriate pool size can significantly enhance the power and resolution of QTL detection in BSA-seq, with F_(3)populations offering notable advantages over F2populations. To provide an experimental demonstration, we tested the power of BSA-seq to identify QTL controlling days from sowing to heading(DTH) in a 7200-plant rice F_(3)population in two environments, with a pool size of approximately 500. Each experiment identified 34 QTL, an order of magnitude greater than reported in most BSA-seq experiments, of which 23 were detected in both experiments, with 17 of these located near41 previously reported QTL and eight cloned genes known to control DTH in rice. These results indicate that QTL mapping by BSA-seq in large F_(3)populations and multi-environment experiments can achieve high power, resolution, and reliability.展开更多
Peanut,with high oil content,has been a major oil and food crop globally.The compositions of the fatty acids are the common factors in determining the oil quality.In the present study,an F2 segregated population with ...Peanut,with high oil content,has been a major oil and food crop globally.The compositions of the fatty acids are the common factors in determining the oil quality.In the present study,an F2 segregated population with 140 individuals derived from the cross of Weihua8(a cultivar)and 12L49(a line with high oleic acid concentration)was used to construct a genetic map and conduct QTL mapping analysis.A total of 103 polymorphic SSR primers were utilized for genotyping the RILs and finally generating the SSR loci.Within the 103 SSR loci,a genetic linkage map,covering a total length of 3592.35 cM of the whole peanut genome,was constructed.Based on the genetic map,sixteen QTLs located on nine linkage groups related to peanut fatty acids were finally identified.Among them,four QTLs were detected associated with various traits simultaneously,which showed genetic stability in relation to fatty acids of peanut.Except for the QTLs for oleic acid,linoleic acid,and linolenic acid,three novel QTLs for arachidic acid and behenic acid were also detected.These QTLs might be helpful for further fine mapping analysis and marker-assisted selection of fatty acids in peanut.展开更多
Grape berry shape is an important agricultural trait.Clarifying its genetic basis is significant for cultivating grape varieties that meet market demands.However,the current study by forward genetics has not achieved ...Grape berry shape is an important agricultural trait.Clarifying its genetic basis is significant for cultivating grape varieties that meet market demands.However,the current study by forward genetics has not achieved in-depth results.Here,a high-density map was constructed to identify quantitative trait loci(QTLs)for berry shape.A total of 358709 polymorphic SNPs were obtained using whole-genome resequencing(WGS)based on 208 F2 individuals derived from round grape‘E42-6’and oblong grape‘Rizamat’.The 1635.65 cM high-density map was divided into 19 linkage groups with an average distance of 0.37 cM.Using this map,three significant QTLs for fruit shape index(ShI:ratio of berry length to berry width)identified over three years were mapped onto LG4 and LG5,including one stable QTL on Chr5 with the genomic region of 0.47–1.94 Mb.Combining with gene annotation and expression patterns based on RNA-seq data from two contrasting F2 individuals with round and oblong berry(their average ShI was 1.89 and 1.10,respectively)at four developmental stages,four candidate genes were selected from the above QTLs.They were mainly involved in DNA replication,cell wall modification,and phytohormone biosynthesis.Further analysis of RNA-seq data revealed that several important phytohormone synthesis and metabolic pathways were enriched based on differentially expressed genes(DEGs),which was consistent with the results of QTL mapping for genes related to plant hormone biosynthesis in the F2 population.Furthermore,a comparison of plant hormone content showed that there were significant differences in IAA and tZ content between the two contrasting F2 individuals at different developmental stages.Our findings provide molecular insights into the genetic variation in grape berry shape.Stable QTLs and their tightly linked markers offer the possibility of marker-assisted selection to accelerate berry shape breeding.展开更多
通过对水稻萌发耐淹性进行QTL定位和稳定位点的聚合效应分析,可以为萌发耐淹性基因的精细定位及后续分子辅助育种奠定基础。本研究利用一个包含144份家系的强萌发耐淹性粳型杂草稻WR-4与籼稻品种广百香占的F2:3定位群体,基于1K m GPS SN...通过对水稻萌发耐淹性进行QTL定位和稳定位点的聚合效应分析,可以为萌发耐淹性基因的精细定位及后续分子辅助育种奠定基础。本研究利用一个包含144份家系的强萌发耐淹性粳型杂草稻WR-4与籼稻品种广百香占的F2:3定位群体,基于1K m GPS SNP芯片构建了一个包含825个Bin标记的高密度遗传图谱,利用完备区间作图法共检测到10个萌发耐淹性QTL,分布于水稻第3、4、7、8、9和10染色体上,LOD值介于3.6~21.3之间,可解释3.0%~21.1%的表型变异。其中,具有较高LOD值和贡献率的2个主效QTL(q GS4-1和q GS7-1)能够被重复检测到,是后续基因克隆的候选位点。根据Bin标记分型结果将不同子代在两个稳定QTL区间内分为WR型和广百香占型,在F2:3群体中进行聚合效应分析,发现聚合增效等位基因数量越多的家系,其淹水条件下的胚芽鞘越长,这些携带多个耐性QTL的株系可为分子育种培育耐低氧萌发水稻新品种提供亲本资源。展开更多
Owing to the limitation of a large genome size(~13 Gb),the genetic and gene mapping studies on faba bean(Vicia faba L.)are lagging far behind those for other legumes.In this study,we selected three purified faba bean ...Owing to the limitation of a large genome size(~13 Gb),the genetic and gene mapping studies on faba bean(Vicia faba L.)are lagging far behind those for other legumes.In this study,we selected three purified faba bean lines(Yundou 8137,H0003712,and H000572)as parents and constructed two F2 populations.These two F2 populations,namely 167 F2 plants in Pop1(Yundou 8137×H0003712)and 204 F2 plants in Pop2(H000572×Yundou 8137),were genotyped using a targeted next-generation sequencing(TNGS)genotyping platform,and two high-density single nucleotide polymorphisms(SNP)genetic linkage maps of faba bean were constructed.The map constructed from Pop1 contained 5103 SNPs with a length of 1333.31 cM and an average marker density of 0.26 cM.The map constructed from Pop2 contained 1904 SNPs with a greater length of 1610.61 cM.In these two F2 populations,QTL mapping identified 98 QTLs for 14 agronomic traits related to the flowers,pods,plant types and grains.The two maps were then merged into an integrated genetic linkage map containing 6895 SNPs,with a length of 3324.48 cM.These results not only lay the foundation for fine mapping and map-based cloning of related genes,but can also accelerate the molecular marker-assisted breeding of faba bean.展开更多
Flesh firmness(FF) is an important and complex trait for melon breeders and consumers. However, the genetic mechanism underlying FF is unclear. Here, a soft fruit melon(P5) and a hard fruit melon(P10) were crossed to ...Flesh firmness(FF) is an important and complex trait for melon breeders and consumers. However, the genetic mechanism underlying FF is unclear. Here, a soft fruit melon(P5) and a hard fruit melon(P10) were crossed to generate F2, and the FF and fruit-related traits were recorded for two years. By performing quantitative trait locus(QTL) specificlocus amplified fragment(SLAF)(QTL-SLAF) sequencing and molecular marker-linkage analysis, 112 844 SLAF markers were identified, and 5 919 SNPs were used to construct a genetic linkage map with a total genetic distance of1 356.49 cM. Ten FF-and fruit-related QTLs were identified. Consistent QTLs were detected for fruit length(FL) and fruit diameter(FD) in both years, and QTLs for single fruit weight(SFW) were detected on two separate chromosomes in both years. For FF, the consistent major locus(ff2.1) was located in a 0.17-Mb candidate region on chromosome 2. Using 429 F2individuals derived from a cross between P5 and P10, we refined the ff2.1 locus to a 28.3-kb region harboring three functional genes. These results provide not only a new candidate QTL for melon FF breeding but also a theoretical foundation for research on the mechanism underlying melon gene function.展开更多
Huanglongbing(HLB)is the most devastating disease for citrus worldwide.Candidatus Liberibacter asiaticus(C Las),vectored by Asian citrus psyllid(ACP,Diaphorina citri Kuwayama),is the most common pathogen causing the d...Huanglongbing(HLB)is the most devastating disease for citrus worldwide.Candidatus Liberibacter asiaticus(C Las),vectored by Asian citrus psyllid(ACP,Diaphorina citri Kuwayama),is the most common pathogen causing the disease.Commercial citrus varieties are highly susceptible to HLB,whereas trifoliate orange(Poncirus trifoliata)is considered highly tolerant to HLB.An F1 segregating population and their parent trifoliate orange and sweet orange,which had been exposed to intense HLB pressure for three years,was evaluated for disease symptoms,ACP colonization,C Las titer and tree vigor repeatedly for two to three years.Trifoliate orange and sweet orange showed significant differences for most of the phenotypic traits,and the F1 population exhibited a large variation.A high-density SNP-based genetic map with 1402 markers was constructed for trifoliate orange,which exhibited high synteny and high coverage of its reference genome.A total of 26 quantitative trait locus(QTLs)were identified in four linkage groups LG-t6,LG-t7,LG-t8 and LG-t9,of which four QTL clusters exhibit a clear co-localization of QTLs associated with different traits.Through genome-wide analysis of gene expression in response to C Las infection in‘Flying Dragon’and‘Larger-Flower DPI-50-7’trifoliate orange,85 differentially expressed genes were found located within the QTL clusters.Among them,seven genes were classified as defense or immunity protein which exhibited the highest transcriptional change after C Las infection.Our results indicate a quantitative genetic nature of HLB tolerance and identified candidate genes that should be valuable for searching for genetic solutions to HLB through breeding or genetic engineering.展开更多
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
Soil salinity is one of the major environmental constraints that limits crop yield and nearly 7%of the total area worldwide is affected by salinity.Salinity-induced oxidative stress causes membrane damage during germi...Soil salinity is one of the major environmental constraints that limits crop yield and nearly 7%of the total area worldwide is affected by salinity.Salinity-induced oxidative stress causes membrane damage during germination and seedling growth.Indian mustard is a major oilseed crop in India and its production and productivity are severely affected by salt stress.Breeding Brassica cultivars for salinity tolerance by conventional means is very difficult and time-consuming.Therefore,understanding the molecular components associated with salt tolerance is needed to facilitate breeding for salt tolerance in Brassica.In this investigation,quantitative trait loci(QTLs)associated with salt tolerance were identified using F_(2:3)mapping population developed from a cross between CS52(salinity tolerant)and RH30(salinity sensitive).Parents and F_(2:3)were evaluated under controlled and salinity stress conditions for 14 morpho-physiological traits for two consecutive generations(F2 and F_(2:3)),explaining proportion of the phenotypic variance under control condition.Simple sequence repeat(SSR)markers were used for mapping studies.A genetic linkage map based on 42 simple sequence repeats(SSRs)markers was constructed covering 2298.5 cM(Haldane)to identify the loci associated with salt tolerance in Brassica juncea.Forty-one SSRs showing polymorphism in the parents(CS52 and RH30)were mapped on 8 linkage groups(C1–C8).One marker(nga 129)did not map to any of the linkage group and was excluded from mapping.Linkage group 5(C5;317.9 cM)was longest and linkage group 1(C1,255.0 cM)was shortest.Further,we identified 15 QTLs controlling 8 traits using F_(2:3)population.These QTLs explained 12.44–60.63%of the phenotypic variation with a LOD score range of 3.62–5.97.Out of these QTLs,QMI4.1 related to membrane injury showed 51.28%phenotypic variance with a LOD score of 3.34.QTL QBYP8.1 related to biological yield per plant showed 60.63%phenotypic variance at a LOD score of 3.62.The highest LOD score of 5.97 was recorded for QTL related to seed yield per plant(QSYP4.1).Major QTLs were QTL for biological yield per plant(QBYP8.1),QTL for siliquae per plant(QSP4.1),QTL for primary branches(QPB4.1),QTLs for seed per siliqua(QSS4.1,QSS4.2),QTL for seed yield per plant(QSYP4.1),and QTL for membrane injury(QMI8.1)which showed more than 50%phenotypic variance.These QTLs identified in our study need to be confirmed in other populations as well so that these can be used in marker-assisted selection and breeding to enhance salt tolerance in Brassica juncea.展开更多
Red tilapia(Oreochromis spp.)is one of the most popular fish in China due to its bright red appearance,fast growth rate,and strong adaptability.Understanding the sex determination mechanisms is of vital importance for...Red tilapia(Oreochromis spp.)is one of the most popular fish in China due to its bright red appearance,fast growth rate,and strong adaptability.Understanding the sex determination mechanisms is of vital importance for the selection of all-male lines to increase aquacultural production of red tilapia.In this research,the genetic architecture for sex from four mapping populations(n=1090)of red tilapia was analyzed by quantitative trait loci(QTL)-seq,linkage-based QTL mapping,and linkage disequilibrium(LD)-based genome-wide association studies.Two genome-wide significant QTL intervals associated with sex were identified on ChrLG1(22.4-23.9 Mb)and ChrLG23(32.0-35.9 Mb),respectively.The QTL on ChrLG1 was detected in family 1(FAM1),FAM2,and FAM4,and the other QTL on ChrLG23 was detected in FAM3 and FAM4.Four microsatellite markers located within the QTL were successfully developed for marker-assisted selection.Interestingly,three(Ipp,sox14,and amh)of the 12 candidate genes located near or on the two QTL intervals were abundantly expressed in males,while the remaining genes were more highly expressed in females.Seven genes(scly,ube3a,Ipp,gpr17,oca2,cog4,and atp10a)were significantly differentially expressed between the male and female groups.Furthermore,LD block analysis suggested that a cluster of genes on ChrLG23 may participate in regulating sex development in red tilapia.Our study provides important information on the genetic architecture of sex in red tilapia and should facilitate further exploration of sex determination mechanisms in this species.展开更多
Growth traits are among the most important economic traits in pigs and are regulated by polygenes with complex regulatory mechanisms.As the major indicators of growth performance,the backfat thickness(BFT),loin eye ar...Growth traits are among the most important economic traits in pigs and are regulated by polygenes with complex regulatory mechanisms.As the major indicators of growth performance,the backfat thickness(BFT),loin eye area(LEA),and days to 100 kg(D100)traits are commonly used to the genetics improvement in pigs.However,the available genetic markers for these traits are limited.To uncover novel loci and candidate genes associated with growth performance,we collected the phenotypic information of BFT,LEA,and D100 in 1,186 pigs and genotyped all these individuals using the Neogen GGP porcine 80K BeadChip.We performed a genome-wide association study(GWAS)using 4 statistical models,including mixed linear models(MLM),fixed and random model circulating probability unification(FarmCPU),settlement of MLM under progressively exclusive relationships(SUPER),Bayesian-information and linkage-disequilibrium Iteratively nested keyway(Blink),and identified 5,3,and 6 high-confidence single nucleotide polymorphisms(SNPs)associated with BFT,LEA,and D100,respectively.Variant annotation and quantitative trait locus(QTL)mapping analysis suggested that6 genes(SKAP2,SATB1,PDE7B,PPP1R16B,WNT3,and WNT9B)were potentially associated with growth performance in pigs.Transcriptome analysis suggested that the expression of Src Kinase Associated Phosphoprotein 2(SKAP2)was higher in prenatal muscles than in postnatal muscles,and the expression of Phosphodiesterase 7B(PDE7B)continuously increased during the prenatal stages and gradually decreased after birth,implying their potential roles in prenatal skeletal muscle development.Overall,this study provides new candidate loci and genes for the genetic improvement of pigs.展开更多
The seed storage materials accumulate during seed development,and are essential for seed germination and seedling establishment.Here we employed two bi-parental populations of an F2:3 population developed from a cross...The seed storage materials accumulate during seed development,and are essential for seed germination and seedling establishment.Here we employed two bi-parental populations of an F2:3 population developed from a cross of improved 220(I220,small seeds with low starch)and PH4CV(large seeds with high starch),as well as recombinant-inbred lines(RILs)of X178(high starch)and its improved introgression line I178(low starch),to identify the genes that control seed storage materials.We identified a total of 12 QTLs for starch,protein and oil,which explained 3.44-10.79%of the phenotypic variances.Among them,qSTA2-1 identified in F2:3 and qSTA2-2 identified in the RILs partially overlapped at an interval of 7.314-9.554 Mb,and they explained 3.44-10.21%of the starch content variation,so they were selected for further study.Fine mapping of qSTA2-2 with the backcrossed populations of ^(I220)/PH4CV in each generation narrowed it down to a 199.7 kb interval that contains 14 open reading frames(ORFs).Transcriptomic analysis of developing seeds from the near-isogenic lines(NILs)of ^(I220)/PH4CV(BC_(5)F_(2))showed that only 11 ORFs were expressed in 20 days after pollination(DAP)seeds.Five of them were upregulated and six of them were downregulated in NIL^(I220),and the differentially expressed genes(DEGs)between NIL^(I220) and NIL^(PH4CV) were enriched in starch metabolism,hormone signal transduction and glycosaminoglycan degradation.Of the eleven NIL^(I220) differential expressed ORFs,ORF4(Zm00001d002260)and ORF5(Zm00001d002261)carry 75%protein sequence similarity,both encodes an glycolate oxidase,were the possible candidates of qSTA2-2.Further analysis and validation indicated that mutation of the qSTA2-2 locus resulted in the dysfunction of ABA accumulation,the embryo/endosperm ratio and the starch and hormone levels.展开更多
Grain weight is one of the key components of wheat(Triticum aestivum L.)yield.Genetic manipulation of grain weight is an efficient approach for improving yield potential in breeding programs.A recombinant inbred line(...Grain weight is one of the key components of wheat(Triticum aestivum L.)yield.Genetic manipulation of grain weight is an efficient approach for improving yield potential in breeding programs.A recombinant inbred line(RIL)population derived from a cross between W7268 and Chuanyu 12(CY12)was employed to detect quantitative trait loci(QTLs)for thousand-grain weight(TGW),grain length(GL),grain width(GW),and the ratio of grain length to width(GLW)in six environments.Seven major QTLs,QGl.cib-2D,QGw.cib-2D,QGw.cib-3B,QGw.cib-4B.1,QGlw.cib-2D.1,QTgw.cib-2D.1 and QTgw.cib-3B.1,were consistently identified in at least four environments and the best linear unbiased estimation(BLUE)datasets,and they explained 2.61 to 34.85%of the phenotypic variance.Significant interactions were detected between the two major TGW QTLs and three major GW loci.In addition,QTgw.cib-3B.1 and QGw.cib-3B were co-located,and the improved TGW at this locus was contributed by GW.Unlike other loci,QTgw.cib-3B.1/QGw.cib-3B had no effect on grain number per spike(GNS).They were further validated in advanced lines using Kompetitive Allele Specific PCR(KASP)markers,and a comparison analysis indicated that QTgw.cib-3B.1/QGw.cib-3B is likely a novel locus.Six haplotypes were identified in the region of this QTL and their distribution frequencies varied between the landraces and cultivars.According to gene annotation,spatial expression patterns,ortholog analysis and sequence variation,the candidate gene of QTgw.cib-3B.1/QGw.cib-3B was predicted.Collectively,the major QTLs and KASP markers reported here provide valuable information for elucidating the genetic architecture of grain weight and for molecular marker-assisted breeding in grain yield improvement.展开更多
基金supported by Natural Science Foundation of Fujian Province (CN) (2020I0009, 2022J01596)Cooperation Project on University Industry-Education-Research of Fujian Provincial Science and Technology Plan (CN) (2022N5011)+1 种基金Lancang-Mekong Cooperation Special Fund (2017-2020)International Sci-Tech Cooperation and Communication Program of Fujian Agriculture and Forestry University (KXGH17014)。
文摘Bulked-segregant analysis by deep sequencing(BSA-seq) is a widely used method for mapping QTL(quantitative trait loci) due to its simplicity, speed, cost-effectiveness, and efficiency. However, the ability of BSA-seq to detect QTL is often limited by inappropriate experimental designs, as evidenced by numerous practical studies. Most BSA-seq studies have utilized small to medium-sized populations, with F2populations being the most common choice. Nevertheless, theoretical studies have shown that using a large population with an appropriate pool size can significantly enhance the power and resolution of QTL detection in BSA-seq, with F_(3)populations offering notable advantages over F2populations. To provide an experimental demonstration, we tested the power of BSA-seq to identify QTL controlling days from sowing to heading(DTH) in a 7200-plant rice F_(3)population in two environments, with a pool size of approximately 500. Each experiment identified 34 QTL, an order of magnitude greater than reported in most BSA-seq experiments, of which 23 were detected in both experiments, with 17 of these located near41 previously reported QTL and eight cloned genes known to control DTH in rice. These results indicate that QTL mapping by BSA-seq in large F_(3)populations and multi-environment experiments can achieve high power, resolution, and reliability.
基金supported by the Development Plan of Science and Technology Project of Jilin Province in China[20220508054RC].
文摘Peanut,with high oil content,has been a major oil and food crop globally.The compositions of the fatty acids are the common factors in determining the oil quality.In the present study,an F2 segregated population with 140 individuals derived from the cross of Weihua8(a cultivar)and 12L49(a line with high oleic acid concentration)was used to construct a genetic map and conduct QTL mapping analysis.A total of 103 polymorphic SSR primers were utilized for genotyping the RILs and finally generating the SSR loci.Within the 103 SSR loci,a genetic linkage map,covering a total length of 3592.35 cM of the whole peanut genome,was constructed.Based on the genetic map,sixteen QTLs located on nine linkage groups related to peanut fatty acids were finally identified.Among them,four QTLs were detected associated with various traits simultaneously,which showed genetic stability in relation to fatty acids of peanut.Except for the QTLs for oleic acid,linoleic acid,and linolenic acid,three novel QTLs for arachidic acid and behenic acid were also detected.These QTLs might be helpful for further fine mapping analysis and marker-assisted selection of fatty acids in peanut.
基金financially supported by National Key R&D Program of China(Grant No.2019YFD1001401)Project of Construction of Grape Germplasm Resources Sharing Platform(Grant No.PT2029)+2 种基金Zhengzhou Major Scientific and Technological Innovation Projects(Grant No.2020CXZX0082)National Modern Agricultural Industry Technology System Construction Special Project(Grant No.CARS-29-yc-1)Special Project of Science,Technology Innovation Project of Chinese Academy of Agricultural Sciences(Grant No.CAAS-ASTIP-2019-ZFRI).
文摘Grape berry shape is an important agricultural trait.Clarifying its genetic basis is significant for cultivating grape varieties that meet market demands.However,the current study by forward genetics has not achieved in-depth results.Here,a high-density map was constructed to identify quantitative trait loci(QTLs)for berry shape.A total of 358709 polymorphic SNPs were obtained using whole-genome resequencing(WGS)based on 208 F2 individuals derived from round grape‘E42-6’and oblong grape‘Rizamat’.The 1635.65 cM high-density map was divided into 19 linkage groups with an average distance of 0.37 cM.Using this map,three significant QTLs for fruit shape index(ShI:ratio of berry length to berry width)identified over three years were mapped onto LG4 and LG5,including one stable QTL on Chr5 with the genomic region of 0.47–1.94 Mb.Combining with gene annotation and expression patterns based on RNA-seq data from two contrasting F2 individuals with round and oblong berry(their average ShI was 1.89 and 1.10,respectively)at four developmental stages,four candidate genes were selected from the above QTLs.They were mainly involved in DNA replication,cell wall modification,and phytohormone biosynthesis.Further analysis of RNA-seq data revealed that several important phytohormone synthesis and metabolic pathways were enriched based on differentially expressed genes(DEGs),which was consistent with the results of QTL mapping for genes related to plant hormone biosynthesis in the F2 population.Furthermore,a comparison of plant hormone content showed that there were significant differences in IAA and tZ content between the two contrasting F2 individuals at different developmental stages.Our findings provide molecular insights into the genetic variation in grape berry shape.Stable QTLs and their tightly linked markers offer the possibility of marker-assisted selection to accelerate berry shape breeding.
基金supported by the National Key R&D Program of China(2019YFD1001300 and 2019YFD1001303)the Construction of Molecular Database of Faba Bean and Pea and Identification of Maize Germplasm Project,Ministry of Agriculture and Rural Affairs,China(19200030)+3 种基金the Yunnan Key R&D Program,China(202202AE090003)the earmarked fund for China Agriculture Research System(CARS-08)the Crop Germplasm Resources Protection(2130135)the Major Agricultural Science and Technology Program of Chinese Academy of Agricultural Sciences(CAAS-XTCX20190025)。
文摘Owing to the limitation of a large genome size(~13 Gb),the genetic and gene mapping studies on faba bean(Vicia faba L.)are lagging far behind those for other legumes.In this study,we selected three purified faba bean lines(Yundou 8137,H0003712,and H000572)as parents and constructed two F2 populations.These two F2 populations,namely 167 F2 plants in Pop1(Yundou 8137×H0003712)and 204 F2 plants in Pop2(H000572×Yundou 8137),were genotyped using a targeted next-generation sequencing(TNGS)genotyping platform,and two high-density single nucleotide polymorphisms(SNP)genetic linkage maps of faba bean were constructed.The map constructed from Pop1 contained 5103 SNPs with a length of 1333.31 cM and an average marker density of 0.26 cM.The map constructed from Pop2 contained 1904 SNPs with a greater length of 1610.61 cM.In these two F2 populations,QTL mapping identified 98 QTLs for 14 agronomic traits related to the flowers,pods,plant types and grains.The two maps were then merged into an integrated genetic linkage map containing 6895 SNPs,with a length of 3324.48 cM.These results not only lay the foundation for fine mapping and map-based cloning of related genes,but can also accelerate the molecular marker-assisted breeding of faba bean.
基金supported by the grants from the National Natural Science Foundation of China (31772330 and 32002043)the Natural Science Foundation of the Heilongjiang Province, China (LH2022C065)the Heilongjiang Bayi Agricultural University Support Program for SanHengSanZong, China (TDJH202004)。
文摘Flesh firmness(FF) is an important and complex trait for melon breeders and consumers. However, the genetic mechanism underlying FF is unclear. Here, a soft fruit melon(P5) and a hard fruit melon(P10) were crossed to generate F2, and the FF and fruit-related traits were recorded for two years. By performing quantitative trait locus(QTL) specificlocus amplified fragment(SLAF)(QTL-SLAF) sequencing and molecular marker-linkage analysis, 112 844 SLAF markers were identified, and 5 919 SNPs were used to construct a genetic linkage map with a total genetic distance of1 356.49 cM. Ten FF-and fruit-related QTLs were identified. Consistent QTLs were detected for fruit length(FL) and fruit diameter(FD) in both years, and QTLs for single fruit weight(SFW) were detected on two separate chromosomes in both years. For FF, the consistent major locus(ff2.1) was located in a 0.17-Mb candidate region on chromosome 2. Using 429 F2individuals derived from a cross between P5 and P10, we refined the ff2.1 locus to a 28.3-kb region harboring three functional genes. These results provide not only a new candidate QTL for melon FF breeding but also a theoretical foundation for research on the mechanism underlying melon gene function.
基金supported by grants from the Citrus Research and Development Foundation,USA(Grant No.CRDF#15-010)the New Varieties Development and Management Corporation(NVDMC),on behalf of the Florida citrus industry,USA,the Fundamental Research Funds for the Central Universities,China(Grant No.2022CDJXY-004)from the USDA-NIFA-SCRI,USA(Grant No.2015-70016-2302).
文摘Huanglongbing(HLB)is the most devastating disease for citrus worldwide.Candidatus Liberibacter asiaticus(C Las),vectored by Asian citrus psyllid(ACP,Diaphorina citri Kuwayama),is the most common pathogen causing the disease.Commercial citrus varieties are highly susceptible to HLB,whereas trifoliate orange(Poncirus trifoliata)is considered highly tolerant to HLB.An F1 segregating population and their parent trifoliate orange and sweet orange,which had been exposed to intense HLB pressure for three years,was evaluated for disease symptoms,ACP colonization,C Las titer and tree vigor repeatedly for two to three years.Trifoliate orange and sweet orange showed significant differences for most of the phenotypic traits,and the F1 population exhibited a large variation.A high-density SNP-based genetic map with 1402 markers was constructed for trifoliate orange,which exhibited high synteny and high coverage of its reference genome.A total of 26 quantitative trait locus(QTLs)were identified in four linkage groups LG-t6,LG-t7,LG-t8 and LG-t9,of which four QTL clusters exhibit a clear co-localization of QTLs associated with different traits.Through genome-wide analysis of gene expression in response to C Las infection in‘Flying Dragon’and‘Larger-Flower DPI-50-7’trifoliate orange,85 differentially expressed genes were found located within the QTL clusters.Among them,seven genes were classified as defense or immunity protein which exhibited the highest transcriptional change after C Las infection.Our results indicate a quantitative genetic nature of HLB tolerance and identified candidate genes that should be valuable for searching for genetic solutions to HLB through breeding or genetic engineering.
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.
文摘Soil salinity is one of the major environmental constraints that limits crop yield and nearly 7%of the total area worldwide is affected by salinity.Salinity-induced oxidative stress causes membrane damage during germination and seedling growth.Indian mustard is a major oilseed crop in India and its production and productivity are severely affected by salt stress.Breeding Brassica cultivars for salinity tolerance by conventional means is very difficult and time-consuming.Therefore,understanding the molecular components associated with salt tolerance is needed to facilitate breeding for salt tolerance in Brassica.In this investigation,quantitative trait loci(QTLs)associated with salt tolerance were identified using F_(2:3)mapping population developed from a cross between CS52(salinity tolerant)and RH30(salinity sensitive).Parents and F_(2:3)were evaluated under controlled and salinity stress conditions for 14 morpho-physiological traits for two consecutive generations(F2 and F_(2:3)),explaining proportion of the phenotypic variance under control condition.Simple sequence repeat(SSR)markers were used for mapping studies.A genetic linkage map based on 42 simple sequence repeats(SSRs)markers was constructed covering 2298.5 cM(Haldane)to identify the loci associated with salt tolerance in Brassica juncea.Forty-one SSRs showing polymorphism in the parents(CS52 and RH30)were mapped on 8 linkage groups(C1–C8).One marker(nga 129)did not map to any of the linkage group and was excluded from mapping.Linkage group 5(C5;317.9 cM)was longest and linkage group 1(C1,255.0 cM)was shortest.Further,we identified 15 QTLs controlling 8 traits using F_(2:3)population.These QTLs explained 12.44–60.63%of the phenotypic variation with a LOD score range of 3.62–5.97.Out of these QTLs,QMI4.1 related to membrane injury showed 51.28%phenotypic variance with a LOD score of 3.34.QTL QBYP8.1 related to biological yield per plant showed 60.63%phenotypic variance at a LOD score of 3.62.The highest LOD score of 5.97 was recorded for QTL related to seed yield per plant(QSYP4.1).Major QTLs were QTL for biological yield per plant(QBYP8.1),QTL for siliquae per plant(QSP4.1),QTL for primary branches(QPB4.1),QTLs for seed per siliqua(QSS4.1,QSS4.2),QTL for seed yield per plant(QSYP4.1),and QTL for membrane injury(QMI8.1)which showed more than 50%phenotypic variance.These QTLs identified in our study need to be confirmed in other populations as well so that these can be used in marker-assisted selection and breeding to enhance salt tolerance in Brassica juncea.
基金supported by the Guangdong Provincial Key R&D Program(2021B0202020001)Independent Research and Development Projects of Maoming Laboratory(2021ZZ007)+1 种基金National Natural Science Foundation of China(32072970)Special Science and Technology Program of Maoming,Guangdong,China(2019S002004)。
文摘Red tilapia(Oreochromis spp.)is one of the most popular fish in China due to its bright red appearance,fast growth rate,and strong adaptability.Understanding the sex determination mechanisms is of vital importance for the selection of all-male lines to increase aquacultural production of red tilapia.In this research,the genetic architecture for sex from four mapping populations(n=1090)of red tilapia was analyzed by quantitative trait loci(QTL)-seq,linkage-based QTL mapping,and linkage disequilibrium(LD)-based genome-wide association studies.Two genome-wide significant QTL intervals associated with sex were identified on ChrLG1(22.4-23.9 Mb)and ChrLG23(32.0-35.9 Mb),respectively.The QTL on ChrLG1 was detected in family 1(FAM1),FAM2,and FAM4,and the other QTL on ChrLG23 was detected in FAM3 and FAM4.Four microsatellite markers located within the QTL were successfully developed for marker-assisted selection.Interestingly,three(Ipp,sox14,and amh)of the 12 candidate genes located near or on the two QTL intervals were abundantly expressed in males,while the remaining genes were more highly expressed in females.Seven genes(scly,ube3a,Ipp,gpr17,oca2,cog4,and atp10a)were significantly differentially expressed between the male and female groups.Furthermore,LD block analysis suggested that a cluster of genes on ChrLG23 may participate in regulating sex development in red tilapia.Our study provides important information on the genetic architecture of sex in red tilapia and should facilitate further exploration of sex determination mechanisms in this species.
基金supported by the National Natural Science Foundation of China(32172697,31830090,and 32002151)the Guangdong Provincial Natural Science Foundation,China(2021A1515011336)the Chinese Academy of Agricultural Sciences(CAAS-ZDRW202006)。
文摘Growth traits are among the most important economic traits in pigs and are regulated by polygenes with complex regulatory mechanisms.As the major indicators of growth performance,the backfat thickness(BFT),loin eye area(LEA),and days to 100 kg(D100)traits are commonly used to the genetics improvement in pigs.However,the available genetic markers for these traits are limited.To uncover novel loci and candidate genes associated with growth performance,we collected the phenotypic information of BFT,LEA,and D100 in 1,186 pigs and genotyped all these individuals using the Neogen GGP porcine 80K BeadChip.We performed a genome-wide association study(GWAS)using 4 statistical models,including mixed linear models(MLM),fixed and random model circulating probability unification(FarmCPU),settlement of MLM under progressively exclusive relationships(SUPER),Bayesian-information and linkage-disequilibrium Iteratively nested keyway(Blink),and identified 5,3,and 6 high-confidence single nucleotide polymorphisms(SNPs)associated with BFT,LEA,and D100,respectively.Variant annotation and quantitative trait locus(QTL)mapping analysis suggested that6 genes(SKAP2,SATB1,PDE7B,PPP1R16B,WNT3,and WNT9B)were potentially associated with growth performance in pigs.Transcriptome analysis suggested that the expression of Src Kinase Associated Phosphoprotein 2(SKAP2)was higher in prenatal muscles than in postnatal muscles,and the expression of Phosphodiesterase 7B(PDE7B)continuously increased during the prenatal stages and gradually decreased after birth,implying their potential roles in prenatal skeletal muscle development.Overall,this study provides new candidate loci and genes for the genetic improvement of pigs.
基金supported by grants from the STI 2030-Major Projects,China(2022ZD040190101,2022ZD040190502)the National Natural Science Foundation of China(32072130,32272162 and 31701437)+1 种基金the Project of Sanya Yazhou Bay Science and Technology City,China(SCKJ-JYRC-2023-64)the 2115 Talent Development Program of China Agricultural University,and the China Agriculture Research System(CARS-02-13)。
文摘The seed storage materials accumulate during seed development,and are essential for seed germination and seedling establishment.Here we employed two bi-parental populations of an F2:3 population developed from a cross of improved 220(I220,small seeds with low starch)and PH4CV(large seeds with high starch),as well as recombinant-inbred lines(RILs)of X178(high starch)and its improved introgression line I178(low starch),to identify the genes that control seed storage materials.We identified a total of 12 QTLs for starch,protein and oil,which explained 3.44-10.79%of the phenotypic variances.Among them,qSTA2-1 identified in F2:3 and qSTA2-2 identified in the RILs partially overlapped at an interval of 7.314-9.554 Mb,and they explained 3.44-10.21%of the starch content variation,so they were selected for further study.Fine mapping of qSTA2-2 with the backcrossed populations of ^(I220)/PH4CV in each generation narrowed it down to a 199.7 kb interval that contains 14 open reading frames(ORFs).Transcriptomic analysis of developing seeds from the near-isogenic lines(NILs)of ^(I220)/PH4CV(BC_(5)F_(2))showed that only 11 ORFs were expressed in 20 days after pollination(DAP)seeds.Five of them were upregulated and six of them were downregulated in NIL^(I220),and the differentially expressed genes(DEGs)between NIL^(I220) and NIL^(PH4CV) were enriched in starch metabolism,hormone signal transduction and glycosaminoglycan degradation.Of the eleven NIL^(I220) differential expressed ORFs,ORF4(Zm00001d002260)and ORF5(Zm00001d002261)carry 75%protein sequence similarity,both encodes an glycolate oxidase,were the possible candidates of qSTA2-2.Further analysis and validation indicated that mutation of the qSTA2-2 locus resulted in the dysfunction of ABA accumulation,the embryo/endosperm ratio and the starch and hormone levels.
基金supported by the Major Program of National Agricultural Science and Technology of China(NK20220607)the West Light Foundation of the Chinese Academy of Sciences(2022XBZG_XBQNXZ_A_001)the Sichuan Science and Technology Program,China(2022ZDZX0014)。
文摘Grain weight is one of the key components of wheat(Triticum aestivum L.)yield.Genetic manipulation of grain weight is an efficient approach for improving yield potential in breeding programs.A recombinant inbred line(RIL)population derived from a cross between W7268 and Chuanyu 12(CY12)was employed to detect quantitative trait loci(QTLs)for thousand-grain weight(TGW),grain length(GL),grain width(GW),and the ratio of grain length to width(GLW)in six environments.Seven major QTLs,QGl.cib-2D,QGw.cib-2D,QGw.cib-3B,QGw.cib-4B.1,QGlw.cib-2D.1,QTgw.cib-2D.1 and QTgw.cib-3B.1,were consistently identified in at least four environments and the best linear unbiased estimation(BLUE)datasets,and they explained 2.61 to 34.85%of the phenotypic variance.Significant interactions were detected between the two major TGW QTLs and three major GW loci.In addition,QTgw.cib-3B.1 and QGw.cib-3B were co-located,and the improved TGW at this locus was contributed by GW.Unlike other loci,QTgw.cib-3B.1/QGw.cib-3B had no effect on grain number per spike(GNS).They were further validated in advanced lines using Kompetitive Allele Specific PCR(KASP)markers,and a comparison analysis indicated that QTgw.cib-3B.1/QGw.cib-3B is likely a novel locus.Six haplotypes were identified in the region of this QTL and their distribution frequencies varied between the landraces and cultivars.According to gene annotation,spatial expression patterns,ortholog analysis and sequence variation,the candidate gene of QTgw.cib-3B.1/QGw.cib-3B was predicted.Collectively,the major QTLs and KASP markers reported here provide valuable information for elucidating the genetic architecture of grain weight and for molecular marker-assisted breeding in grain yield improvement.
