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
BACKGROUND Left atrial flutter without prior cardiac interventions is uncommon,especially dual-loop macro-reentry atrial flutter.The critical step to ablate dual-loop macroreentry atrial flutter is to identify the dom...BACKGROUND Left atrial flutter without prior cardiac interventions is uncommon,especially dual-loop macro-reentry atrial flutter.The critical step to ablate dual-loop macroreentry atrial flutter is to identify the dominant loop and key isthmus.Although entrainment mapping could help identify the dominant loop and key isthmus,it may alter or terminate tachycardia.High-density mapping allows the generation of electroanatomic maps without altering or terminating tachycardia.CASE SUMMARY Here,we report a case of symptomatic left atrial flutter without prior intervention.In this case,high-density mapping revealed a dual-loop macro-reentry around the mitral annulus and central scar of the anterior wall.The propagation result showed that the dominant loop was around the mitral annulus,and the key isthmus was between the central scar and mitral annulus.The atrial flutter terminated successfully after ablation was performed.CONCLUSION In this case,we demonstrate that high-density mapping technology may help identify the dominant loop of dual-loop atrial flutter without entrainment,which makes ablation easier.展开更多
General combining abilities （GCAs） are very important in utilization of heterosis in maize breeding. However, its genetic basis is unclear. In the present study, a set of 118 doubled haploid （DH） lines were induce...General combining abilities （GCAs） are very important in utilization of heterosis in maize breeding. However, its genetic basis is unclear. In the present study, a set of 118 doubled haploid （DH） lines were induced from F1 generations produced from the cross between the inbred line Zheng 58 and the inbred line W499 belonging to the Reid subgroup. Using the MaizeSNP50 BeadChip, a high-density genetic map was constructed based on the DH population which included 1 147 bin markers with an average interval length of 2.00 cM. Meanwhile, the DH population was crossed with three testers including W16-5, HD568, and W556, which belong to the Sipingtou subgroup. The GCAs of the ear height （EH）, the kernel moisture content （KMC）, the kernel ratio （KR）, and the yield per plant （YPP） were estimated using these hybrids in three environments. Combining the high-density genetic map and the GCAs, a total of 14 QTLs were detected for the GCAs of the four traits. Especially, one pleiotropic QTL was identified on chromosome 1 between the SNP SYN16067 and the SNP PZE-101169244 which was simultaneously associated with the GCAs of the EH, the KR, and the YPP. These QTLs pave the way for further dissecting the genetic architecture underlying GCAs of the traits, and they may be used to enhance GCAs of inbred lines under the fixed heterotic pattern ReidxSipingtou in China through a marker-assisted selection approach.展开更多
Grain number per spikelet (GNS) is a key determinant of grain yield in wheat.A recombinant inbred line population comprising 300 lines was developed from a cross between a high GNS variety H461 and Chinese Spring from...Grain number per spikelet (GNS) is a key determinant of grain yield in wheat.A recombinant inbred line population comprising 300 lines was developed from a cross between a high GNS variety H461 and Chinese Spring from which the reference genome assembly of bread wheat was obtained.Both parents and the recombinant inbred lines were genotyped using the wheat 55K single nucleotide polymorphism(SNP) array.A high-density genetic map containing 21,197 SNPs was obtained.These markers covered each of the 21 chromosomes with a total linkage distance of 3792.71 c M.Locations of these markers in this linkage map were highly consistent with their physical locations in the genome assembly of Chinese Spring.The two parents and the whole RIL population were assessed for GNS in two consecutive years at two different locations.Based on multi-environment phenotype data and best liner unbiased prediction values,three quantitative trait loci (QTL) for GNS were identified.One of them located on chromosomes 2B and the other two on 2D.Phenotypic variation explained by these loci varied from 3.07%to26.57%.One of these QTL,QGns.sicau-2D-2,was identified in each of all trials conducted.Based on the best linear unbiased prediction values,this locus explained 19.59%–26.57%of phenotypic variation.A KASP(Kompetitive Allele-Specific PCR) marker closely linked with this locus was generated and used to validate the effects of this locus in three different genetic backgrounds.The identified QTL and the KASP marker developed for it will be highly valuable in fine-mapping the locus and in exploiting it for markerassisted selection in wheat breeding programs.展开更多
Long-day length and high temperature inhibit sex expression in pumpkin(Cucurbita moschata Duch.),and therefore directly impact the production potential.In this study,female flowering patterns in photoperiod-insensitiv...Long-day length and high temperature inhibit sex expression in pumpkin(Cucurbita moschata Duch.),and therefore directly impact the production potential.In this study,female flowering patterns in photoperiod-insensitive(PPIS)and photoperiod-sensitive(PPS)germplasms differed significantly in a moderately long day and high temperature environment.However,both germplasms exhibited a similar response in short day with either low temperature or high temperature environment.Photoperiod sensitivity led to this difference in sex expression between the germplasms.For the traits of 1st female flowering node(FFFN)and number of female flowers(NFF),high-density linkage map construction and quantitative trait locus(QTL)mapping were performed using SLAF-seq technology and 162 F_(2) individuals generated from PPIS and PPS.In total,4655 SLAFs were selected and mapped on 20 linkage groups(LGs).The total map length was 2502.01 cM with an average interval distance of 0.75 cM.Major QTLs for both FFFN and NFF were detected on LG6 with intervals of 7.89 and 17.67 cM and PVE values of 30.5%and 22.9%,respectively.Further analyses of the major locus for FFFN revealed 73 protein-coding genes.Among them,4 were related to sex expression,photoperiod flowering,and hormone response.An InDel(insertion and deletion)marker partially correlated with FFFN of the F_(2) population was also developed.Our study identified the QTL for the sex expression response to environmental factors using the high-density linkage map.The identified candidate genes and markers will provide useful information about the molecular interaction between the environment and sex expression and for marker-assisted selection of pumpkin environment-insensitive resources.展开更多
Ancherythroculter nigrocauda is a fish endemic to the upper areas of the Changjiang(Yangtze)River in China.Quantitative trait locus(QTL)mapping is a powerful tool to identify potential genes affecting traits of econom...Ancherythroculter nigrocauda is a fish endemic to the upper areas of the Changjiang(Yangtze)River in China.Quantitative trait locus(QTL)mapping is a powerful tool to identify potential genes affecting traits of economic importance in domestic animals.In this study,a high-density genetic map was constructed with 5901 single nucleotide polymorphism(SNP)makers by sequencing 92 individual fish from a F1 family using the specific-locus amplified fragment sequencing approach.Initially,48 QTLs for total length,body length,body height,and body weight were identified according to the high density of the genetic map with 24 LGs,a total length of 3839.4 cM,and marker spacing of about 0.82 cM.These QTLs explained 27.1%-49.9%of phenotypic variance.The results of this study suggest that major QTLs are responsible for the growth of A.nigrocauda,and these are potentially useful in comparative genomics research,genome assembly,and marker-assisted breeding programs for this species.展开更多
High-density linkage maps are essential tools for genome analysis of various biological traits. Our developed compact multi-gel system, HEGS （high efficiency genome scanning） is a high-throughput and high-cost-perfo...High-density linkage maps are essential tools for genome analysis of various biological traits. Our developed compact multi-gel system, HEGS （high efficiency genome scanning） is a high-throughput and high-cost-performance electrophoresis apparatus. Using this system, a high-density （average interval 2.3 cM） map with 1 065 AFLP and 63 SSR markers was constructed from recombinant inbred lines of a japonica and indica hybrid in just two months of electrophoreses by a single person. More than 50% of the mapped AFLP markers were commonly polymorphic for several combinations between japonica and indica rice and 15% were applicable for genetically closer crosses between upland and lowland types of japonica rice. This system can be used for rapid analyses of all kinds of markers.展开更多
Pyropia yezoensis is an important macroalga because of its extensive global distribution and economic importance.Color is an important trait in the thalli of P.yezoensis,it is also an effective marker to identify the ...Pyropia yezoensis is an important macroalga because of its extensive global distribution and economic importance.Color is an important trait in the thalli of P.yezoensis,it is also an effective marker to identify the hybridization in genetic breeding.In this study,a high-density genetic linkage map was constructed based on high-throughput single nucleotide polymorphism(SNP)markers,and used for analyzing the quantitative trait loci(QTLs)of red color trait in the thalli of P.yezoensis.The conchospore undergoes meiosis to develop into an ordered tetrad,and each cell has a haploid phenotype and can grow into a single individual.Based on this theory,F1 haploid population was used as the mapping population.The map included 531 SNP markers,394.57 cM long on average distance of 0.74 cM.Collinear analysis of the genetic linkage map and the physical map indicated that the coverage between the two maps was 79.42%.Furthermore,QTL mapping identified six QTLs for the chromosomal regions associated with the red color trait of the thalli.The value of phenotypic variance explained(PVE)by an individual QTL ranged from 4.71%-63.11%.And QTL qRed-1-1,with a PVE of 63.11%,was considered the major QTL.Thus,these data may provide a platform for gene and QTL fine mapping,and marker-assisted breeding in P.yezoensis in the future.展开更多
The construction of high density genetic linkage map provides a powerful tool to detect and map quantitative trait loci(QTLs) controlling agronomically important traits. In this study, simple sequence repeat(SSR) mark...The construction of high density genetic linkage map provides a powerful tool to detect and map quantitative trait loci(QTLs) controlling agronomically important traits. In this study, simple sequence repeat(SSR) markers and Illumina 9K i Select single nucleotide polymorphism(SNP) genechip were employed to construct one genetic linkage map of common wheat(Triticum aestivum L.) using 191 recombinant inbred lines(RILs) derived from cross Yu 8679×Jing 411. This map included 1 901 SNP loci and 178 SSR loci, covering 1 659.9 c M and 1 000 marker bins, with an average interval distance of 1.66 c M. A, B and D genomes covered 719.1, 703.5 and 237.3 c M, with an average interval distance of 1.66, 1.45 and 2.9 c M, respectively. Notably, the genetic linkage map covered 20 chromosomes, with the exception of chromosome 5D. Bioinformatics analysis revealed that 1 754(92.27%) of 1 901 mapped SNP loci could be aligned to 1 215 distinct wheat unigenes, among which 1 184(97.4%) were located on o ne single chromosome, and the rest 31(2.6%) were located on 2 to 3 chromosomes. By performing in silico comparison, 214 chromosome deletion bin-mapped expressed sequence tags(ESTs), 1 043 Brachypodium genes and 1 033 rice genes were further added onto the genetic linkage map. This map not only integrated genetic and physical maps, SSR and SNP loci, respectively, but also provided the information of Brachypodium and rice genes corresponding to 1 754 SNP loci. Therefore, it will be a useful tool for comparative genomics analysis, fine mapping of QTL/gene controlling agronomically important traits and marker-assisted selection breeding in wheat.展开更多
Plant height is an important agronomic trait, which is governed by multiple genes with major or minor effects. Of numerous QTLs for plant height reported in soybean, most are in large genomic regions, which results in...Plant height is an important agronomic trait, which is governed by multiple genes with major or minor effects. Of numerous QTLs for plant height reported in soybean, most are in large genomic regions, which results in a still unknown molecular mechanism for plant height. Increasing the density of molecular markers in genetic maps will significantly improve the efficiency and accuracy of QTL mapping. This study constructed a high-density genetic map using 4 011 recombination bin markers developed from whole genome re-sequencing of 241 recombinant inbred lines(RILs) and their bi-parents, Zhonghuang 13(ZH) and Zhongpin 03-5373(ZP). The total genetic distance of this bin map was 3 139.15 cM,with an average interval of 0.78 cM between adjacent bin markers. Comparative genomic analysis indicated that this genetic map showed a high collinearity with the soybean reference genome. Based on this bin map, nine QTLs for plant height were detected across six environments, including three novel loci(qPH-b_11, qPH-b_17 and qPH-b_18). Of them, two environmentally stable QTLs qPH-b_13 and qPH-b_19-1 played a major role in plant height, which explained 10.56-32.7% of the phenotypic variance. They were fine-mapped to 440.12 and 237.06 kb region, covering 54 and 28 annotated genes, respectively. Via the function of homologous genes in Arabidopsis and expression analysis, two genes of them were preferentially predicted as candidate genes for further study.展开更多
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the National Science Foundation of China,No.81800292.
文摘BACKGROUND Left atrial flutter without prior cardiac interventions is uncommon,especially dual-loop macro-reentry atrial flutter.The critical step to ablate dual-loop macroreentry atrial flutter is to identify the dominant loop and key isthmus.Although entrainment mapping could help identify the dominant loop and key isthmus,it may alter or terminate tachycardia.High-density mapping allows the generation of electroanatomic maps without altering or terminating tachycardia.CASE SUMMARY Here,we report a case of symptomatic left atrial flutter without prior intervention.In this case,high-density mapping revealed a dual-loop macro-reentry around the mitral annulus and central scar of the anterior wall.The propagation result showed that the dominant loop was around the mitral annulus,and the key isthmus was between the central scar and mitral annulus.The atrial flutter terminated successfully after ablation was performed.CONCLUSION In this case,we demonstrate that high-density mapping technology may help identify the dominant loop of dual-loop atrial flutter without entrainment,which makes ablation easier.
基金financially supported by the National Key Research and Development Plan of China(2016YFD0101200)
文摘General combining abilities （GCAs） are very important in utilization of heterosis in maize breeding. However, its genetic basis is unclear. In the present study, a set of 118 doubled haploid （DH） lines were induced from F1 generations produced from the cross between the inbred line Zheng 58 and the inbred line W499 belonging to the Reid subgroup. Using the MaizeSNP50 BeadChip, a high-density genetic map was constructed based on the DH population which included 1 147 bin markers with an average interval length of 2.00 cM. Meanwhile, the DH population was crossed with three testers including W16-5, HD568, and W556, which belong to the Sipingtou subgroup. The GCAs of the ear height （EH）, the kernel moisture content （KMC）, the kernel ratio （KR）, and the yield per plant （YPP） were estimated using these hybrids in three environments. Combining the high-density genetic map and the GCAs, a total of 14 QTLs were detected for the GCAs of the four traits. Especially, one pleiotropic QTL was identified on chromosome 1 between the SNP SYN16067 and the SNP PZE-101169244 which was simultaneously associated with the GCAs of the EH, the KR, and the YPP. These QTLs pave the way for further dissecting the genetic architecture underlying GCAs of the traits, and they may be used to enhance GCAs of inbred lines under the fixed heterotic pattern ReidxSipingtou in China through a marker-assisted selection approach.
基金supported by the National Natural Science Foundation of China (31771794)the National Key Research and Development Program of China (2016YFD0101004 and 2017YFD0100900)the International Science & Technology Cooperation Program of the Bureau of Science and Technology of Chengdu China (2015DFA306002015-GH03-00008-HZ)。
文摘Grain number per spikelet (GNS) is a key determinant of grain yield in wheat.A recombinant inbred line population comprising 300 lines was developed from a cross between a high GNS variety H461 and Chinese Spring from which the reference genome assembly of bread wheat was obtained.Both parents and the recombinant inbred lines were genotyped using the wheat 55K single nucleotide polymorphism(SNP) array.A high-density genetic map containing 21,197 SNPs was obtained.These markers covered each of the 21 chromosomes with a total linkage distance of 3792.71 c M.Locations of these markers in this linkage map were highly consistent with their physical locations in the genome assembly of Chinese Spring.The two parents and the whole RIL population were assessed for GNS in two consecutive years at two different locations.Based on multi-environment phenotype data and best liner unbiased prediction values,three quantitative trait loci (QTL) for GNS were identified.One of them located on chromosomes 2B and the other two on 2D.Phenotypic variation explained by these loci varied from 3.07%to26.57%.One of these QTL,QGns.sicau-2D-2,was identified in each of all trials conducted.Based on the best linear unbiased prediction values,this locus explained 19.59%–26.57%of phenotypic variation.A KASP(Kompetitive Allele-Specific PCR) marker closely linked with this locus was generated and used to validate the effects of this locus in three different genetic backgrounds.The identified QTL and the KASP marker developed for it will be highly valuable in fine-mapping the locus and in exploiting it for markerassisted selection in wheat breeding programs.
基金supported by Key Realm R&D Program of Guangdong Province(Grant No.2020B020220003)the National Natural Science Foundation of China(Grant No.31601748)the Agricultural competitive industry discipline team building project of Guangdong Academy of Agricultural Sciences(Grant No.202103TD).
文摘Long-day length and high temperature inhibit sex expression in pumpkin(Cucurbita moschata Duch.),and therefore directly impact the production potential.In this study,female flowering patterns in photoperiod-insensitive(PPIS)and photoperiod-sensitive(PPS)germplasms differed significantly in a moderately long day and high temperature environment.However,both germplasms exhibited a similar response in short day with either low temperature or high temperature environment.Photoperiod sensitivity led to this difference in sex expression between the germplasms.For the traits of 1st female flowering node(FFFN)and number of female flowers(NFF),high-density linkage map construction and quantitative trait locus(QTL)mapping were performed using SLAF-seq technology and 162 F_(2) individuals generated from PPIS and PPS.In total,4655 SLAFs were selected and mapped on 20 linkage groups(LGs).The total map length was 2502.01 cM with an average interval distance of 0.75 cM.Major QTLs for both FFFN and NFF were detected on LG6 with intervals of 7.89 and 17.67 cM and PVE values of 30.5%and 22.9%,respectively.Further analyses of the major locus for FFFN revealed 73 protein-coding genes.Among them,4 were related to sex expression,photoperiod flowering,and hormone response.An InDel(insertion and deletion)marker partially correlated with FFFN of the F_(2) population was also developed.Our study identified the QTL for the sex expression response to environmental factors using the high-density linkage map.The identified candidate genes and markers will provide useful information about the molecular interaction between the environment and sex expression and for marker-assisted selection of pumpkin environment-insensitive resources.
基金Supported by the Technical Innovation Project of Hubei Province(No.2018ABA105)the Enterprise Technology Innovation Project of Wuhan(No.39 of 2019 WuKe)。
文摘Ancherythroculter nigrocauda is a fish endemic to the upper areas of the Changjiang(Yangtze)River in China.Quantitative trait locus(QTL)mapping is a powerful tool to identify potential genes affecting traits of economic importance in domestic animals.In this study,a high-density genetic map was constructed with 5901 single nucleotide polymorphism(SNP)makers by sequencing 92 individual fish from a F1 family using the specific-locus amplified fragment sequencing approach.Initially,48 QTLs for total length,body length,body height,and body weight were identified according to the high density of the genetic map with 24 LGs,a total length of 3839.4 cM,and marker spacing of about 0.82 cM.These QTLs explained 27.1%-49.9%of phenotypic variance.The results of this study suggest that major QTLs are responsible for the growth of A.nigrocauda,and these are potentially useful in comparative genomics research,genome assembly,and marker-assisted breeding programs for this species.
文摘High-density linkage maps are essential tools for genome analysis of various biological traits. Our developed compact multi-gel system, HEGS （high efficiency genome scanning） is a high-throughput and high-cost-performance electrophoresis apparatus. Using this system, a high-density （average interval 2.3 cM） map with 1 065 AFLP and 63 SSR markers was constructed from recombinant inbred lines of a japonica and indica hybrid in just two months of electrophoreses by a single person. More than 50% of the mapped AFLP markers were commonly polymorphic for several combinations between japonica and indica rice and 15% were applicable for genetically closer crosses between upland and lowland types of japonica rice. This system can be used for rapid analyses of all kinds of markers.
基金Supported by the National Natural Science Foundation of China(Nos.41976146,31672641)the Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology(Qingdao)(No.2018SDKJ0302-4)+1 种基金the National Key R&D Program of China(No.2018YFD0900106)the Shandong Province Key Research and Development Program(No.2019GHY112008)。
文摘Pyropia yezoensis is an important macroalga because of its extensive global distribution and economic importance.Color is an important trait in the thalli of P.yezoensis,it is also an effective marker to identify the hybridization in genetic breeding.In this study,a high-density genetic linkage map was constructed based on high-throughput single nucleotide polymorphism(SNP)markers,and used for analyzing the quantitative trait loci(QTLs)of red color trait in the thalli of P.yezoensis.The conchospore undergoes meiosis to develop into an ordered tetrad,and each cell has a haploid phenotype and can grow into a single individual.Based on this theory,F1 haploid population was used as the mapping population.The map included 531 SNP markers,394.57 cM long on average distance of 0.74 cM.Collinear analysis of the genetic linkage map and the physical map indicated that the coverage between the two maps was 79.42%.Furthermore,QTL mapping identified six QTLs for the chromosomal regions associated with the red color trait of the thalli.The value of phenotypic variance explained(PVE)by an individual QTL ranged from 4.71%-63.11%.And QTL qRed-1-1,with a PVE of 63.11%,was considered the major QTL.Thus,these data may provide a platform for gene and QTL fine mapping,and marker-assisted breeding in P.yezoensis in the future.
基金financially supported by the National Natural Science Foundation of China (91435204, 31271710)the National 863 Program of China (2012AA10A309)the Program of Conservation and Sustainable Utilization of Wild Relatives of Crops by the Ministry of Agriculture of China (201003021)
文摘The construction of high density genetic linkage map provides a powerful tool to detect and map quantitative trait loci(QTLs) controlling agronomically important traits. In this study, simple sequence repeat(SSR) markers and Illumina 9K i Select single nucleotide polymorphism(SNP) genechip were employed to construct one genetic linkage map of common wheat(Triticum aestivum L.) using 191 recombinant inbred lines(RILs) derived from cross Yu 8679×Jing 411. This map included 1 901 SNP loci and 178 SSR loci, covering 1 659.9 c M and 1 000 marker bins, with an average interval distance of 1.66 c M. A, B and D genomes covered 719.1, 703.5 and 237.3 c M, with an average interval distance of 1.66, 1.45 and 2.9 c M, respectively. Notably, the genetic linkage map covered 20 chromosomes, with the exception of chromosome 5D. Bioinformatics analysis revealed that 1 754(92.27%) of 1 901 mapped SNP loci could be aligned to 1 215 distinct wheat unigenes, among which 1 184(97.4%) were located on o ne single chromosome, and the rest 31(2.6%) were located on 2 to 3 chromosomes. By performing in silico comparison, 214 chromosome deletion bin-mapped expressed sequence tags(ESTs), 1 043 Brachypodium genes and 1 033 rice genes were further added onto the genetic linkage map. This map not only integrated genetic and physical maps, SSR and SNP loci, respectively, but also provided the information of Brachypodium and rice genes corresponding to 1 754 SNP loci. Therefore, it will be a useful tool for comparative genomics analysis, fine mapping of QTL/gene controlling agronomically important traits and marker-assisted selection breeding in wheat.
基金supported by the National Key R&D Program of China(2016YFD0100201)the Agricultural Science and Technology Innovation Program(ASTIP)of Chinese Academy of Agricultural Sciences。
文摘Plant height is an important agronomic trait, which is governed by multiple genes with major or minor effects. Of numerous QTLs for plant height reported in soybean, most are in large genomic regions, which results in a still unknown molecular mechanism for plant height. Increasing the density of molecular markers in genetic maps will significantly improve the efficiency and accuracy of QTL mapping. This study constructed a high-density genetic map using 4 011 recombination bin markers developed from whole genome re-sequencing of 241 recombinant inbred lines(RILs) and their bi-parents, Zhonghuang 13(ZH) and Zhongpin 03-5373(ZP). The total genetic distance of this bin map was 3 139.15 cM,with an average interval of 0.78 cM between adjacent bin markers. Comparative genomic analysis indicated that this genetic map showed a high collinearity with the soybean reference genome. Based on this bin map, nine QTLs for plant height were detected across six environments, including three novel loci(qPH-b_11, qPH-b_17 and qPH-b_18). Of them, two environmentally stable QTLs qPH-b_13 and qPH-b_19-1 played a major role in plant height, which explained 10.56-32.7% of the phenotypic variance. They were fine-mapped to 440.12 and 237.06 kb region, covering 54 and 28 annotated genes, respectively. Via the function of homologous genes in Arabidopsis and expression analysis, two genes of them were preferentially predicted as candidate genes for further study.
