Inheritance analysis and gene mapping of the glabrous trait were conducted using the crosses between a pubescent rice material Chuanxiang 29B （an aromatic elite maintainer line of hybrid rice）, and two glabrous rice...Inheritance analysis and gene mapping of the glabrous trait were conducted using the crosses between a pubescent rice material Chuanxiang 29B （an aromatic elite maintainer line of hybrid rice）, and two glabrous rice materials, Lemont and R2 （R2 is a new restorer line of hybrid rice）. All F1 plants from the two crosses had pubescent leaves, confirming that the pubescence trait in Chuanxiang 29B is dominant over the glabrous trait. In F2 individuals, the segregation ratio of three pubescent to one glabrous plant suggests that a single glabrous gene was present in Lemont and R2. Using the bulked segregant analysis, the linkage analysis of the simple sequence repeat markers showed that the glabrous gene, gl-1, was flanked by GL311 and GL8 with the genetic distances of 0.19 and 0.92 cM on chromosome 5, respectively.展开更多
The genetic diversity and relationship among 40 elite barley varieties were analyzed based on simple sequence repeat （SSR） genotyping data. The amplified fragments from SSR primers were highly polymorphic in the bad...The genetic diversity and relationship among 40 elite barley varieties were analyzed based on simple sequence repeat （SSR） genotyping data. The amplified fragments from SSR primers were highly polymorphic in the badey accessions investigated. A total of 85 alleles were detected at 35 SSR loci, and allelic variations existed at 29 SSR loci. The allele number per locus ranged from 1 to 5 with an average of 2.4 alleles per locus detected from the 40 badey accessions. A cluster analysis based on the genetic similarity coefficients was conducted and the 40 varieties were classified into two groups. Seven malting barley varieties from China fell into the same subgroup. It was found that the genetic diversity within the Chinese malting barley varieties was narrower than that in other barley germplasm sources, suggesting the importance and feasibility of introducing elite genotypes from different origins for malting barley breeding in China.展开更多
Salt stress is a major problem in most of the rice growing areas in the world. A major QTLSaltol associated with salt tolerance at the seedling stage has been mapped on chromosome 1 in rice.This study aimed to charact...Salt stress is a major problem in most of the rice growing areas in the world. A major QTLSaltol associated with salt tolerance at the seedling stage has been mapped on chromosome 1 in rice.This study aimed to characterize the haplotype diversity at Saltol and additional QTLs associated withsalt tolerance. Salt tolerance at the seedling stage was assessed in 54 rice genotypes in the scale of 1to 9 score at EC = 10 dSm^-1 under controlled environmental conditions. Seven new breeding linesincluding three KMR3/O. rufipogon introgression lines showed similar salt tolerant ability as FL478 andcan be good sources of new genes/alleles for salt tolerance. Simple sequence repeat （SSR） markerRM289 showed only two alleles and RM8094 showed seven alleles. Polymorphic information contentvalue varied from 0.55 for RM289 to 0.99 for RM8094 and RM493. Based on 14 SSR markers, the 54lines were clearly separated into two major clusters. Fourteen haplotypes were identified based onSaltol linked markers with FL478 as the reference. Alleles of RM8094 and RM3412 can discriminatebetween the salt tolerant and susceptible genotypes clearly and hence can be useful in marker-assistedselection at the seedling stage. Other markers RM10720 on chromosome 1 and RM149 and RM264 onchromosome 8 can also distinguish tolerant and susceptible lines but with lesser stringency.展开更多
The genetic diversity of 41 parental lines popularized in commercial hybrid rice production in China was studied by using cluster analysis of morphological traits and simple sequence repeat （SSR） markers. Forty-one ...The genetic diversity of 41 parental lines popularized in commercial hybrid rice production in China was studied by using cluster analysis of morphological traits and simple sequence repeat （SSR） markers. Forty-one entries were assigned into two clusters （i.e. early or medium-maturing cluster; medium or late-maturing cluster） and further assigned into six sub-clusters based on morphological trait cluster analysis, The early or medium-maturing cluster was composed of 15 maintainer lines, four early-maturing restorer lines and two thermo-sensitive genic male sterile lines, and the medium or late-maturing cluster included 16 restorer lines and 4 medium or late-maturing maintainer lines. Moreover, the SSR cluster analysis classified 41 entries into two groups （i.e, maintainer line group and restorer line group） and seven sub-groups. The maintainer line group consisted of all 19 maintainer lines, two thermo-sensitive genic male sterile lines, while the restorer line group was composed of all 20 restorer lines. The SSR analysis fitted better with the pedigree information. From the views on hybrid rice breeding, the results suggested that SSR analysis might be a better method to study the diversity of parental lines in indica hybrid rice.展开更多
Puccinia striiformis f. sp. tritici （Pst） is the obligate biotrophic fungus responsible for stripe rust wheat. In this study, we developed and characterized 20 polymorphic microsatelUte markers from the genomic sequ...Puccinia striiformis f. sp. tritici （Pst） is the obligate biotrophic fungus responsible for stripe rust wheat. In this study, we developed and characterized 20 polymorphic microsatelUte markers from the genomic sequence of an isolate of Chinese Pst race C^32. Polymorphism at each simple sequence repeat （SSR） locus was determined using 32 Pst isolates from 7 countries. The number of alleles varied from 2 to 7 across isolates, and the observed and expected heterozygosities ranged from 0.33 to 0.97 （mean 0.62） and 0.23 to 0.73 （mean 0.51 ）, respectively. As expected the genomic SSR markers were more polymorphic than the expressed sequence tag （EST）-SSR markers developed previously. These markers will be more useful for population genetics and molecular genetics studies in Pst.展开更多
Weedy rice exerts a severe impact on rice production by competing for sunlight, water and nutrients. This study assayed the population structure, genetic diversity and origin of Northeast Asia weedy rice by using 48 s...Weedy rice exerts a severe impact on rice production by competing for sunlight, water and nutrients. This study assayed the population structure, genetic diversity and origin of Northeast Asia weedy rice by using 48 simple sequence repeat markers. The results showed that weedy rice in Northeast Asia had a high genetic diversity, with Shannon＇s diversity index （I） of 0.748 and the heterozygosity （He） of 0.434. In each regional population, I value varied widely. The widest range of I （0.228-0.489） was observed in the weedy rice of Eastern China, which was larger than that of Northeast China and Korea （0.168-0.270）. The F-statistics of regional populations （Fis, Fit and Fst） also showed higher values in the weedy rice of Eastern China than those of Northeast China and Korea All weedy rice accessions were grouped into two clusters in the unweighted pair group method with arithmetic mean cluster analysis dendrogram, namely Eastern China branch and Northeastern China plus Korea branch. There was significant differentiation in genetic characteristics in weedy rice of northeastern and eastern Asia, especially in Eastern China.展开更多
The cultivation of grapes is severely impacted by the emergence of downy mildew (DM) disease which negatively affects quality and yield possibly resulting in heavy losses. Due to certain shortcomings in the usage of f...The cultivation of grapes is severely impacted by the emergence of downy mildew (DM) disease which negatively affects quality and yield possibly resulting in heavy losses. Due to certain shortcomings in the usage of fungicides and the development of new cultivars by plant breeding, marker assisted selection (MAS) will be an efficient alternative method to introduce desired genes into the cultivated varieties in a short time period. The Simple sequence repeats (SSR) markers seem to be the most popular genetic marker of choice for MAS. In the present study, we identified 14 new SSR markers in <i>RPV1</i> locus that are associated with downy mildew resistance in grapes. The characterization of the identified markers was carried out on the basis of various parameters such as types of repeat motifs, number of repeats, different classes and structure of microsatellites. Additionally, SSR genotyping in 56 different grape accessions was done to determine the susceptibility or resistance of these accessions to DM.展开更多
Octopus minor(Sasaki 1920)is an important commercial cephalopod species in China.This species has declined sharply in recent years.Hence,genetic studies of O.minor are imperative to exploit and manage the wild resourc...Octopus minor(Sasaki 1920)is an important commercial cephalopod species in China.This species has declined sharply in recent years.Hence,genetic studies of O.minor are imperative to exploit and manage the wild resource.In this study,46192 microsatellite loci were discovered in 70174 unigenes from the transcriptomic data.Among all of the simple sequence repeat(SSR)unit categories,di-nucleotide and tri-nucleotide SSRs accounted for 45.26%and 14.49%,respectively.A total of 108 SSRs were tested,of which 21 were neutral and polymorphic.Seven SSRs were selected for genetics analyses of the O.minor populations in the Bohai Sea,the Yellow Sea,and the southwest coast of the Taiwan Strait region.Significant pairwise F_(st) values were detected among the samples.The UPGMA tree based on genetic distances suggested that the sampling locations could be arranged in three clusters.These markers are evidence that the populations in this region may be structured,with samples from Penghu differing remarkably from those in northern China.The present study characterized genetic markers for population assessment,management,and conservation of O.minor.展开更多
Simple sequence repeats （SSRs） or microsatellites, as genetic markers, are ubiquitous in genomes of various organisms. The analysis of SSR in rhizobia genome provides useful information for a variety of applications...Simple sequence repeats （SSRs） or microsatellites, as genetic markers, are ubiquitous in genomes of various organisms. The analysis of SSR in rhizobia genome provides useful information for a variety of applications in population genetics of rhizobia. We analyzed the occurrences, relative abundance, and relative density of SSRs, the most common in Bradyrhizobium japonicum, Mesorhizobium loti, and Sinorhizobium meliloti genomes se- quenced in the microorganisms tandem repeats database, and SSRs in the three species genomes were compared with each other. The result showed that there were 1 410, 859, and 638 SSRs in B. japonicum, M. loti, and S. meliloti genomes, respectively. In the genomes of B. japonicum, M. loti, and S. meliloti, tetranucleotide, pentanucleotide, and hexanucleotide repeats were more abundant and indicated higher mutation rates in these species. The least abundance was mononucleotide repeat. The SSRs type and distribution were similar among these species.展开更多
Every breeding program that aims to create new and improved cultivars with desired traits mostly relies on information related to genetic diversity.Therefore,molecular characterization of germplasms is important to ob...Every breeding program that aims to create new and improved cultivars with desired traits mostly relies on information related to genetic diversity.Therefore,molecular characterization of germplasms is important to obtain target cultivars with desirable traits.Sweet potato[Ipomoea batatas(L.)Lam]is widely considered the world’s most important crop,with great diversity in morphological and phenotypic traits.The genetic diversity of 20 sweet potato germplasms originating from Bangladesh,CIP,Philippines,Taiwan,and Malaysia were compared,which was accomplished by genetic diversity analysis by exploring 20 microsatellite DNA markers for germplasm characterization and utilization.This information was effective in differentiating or clustering the sweet potato genotypes.A total of 64 alleles were generated using the 20 primers throughout the 20 germplasm samples,with locus IBS97 having the highest number of alleles(5),whereas locus IbU33 had the fewest alleles(2).The alleles varied in size from 105(IbU31)to 213 base pairs(IBS34).The Polymorphism Information Content(PIC)values for the loci IbL46 and IBS97 varied from 0.445 to 0.730.IBS97 has the highest number of effective alleles(3.704),compared to an average of 2.520.The average Shannon’s diversity index(H)was 1.003,ranging from 0.673 in IbU3 to 1.432 in IBS97.The value of gene flow(Nm)varied between 0.000 and 0.005,with an average of 0.003,whereas genetic differentiation(FST-values)ranged between 0.901 and 1.000.The sweet potato germplasm included in this study had a broad genetic base.SP1 vs.SP9 and SP12 vs.SP18 germplasm pairings had the greatest genetic distance(GD=0.965),while SP1 vs.SP2 germplasm couples had the least genetic diversity(GD=0.093).Twenty genotypes were classified into two groups in the UPGMA dendrogram,with 16 genotypes classified as group“A”and the remaining four genotypes,SP10,SP18,SP19,and SP20,classified as group“B.”According to cluster analysis,the anticipated heterozygosity(gene diversity)of Nei(1973)was 0.591 on average.In summary,SSR markers successfully evaluated the genetic relationships among the sweet potato accessions used and generated a high level of polymorphism.The results of the present study will be useful for the management of germplasm,improvement of the current breeding strategies,and the release of new cultivars as varieties.展开更多
Chinese bayberry （Myrica rubra Sieb. et Zucc.） is one of the important subtropical fruit crops native to the South of China and Asian countries. In this study, 107 novel simple sequence repeat （SSR） molecular mark...Chinese bayberry （Myrica rubra Sieb. et Zucc.） is one of the important subtropical fruit crops native to the South of China and Asian countries. In this study, 107 novel simple sequence repeat （SSR） molecular markers, a powerful tool for genetic diversity studies, cultivar identification, and linkage map construction, were developed and characterized from whole genome shotgun sequences. M13 tailing for forward primers was applied as a simple method in different situations. In total, 828 alleles across 45 accessions were detected, with an average of 8 alleles per locus. The number of effective alleles ranged from 1.22 to 10.41 with an average of 4.08. The polymorphic information content （PIC） varied from 0.13 to 0.89, with an average of 0.63. Moreover, these markers could also be amplified in their related species Myrica cerifera （syn. More/la cerifera） and Myrica adenophora. Seventy-eight SSR markers can be used to produce a genetic map of a cross between ＇Biqi＇ and ＇Dongkui＇. A neighbor-joining （N J） tree was con- structed to assess the genetic relationships among accessions, and the elite accessions ＇Y2010-70＇, ＇Y2012-140＇, and ＇Y2012-145＇, were characterized as potential new genotypes for cultivation.展开更多
Abundance of simple sequence repeat (SSR) in Citrus sequences from EMBL database was investigated by usingcomputer program MISA (MIcroSAtellite), which aimed to provide useful information for the development of SSR ma...Abundance of simple sequence repeat (SSR) in Citrus sequences from EMBL database was investigated by usingcomputer program MISA (MIcroSAtellite), which aimed to provide useful information for the development of SSR markers.Among 32 896 sequences of Citrus, 4 987 SSRs were found in 4 167 sequences and the average distance between SSRs wasapproximately 3.5 kb. Mononucleotide repeats (50.6%) were the most abundant repeats. And di-, tri-, tetra-, penta- andhexa-nucleotide repeats were 22.8, 25.2, 1, 0.08, and 0.36%, respectively. The most abundant motif was A/T followed indescending order by AG/CT, AC/GT, AT/TA. AAT/ATT, AAG/CTT, AGC/CGT, ACG/CTG and C/G. They comprised about90% of all microsatellites. Ten primer pairs were designed, and three of them produced clear visible bands among Citrusand its related genera.展开更多
Yellowfin seabream Acanthopagrus latus is an important economic fish in Chinese coastal areas.Given its narrow distribution and overfishing,the genetic diversity of yellowfin seabream has been restricted for artificia...Yellowfin seabream Acanthopagrus latus is an important economic fish in Chinese coastal areas.Given its narrow distribution and overfishing,the genetic diversity of yellowfin seabream has been restricted for artificial breeding and reproduction.We performed full-length transcriptome sequencing and assembly of the genome of yellowfin seabream.A total of 68086 unigenes were obtained,with an N50 of 3391 bp on average length of 2933 bp.A total number of 50593 expressed sequence tags linked to simple sequence repeats(EST-SSR)were identified,among them dinucleotide repeats(40.6%)and AC/GT motifs(38.5%)were the most frequent.Of the 190 EST-SSRs for which PCR primer pairs were designed,150 primer pairs successfully amplified target loci and 15 SSRs showed high polymorphism.The alleles per locus ranged 6-50 on average of 25.3.The expected and observed heterozygosity varied from 0.632 to 0.969 and from 0.519 to 0.953,respectively.The polymorphic index content(PIC)values of each locus ranged 0.587-0.966 on average of 0.851.Among six yellowfin seabream population samples preliminarily tested for genetic diversity and differentiation,the Fangchenggang(FCG)population in Guangxi Province had the highest mean observed heterozygosity(H_(o))value(0.786),whereas the Zhangzhou(ZZ)population in Fujian Province had the lowest(0.678).The pairwise fixation index(Fst)values indicated significant population differentiation among six yellowfin seabream populations.This study provided evidence for the usefulness of the transcriptomic resource information and EST-SSR markers for natural resource conservation,population genetics,and breeding studies of yellowfin seabream in South China.展开更多
The present study investigated the genetic diversity of 24 germplasms of Polianthes tuberosa L.via 16 inter simple sequence repeat(ISSR)marker techniques.The research findings revealed that the ISSR markers presented ...The present study investigated the genetic diversity of 24 germplasms of Polianthes tuberosa L.via 16 inter simple sequence repeat(ISSR)marker techniques.The research findings revealed that the ISSR markers presented higher levels of band reproducibility andweremore efficient at clustering germplasms.Among the 16markers examined in this study,12 had a complete polymorphism rate of 100%.Themolecular analysis revealed a PICranging from0.079 to 0.373,with amean value of 0.30,whereas the range of themarker index was from0.0001 to 0.409,with an average value of 0.03,and the primer resolving power ranged from 0.173 to 4.173,with a mean value of 2.02.The UPGMA clustering dendrogram indicated that all 24 germplasms were grouped into three main clusters.The study revealed a variable range of tree distances between 0.185 and 0.621,with the highest tree distance(0.621)detected between germplasms BR-24 and BR-1.Through these studies,the dissimilarity among the germplasms was evaluated,and diverse parents were identified for further crop improvement programs.展开更多
To assess the population development of submerged plant species in disturbed lake ecosystems,we need to better understand the genetic diversity and spatial genetic structure at a fine scale,as well as the impact of di...To assess the population development of submerged plant species in disturbed lake ecosystems,we need to better understand the genetic diversity and spatial genetic structure at a fine scale,as well as the impact of disturbances on the populations.Caohai Lake,in southwest China,is a suitable natural sampling lake because of its abundance of submerged plants and the intense human disturbance.Three widely distributed species,Potamogeton lucens,Ceratophyllum demersum,and Myriophyllum spicatum,were sampled;the spatial position of each individual was recorded in two-dimensional coordinates;and the species were analyzed genetically using microsatellite markers.Among the species studied,M.spicatum exhibited the highest genetic and clonal diversities.All P.lucens subpopulations but one showed a significant fine-scale spatial genetic structure(FSGS),which may result from the limited gene dispersal.However,M.spicatum and C.demersum,with a relatively large distance of gene dispersal,had no significant FSGS.The FSGS pattern of P.lucens at the dock site with intense boat disturbance was significantly different from that at other sites.Our results imply that the FSGS of submerged plants is affected by many factors including seed dispersal,vegetative reproduction and disturbance from birds and boats.Most subpopulations of the three species hadσ_(sex)^(2)/σ_(veg)^(2)values greater than one,implying that the sexual dispersal contributes more than vegetative dispersal to total gene dispersal.Therefore,it is worth paying attention to the importance of seed dispersal for population development of submerged plants in lake ecosystems.展开更多
Chloroplast simple sequence repeat (cpSSR) markers in Citrus were developed and successfully used to analyze chloroplast genome inheritance of Citrus somatic hybrids. Twenty-two previously reported cpSSR primer pairs ...Chloroplast simple sequence repeat (cpSSR) markers in Citrus were developed and successfully used to analyze chloroplast genome inheritance of Citrus somatic hybrids. Twenty-two previously reported cpSSR primer pairs from pine (Pinus thunbergii Parl.), rice (Otyza sativa L.) and tobacco (Nicotiana tabacum L.) were tested in Citrus, nine of which could amplify intensive PCR products by agarose gel electrophoresis. Chloroplast genome inheritance of Citrus somatic hybrids from nine fusions was then analyzed, and five of the nine pre-screened primer pairs showed polymorphisms by polyacrylamide gel electrophoresis. The results revealed the random inheritance nature of chloroplast genome in all analyzed Citrus somatic hybrids, which was in agreement with previous reports based on RFLP or CAPS analyses. It was also shown that cpSSR is a more efficient tool in chloroplast genome analyses of somatic hybrids in higher plants, compared with the conventional RFLP or CAPS analyses.展开更多
Genetic relationships of eight species of genus Betula were evaluated using ISSR marks. A total of 236 loci were generated from 17 ISSR primers. Percentage of polymorphic bands (PPB) varied from 5.93 to 19.92. The hig...Genetic relationships of eight species of genus Betula were evaluated using ISSR marks. A total of 236 loci were generated from 17 ISSR primers. Percentage of polymorphic bands (PPB) varied from 5.93 to 19.92. The highest and the lowest level of genetic differentiation were detected in B. ovalifolia and B. maximowicziana Regel respectively. In these eight species, genetic diversity of birch (HT) was 24.38 %, and the genetic variation (GST ) interspecies was accounting for 79.36% of total genetic variation. According to the cluster results of genetic distance, the eight species were classified into three groups as B. davurica, B. ovalifolia, B. platyphylla and B. pendula for one group; B. schmidtii, B. costata and B. ermanii Cham. var. communis for one group, and B. maximowicziana Regel for another group. The result of cluster is consistent with traditional morphological classification.展开更多
[Objective]The aim was to optimize SSR reaction system applied in the identification of authenticity of maize variety.[Method]The technical parameters of SSR including PCR reaction system,annealing temperature and ele...[Objective]The aim was to optimize SSR reaction system applied in the identification of authenticity of maize variety.[Method]The technical parameters of SSR including PCR reaction system,annealing temperature and electrophoresis time were optimized to identify 10 major maize varieties in Liaoning Province.[Result]The optimum PCR reaction system was：14.60 μl sterile ultrapure water,2.00 μl 10 × Buffer（Mg2＋）,1.20 μl dNTPs,0.20 μl Taq enzyme,0.50 μl each of the forward and reverse primers and1.00 μl DNA stock solution.Annealing temperature and electrophoresis time could greatly influence the results of PCR amplification.The optimal annealing temperature and electrophoresis time required for the ideal electrophoresis bands under the same conditions were different when different primers were used.[Conclusion]The system was feasible to be applied in rapid identification of authenticity of hybrid maize varieties.展开更多
In an effort to simplify the procedure and to reduce the cost of fluorescence SSR analysis, the conditions of the multiplex PCR and the multiplex gel electrophoresis were optimized in the genetic analysis of sunflower...In an effort to simplify the procedure and to reduce the cost of fluorescence SSR analysis, the conditions of the multiplex PCR and the multiplex gel electrophoresis were optimized in the genetic analysis of sunflower (Helianthus annuus L.) inbred lines. Results indicated that factors for a successful multiplex PCR assay were related to the cycling touchdown annealing temperature, the balance of primer concentration at the various loci, the concentration of PCR buffer and the Taq DNA polymerase. Based on the optimization, a tailed primer strategy was outlined, and the effective ways were proposed to overcome the troubleshootings commonly encountered in the multiplex PCR and the multiplex gel electrophoresis.展开更多
基金supported by the grants of the National High Technology Research and Development Program of China(Grant No.2006AA100101)the ‘948’program of China(Grant No.2006-G1)the National Technology Foundation from Ministry of Agriculture,China(Grant No.2006BAD01A01-1)
文摘Inheritance analysis and gene mapping of the glabrous trait were conducted using the crosses between a pubescent rice material Chuanxiang 29B （an aromatic elite maintainer line of hybrid rice）, and two glabrous rice materials, Lemont and R2 （R2 is a new restorer line of hybrid rice）. All F1 plants from the two crosses had pubescent leaves, confirming that the pubescence trait in Chuanxiang 29B is dominant over the glabrous trait. In F2 individuals, the segregation ratio of three pubescent to one glabrous plant suggests that a single glabrous gene was present in Lemont and R2. Using the bulked segregant analysis, the linkage analysis of the simple sequence repeat markers showed that the glabrous gene, gl-1, was flanked by GL311 and GL8 with the genetic distances of 0.19 and 0.92 cM on chromosome 5, respectively.
基金Project supported by the National Natural Science Foundation of China (Nos. 30700485 and 30771333)the Zhejiang Provincial Natural Science Foundation (No. Y306641),China
文摘The genetic diversity and relationship among 40 elite barley varieties were analyzed based on simple sequence repeat （SSR） genotyping data. The amplified fragments from SSR primers were highly polymorphic in the badey accessions investigated. A total of 85 alleles were detected at 35 SSR loci, and allelic variations existed at 29 SSR loci. The allele number per locus ranged from 1 to 5 with an average of 2.4 alleles per locus detected from the 40 badey accessions. A cluster analysis based on the genetic similarity coefficients was conducted and the 40 varieties were classified into two groups. Seven malting barley varieties from China fell into the same subgroup. It was found that the genetic diversity within the Chinese malting barley varieties was narrower than that in other barley germplasm sources, suggesting the importance and feasibility of introducing elite genotypes from different origins for malting barley breeding in China.
基金Financial support of Department of Biotechnology,Government of India[Grant Nos.BT/AB/FG-2(PH-II)2009 and BT/PR13357/AGR/02/695/2009]
文摘Salt stress is a major problem in most of the rice growing areas in the world. A major QTLSaltol associated with salt tolerance at the seedling stage has been mapped on chromosome 1 in rice.This study aimed to characterize the haplotype diversity at Saltol and additional QTLs associated withsalt tolerance. Salt tolerance at the seedling stage was assessed in 54 rice genotypes in the scale of 1to 9 score at EC = 10 dSm^-1 under controlled environmental conditions. Seven new breeding linesincluding three KMR3/O. rufipogon introgression lines showed similar salt tolerant ability as FL478 andcan be good sources of new genes/alleles for salt tolerance. Simple sequence repeat （SSR） markerRM289 showed only two alleles and RM8094 showed seven alleles. Polymorphic information contentvalue varied from 0.55 for RM289 to 0.99 for RM8094 and RM493. Based on 14 SSR markers, the 54lines were clearly separated into two major clusters. Fourteen haplotypes were identified based onSaltol linked markers with FL478 as the reference. Alleles of RM8094 and RM3412 can discriminatebetween the salt tolerant and susceptible genotypes clearly and hence can be useful in marker-assistedselection at the seedling stage. Other markers RM10720 on chromosome 1 and RM149 and RM264 onchromosome 8 can also distinguish tolerant and susceptible lines but with lesser stringency.
文摘The genetic diversity of 41 parental lines popularized in commercial hybrid rice production in China was studied by using cluster analysis of morphological traits and simple sequence repeat （SSR） markers. Forty-one entries were assigned into two clusters （i.e. early or medium-maturing cluster; medium or late-maturing cluster） and further assigned into six sub-clusters based on morphological trait cluster analysis, The early or medium-maturing cluster was composed of 15 maintainer lines, four early-maturing restorer lines and two thermo-sensitive genic male sterile lines, and the medium or late-maturing cluster included 16 restorer lines and 4 medium or late-maturing maintainer lines. Moreover, the SSR cluster analysis classified 41 entries into two groups （i.e, maintainer line group and restorer line group） and seven sub-groups. The maintainer line group consisted of all 19 maintainer lines, two thermo-sensitive genic male sterile lines, while the restorer line group was composed of all 20 restorer lines. The SSR analysis fitted better with the pedigree information. From the views on hybrid rice breeding, the results suggested that SSR analysis might be a better method to study the diversity of parental lines in indica hybrid rice.
基金supported by the National Basic Research Program(973)of China(No.2013CB127700)the Special Fund for Agro-Scientific Research in the Public Interest(No.201303023)+1 种基金the National Natural Science Foundation of China(No.31371882)the 111 Project from the Ministry of Education of China(No.B07049)
文摘Puccinia striiformis f. sp. tritici （Pst） is the obligate biotrophic fungus responsible for stripe rust wheat. In this study, we developed and characterized 20 polymorphic microsatelUte markers from the genomic sequence of an isolate of Chinese Pst race C^32. Polymorphism at each simple sequence repeat （SSR） locus was determined using 32 Pst isolates from 7 countries. The number of alleles varied from 2 to 7 across isolates, and the observed and expected heterozygosities ranged from 0.33 to 0.97 （mean 0.62） and 0.23 to 0.73 （mean 0.51 ）, respectively. As expected the genomic SSR markers were more polymorphic than the expressed sequence tag （EST）-SSR markers developed previously. These markers will be more useful for population genetics and molecular genetics studies in Pst.
基金funded by Shanghai Municipal Key Task Projects of Prospering Agriculture by Science and Technology Plan in China (Grant No. Hu Nong Ke Gong Zi 2008: 2-1)
文摘Weedy rice exerts a severe impact on rice production by competing for sunlight, water and nutrients. This study assayed the population structure, genetic diversity and origin of Northeast Asia weedy rice by using 48 simple sequence repeat markers. The results showed that weedy rice in Northeast Asia had a high genetic diversity, with Shannon＇s diversity index （I） of 0.748 and the heterozygosity （He） of 0.434. In each regional population, I value varied widely. The widest range of I （0.228-0.489） was observed in the weedy rice of Eastern China, which was larger than that of Northeast China and Korea （0.168-0.270）. The F-statistics of regional populations （Fis, Fit and Fst） also showed higher values in the weedy rice of Eastern China than those of Northeast China and Korea All weedy rice accessions were grouped into two clusters in the unweighted pair group method with arithmetic mean cluster analysis dendrogram, namely Eastern China branch and Northeastern China plus Korea branch. There was significant differentiation in genetic characteristics in weedy rice of northeastern and eastern Asia, especially in Eastern China.
文摘The cultivation of grapes is severely impacted by the emergence of downy mildew (DM) disease which negatively affects quality and yield possibly resulting in heavy losses. Due to certain shortcomings in the usage of fungicides and the development of new cultivars by plant breeding, marker assisted selection (MAS) will be an efficient alternative method to introduce desired genes into the cultivated varieties in a short time period. The Simple sequence repeats (SSR) markers seem to be the most popular genetic marker of choice for MAS. In the present study, we identified 14 new SSR markers in <i>RPV1</i> locus that are associated with downy mildew resistance in grapes. The characterization of the identified markers was carried out on the basis of various parameters such as types of repeat motifs, number of repeats, different classes and structure of microsatellites. Additionally, SSR genotyping in 56 different grape accessions was done to determine the susceptibility or resistance of these accessions to DM.
基金supported by the National Natural Science Foundation of China(No.31672257)the National Key Research and Development Program of China(No.2020YFD0900705).
文摘Octopus minor(Sasaki 1920)is an important commercial cephalopod species in China.This species has declined sharply in recent years.Hence,genetic studies of O.minor are imperative to exploit and manage the wild resource.In this study,46192 microsatellite loci were discovered in 70174 unigenes from the transcriptomic data.Among all of the simple sequence repeat(SSR)unit categories,di-nucleotide and tri-nucleotide SSRs accounted for 45.26%and 14.49%,respectively.A total of 108 SSRs were tested,of which 21 were neutral and polymorphic.Seven SSRs were selected for genetics analyses of the O.minor populations in the Bohai Sea,the Yellow Sea,and the southwest coast of the Taiwan Strait region.Significant pairwise F_(st) values were detected among the samples.The UPGMA tree based on genetic distances suggested that the sampling locations could be arranged in three clusters.These markers are evidence that the populations in this region may be structured,with samples from Penghu differing remarkably from those in northern China.The present study characterized genetic markers for population assessment,management,and conservation of O.minor.
基金the program of Key Sci-ence and Technology Research from the Department of Science and Technology of General Bureau of Land Reclamation of Heilongjiang Province, China (HNKXIV-02-03-03)
文摘Simple sequence repeats （SSRs） or microsatellites, as genetic markers, are ubiquitous in genomes of various organisms. The analysis of SSR in rhizobia genome provides useful information for a variety of applications in population genetics of rhizobia. We analyzed the occurrences, relative abundance, and relative density of SSRs, the most common in Bradyrhizobium japonicum, Mesorhizobium loti, and Sinorhizobium meliloti genomes se- quenced in the microorganisms tandem repeats database, and SSRs in the three species genomes were compared with each other. The result showed that there were 1 410, 859, and 638 SSRs in B. japonicum, M. loti, and S. meliloti genomes, respectively. In the genomes of B. japonicum, M. loti, and S. meliloti, tetranucleotide, pentanucleotide, and hexanucleotide repeats were more abundant and indicated higher mutation rates in these species. The least abundance was mononucleotide repeat. The SSRs type and distribution were similar among these species.
基金The work was financially supported by National Agricultural Technology Program-II Project(NATP-2)BARC Component Bangladesh Agricultural Research Council,Farmgate,Dhaka-1215+2 种基金Bangladesh Agricultural Research Institute(BARI),Joydebpur,Gazipur 1701The work was partially supported by the Taif University Researchers Supporting Project No.(TURSP-2020/39)Taif University,Taif,Saudi Arabia.
文摘Every breeding program that aims to create new and improved cultivars with desired traits mostly relies on information related to genetic diversity.Therefore,molecular characterization of germplasms is important to obtain target cultivars with desirable traits.Sweet potato[Ipomoea batatas(L.)Lam]is widely considered the world’s most important crop,with great diversity in morphological and phenotypic traits.The genetic diversity of 20 sweet potato germplasms originating from Bangladesh,CIP,Philippines,Taiwan,and Malaysia were compared,which was accomplished by genetic diversity analysis by exploring 20 microsatellite DNA markers for germplasm characterization and utilization.This information was effective in differentiating or clustering the sweet potato genotypes.A total of 64 alleles were generated using the 20 primers throughout the 20 germplasm samples,with locus IBS97 having the highest number of alleles(5),whereas locus IbU33 had the fewest alleles(2).The alleles varied in size from 105(IbU31)to 213 base pairs(IBS34).The Polymorphism Information Content(PIC)values for the loci IbL46 and IBS97 varied from 0.445 to 0.730.IBS97 has the highest number of effective alleles(3.704),compared to an average of 2.520.The average Shannon’s diversity index(H)was 1.003,ranging from 0.673 in IbU3 to 1.432 in IBS97.The value of gene flow(Nm)varied between 0.000 and 0.005,with an average of 0.003,whereas genetic differentiation(FST-values)ranged between 0.901 and 1.000.The sweet potato germplasm included in this study had a broad genetic base.SP1 vs.SP9 and SP12 vs.SP18 germplasm pairings had the greatest genetic distance(GD=0.965),while SP1 vs.SP2 germplasm couples had the least genetic diversity(GD=0.093).Twenty genotypes were classified into two groups in the UPGMA dendrogram,with 16 genotypes classified as group“A”and the remaining four genotypes,SP10,SP18,SP19,and SP20,classified as group“B.”According to cluster analysis,the anticipated heterozygosity(gene diversity)of Nei(1973)was 0.591 on average.In summary,SSR markers successfully evaluated the genetic relationships among the sweet potato accessions used and generated a high level of polymorphism.The results of the present study will be useful for the management of germplasm,improvement of the current breeding strategies,and the release of new cultivars as varieties.
基金supported by the Ningbo Science and Technology Bureau(No.2012C10012)the Science and Technology Project of Zhejiang Province(No.2012C12904)the Yuyao Financial Bureau for Chinese Bayberry Breeding Program,China
文摘Chinese bayberry （Myrica rubra Sieb. et Zucc.） is one of the important subtropical fruit crops native to the South of China and Asian countries. In this study, 107 novel simple sequence repeat （SSR） molecular markers, a powerful tool for genetic diversity studies, cultivar identification, and linkage map construction, were developed and characterized from whole genome shotgun sequences. M13 tailing for forward primers was applied as a simple method in different situations. In total, 828 alleles across 45 accessions were detected, with an average of 8 alleles per locus. The number of effective alleles ranged from 1.22 to 10.41 with an average of 4.08. The polymorphic information content （PIC） varied from 0.13 to 0.89, with an average of 0.63. Moreover, these markers could also be amplified in their related species Myrica cerifera （syn. More/la cerifera） and Myrica adenophora. Seventy-eight SSR markers can be used to produce a genetic map of a cross between ＇Biqi＇ and ＇Dongkui＇. A neighbor-joining （N J） tree was con- structed to assess the genetic relationships among accessions, and the elite accessions ＇Y2010-70＇, ＇Y2012-140＇, and ＇Y2012-145＇, were characterized as potential new genotypes for cultivation.
基金The authors acknowledge the financial support by the National Natural Science Foundation of China(30170472,30471201)International Plant Genetic Resources Institute(IPGRI/AM-LOA-002-2002).
文摘Abundance of simple sequence repeat (SSR) in Citrus sequences from EMBL database was investigated by usingcomputer program MISA (MIcroSAtellite), which aimed to provide useful information for the development of SSR markers.Among 32 896 sequences of Citrus, 4 987 SSRs were found in 4 167 sequences and the average distance between SSRs wasapproximately 3.5 kb. Mononucleotide repeats (50.6%) were the most abundant repeats. And di-, tri-, tetra-, penta- andhexa-nucleotide repeats were 22.8, 25.2, 1, 0.08, and 0.36%, respectively. The most abundant motif was A/T followed indescending order by AG/CT, AC/GT, AT/TA. AAT/ATT, AAG/CTT, AGC/CGT, ACG/CTG and C/G. They comprised about90% of all microsatellites. Ten primer pairs were designed, and three of them produced clear visible bands among Citrusand its related genera.
基金Supported by the National Key R&D Program of China (No. 2019YFD0901202)the Key-Area Research and Development Program of Guangdong Province (No. 2021B0202020002)+1 种基金the China Postdoctoral Science Foundation (No. 2021M693677)the Yellow Fin Bream Seed System Building Project (2021)
文摘Yellowfin seabream Acanthopagrus latus is an important economic fish in Chinese coastal areas.Given its narrow distribution and overfishing,the genetic diversity of yellowfin seabream has been restricted for artificial breeding and reproduction.We performed full-length transcriptome sequencing and assembly of the genome of yellowfin seabream.A total of 68086 unigenes were obtained,with an N50 of 3391 bp on average length of 2933 bp.A total number of 50593 expressed sequence tags linked to simple sequence repeats(EST-SSR)were identified,among them dinucleotide repeats(40.6%)and AC/GT motifs(38.5%)were the most frequent.Of the 190 EST-SSRs for which PCR primer pairs were designed,150 primer pairs successfully amplified target loci and 15 SSRs showed high polymorphism.The alleles per locus ranged 6-50 on average of 25.3.The expected and observed heterozygosity varied from 0.632 to 0.969 and from 0.519 to 0.953,respectively.The polymorphic index content(PIC)values of each locus ranged 0.587-0.966 on average of 0.851.Among six yellowfin seabream population samples preliminarily tested for genetic diversity and differentiation,the Fangchenggang(FCG)population in Guangxi Province had the highest mean observed heterozygosity(H_(o))value(0.786),whereas the Zhangzhou(ZZ)population in Fujian Province had the lowest(0.678).The pairwise fixation index(Fst)values indicated significant population differentiation among six yellowfin seabream populations.This study provided evidence for the usefulness of the transcriptomic resource information and EST-SSR markers for natural resource conservation,population genetics,and breeding studies of yellowfin seabream in South China.
基金funded by Uttar Banga Krishi Viswavidyalaya,IndiaBangladesh Wheat and Maize Research Institute,Dinajpur 5200,Bangladeshfunded by Taif University,Saudi Arabia,Project No.(TU-DSPP-2025-30).
文摘The present study investigated the genetic diversity of 24 germplasms of Polianthes tuberosa L.via 16 inter simple sequence repeat(ISSR)marker techniques.The research findings revealed that the ISSR markers presented higher levels of band reproducibility andweremore efficient at clustering germplasms.Among the 16markers examined in this study,12 had a complete polymorphism rate of 100%.Themolecular analysis revealed a PICranging from0.079 to 0.373,with amean value of 0.30,whereas the range of themarker index was from0.0001 to 0.409,with an average value of 0.03,and the primer resolving power ranged from 0.173 to 4.173,with a mean value of 2.02.The UPGMA clustering dendrogram indicated that all 24 germplasms were grouped into three main clusters.The study revealed a variable range of tree distances between 0.185 and 0.621,with the highest tree distance(0.621)detected between germplasms BR-24 and BR-1.Through these studies,the dissimilarity among the germplasms was evaluated,and diverse parents were identified for further crop improvement programs.
基金Supported by the National Natural Science Foundation of China(No.31600325)the Self-determined Research Funds of the Central China Normal University(CCNU)from the Colleges’Basic Research and Operation of MOE(No.CCNU20TS022)。
文摘To assess the population development of submerged plant species in disturbed lake ecosystems,we need to better understand the genetic diversity and spatial genetic structure at a fine scale,as well as the impact of disturbances on the populations.Caohai Lake,in southwest China,is a suitable natural sampling lake because of its abundance of submerged plants and the intense human disturbance.Three widely distributed species,Potamogeton lucens,Ceratophyllum demersum,and Myriophyllum spicatum,were sampled;the spatial position of each individual was recorded in two-dimensional coordinates;and the species were analyzed genetically using microsatellite markers.Among the species studied,M.spicatum exhibited the highest genetic and clonal diversities.All P.lucens subpopulations but one showed a significant fine-scale spatial genetic structure(FSGS),which may result from the limited gene dispersal.However,M.spicatum and C.demersum,with a relatively large distance of gene dispersal,had no significant FSGS.The FSGS pattern of P.lucens at the dock site with intense boat disturbance was significantly different from that at other sites.Our results imply that the FSGS of submerged plants is affected by many factors including seed dispersal,vegetative reproduction and disturbance from birds and boats.Most subpopulations of the three species hadσ_(sex)^(2)/σ_(veg)^(2)values greater than one,implying that the sexual dispersal contributes more than vegetative dispersal to total gene dispersal.Therefore,it is worth paying attention to the importance of seed dispersal for population development of submerged plants in lake ecosystems.
文摘Chloroplast simple sequence repeat (cpSSR) markers in Citrus were developed and successfully used to analyze chloroplast genome inheritance of Citrus somatic hybrids. Twenty-two previously reported cpSSR primer pairs from pine (Pinus thunbergii Parl.), rice (Otyza sativa L.) and tobacco (Nicotiana tabacum L.) were tested in Citrus, nine of which could amplify intensive PCR products by agarose gel electrophoresis. Chloroplast genome inheritance of Citrus somatic hybrids from nine fusions was then analyzed, and five of the nine pre-screened primer pairs showed polymorphisms by polyacrylamide gel electrophoresis. The results revealed the random inheritance nature of chloroplast genome in all analyzed Citrus somatic hybrids, which was in agreement with previous reports based on RFLP or CAPS analyses. It was also shown that cpSSR is a more efficient tool in chloroplast genome analyses of somatic hybrids in higher plants, compared with the conventional RFLP or CAPS analyses.
基金This paper was supported by Northeast Forestry University.
文摘Genetic relationships of eight species of genus Betula were evaluated using ISSR marks. A total of 236 loci were generated from 17 ISSR primers. Percentage of polymorphic bands (PPB) varied from 5.93 to 19.92. The highest and the lowest level of genetic differentiation were detected in B. ovalifolia and B. maximowicziana Regel respectively. In these eight species, genetic diversity of birch (HT) was 24.38 %, and the genetic variation (GST ) interspecies was accounting for 79.36% of total genetic variation. According to the cluster results of genetic distance, the eight species were classified into three groups as B. davurica, B. ovalifolia, B. platyphylla and B. pendula for one group; B. schmidtii, B. costata and B. ermanii Cham. var. communis for one group, and B. maximowicziana Regel for another group. The result of cluster is consistent with traditional morphological classification.
文摘[Objective]The aim was to optimize SSR reaction system applied in the identification of authenticity of maize variety.[Method]The technical parameters of SSR including PCR reaction system,annealing temperature and electrophoresis time were optimized to identify 10 major maize varieties in Liaoning Province.[Result]The optimum PCR reaction system was：14.60 μl sterile ultrapure water,2.00 μl 10 × Buffer（Mg2＋）,1.20 μl dNTPs,0.20 μl Taq enzyme,0.50 μl each of the forward and reverse primers and1.00 μl DNA stock solution.Annealing temperature and electrophoresis time could greatly influence the results of PCR amplification.The optimal annealing temperature and electrophoresis time required for the ideal electrophoresis bands under the same conditions were different when different primers were used.[Conclusion]The system was feasible to be applied in rapid identification of authenticity of hybrid maize varieties.
文摘In an effort to simplify the procedure and to reduce the cost of fluorescence SSR analysis, the conditions of the multiplex PCR and the multiplex gel electrophoresis were optimized in the genetic analysis of sunflower (Helianthus annuus L.) inbred lines. Results indicated that factors for a successful multiplex PCR assay were related to the cycling touchdown annealing temperature, the balance of primer concentration at the various loci, the concentration of PCR buffer and the Taq DNA polymerase. Based on the optimization, a tailed primer strategy was outlined, and the effective ways were proposed to overcome the troubleshootings commonly encountered in the multiplex PCR and the multiplex gel electrophoresis.
