A repeated sequence DNA fragment, L5B-4, was cloned from the 5 kb BamHI DNA fragments of rat genomic DNA. The expressions of the L5B-4 DNA fragment are different in liver and hepatoma cells. The amounts of transcripts...A repeated sequence DNA fragment, L5B-4, was cloned from the 5 kb BamHI DNA fragments of rat genomic DNA. The expressions of the L5B-4 DNA fragment are different in liver and hepatoma cells. The amounts of transcripts in hepatoma cells are lower in nucleus and higher in cytoplasm, especially in polysomal RNA, as compared with that in liver cells. The alteration shown in polysomal RNA of hepatoma cells seems to be specific. These results are discussed with respect to the possible function of this repeated DNA and its variation in hepatoma cells.展开更多
Pyrola atropurpurea Franch is an important annual herbaceous plant.Few genomic analyses have been conducted on this plant,and chloroplast genome research will enrich its genomics basis.This study is based on high-thro...Pyrola atropurpurea Franch is an important annual herbaceous plant.Few genomic analyses have been conducted on this plant,and chloroplast genome research will enrich its genomics basis.This study is based on high-throughput sequencing technology and Bioinformatics methods to obtain the sequence,structure,and other characteristics of the P.atropurpurea chloroplast genome.The result showed that the chloroplast genome of P.atropurpurea has a double-stranded circular structure with a total length of 172,535 bp and a typical four-segment structure.The genome has annotated a total of 132 functional genes,including 43 tRNAs,8 rRNAs,76 protein-coding genes,and 5 pseudo-genes.In total,358 SSR loci were checked out,mainly composed of mononucleotide and trinucleotide repeat.There are three types of scattered repetitive sequences,totaling 4223,including 2452 forward repeats,1763 palindrome repeats,and eight reverse repeats.The optimal codon usage frequency is relatively high with AT usage preference in this genome.Chloroplast genome comparative analysis in the family Ericaceae shows that the overall sequence is more complex,and there are more variations in the gene interval region.The collinearity analysis indicated that there is a complex rearrangement of species between different genera in Ericaceae.The selection pressure analysis showed that the protein-encoding genes rpl33 and rps16 were positively selected among the seven medicinal plants in Ericaceae.The maximum likelihood tree shows that the genetic relationship among P.atropurpurea,Pyrola rotundifolia,and Chimaphila japonica is relatively close.Therefore,an important data basis was provided for species identification,genetic diversity,and phylogenetic studies of P.atropurpurea and even this genus of plants.展开更多
According to the distribution characteristics of short and repeated sequence （SRS）, a steganaiytic method based on the correlation of image bit planes is proposed. Firstly, we provide the conception of SRS distance ...According to the distribution characteristics of short and repeated sequence （SRS）, a steganaiytic method based on the correlation of image bit planes is proposed. Firstly, we provide the conception of SRS distance statistics and deduce its statistical distribution. Because the SRS distance statistics can effectively reflect the correlation of the sequence, SRS has statistical features when the image bit plane sequence equals the image width. Using this characteristic, the steganalytic method is fulfilled by the distinct test of Poisson distribution. Experimental results show a good performance for detecting LSB matching steganographic method in still images. By the way, the proposed method is not designed for specific steganographic algorithms and has good generality.展开更多
Rorippa indica is a wild oilseed crop of Brassicaceae with good environmental adaptability and strong stress resistance.This plant has become an important wild relative species for rapeseed(Brassica napus L.)and is us...Rorippa indica is a wild oilseed crop of Brassicaceae with good environmental adaptability and strong stress resistance.This plant has become an important wild relative species for rapeseed(Brassica napus L.)and is used to improve its agronomic traits,with important development and utilization value.However,the research of R.indica genetics is still lacking.And no mitochondrial genome(mitogenome)in the genus Rorippa has been expounded.To analyze the structural characteristics of the R.indica mitogenome,second-generation and third-generation sequencing techniques were made to assemble its mitogenome.The results showed that its mitogenome is composed of a single master circle DNA molecule,with 59 genes(33 protein-coding,23 tRNA,and 3 ribosomal RNA genes)annotated.The length of the circular genome is 219,775 bp,with aGCcontent of 45.24%.Themitochondrial genome contains 55 SSRs,17 tandem repeats,and 252 scattered repeat sequences,with scattered repeat sequences accounting for 77.78%.The top two codons with the highest expression levels are TTT and AUU.Moreover,377 RNA editing sites were forecasted in the R.indica mitogenome.And 22 collinear gene fragments were discriminated in the R.indica chloroplast andmitogenomes,with a total 13,153 bp length,accounting for 4.08%of the mitogenome sequence.The longest gene migration fragment is 2186 bp,and the shortest fragment is 42 bp.Furthermore,12 genes undergo complete migration between the two genomes,and 10 genes undergo partial migration.Systematic evolutionary analysis shows that R.indica and Brassica napus are grouped,indicating a close genetic relationship between the two.Herein,the R.indica mitogenome was sequenced and annotated,and it was compared with other Brassicaceae mitogenomes.A genomic data foundation was supplied for elucidating the R.indica origin and evolution.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
We have compared genetic diversity of 24 Chinese weak-winter, Swedish winter and spring B. napus accessions by inter-simple sequence repeats (ISSRs). By cluster analysis (UPGMA) based on 125 polymorphism bands amplifi...We have compared genetic diversity of 24 Chinese weak-winter, Swedish winter and spring B. napus accessions by inter-simple sequence repeats (ISSRs). By cluster analysis (UPGMA) based on 125 polymorphism bands amplified with 20 primers, the 24 accessions were divided into three groups. Six Swedish winter lines and eight Chinese weak-winter lines were in the group I and the groupⅡwere two Chinese weak-winter lines XiangyoulS and Bao81. The third group contained eight Swedish spring lines. Principal co-ordinates analysis (PCO) showed similar groupings to cluster analysis. Results from cluster analysis and PCO analysis showed very clearly that Chinese weak-winter, Swedish spring and winter accessions were distinguished from each other and Chinese weak-winter accessions in this study were genetically closer to Swedish winter accessions than to Swedish spring accessions. The Chinese weak-winter accessions had larger diversity than Swedish spring or winter accessions did. This study indicated that ISSR is a suitable and effective tool to evaluate genetic diversity among rapeseed germplasm.展开更多
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
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
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
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 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
To confirm a hybrid swarm population of Pinus densiflora × P. sylvestris in Jilin, China, we used needles and seeds from P. densiflora, P. sylvestris, and P. densiflora × P. sylvestris collected from natural...To confirm a hybrid swarm population of Pinus densiflora × P. sylvestris in Jilin, China, we used needles and seeds from P. densiflora, P. sylvestris, and P. densiflora × P. sylvestris collected from natural stands or experimental stations to study whether shoot apex morphology of 4-year old seedlings can be correlated with the sequence of a chloroplast DNA simple sequence repeat marker （cpDNA SSRs）. Total genomic DNA was extracted and subjected to sequence analysis of the pine cpDNA SSR marker Pt15169. Results show that morphological characters from 4-year old seedlings did not correlate with sequence variants of this marker. Marker haplotypes from all P. sylvestris trees had a CTAT element that was absent from all sampled P. densiflora trees. However, both haplotype classes involving this insertion/deletion element were found in a P. densiflora × P. sylvestris population and its seedling progeny. It was concluded that the P. densiflora × P. sylvestris accessions sampled from Jilin, China resulted from bi-directional crosses, as evidenced by both species’ cpDNA haplotypes within the hybrid swarm population.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
文摘A repeated sequence DNA fragment, L5B-4, was cloned from the 5 kb BamHI DNA fragments of rat genomic DNA. The expressions of the L5B-4 DNA fragment are different in liver and hepatoma cells. The amounts of transcripts in hepatoma cells are lower in nucleus and higher in cytoplasm, especially in polysomal RNA, as compared with that in liver cells. The alteration shown in polysomal RNA of hepatoma cells seems to be specific. These results are discussed with respect to the possible function of this repeated DNA and its variation in hepatoma cells.
基金supported by the Education Reform Program of Jiangxi Provincial Department of Education(JXJG-22-23-3,JXJG-23-23-5)the“Biology and Medicine”Discipline Construction Project of Nanchang NormalUniversity(100/20149)+2 种基金Jiangxi Province Key Laboratory of Oil Crops Biology(YLKFKT202203)the Education Reform Program of Nanchang Normal University(NSJG-21-25)Nanchang Key Laboratory of Comprehensive Research and Development of Brasenia schreberi(32060078).
文摘Pyrola atropurpurea Franch is an important annual herbaceous plant.Few genomic analyses have been conducted on this plant,and chloroplast genome research will enrich its genomics basis.This study is based on high-throughput sequencing technology and Bioinformatics methods to obtain the sequence,structure,and other characteristics of the P.atropurpurea chloroplast genome.The result showed that the chloroplast genome of P.atropurpurea has a double-stranded circular structure with a total length of 172,535 bp and a typical four-segment structure.The genome has annotated a total of 132 functional genes,including 43 tRNAs,8 rRNAs,76 protein-coding genes,and 5 pseudo-genes.In total,358 SSR loci were checked out,mainly composed of mononucleotide and trinucleotide repeat.There are three types of scattered repetitive sequences,totaling 4223,including 2452 forward repeats,1763 palindrome repeats,and eight reverse repeats.The optimal codon usage frequency is relatively high with AT usage preference in this genome.Chloroplast genome comparative analysis in the family Ericaceae shows that the overall sequence is more complex,and there are more variations in the gene interval region.The collinearity analysis indicated that there is a complex rearrangement of species between different genera in Ericaceae.The selection pressure analysis showed that the protein-encoding genes rpl33 and rps16 were positively selected among the seven medicinal plants in Ericaceae.The maximum likelihood tree shows that the genetic relationship among P.atropurpurea,Pyrola rotundifolia,and Chimaphila japonica is relatively close.Therefore,an important data basis was provided for species identification,genetic diversity,and phylogenetic studies of P.atropurpurea and even this genus of plants.
基金the National Natural Science Foundation of China (Grant No.60473022)
文摘According to the distribution characteristics of short and repeated sequence （SRS）, a steganaiytic method based on the correlation of image bit planes is proposed. Firstly, we provide the conception of SRS distance statistics and deduce its statistical distribution. Because the SRS distance statistics can effectively reflect the correlation of the sequence, SRS has statistical features when the image bit plane sequence equals the image width. Using this characteristic, the steganalytic method is fulfilled by the distinct test of Poisson distribution. Experimental results show a good performance for detecting LSB matching steganographic method in still images. By the way, the proposed method is not designed for specific steganographic algorithms and has good generality.
基金supported by the Jiangxi Province Higher Education Teaching Research Project(JXJG-22-23-3,NSJG-21-25)Jiangxi Province Key Laboratory of Oil Crops Biology(YLKFKT202203).
文摘Rorippa indica is a wild oilseed crop of Brassicaceae with good environmental adaptability and strong stress resistance.This plant has become an important wild relative species for rapeseed(Brassica napus L.)and is used to improve its agronomic traits,with important development and utilization value.However,the research of R.indica genetics is still lacking.And no mitochondrial genome(mitogenome)in the genus Rorippa has been expounded.To analyze the structural characteristics of the R.indica mitogenome,second-generation and third-generation sequencing techniques were made to assemble its mitogenome.The results showed that its mitogenome is composed of a single master circle DNA molecule,with 59 genes(33 protein-coding,23 tRNA,and 3 ribosomal RNA genes)annotated.The length of the circular genome is 219,775 bp,with aGCcontent of 45.24%.Themitochondrial genome contains 55 SSRs,17 tandem repeats,and 252 scattered repeat sequences,with scattered repeat sequences accounting for 77.78%.The top two codons with the highest expression levels are TTT and AUU.Moreover,377 RNA editing sites were forecasted in the R.indica mitogenome.And 22 collinear gene fragments were discriminated in the R.indica chloroplast andmitogenomes,with a total 13,153 bp length,accounting for 4.08%of the mitogenome sequence.The longest gene migration fragment is 2186 bp,and the shortest fragment is 42 bp.Furthermore,12 genes undergo complete migration between the two genomes,and 10 genes undergo partial migration.Systematic evolutionary analysis shows that R.indica and Brassica napus are grouped,indicating a close genetic relationship between the two.Herein,the R.indica mitogenome was sequenced and annotated,and it was compared with other Brassicaceae mitogenomes.A genomic data foundation was supplied for elucidating the R.indica origin and evolution.
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.
文摘We have compared genetic diversity of 24 Chinese weak-winter, Swedish winter and spring B. napus accessions by inter-simple sequence repeats (ISSRs). By cluster analysis (UPGMA) based on 125 polymorphism bands amplified with 20 primers, the 24 accessions were divided into three groups. Six Swedish winter lines and eight Chinese weak-winter lines were in the group I and the groupⅡwere two Chinese weak-winter lines XiangyoulS and Bao81. The third group contained eight Swedish spring lines. Principal co-ordinates analysis (PCO) showed similar groupings to cluster analysis. Results from cluster analysis and PCO analysis showed very clearly that Chinese weak-winter, Swedish spring and winter accessions were distinguished from each other and Chinese weak-winter accessions in this study were genetically closer to Swedish winter accessions than to Swedish spring accessions. The Chinese weak-winter accessions had larger diversity than Swedish spring or winter accessions did. This study indicated that ISSR is a suitable and effective tool to evaluate genetic diversity among rapeseed germplasm.
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.
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.
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 a grant from the Next-Generation BioGreen 21 Program, Rural Development Administration, Republic of Korea (PJ009052)
文摘To confirm a hybrid swarm population of Pinus densiflora × P. sylvestris in Jilin, China, we used needles and seeds from P. densiflora, P. sylvestris, and P. densiflora × P. sylvestris collected from natural stands or experimental stations to study whether shoot apex morphology of 4-year old seedlings can be correlated with the sequence of a chloroplast DNA simple sequence repeat marker （cpDNA SSRs）. Total genomic DNA was extracted and subjected to sequence analysis of the pine cpDNA SSR marker Pt15169. Results show that morphological characters from 4-year old seedlings did not correlate with sequence variants of this marker. Marker haplotypes from all P. sylvestris trees had a CTAT element that was absent from all sampled P. densiflora trees. However, both haplotype classes involving this insertion/deletion element were found in a P. densiflora × P. sylvestris population and its seedling progeny. It was concluded that the P. densiflora × P. sylvestris accessions sampled from Jilin, China resulted from bi-directional crosses, as evidenced by both species’ cpDNA haplotypes within the hybrid swarm population.
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.
