Genetic algorithms (GAs) employ the evolutionary process of Darwin’s nature selection theory to find the solutions of optimization problems. In this paper, an implementation of genetic algorithm is put forward to sol...Genetic algorithms (GAs) employ the evolutionary process of Darwin’s nature selection theory to find the solutions of optimization problems. In this paper, an implementation of genetic algorithm is put forward to solve a classical transportation problem, namely the Hitchcock’s Transportation Problem (HTP), and the GA is improved to search for all optimal solutions and identify them automatically. The algorithm is coded with C++ and validated by numerical examples. The computational results show that the algorithm is efficient for solving the Hitchcock’s transportation problem.展开更多
A total 23 morphological traits, 19 AFLP-primer combinations, 80 RAPD primers and 32 SSR primer pair were used to compare the informativeness and efficiency of random amplified polymorphic DNA (RAPD), amplified fragme...A total 23 morphological traits, 19 AFLP-primer combinations, 80 RAPD primers and 32 SSR primer pair were used to compare the informativeness and efficiency of random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers in establishing genetic relationships among 29 almond cultivars and three related wild species. SSRs presented a high level of polymorphism and greater information content, as assessed by the expected hetrozygosity, compared to AFLPs and RAPDs. The lowest values of expected hetrozygosity were obtained for AFLPs; however AFLPs showed the highest efficiency, owing to their capacity to reveal large numbers of bands per reaction, which led to high values for various types of indices of diversity. All the three techniques discriminated almond genotypes very effectively, except that SSRs failed to discriminate between ‘Monagha’ and ‘Sefied’ almond genotypes. The correlation coefficients of similarity were statistically significant for all the three marker systems, but were lower for the SSR data than for RAPDs and AFLPs. For all the markers, high similarity in dendrogram topologies was obtained, although some differences were observed. All the dendrograms, including that obtained by the combined use of all the marker data, reflect relationships for most of cultivars according to their geographic diffusion. AMOVA detected more variation among cultivated and related wild species of almond within each geographic group. Bootstrap analysis revealed that the number of markers used was sufficient for reliable estimation of genetic similarity and for meaningful comparisons of marker types.展开更多
Understanding the intra-population genetic diversity and population genetic structure is beneficial for plant protection and breeding.Dendrobium huoshanense is an endangered authentic medicinal herb.To analyze the pop...Understanding the intra-population genetic diversity and population genetic structure is beneficial for plant protection and breeding.Dendrobium huoshanense is an endangered authentic medicinal herb.To analyze the population differentiation and genetic diversity in D.huoshanense,simple sequence repeat(SSR)markers were obtained by high-throughput transcriptome sequencing,and 10 expressed sequence tag(EST)-SSRs were studied in 182 Dendrobium individual samples from 15 populations distributed in Huoshan County,southwest Anhui Province.After deep sequencing of D.huoshanense transcriptome,a total of 58202 unigenes were obtained,and 7781 SSRs with 1~6 base repeats were detected.Among them,dinucleotide SSRs were the dominant repeating motifs(3119,40.085%),and the most common was AG/CT(2666,54.01%).Ten SSR primers were screened out from the designed 120 primer pairs for further polymorphism verification.The results showed that 75 alleles were detected,and the number of alleles at each locus ranged from 4 to 11,with an average of 7.5.The mean expected heterozygosity(H_(e)),observed heterozygosity(H_(o))and polymorphism information content(C_(pi))of the 10 SSR loci were 0.646,0.574,and 0.607,respectively.D.huoshanense populations exhibited a high level of genetic diversity(H_(o)=0.591,H_(e)=0.557)and a moderate level of differentiation(F_(ST)=0.10069),and the genetic variation mainly existed within populations.The results of Structure and neighbour-joining(NJ)analysis based on 10 polymorphic primers showed that D.huoshanense populations were clustered into 2 groups,and the populations KS,HSD,and JXZ had rich genetic diversity and multiple private alleles,suggesting that these populations could be used for genetic improvement of the species.The study revealed frequency distribution of D.huoshanense SSR loci,and successfully developed microsatellite genetic markers,which are expected to expand the repertoire of DNA markers for genetic study of D.huoshanense.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
Over 50 years of efforts, cellular reprogram- ruing opens a new door for disease modeling and regen- erative medicine. Although induction of pluripotency by transcription factors has become common, only a small portio...Over 50 years of efforts, cellular reprogram- ruing opens a new door for disease modeling and regen- erative medicine. Although induction of pluripotency by transcription factors has become common, only a small portion of basic mechanisms of epigenetic modifications during this process have been revealed. To clearly under- stand reprogramming and devise ways to promote full transition towards pluripotency, we must gain insight from comprehensive characterizations of cells at distinct repro- gramming stages, which involves gene expression profil- ing, chromatin state maps of key activating and repressive marks, and DNA modifications. Here, we review recent advances in epigenetic reprogramming to pluripotency with a focus on the principal molecular regulators and attach importance to the combination of high-throughput sequencing and systematic biology approaches in uncov- ering underlying molecular mechanisms of this unique platform in future researches.展开更多
文摘Genetic algorithms (GAs) employ the evolutionary process of Darwin’s nature selection theory to find the solutions of optimization problems. In this paper, an implementation of genetic algorithm is put forward to solve a classical transportation problem, namely the Hitchcock’s Transportation Problem (HTP), and the GA is improved to search for all optimal solutions and identify them automatically. The algorithm is coded with C++ and validated by numerical examples. The computational results show that the algorithm is efficient for solving the Hitchcock’s transportation problem.
文摘A total 23 morphological traits, 19 AFLP-primer combinations, 80 RAPD primers and 32 SSR primer pair were used to compare the informativeness and efficiency of random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers in establishing genetic relationships among 29 almond cultivars and three related wild species. SSRs presented a high level of polymorphism and greater information content, as assessed by the expected hetrozygosity, compared to AFLPs and RAPDs. The lowest values of expected hetrozygosity were obtained for AFLPs; however AFLPs showed the highest efficiency, owing to their capacity to reveal large numbers of bands per reaction, which led to high values for various types of indices of diversity. All the three techniques discriminated almond genotypes very effectively, except that SSRs failed to discriminate between ‘Monagha’ and ‘Sefied’ almond genotypes. The correlation coefficients of similarity were statistically significant for all the three marker systems, but were lower for the SSR data than for RAPDs and AFLPs. For all the markers, high similarity in dendrogram topologies was obtained, although some differences were observed. All the dendrograms, including that obtained by the combined use of all the marker data, reflect relationships for most of cultivars according to their geographic diffusion. AMOVA detected more variation among cultivated and related wild species of almond within each geographic group. Bootstrap analysis revealed that the number of markers used was sufficient for reliable estimation of genetic similarity and for meaningful comparisons of marker types.
文摘Understanding the intra-population genetic diversity and population genetic structure is beneficial for plant protection and breeding.Dendrobium huoshanense is an endangered authentic medicinal herb.To analyze the population differentiation and genetic diversity in D.huoshanense,simple sequence repeat(SSR)markers were obtained by high-throughput transcriptome sequencing,and 10 expressed sequence tag(EST)-SSRs were studied in 182 Dendrobium individual samples from 15 populations distributed in Huoshan County,southwest Anhui Province.After deep sequencing of D.huoshanense transcriptome,a total of 58202 unigenes were obtained,and 7781 SSRs with 1~6 base repeats were detected.Among them,dinucleotide SSRs were the dominant repeating motifs(3119,40.085%),and the most common was AG/CT(2666,54.01%).Ten SSR primers were screened out from the designed 120 primer pairs for further polymorphism verification.The results showed that 75 alleles were detected,and the number of alleles at each locus ranged from 4 to 11,with an average of 7.5.The mean expected heterozygosity(H_(e)),observed heterozygosity(H_(o))and polymorphism information content(C_(pi))of the 10 SSR loci were 0.646,0.574,and 0.607,respectively.D.huoshanense populations exhibited a high level of genetic diversity(H_(o)=0.591,H_(e)=0.557)and a moderate level of differentiation(F_(ST)=0.10069),and the genetic variation mainly existed within populations.The results of Structure and neighbour-joining(NJ)analysis based on 10 polymorphic primers showed that D.huoshanense populations were clustered into 2 groups,and the populations KS,HSD,and JXZ had rich genetic diversity and multiple private alleles,suggesting that these populations could be used for genetic improvement of the species.The study revealed frequency distribution of D.huoshanense SSR loci,and successfully developed microsatellite genetic markers,which are expected to expand the repertoire of DNA markers for genetic study of D.huoshanense.
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supported by the National Natural Science Foundation of China(31325019,91319306 and31401247)Ministry of Science and Technology of China(2015CB964800 and 2014CB964601)
文摘Over 50 years of efforts, cellular reprogram- ruing opens a new door for disease modeling and regen- erative medicine. Although induction of pluripotency by transcription factors has become common, only a small portion of basic mechanisms of epigenetic modifications during this process have been revealed. To clearly under- stand reprogramming and devise ways to promote full transition towards pluripotency, we must gain insight from comprehensive characterizations of cells at distinct repro- gramming stages, which involves gene expression profil- ing, chromatin state maps of key activating and repressive marks, and DNA modifications. Here, we review recent advances in epigenetic reprogramming to pluripotency with a focus on the principal molecular regulators and attach importance to the combination of high-throughput sequencing and systematic biology approaches in uncov- ering underlying molecular mechanisms of this unique platform in future researches.
