SFGA-CPA: A Novel Screening Correlation Power Analysis Framework Based on Genetic Algorithm

Correlation power analysis(CPA)combined with genetic algorithms(GA)now achieves greater attack efficiency and can recover all subkeys simultaneously.However,two issues in GA-based CPA still need to be addressed:key degeneration and slow evolution within populations.These challenges significantly hinder key recovery efforts.This paper proposes a screening correlation power analysis framework combined with a genetic algorithm,named SFGA-CPA,to address these issues.SFGA-CPA introduces three operations designed to exploit CPA characteris-tics:propagative operation,constrained crossover,and constrained mutation.Firstly,the propagative operation accelerates population evolution by maximizing the number of correct bytes in each individual.Secondly,the constrained crossover and mutation operations effectively address key degeneration by preventing the compromise of correct bytes.Finally,an intelligent search method is proposed to identify optimal parameters,further improving attack efficiency.Experiments were conducted on both simulated environments and real power traces collected from the SAKURA-G platform.In the case of simulation,SFGA-CPA reduces the number of traces by 27.3%and 60%compared to CPA based on multiple screening methods(MS-CPA)and CPA based on simple GA method(SGA-CPA)when the success rate reaches 90%.Moreover,real experimental results on the SAKURA-G platform demonstrate that our approach outperforms other methods.

Population genomic analysis reveals key genetic variations and the driving force for embryonic callus induction capability in maize

Genetic transformation has been an effective technology for improving the agronomic traits of maize.However,it is highly reliant on the use of embryonic callus(EC)and shows a serious genotype dependence.In this study,we performed genomic sequencing for 80 core maize germplasms and constructed a high-density genomic variation map using our newly developed pipeline(MQ2Gpipe).Based on the induction rate of EC(REC),these inbred lines were categorized into three subpopulations.The low-REC germplasms displayed more abundant genetic diversity than the high-REC germplasms.By integrating a genome-wide selective signature screen and region-based association analysis,we revealed 95.23 Mb of selective regions and 43 REC-associated variants.These variants had phenotypic variance explained values ranging between 21.46 and 49.46%.In total,103 candidate genes were identified within the linkage disequilibrium regions of these REC-associated loci.These genes mainly participate in regulation of the cell cycle,regulation of cytokinesis,and other functions,among which MYB15 and EMB2745 were located within the previously reported QTL for EC induction.Numerous leaf area-associated variants with large effects were closely linked to several REC-related loci,implying a potential synergistic selection of REC and leaf size during modern maize breeding.

Integrated classification method of tight sandstone reservoir based on principal component analysise simulated annealing genetic algorithmefuzzy cluster means

In this research,an integrated classification method based on principal component analysis-simulated annealing genetic algorithm-fuzzy cluster means(PCA-SAGA-FCM)was proposed for the unsupervised classification of tight sandstone reservoirs which lack the prior information and core experiments.A variety of evaluation parameters were selected,including lithology characteristic parameters,poro-permeability quality characteristic parameters,engineering quality characteristic parameters,and pore structure characteristic parameters.The PCA was used to reduce the dimension of the evaluation pa-rameters,and the low-dimensional data was used as input.The unsupervised reservoir classification of tight sandstone reservoir was carried out by the SAGA-FCM,the characteristics of reservoir at different categories were analyzed and compared with the lithological profiles.The analysis results of numerical simulation and actual logging data show that:1)compared with FCM algorithm,SAGA-FCM has stronger stability and higher accuracy;2)the proposed method can cluster the reservoir flexibly and effectively according to the degree of membership;3)the results of reservoir integrated classification match well with the lithologic profle,which demonstrates the reliability of the classification method.

Genetic Analysis of the First Female Flower Node and the First Male Flower Node in Bitter Gourd

Exploring genetic mechanism of the first female flower node and the first male flower node in bitter gourd has practical significance for formulating breeding strategy. In this article, a cross was made between CN19-1 and Thai4-6, and the F2segregation population was also constructed through F1selfing. The genetic characteristics of the first female flower node and the first male flower node were analyzed by adopting the major gene plus polygene mixed genetic model. The data analysis results showed that the first female flower node and the first male flower node were continuous distribution in the F2segregation population. E-2 model was the most suitable model for the genetic analysis of the first female flower node and the first male flower node. The additive effect values of the 2 pairs of major genes controlling the first female flower node were 2.722 and 1.862 8 respectively, the dominant effect values were-2.721 6 and-0.171 8, respectively. The additive effect value of polygene was-0.839 2, and the dominant effect value of polygene was 2.225 4. The heritability of major genes and polygene were 83.73% and 1.54%, respectively. The additive effect values of the 2 pairs of major genes controlling the first male flower node were 17.746 9 and 3.972, respectively, the dominant effect values were 5.191 6 and-3.972, respectively. The additive effect value of polygene was-20.530 5, and the dominant effect value was-4.141 4. The heritability of major genes and polygene was 92.34% and 4.7%, respectively. This study could provide a theoretical basis for bitter gourd breeding.

Genetic Analysis of Notched Grain in Rice水稻腹缺米的遗传分析

调查了1366份水稻品种和品系,腹缺米的发生频率为5.63%,腹缺米频率与粒重的相关r=+0.6195。1978、1979和1981年,用腹缺米和饱满米配制了17个组合,F_1、F_2和 BF的分析发现,腹缺米受两对显性互补基因控制,环境条件只影响腹缺米的程度。这种障碍在早期世代进行连续选择即可消除。

Epidemiological Surveillance: Genetic Diversity of Rotavirus Group A in the Pearl River Delta, Guangdong, China in 2019

Objective This study aimed to understand the epidemic status and phylogenetic relationships of rotavirus group A(RVA)in the Pearl River Delta region of Guangdong Province,China.Methods This study included individuals aged 28 days–85 years.A total of 706 stool samples from patients with acute gastroenteritis collected between January 2019 and January 2020 were analyzed for 17 causative pathogens,including RVA,using a Gastrointestinal Pathogen Panel,followed by genotyping,virus isolation,and complete sequencing to assess the genetic diversity of RVA.Results The overall RVA infection rate was 14.59%(103/706),with an irregular epidemiological pattern.The proportion of co-infection with RVA and other pathogens was 39.81%(41/103).Acute gastroenteritis is highly prevalent in young children aged 0–1 year,and RVA is the key pathogen circulating in patients 6–10 months of age with diarrhea.G9P[8](58.25%,60/103)was found to be the predominant genotype in the RVA strains,and the 41 RVA-positive strains that were successfully sequenced belonged to three different RVA genotypes in the phylogenetic analysis.Recombination analysis showed that gene reassortment events,selection pressure,codon usage bias,gene polymorphism,and post-translational modifications(PTMs)occurred in the G9P[8]and G3P[8]strains.Conclusion This study provides molecular evidence of RVA prevalence in the Pearl River Delta region of China,further enriching the existing information on its genetics and evolutionary characteristics and suggesting the emergence of genetic diversity.Strengthening the surveillance of genotypic changes and gene reassortment in RVA strains is essential for further research and a better understanding of strain variations for further vaccine development.

Surface wave inversion with unknown number of soil layers based on a hybrid learning procedure of deep learning and genetic algorithm

Surface wave inversion is a key step in the application of surface waves to soil velocity profiling.Currently,a common practice for the process of inversion is that the number of soil layers is assumed to be known before using heuristic search algorithms to compute the shear wave velocity profile or the number of soil layers is considered as an optimization variable.However,an improper selection of the number of layers may lead to an incorrect shear wave velocity profile.In this study,a deep learning and genetic algorithm hybrid learning procedure is proposed to perform the surface wave inversion without the need to assume the number of soil layers.First,a deep neural network is adapted to learn from a large number of synthetic dispersion curves for inferring the layer number.Then,the shear-wave velocity profile is determined by a genetic algorithm with the known layer number.By applying this procedure to both simulated and real-world cases,the results indicate that the proposed method is reliable and efficient for surface wave inversion.

Rapid Prototype Development Approach for Genetic Programming

Genetic Programming (GP) is an important approach to deal with complex problem analysis and modeling, and has been applied in a wide range of areas. The development of GP involves various aspects, including design of genetic operators, evolutionary controls and implementations of heuristic strategy, evaluations and other mechanisms. When designing genetic operators, it is necessary to consider the possible limitations of encoding methods of individuals. And when selecting evolutionary control strategies, it is also necessary to balance search efficiency and diversity based on representation characteristics as well as the problem itself. More importantly, all of these matters, among others, have to be implemented through tedious coding work. Therefore, GP development is both complex and time-consuming. To overcome some of these difficulties that hinder the enhancement of GP development efficiency, we explore the feasibility of mutual assistance among GP variants, and then propose a rapid GP prototyping development method based on πGrammatical Evolution (πGE). It is demonstrated through regression analysis experiments that not only is this method beneficial for the GP developers to get rid of some tedious implementations, but also enables them to concentrate on the essence of the referred problem, such as individual representation, decoding means and evaluation. Additionally, it provides new insights into the roles of individual delineations in phenotypes and semantic research of individuals.

Identification, Genetic Analysis and Mapping of Resistance to Phytophthora sojae of Pm28 in Soybean

Phytophthora sojae Kanfman and Gerdemann （P. sojae） is one of the most prevalent pathogens and causes Phytophthora root rot, which limits soybean production worldwide. Development of resistant cultivars is a cost-effective approach to controlling this disease. In this study, 127 soybean germplasm were evaluated for their responses to Phytophthora sojae strain Pm28 using the hypocotyl inoculation technique, and 49 were found resistant to the strain. The hypocotyl of P1, P2, F1, and F2：3 of two crosses of Ludou 4 （resistant）×Youchu 4 （susceptible） and Cangdou 5 （resistant）×Williams （susceptible） were inoculated with Pm28, and were used to analyze the inheritance of resistance. The population derived from the cross of Ludou 4×Youchu 4 was used to map the resistance gene （designated as Rps9） to a linkage group. 932 pairs of SSR primers were used to detect polymorphism, and seven SSR markers were mapped near the resistance gene. The results showed that the resistance to Pm28 in Ludou 4 and Cangdou 5 was controlled by a single dominant gene Rps9, which was located on the molecular linkage group N between the SSR markers Satt631 （7.5 cM） and Sat_186 （4.3 cM）.

Analysis of Genetic Diversity of Processing Apple Varieties

Genetic diversity of 18 processing apple varieties and two fresh varieties were evaluated using 12 simple sequence repeats （SSR） primer pairs previously identified in Malus domestica Borkh. A total of 87 alleles in 10 loci were detected using 10 polymorphic SSR markers selected within the range of 5-14 alleles per locus. All the 20 varieties could be distinguished using two primer pairs and they were divided into four groups using cluster analysis. The genetic similarity （GS） of groups analyzed using cluster analysis varied from 0.14 to 0.83. High acid variety Avrolles separated from other varieties with GS less than 0.42. The second group contained Longfeng and Dolgo from Northeast of China, the inherited genes of Chinese crab apple. The five cider varieties with high tannin contents, namely, Dabinette, Frequin rouge, Kermerrien, M.Menard, and D.Coetligne were clustered into the third group. The fourth group was mainly composed of 12 juice and fresh varieties. Principal coordinate analysis （PCO） also divided all the varieties into four groups. Juice and fresh apple varieties, Longfeng and Dolgo were clustered together, respectively, using both the analyses. Both the analyses showed there was much difference between cider and juice varieties, cider and fresh varieties, as well as Chinese crab apple and western European crab apple, whereas juice varieties and fresh varieties had a similar genetic background. The genetic diversity and differentiation could be sufficiently reflected by combining the two analytical methods.

Genetic Analysis and Molecular Mapping of a Novel Chlorophyll-Deficit Mutant Gene in Rice

A rice etiolation mutant 824ys featured with chlorophyll deficiency was identified from a normal green rice variety 824B. It showed whole green-yellow plant from the seedling stage, reduced number of tillers and longer growth duration. The contents of chlorophyll, chlorophyll a, chlorophyll b and net photosynthetic rate in leaves of the mutant obviously decreased, as well as the number of spikelets per panicle, seed setting rate and 1000-grain weight compared with its wild-type parent. Genetic analyses on F1 and F2 generations of 824ys crossed with three normal green varieties showed that the chlorophyll-deficit mutant character was controlled by a pair of recessive nuclear gene. Genetic mapping of the mutant gene was conducted by using microsatellite markers and F2 mapping population of 495R/824ys, and the mutant gene of 824ys was mapped on the short arm of rice chromosome 3. The genetic distances from the target gene to the markers RM218, RM282 and RM6959 were 25.6 cM, 5.2 cM and 21.8 cM, respectively. It was considered to be a new chlorophyll-deficit mutant gene and tentatively named as chill（t）.

Analysis of the Germplasm Resources and Genetic Relationships Among Hybrid Cymbidium Cultivars and Native Species with RAPD Markers

The random amplified polymorphic DNA （RAPD） marker was assessed to detect the genetic relationships among 48 hybrid Cymbidium cultivars from Japan, Korea, China, and USA, and 2 species of native Cymbidium. Twenty primers were screened from 100 random decamer primers, and a total of 258 DNA bands were amplified, 253 of which （98.1%） were polymorphic. The average number of polymorphic DNA bands amplified by each primer was 12.6. All cultivars were distinguishable when a number of primers were considered. Genetic similarities among the cultivars and species were estimated based on the amount of band sharing ranging from 0.364-0.817 with an average of 0.581. According to the data, a dendrogram of genetic relationship, which was constructed using the UPGMA method, showed that all the tested cultivars and native species were classified into five cluster groups with the similarity coefficient of 0.592. It revealed that the genetic relationships among tested accessions were to some extent related with their origin, flower colour, branch type, and genealogy. It further indicated that the RAPD technique is a useful tool for studying the genetic relationships among hybrid Cymbidium cultivars.

Genetic Analysis and Primary Mapping of pms4, a Photoperiod-Sensitive Genic Male Sterility Gene in Rice (Oryza sativa)

To understand the genetic characteristics of a new photoperiod-sensitive genic male sterile line Mian 9S, some reciprocal crosses were made between Mian 9S and six indica rice materials, Yangdao 6, Luhui 602, Shuihui 527, Mianhui 725, Fuhui 838 and Yixiang 1B. Genetic analysis results suggested that the photoperiod-sensitive genic male sterility （PGMS） of Mian 9S was controlled by a single recessive nuclear gene. Thus, the F2 population derived from the cross of Yangdao 6/Mian 9S was used to map the PGMS gene in Mian 9S. By using SSR markers, the PGMS gene of Mian 9S was mapped on one side of the markers, RM6659 and RM1305, on rice chromosome 4, with the genetic distances of 3.0 cM and 3.5 cM, respectively. The gene was a novel PGMS gene and designated tentatively as pms4. In addition, the application of the pms4 gene was discussed.

Genetic Analysis and Mapping of TWH Gene in Rice Twisted Hull Mutant

A mutant with twisted hulls was found in a breeding population of rice （Oryza sativa L.）. The mutant shows less grain weight and inferior grain quality in addition to twisted hulls. Genetic analysis indicated that the phenotype of mutant was controlled by a single recessive gene （temporarily designated as TW（H）. To map the TWH gene, an F2 population was generated by crossing the twh mutant to R725, an indica rice variety with normal hulls. For bulked segregant analysis, the bulk of mutant plants was prepared by mixing equal amount of plant tissue from 10 twisted-hull plants and the bulk of normal plants was obtained by pooling equal amount tissue of 10 normal-hull plants. Two hundred and seven pairs of simple sequence repeat （SSR） primers, which are distributed on 12 rice chromosomes, were used for polymorphism analysis of the parents and the two bulks. The TWH locus was initially mapped close to the SSR marker RM526 on chromosome 2. Therefore, further mapping was performed using 50 pairs of SSR primers around the marker RM526. The TWH was delimited between the SSR markers RM14128 and RM208 on the long arm of chromosome 2 at the genetic distances of 1.4 cM and 2.7 cM, respectively. These results provide the foundation for further fine mapping, cloning and functional analysis of the TWH gene.

RAPD-PCR Analysis on Genetic Relationships Between Cultivars of Tree Peony

Random amplified polymorphic DNA (RAPD) was used to analyze genetic polymophism of 35 Tree Peony cultivars with 7 different color groups. Thirty four primers amplified 418 DNA fragments and 337 polymorphic bands (80.6%), including specific DNA markers for 18 cultivars that could be used to differentiate cultivars. The UPCMA method was used to analyze the genetic relationship among cultivars. The results showed that 35 Peony cultivars could be divided into 2 cluster groups when using similarity criteria of 1.5, and into 4 cluster groups when using similarity criteria of 1.0. The result confirmed that the flower color has no relation to the genetic clusters and the Tree Peony cultivars originated from the same area has close genetic relationship. Therefore, genetic background has no large effect on the genetic relationship. The sequence based on polymorphic rate from high to low was Blue groups > Yellow groups > Bark red groups > Blake groups > White groups>Green groups>Red groups.

Clinicopathological and molecular genetic analysis of 4 typical Chinese HNPCC families

AIM: To study the clinicopathological and molecular genetic characteristics of typical Chinese hereditary nonpolyposis cotorectal cancer (HNPCC) families.METHODS: Four typical Chinese HNPCC families were analyzed using microdissection, microsatellite instability analysis, immunostaining of hMSH2 and hMLH1 proteins and direct DNA sequencing of hMSH2 and hMLH1 genes.RESULTS: All five tumor tissues of 4 probands from the 4typical Chinese HNPCC families showed microsatellite instability at more than two loci (MSI-H or RER +phenotype). Three out of the 4 cases lost hMSH2 protein expression and the other case showed no hMLH1 protein expression. Three pathological germline mutations (2 in hMSH2 and 1 in hMLH1 ), which had not been reported previously, were identified. The same mutations were also found in otler affected members of two HNPCC families,respectively.CONCLUSION: Typical Chinese HNPCC families showed relatively frequent germline mutation of mismstch repair genes. High-level microsateliita instability and loss of expression of mismatch repair genes correlated closely with germline mutation of mismatch repair genes. Microsatellite instability analysis and immunostaining of miamstch repair gens might serve as effective screening methods before direct DNA sequencing. It is necessary to establish clinical criteria and molecular diagnostic strategies more suitable for Chinese HNPCC families.

Comparative Analysis of Genetic Diversity and Structure in Rice Using ILP and SSR Markers

Genetic diversity of 36 rice entries from the United States Department of Agriculture （USDA） rice collection was assessed using 103 ILP （intron length polymorphism） and 54 SSR （simple sequence repeats） markers. A total of 236 and 332 alleles were detected by the ILP and SSR markers, respectively. On average, the SSR markers produced higher polymorphism information content value and number of alleles than the ILP markers. Whereas the Nei＇s genetic distance measured using the SSR markers was much higher than that measured using the ILP markers. Manters test indicated that there was a statistically significant correlation （r=0.827, P〈0.001 ） between the two marker systems. UPGMA clustering based on the ILP and SSR markers resulted in consensus dendrograms. The cophenetic correlation coefficient （r=0.918, 0.878 and 0.924, P〈0.001 for the ILP, SSR and combined markers, respectively） showed a highly accurate dendrogram represented the genetic distance among these entries. The 36 entries were divided into four groups. Four African Oryza glaberrima accessions were clustered within a distinct group （I）, and the remaining entries were separated into three groups （11, III and IV）. All the entries could be also clustered into two main groups： One was composed of III and IV, considered as indica group, and the other was composed of I （O. glaberrima） and II （japonica-like）. Model-based cluster analysis revealed that the japonica-like group maintained very pure ancestry while the indica group shared mixed ancestry, especially for group III, which had seven admixtures sharing from 19.5% to 30.0% of ancestry with group IV （based on SSR markers）. It is suggested that ILP and SSR markers could be very useful for the genetic study and breeding in rice.

Reverse Genetic Analysis of Transcription Factor Os Hox9, a Member of Homeobox Family, in Rice

Homeobox transcription factors participate in the growth and development of plants by regulating cell differentiation, morphogenesis and environmental signal response. To reveal the functions of these transcription factors in rice, we constructed the RNAi vectors of OsHox9, a member of homeobox family, and analyzed the function of OsHox9 using reverse genetics. The plant height and tillering number of RNAi transgenic plants decreased compared with those of wild-type plants. Reverse transcdption-polymerase chain reaction analysis showed that OsHox9 expression reduced in the transgenic plants with phenotypic variance, whereas that in the transgenic plants without phenotypic variance was similar to that in the wild-type plants. This result suggests that the phenotypes of the transgenic plants were caused by RNAi effects. The tissue-specificity of OsHox9 expression indicated that it was expressed in different organs, with high expression in stem apical medstem and young panicles. Subcellular location of OsHox9 demonstrated that it was localized on the cell membrane.

GENETIC MODELS AND ANALYSIS METHODS FOR SEX-LINKED AND MATERNAL GENE EFFECTS

Genetic models are proposed for analyzing sex-linked and maternal effects as well as autosomal gene effects.For the model with no genotype×environment interaction,the total genetic effect is partitioned into direct additive （A）,direct dominance （D）,sexlinked （L）,maternal additive （Am） and maternal dominance （Dm） genetic components.For the model including genotype×environment interaction （GE）,GE can also be partitioned into components of direct additive by environment interaction （AE）,direct dominance by environment interaction （DE）,sex-linked by environment interaction （LE）,maternal additive by environment interaction （AmE ）,and maternal dominance by environment interaction （DmE）.Linear functions of genetic components are listed for parent,F1,and F2.A set of parents,their reciprocal F1’s and F2’s is applicable for efficient analysis.Variance and covariance components can be well mated by MINQUE（O/l） with the jackknife procedure.The t-test conducted by the jackknife procedure is applicable for detecting significance of variation.Adjusted Unbiased Prediction （AUP） method is suggested for predicting genetic effects.

Morphogenesis,Anatomical Observation and Primary Genetic Analysis of a Multi-glume Floral Organ Mutant in Rice

A multi-glume （mg） mutant was obtained by screening the T-DNA inserted mutant pool. Anatomical observation revealed that the florets of the mutant showed elongated leafy paleas/lemmas and palea/lemma-like structures, just like multi-glumes. Among the 215 observed florets of the mutant, 14.27% were failed to produce pistil and stamens, 23.72% showed extra floret generated on the same rachilla, while 62.01% consisted of one to nine stamens and one to three pistils in a single floret. On the other hand, in some cases the transparent bulged vesile-like tissue could be observed at the basis of filament. The mutant showed glumaceous Iodicules, which prevented the florets from opening in natural conditions, while the absolute male and female sterility was an obvious character of the current mutant. Observation on the process of floral organ morphogenesis by a scanning electron microscopy （SEM） indicated that no phenotype difference in floret primordia was found between the wild-type and the mutant. Meanwhile, for the mutant, the beginning of stamen and pistil primordial differentiation was later than the wild type and the palea/lemma-like structure continued to differentiate after the formation of normal palea and lemma. Furthermore, in the mutant the asymmetrical division of floral primordial caused variation in the number of stamens and pistils. Therefore, the genetic analyses indicated that the mutation phenotype was a recessive trait controlled by a single gene and co-segregated with the T-DNA. Based on the phenotypic characteristics, it could be deduced that the mutant was the result of homeotic conversion from the function of the class E genes in ABCD model.