Advancing Early Detection of Colorectal Adenomatous Polyps via Genetic Data Analysis: A Hybrid Machine Learning Approach

In this study, a hybrid machine learning (HML)-based approach, incorporating Genetic data analysis (GDA), is proposed to accurately identify the presence of adenomatous colorectal polyps (ACRP) which is a crucial early detector of colorectal cancer (CRC). The present study develops a classification ensemble model based on tuned hyperparameters. Surpassing accuracy percentages of early detection approaches used in previous studies, the current method exhibits exceptional performance in identifying ACRP and diagnosing CRC, overcoming limitations of CRC traditional methods that are based on error-prone manual examination. Particularly, the method demonstrates the following CRP identification accuracy data: 97.7 ± 1.1, precision: 94.3 ± 5, recall: 96.0 ± 3, F1-score: 95.7 ± 4, specificity: 97.3 ± 1.2, average AUC: 0.97.3 ± 0.02, and average p-value: 0.0425 ± 0.07. The findings underscore the potential of this method for early detection of ACRP as well as clinical use in the development of CRC treatment planning strategies. The advantages of this approach are highly expected to contribute to the prevention and reduction of CRC mortality.

Genetic Analysis of a Biomass Mutant in Oryza sativa

[ Objective ] The study aimed to reveal the genetic model of a biomass mutant in Oryza sativa. [ Method ] In the process of screening and identification of Bar-transgenic rice, a biomass mutant was found in 10 lines of T1 progenies. The mutant was investigated for genetic analysis and agronomic traits by herbicide spraying and PCR amplification. [ Result] The segregation ratio is consistent with mendelian law（3：1）. The mutant assumed not only higher plant height, wider straw and earlier florescence, but also more tillers, bigger spikes and resultantly higher biomass. PCR detections indicated that no co-segregation was observed between mutant traits and target gene（Bar） in the T-DNA inserted, proving that the mutant is not caused by the insertion of T-DNA containing target gene （Bar）. [ Conclusion] Our study may avail to understand the cloning of mutant gene and the mechanism of the mutant gene on biomass.

Morphological,Anatomical and Genetic Analysis for a Rice Mutant with Abnormal Hull

A mutant with abnormal hull was first discovered from a twin-seedling strain W2555 in rice （Oryza sativa L.）. The mutant had sparse branches and decreased number of florets from the base to the peak. Frequently, the florets at the top of the panicle did not develop completely. The underdeveloped florets often showed slender and white in their life cycle. Genetic analysis indicated that the mutant traits were controlled by a single recessive gene （temporarily designated as ah）. ah gene controlled the development of inflorescence meristem and the flower organ. The florets of mutant showed degenerated lemma and palea. Stamens and lodicules were homeoticly transformed into pistils and palea/lemma-like structures, respectively. It seemed that ah mutant phenotypes of the homeotic conversions in lodicules and stamens were very similar to that of the B loss-of-function spwl gene reported previously in rice.

Genetic Analysis of the VP2 Hypervariable Region of Thirty-six Infectious Bursal Disease Virus Isolates in China during 2009-2012

[Objective] Infectious bursal disease （IBD） is a highly contagious immuno- suppressive disease caused by infectious bursal disease virus （IBDV）. IBDV is ge- netically prone to mutation, which results in challenges to the disease prevention and control. Thus, it is necessary to continuously monitor the prevalence of IBDV. [Method] 36 IBDVs were identified from ten provinces in China from 2009 to 2012. Partial fragments of VP2, including the hypervariable region （HVR）, from new iso- lates were sequenced and analyzed through comparisons with published sequences of IBDV, including 18 strains isolated previously by our lab and 24 reference strains from China and around the world. [Result] Phylogenetic analysis showed a co-exis- tence of IBDV strains belonging to classic, variant, attenuated, and very virulent IB- DV （wlBDV） in China. wlBDVs remain the predominant strains in China and the new subgroup was emerging. Alignment analysis revealed several distinct amino acid mutations that might be involved in virulence or antigenicity variation. [Conclu- sion] The results offered evolutionary clues showing the emerging trend of obvious variations and diversity of IBDV in major poultry-producing regions of China particu- larly in recent years. These findings will contribute to a better understanding of the genetic evolution of IBDV.

AFLP Analysis of Phylogenetic Relationship of Salvia spp. in Beijing

Twenty-third collections of Salvia spp.in Beijing were analyzed phylogenetically by AFLP technique.6 primer pairs with good repetition and highly polymorphic bands from 21 pairs were selected to amplify the genomic DNA.All of 367 AFLP bands were obtained,in which 359(97.82%)were polymorphic markers.At a genetic distance of 0.32,the collections could be clustered into 7 species i.e.S.splendens,S.farinacea,S.coccinea,S.plebeia,S.miltiorrhiza,S.umbratica and S.officinalis.The respective genetic relationship be...

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。

Creation and Genetic Analysis of a Male Sterility Mutant in Panicum miliaceum

Heterosis plays an important role in the development of new crop varieties with high-yielding, good-quality and biotic/abiotic stresses while male sterile line de- velopment is the key step to determine the success of heterosis utilization. A male sterile mutant, M207A was created in proso millet （Panicum mi/iaceurn, 2n=4x=36） for the first time using 60Co-y ray mutagenesis. Fertility identification and genetic analysis were carried out to characterize the mutant for its possible use for hetero- sis utilization in proso millet. First the sterility was investigated using both field sur- vey and indoor pollen microscopy identification. Then Pollinated by normal fertile proso millet cultivars, F1 and F2 populations from the mutant were obtained. Mean- while primary genetic analysis was also conducted using above populations in dif- ferent experimental sites, seasons and years. The results showed that the male sterile plant exhibited closed glumes, browning and dry anthers with few normal pollens. The sterility was stable and sterility rate was above 95% on average. The segregation ratio of fertile to sterile plants was 35：1 in the fertile selfing F2 popula- tion indicating that the mutant was a genic male sterility belonging to a pollen-less type controlled by a single recessive gene. The creation of the mutant, M207A can play a key role for heterosis utilization in proso millet.

Genetic Variation Analysis of 3D Gene and Molecular Detection of Porcine Kobuvirus in 2013-2014

[Objective] This study aimed to investigate the prevalence and variation of porcine kobuvirus （PKV） in suckling piglets in China. [Method] In 2013-2014, 224 feces samples from suckling piglets with diarrhea in 27 pig farms of five provinces in China were collected to detect 3D genes of PKV with RT-PCR method; the sequences and genetic variation of 29 PKV 3D genes were analyzed. [Result] Total positive rate of PKV in feces samples from suckling piglets with diarrhea was 65.18% （146/224）; total positive rate of PKV in pig farms was 85,2% （23/27）; nucleotide sequences and the deduced amino acid sequences of 29 PKV 3D genes shared 87.0%-100% and 92.7%-100% homologies with six PKV-related 3D sequences, respectively. [Conclusion] PKV infection is prevalent in suckling piglets in China; PKV 3D genes exhibit high diversity.

Genetic Diversity Analysis of the Main Commercial Varieties of Brassica napus in Guizhou Province

[Objective] The aim was to investigate the genetic diversity of the main commercial varieties of Brassica napus in Guizhou Province at the molecular level. [Method] Nine main commercial rapeseed cultivars in Guizhou were detected by 40 pairs of SSR primers used in the national regional trial of B. napus, and then clus-tering analysis was carried out. [Result] A total of 191 bands were amplified, and 143 （accounting for 75%） of them showed polymorphism among the nine rapeseed cultivars. By cluster analysis, the nine cultivars were divided into two groups. Group A included seven varieties, and group B consisted of two cultivars from Guizhou In-stitute of Oil Crops. The cultivars in group A were further divided into sub-groups A1 and A2 at the similarity coefficient of 0.643 4. Sub-group A1 included three culti-vars from Guizhou Rapeseed Institute, and sub-group A2 included the other four cultivars from Guizhou Institute of Oil Crops. [Conclusion] The cultivars bred by the same institute had similar genetic background. The cultivars from Guizhou Institute of Oil Crops showed wider genetic basis. However, the genetic similarity coefficient between Qianyou 17 and Qianyou 29 was up to 0.87, suggesting that they shared closer genetic basis.

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）.

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）.

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 Rescue of a Triple-reassortant H3N2 Influenza A Virus Isolated From Swine in Eastern China

One influenza H3N2 virus, A/swine/Shandong/3/2005 (Sw/SD/3/2005), was isolated from pigs with respiratory disease on a farm in eastern China. Genetic analysis revealed that Sw/SD/3/2005 was a triple-reassortant virus with a PB2 gene from human-like H1N1, NS from classical swine H1N1, and the remaining genes from human-like H3N2 virus. These findings further support the concept that swine can serve as reservoir or mixing vessels of influenza virus strains and maintain genetic and antigenic stability of viruses. Furthermore, we have successfully established a reverse genetics system based on eight plasmids and rescued Sw/SD/3/2005 through cell transfection. HI tests and RT-PCR confirmed that the rescued virus maintained the biological properties of the wild type Sw/SD/3/2005. The successful establishment of the reverse genetics system of Sw/SD/3/2005 will enable us to conduct extensive studies of the molecular evolution of H3N2 influenza viruses in swine.

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.

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.

Distribution of Grain Hardness in Chinese Wheats and Genetic Analysis

A hundred winter wheat and 41 spring wheat cultivars and advanced lines were used to investigate the distribution of grain hardness in Chinese wheats and correlations between grain hardness and other kernel traits. P1, P2, F1 , F2 and F3 from three crosses, i. e. , Liken2/Yumai2, 85Zhong33/Wenmai6 and 85Zhong33/95Zhong459 were sown to study the genetics of grain hardness. Significant correlation was observed between hardness measured by Single Kernel Characteristic System 4100 (SKCS 4100) and Near Infrared (NIR) Spectroscopy, r ranging from 0.85 to 0.94. Chinese wheat is a mixed population in terms of hardness, ranging from very soft to very hard. For autumn-sown wheat, on average, grain hardness decreases from north to south and spring-sown wheat is dominant with hard type. Hardness is negatively associated with flour color, and its associations with flour yield and ash content differ in winter and spring wheats. Grain hardness is controlled by a major gene and several minor genes with additive effect mostly, but dominant effect is also observed, with heritability of 0.78.

Genetic Analysis and Mapping of an Enclosed Panicle Mutant Locus esp1 in Rice (Oryza sativa L.)

A mutant was isolated from the M2 of 60Co-T ray mutagenized male-fertility restorer line Zao-R974 in rice. The mutant showed pleiotropic phenotypes including dwarfism, delayed heading time, short and partially enclosed panicles, short uppermost internode, decreased grain and secondary branch numbers per panicle, and partially degenerated spikelets. The mutant was named as espl （enclosed shorter panicle 1）. Genetic analysis indicated that the mutant phenotype was controlled by a recessive locus. Spraying exogenous GA~ did not rescue the panicle enclosure. Using an F2 and a BC, population of the cross between espl and a japonica cultivar Nipponbare, we mapped the ESP1 locus to a region of-260 kb on chromosome 11. This result provides a basis for further map-based cloning of the ESP1 locus.

Genetic Analysis of the P1 Region of Human Enterovirus 71 Strains and Expression of the 55 F StrainVP1 Protein

Enterovirus 71 （EV71） is a member of the Entero-virus genus of the Picomaviridae family and is the major cause of Hand, foot, and mouth disease （HFMD） in children. Different strains from Gansu were cloned and the P1 protein was sequenced and analysed. Results indicate that there are three kinds of EV71 infections prevalent in Gansu. The VP 1 protein from one of these strains, 55F, was expressed. The recombinant protein was expressed with high level and reacted specifically with the EV71 patient antibody, the recombinant protein was also applied to raise antiserum in rabbits and after the fourth injection a high titer of antiserum was detected by ELISA assay. These data are useful for further clarification of prevalent EV71 strains in the north of China at the molecular level and provide a basis for EV71 diagnosis.

Genetic Analysis and Molecular Mapping of Light-Sensitive Red-Root Mutant in Rice

The light-sensitive red-root mutant, designated as HG1, was newly observed from an indica rice variety, Nankinkodo, when seedlings were grown with roots exposed to natural light. The root color of the mutant began to turn slight-red when the roots were exposed to the light at the intensity of 29 ）Jmol/（m^2·s）, then turned dark-red at the light intensity of 180 pmol/（m^2·s）, suggesting that the root color of the mutant was evidently sensitive to light. Furthermore, genetic analysis showed that the character of light-sensitive red-root of the HG1 mutant was controlled by a single dominant gene, tentatively designated as Lsr. With simple sequence repeat markers, Lsrgene was located between the markers RM252 and RM303 on chromosome 4 with the genetic distances of 9.8 cM and 6.4 cM, respectively. These results could be useful for fine mapping and cloning of Lsrgene in rice.

Genetic analysis of fertility restoring genes for AL-type male sterility in wheat

In order to screen molecular markers linked to fertility restoring genes and further improve the breeding efficiency of restorer lines, in this study, wheat varieties 18A, 18B and 99AR144-1 were used as experimental materials to establish F2 fertility-segregating population. Plant quantitative trait ＂major gene ＋ polygene mixed mo- del＂ separation analysis method and simple sequence repeat （SSR） molecular markers were adopted for genetic analysis of four generations, including the parents （P~ and P2）, and hybrid （G and G） populations. The results show that AL-type fertility restoring gene is controlled by two pairs of additive-dominant-epistatic genes and addi- tive-dominant polygene; two primers linked to fertility restoring genes were selected by SSR molecular markers, including Xgwm95 on chromosome 2A and Barc61 on chromosome 1B, with the linkage distance of 15.0 cM and 18.0 cM, respectively. Based on verification, these two markers are reliable for distinguishing AL-type wheat ste- rile lines and restorer lines.