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.

Diversity Analysis in Selected Non-basmati Scented Rice Collection

Diversity analysis among 23 rice varieties including 16 non-basmati scented accessions, 5 basmati accessions and 2 non-scented accessions was performed by random amplified polymorphic DNA （RAPD） and inter-simple sequence repeat （ISSR） marker systems. The varieties analyzed by 11 RAPD and 8 ISSR primers yielded an average of 65% and 80% polymorphism, respectively. The average number of polymorphic bands generated per RAPD primer was 6 and per ISSR primer was 5.87. RAPD and ISSR data analysis individually could not segregate basmati and non-basmati scented rice accessions. However, the analysis using a combined data could group basmati and non-basmati scented rice accessions separately. The bands present specifically among three accessions of non-basmati scented rice were also identified. The study revealed a high genetic diversity among non-basmati scented rice accessions.

Genetic diversity analysis of Lepidium sativum(Chandrasur) using inter simple sequence repeat(ISSR) markers

Lepidium sativum（commonly known as garden cress） belongs to the family Brassicaceae. It is a fastgrowing erect, annual herbaceous plant. Its seeds possess significant fracture healing, anti-asthmatic, anti-diabetic,hypoglycemic, nephrocurative and nephroprotective activities. In the present study, we assessed the genetic diversity of various genotypes of L. sativum using inter-simple sequence repeat（ISSR） markers. Out of 41 ISSR primers screened, 32 primers showed significant, clear and reproducible bands. A total of 510 amplified bands were obtained using 32 ISSR primers, out of which 422 bands were polymorphic and 88 bands were monomorphic. The percentage of polymorphism was found to be 82. A total of 35 unique alleles ranging insize from 200 to 2,900 bp were observed.Cluster analysis based on unweighted pair-group method,arithmetic mean divided the 18 genotypes into two main clusters, with the first having only HCS-08 genotype of L.sativum and other having all of the other 17 genotypes. The Jaccard similarity coefficient revealed a broad range32–72 % genetic relatedness among the 18 genotypes.

Diversity analysis of acute hepatopancreatic necrosis disease-positive Vibrio parahaemolyticus strains

Acute hepatopancreatic necrosis disease(AHPND),also called early mortality syndrome(EMS),has caused massive economic loss in aquaculture since 2009.It was considered that the disease was caused by a novel type of Vibrio parahaemolyticus which harbors a large plasmid.Two insecticidal Photorhabdus insect-related(pir)genes were found in the plasmid.In this study,81 isolates have been collected from a shrimp farm in Maoming,Guangdong Province,PRC.Suspected isolates were identified using 3 pairs of primer recently made public.Both the 16S rRNA gene and pir gene were sequenced.ERIC-PCR was employed for analysis of strain diversity.12 isolates were amplified by PCR and identified as Vibrio parahaemolyticus by 16S rRNA sequence alignment.Sequence alignments of the pir gene showed few mutations in the 12 strains of V.parahaemolyticus.The 12 strains separated into 3 clusters at a cut of 90%similarity by ERIC-PCR.The virulence gene expression and toxicity profile showed differences between strains.This study generated comprehensive identification of pathogenic bacteria and microbial molecular resources,which will contribute to future research of AHPND.

Estimation of Genetic Divergence and Character Association Studies in Local and Exotic Diversity Panels of Soybean(Glycine max L.)Genotypes

The availability of favorable genetic diversity is a thriving vitality for the success of a breeding program.It provides a firm basis of selecting superior breeding lines for the development of high yielding crop genotypes.In this context,present investigation aimed to generate information on genetic divergence and character association in a diversity panel of 123 local and exotic soybean genotypes.Analysis of variance revealed significant response of the evaluated genotypes based on studied attributes.It depicted the probability of selecting desirable soybean genotypes by focusing on character association studies and genetic diversity analysis.Correlation analysis revealed that seed yield per plant showed high positive correlation with 100-seed weight followed by pods per plant and plant height.Furthermore,path coefficient analysis exposed that pods per plant had maximum direct contribution in seed yield per plant followed by 100-seed weight,days to flowering and SPAD measurement.Genotype named“G-10”showed maximum yield per plant followed by 24607,G-52,24593,Arisoy,24566,17426,A-3127,24570 and 24567.Genetic diversity analysis grouped the evaluated germplasm into 17 clusters.All clusters showed zero intra-cluster variability;while inter-cluster divergence ranged from 9.00 to 91.11.Cluster V showed maximum inter-cluster distance with cluster XII followed by that of between V and VIII.Moreover,cluster IV with superior genotypes(G-10,24607,24593 and 24566),VI(17426 and 24567),XIII(24570)and X(Arisoy and G-52)showed above mean values for most of the studied characters.Overall,the results of hybridization between the superior genotypes of these cluster pairs might be useful for soybean breeding with improving agronomic traits and adaptability.

Association between childhood obesity and gut microbiota:16S rRNA gene sequencing-based cohort study

BACKGROUND This study aimed to identify characteristic gut genera in obese and normal-weight children(8-12 years old)using 16S rDNA sequencing.The research aimed to provide insights for mechanistic studies and prevention strategies for childhood obesity.Thirty normal-weight and thirty age-and sex-matched obese children were included.Questionnaires and body measurements were collected,and fecal samples underwent 16S rDNA sequencing.Significant differences in body mass index(BMI)and body-fat percentage were observed between the groups.Analysis of gut microbiota diversity revealed lowerα-diversity in obese children.Differences in gut microbiota composition were found between the two groups.Prevotella and Firmicutes were more abundant in the obese group,while Bacteroides and Sanguibacteroides were more prevalent in the control group.AIM To identify the characteristic gut genera in obese and normal-weight children(8-12-year-old)using 16S rDNA sequencing,and provide a basis for subsequent mechanistic studies and prevention strategies for childhood obesity.METHODS Thirty each normal-weight,1:1 matched for age and sex,and obese children,with an obese status from 2020 to 2022,were included in the control and obese groups,respectively.Basic information was collected through questionnaires and body measurements were obtained from both obese and normal-weight children.Fecal samples were collected from both groups and subjected to 16S rDNA sequencing using an Illumina MiSeq sequencing platform for gut microbiota diversity analysis.RESULTS Significant differences in BMI and body-fat percentage were observed between the two groups.The Ace and Chao1 indices were significantly lower in the obese group than those in the control group,whereas differences were not significant in the Shannon and Simpson indices.Kruskal-Wallis tests indicated significant differences in unweighted and weighted UniFrac distances between the gut microbiota of normal-weight and obese children(P<0.01),suggesting substantial disparities in both the species and quantity of gut microbiota between the two groups.Prevotella,Firmicutes,Bacteroides,and Sanguibacteroides were more abundant in the obese and control groups,respectively.Heatmap results demonstrated significant differences in the gut microbiota composition between obese and normal-weight children.CONCLUSION Obese children exhibited lowerα-diversity in their gut microbiota than did the normal-weight children.Significant differences were observed in the composition of gut microbiota between obese and normal-weight children.

Analysis on the Main Botanical Characters of 41 Cucurbita moschata Varieties

In order to scientifically evaluate the values of Cucurbita moschata cultivars, main botanical characters including the initial flowering date, the first fruiting node, fruit length, fruit stem length, stem diameter, internode length, the transverse and longitudinal diameters of the largest leaf, single fruit weight, flesh thickness and soluble solid content of 41 cultivars were measured for conducting diversity, correlation and cluster analysis. The results revealed that the pumpkin cultivars showed large variations in fruit stem length, single fruit weight, fruit length and flesh thickness, but small variations in initial flowering date. Significant, even highly significant correlations were found among the tested traits. Cluster analysis demonstrated that the 41 old Cucurbita moschata cultivars were divided into three groups, of which multiple traits of Group 1 were better than those in the other two groups. High similarities existed in three groups and the cultivars in each group. This research provided basis for selecting excellent traits and parents for the breeding of hybrids.

Effects of Topography and Land use on Woody Plant Species Composition and Beta Diversity in an Arid Trans-Himalayan Landscape, Nepal

Distribution patterns of plant species are believed to be impacted by small-scale habitat heterogeneity. However, there have been few comparative studies examining how woody vegetation composition and diversity varies with aspects of different orientations in the Trans-Himalayan region at a local scale. Here, we examined the effects of incoming solar radiation on variation in woody species composition and compared the diversity between the northeast- and southwest-facing slopes in a Trans-Himalayan valley of Nepal. We also examined the implicit interactions between slope orientation and land use in determining the compositional variations between the slopes. We selected two pairs of northeast- and southwest-facing slopes where the first pair has a similar land use and differs in exposure only(Pisang site) while the other pair has clear differences in land use in addition to slope exposure(Braka site). In each site, we sampled 72 plots(36 on each slope) in which the presence and absence of woody species, environmental variables, and disturbance were recorded. Correspondence Analysis(CA) results suggested that the woody species composition significantly varied between northeast- and southwest-facing slopes at both sites, and was significantly correlated with measured environmental variables such as radiation index, altitude, and canopy openness. In the Braka site,mean alpha diversity was significantly higher on southwest-facing slopes. In contrast, beta diversity and gamma diversity were greater on northeast-facing slopes at both sites. Our results suggest that topographic variables(e.g., radiation index) affect species composition between the slopes, likely due to their influence on small scale abiotic environmental variables. However, the effects of land use, such as livestock browsing/grazing may interact with the effects of slope exposure, effectively reducing differences in species composition within slopes but enhancing the differences in beta diversity between contrasting slopes in the Braka. We conclude that slope orientation and land use are important factors in structuring the woody species composition and diversity in the arid Trans-Himalayan region. We suggest that both environmental and land use variables should be taken into consideration in future studies on plant community structure along the cultural landscapes.

Variability and divergence in Pongamia pinnata for further use in tree improvement

A total of 24 candidate plus trees（CPTs） of Pongamia pinnata（L.） Pierre.were selected to elucidate their variation and diversity based on thirteen quantitative traits（4 pod traits,6 seed traits of parent trees and 3 progeny traits） at Forest Research Centre,Institute of Forest Productivity-Mandar,Ranchi district during 2005-2007.The results show that,CPT-19 had maximum for seven traits viz,pod length（65.6 mm）,100-pod weight（542.4 g）,seed 2D（two dimension） area（351.2 mm2）,seed length（27.9 mm）,seed breadth（17.4 mm）,100-seed weight（217.9 g） and plant height（164.3 cm）.The traits,100-pod weight and 100-seed weight had a high heritability（98.4%,96.9%） accompanied with high genetic advance（46.0%,34.9%）.There is a positive significant correlation between 100-pod weight and 100-seed weight traits at both genotypic and phenotypic levels with plant height,collar diameter and volume index at 30 MAS（months after sowing）.Volume index expressed a moderate heritability（47.4%） accompanied with high genetic advance（48.4%）,indicating that the character is governed by additive gene effects.In divergence study,24 accessions were grouped into 6 clusters on the basis of non-hierarchical euclidian cluster analysis.The genotypes in cluster IV（CPT-5,CPT-6,CPT-7,CPT-12,CPT-16,CPT18,CPT-22） and cluster III（CPT-4,CPT-8,CPT-9,CPT-20,CPT-21） were most heterogeneous and can be best used within group hybridization.The wide diversity exists between the cluster V and II,followed by cluster II and I and crosses between CPTs of these clusters may result in substantial segregates.It is revealed that the existence of substantial variation and diversity can be utilized for genetic resource conservation and further tree improvement programmers of the species.

Establishment and application of an SNP molecular identification system for grape cultivars

We aimed to develop a set of single nucleotide polymorphism(SNP) markers that can be used to distinguish the main cultivated grape(Vitis L.) cultivars in China and provide technical support for domestic grape cultivar protection, cultivar registration, and market rights protection. A total of 517 high-quality loci were screened from 4 241 729 SNPs obtained by sequencing 304 grape accessions using specific locus amplified fragment sequencing, of which 442 were successfully designed as Kompetitive Allele Specific PCR(KASP) markers. A set of 27 markers that completely distinguishes 304 sequenced grape accessions was determined by using the program, and 26 effective markers were screened based on 23 representative grape cultivars. Finally, a total of 46 out of 48 KASP markers, including 22 markers selected by the research group in the early stage, were re-screened based on 348 grape accessions. Population structure, principal component, and cluster analyses all showed that the 348 grape accessions were best divided into two populations. In addition, cluster analysis subdivided them into six subpopulations. According to genetic distance, V. labrusca, V. davidii, V. heyneana, and V. amurensis were far from V. vinifera, while V. vinifera×V. labrusca and V. amurensis×V. vinifera were somewhere in between these two groups. Furthermore, a core set of 25 KASP markers could distinguish 95.69% of the 348 grape accessions, and the other 21 markers were used as extended markers. Therefore, SNP molecular markers based on KASP typing technology provide a new way for mapping DNA fingerprints in grape cultivars. With high efficiency and accuracy and low cost, this technology is more competitive than other current identification methods. It also has excellent application prospects in the grape distinctness, uniformity, and stability(DUS) test, as well as in promoting market rights protection in the near future.

Development of a Highly Informative Microsatellite (SSR) Marker Framework for Rice (Oryza sativa L.) Genotyping

To select highly informative microsatellite markers （SSRs） and establish a useful genetic SSR framework for rice genotyping, 15 rice （Oryza sativa L.） cultivars including six indica varieties and nine japonica varieties were used to analyze the polymorphism information content （PIC） value of 489 SSR markers. A total of 1 296 alleles were detected by 405 polymorphic markers with an average of 3.2 per locus. The PIC value of each chromosome was ranged from 0.4039 （chromosome 2） to 0.5840 （chromosome 11）. Among the two rice subspecies, indica （0.3685-0.4952） gave a higher PIC value than japonica （0.1326-0.3164） and displayed a higher genetic diversity. Genetic diversity of indica was high on chromosome 12 （0.4952） and low on chromosome 8 （0.3685）, while that for japonica was high on chromosome 11 （0.3164） and low on chromosome 2 （0.1326）. A SSR framework including 141 highly informative markers for genotyping was selected from 199 SSR markers （PIC〉0.50）. Ninety-three SSR markers distributed on 12 chromosomes were found to be related to indica-japonica differentiation. Of these 93 pairs of SSR primers, 17 pairs were considered as core primers （all the japonica varieties have the same specific alleles, while the indica varieties have another specific alleles）, 48 pairs as the second classic primers （all the japonica or indica varieties have the same specific alleles, while the indica or japanica varieties have two or more other specific alleles ） and 28 pairs as the third classic primers （all the japonica and indica varieties have two or more alleles, but the specific alleles are different between japonica and indica）. Thirty-two SSR markers were selected to be highly informative and useful for genetic diversity analysis of japonica varieties. This work provides a lot of useful information of SSR markers for rice breeding programs, especially for genotyping, diversity analysis and genetic mapping.

Advance of Study on SSR Molecular Marker in Citrus and Its Close Relatives

Simple sequences repeat （SSR） molecular maker, as a new type of DNA molecular marker, the second generation based on the polymerase chain reaction （PCR）, is valuable and of great potential as genetic markers for its characteristics of abundant quantity, high polymorphic, reproducibility, specific site amplification, high occurring frequency, and co-dominant inheritance etc. This paper outlined its principles and characteristics, and introduced its application to variety identification, phylogenetic relationship analysis, genetic diversity analysis, DNA fingerprinting and linkage map constructing etc. in recent years in Citrus and its close relatives.

Soil Microbial Community Composition During Natural Recovery in the Loess Plateau, China

This study aimed to determine the characteristics of soil microbial community composition and its relationship with soil chemical properties during natural recovery in the Loess Plateau.The soil microbial community composition was analyzed by comparing the soil microbial phospholipid fatty acids（PLFAs） of eight croplands abandoned for 1,3,5,10,13,15,20,and 30 yr in the Dunshan watershed,northern Loess Plateau,China.The results showed that soil organic carbon,total nitrogen,soil microbial biomass carbon,and soil microbial biomass nitrogen significantly increased with the abandonment duration,whereas the metabolic quotient significantly decreased.The Shannon richness and Shannon evenness of PLFAs significantly increased after 10 yr of abandonment.Gram-negative,Gram-positive,bacterial,fungal,and total PLFAs linearly increased with increased abandonment duration.Redundancy analysis showed that the abandonment duration was the most important environmental factor in determining the PLFA microbial community composition.The soil microbial PLFAs changed from anteiso-to iso-,unsaturated to saturated,and short-to long-chain during natural recovery.Therefore,in the Loess Plateau,cropland abandonment for natural recovery resulted in the increase of the soil microbial PLFA biomass and microbial PLFA species and changed the microbial from chemolithotrophic to a more heterotrophic community.

Fungal diversity in adult date palm(Phoenix dactylifera L.) revealed by culture-dependent and culture-independent approaches

Endophytic flora plays a vital role in the colonization and survival of host plants, especially in harsh environments, such as arid regions. This flora may, however, contain pathogenic species responsible for various troublesome host diseases. The present study is aimed at investigating the diversity of both cultivable and non-cultivable endophytic fungal floras in the internal tissues(roots and leaves) of Tunisian date palm trees(Phoenix dactylifera). Accordingly, 13 isolates from both root and leaf samples, exhibiting distinct colony morphology, were selected from potato dextrose agar(PDA) medium and identified by a sequence match search wherein their 18S–28S internal transcribed spacer(ITS) sequences were compared to those available in public databases. These findings revealed that the cultivable root and leaf isolates fell into two groups, namely Nectriaceae and Pleosporaceae. Additionally, total DNA from palm roots and leaves was further extracted and ITS fragments were amplified. Restriction fragment length polymorphism(RFLP) analysis of the ITS from 200 fungal clones(leaves: 100; roots: 100) using HaeIII restriction enzyme revealed 13 distinct patterns that were further sequenced and led to the identification of Alternaria, Cladosporium, Davidiella(Cladosporium teleomorph), Pythium, Curvularia, and uncharacterized fungal endophytes. Both approaches confirmed that while the roots were predominantly colonized by Fusaria(members of the Nectriaceae family), the leaves were essentially colonized by Alternaria(members of the Pleosporaceae family). Overall, the findings of the present study constitute, to the authors' knowledge, the first extensive report on the diversity of endophytic fungal flora associated with date palm trees(P. dactylifera).

Assessment of genetic diversity by simple sequence repeat markers among forty elite varieties in the germplasm for malting barley breeding

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.

Features of gut microbiota in patients with anorexia nervosa

Background:Anorexia nervosa(AN)is a psychological disorder,which is characterized by the misunderstanding of body image,food restriction,and low body weight.An increasing number of studies have reported that the pathophysiological mechanism of AN might be associated with the dysbiosis of gut microbiota.The purpose of our study was to explore the features of gut microbiota in patients with AN,hoping to provide valuable information on its pathogenesis and treatment.Methods:In this cross-sectional study,from August 2020 to June 2021,patients with AN who were admitted into Peking University Third Hospital and Peking University Sixth Hospital(n=30)were recruited as the AN group,and healthy controls(HC)were recruited from a middle school and a university in Beijing(n=30).Demographic data,Hamilton Depression Scale(HAMD)scores of the two groups,and length of stay of the AN group were recorded.Microbial diversity analysis of gut microbiota in stool samples from the two groups was analyzed by 16S ribosomal RNA(rRNA)gene sequencing.Results:The weight(AN vs.HC,[39.31±7.90]kg vs.[56.47±8.88]kg,P<0.001)and body mass index(BMI,AN vs.HC,[14.92±2.54]kg/m^(2)vs.[20.89±2.14]kg/m^(2),P<0.001)of patients with AN were statistically significantly lower than those of HC,and HAMD scores in AN group were statistically significantly higher than those of HC.For alpha diversity,there were no statistically significant differences between the two groups;for beta diversity,the two groups differed obviously regarding community composition.Compared to HC,the proportion of Lachnospiraceae in patients with AN was statistically significantly higher(AN vs.HC,40.50%vs.31.21%,Z=-1.981,P=0.048),while that of Ruminococcaceae was lower(AN vs.HC,12.17%vs.19.15%,Z=-2.728,P=0.007);the proportion of Faecalibacterium(AN vs.HC,3.97%vs.9.40%,Z=-3.638,P<0.001)and Subdoligranulum(AN vs.HC,4.60%vs.7.02%,Z=-2.369,P=0.018)were statistically significantly lower,while that of Eubacterium_halli_group was significantly higher(AN vs.HC,7.63%vs.3.43%,Z=-2.115,P=0.035).Linear discriminant effect(LEfSe)analysis(LDA score>3.5)showed that o_Lachnospirales,f_Lachnospiraceae,and g_Eubacterium_halli_group(o,f andg represents order,family and genus respectively)were enriched in patients with AN.Microbial function of nutrient transport and metabolism in AN group were more abundant(P>0.05).In AN group,weight and BMI were significantly negatively correlated with the abundance of Bacteroidota and Bacteroides,while positively correlated with Subdoligranulum.BMI was significantly positively correlated with Firmicutes;HAMD scores were significantly negatively correlated with Faecalibacterium.Conclusions:The composition of gut microbiota in patients with AN was different from that of healthy people.Clinical indicators have correlations with the abundance of gut microbiota in patients with AN.

A high-efficiency pretreatment method for elution of pathogenic bacteria in lettuce

Many current studies on rapid detection of pathogenic bacteria in foods have focused on the construction of detection methods,neglecting pretreatment.It is also a key step to efficiently elute pathogenic bacteria from food samples for rapid detection and can even determine the success or failure of an assay.In this study,we used Escherichia coli(E.coli),Salmonella enteritidis(S.enteritidis),and Listeria monocytogenes(L.monocytogenes)as model bacteria to compare the elution efficiency of different eluants;explore the effect of surfactant,ionic strength,protein(or amino acid and peptide),and enzyme on the recovery rate of bacteria in lettuce;and compare the compound effect caused by multiple factors.Finally,we developed an efficient bacterial recovery method and confirmed the superiority of this method to analyze the bacterial diversity of eluants from lettuce.The results showed that the recovery efficiency of E.coli,S.enteritidis,and L.monocytogenes,which were artificially contaminated with approximately 10^(5)CFU/g in lettuces,could reach 94.4%,90.6%,and 93.7%by using 10 mmol/L Tris·HCl(pH 9.5)with 0.1%peptone and 300 U/100 mL of cellulase,and furthermore,the elution efficiency could reach 99.6%,98.6%,and 100%with the aid of a 2-min stomaching.For the lettuce samples with only native bacteria,the recovery rate reached 92.1%for viable aerobic bacteria by this method,which was approximately 10%higher than that of the modified previous method.The bacterial diversity of the eluted solution was analyzed,and the result was significantly improved.Considering these advantages,it is important to improve the elution efficiency to achieve rapid and accurate detection of pathogenic bacteria in lettuces.