Genetic variations of wood properties and growth characters of Ko-rean pines from different provenances

Totally 26 provenance stands of 17-year-old Korean pine were selected for investigating wood properties and growth characters in Mao抏rshan Experimental Forest Farm of Northeast Forestry University in 1999. The anatomical property indexes, including tracheid length, tracheid diameter and wall-indiameter ratio, and the physical property indexes, such as growth ring width, late wood percentage and growth ring density, were measured for wood properties. Growth character indexes, including tree height and diameter at breast height, were also measured. The analytical results showed that there exited obviously dif-ference in wood property indexes between different provenances, which is suggested that wood properties are controlled by their genetic differences. The growth character indexes of Korean pines presented significant difference and they might also be controlled by their genetic differences. Most parameters of wood properties mainly varied in the direction of longitude, but the parameters of growth characters varied in the direction of latitude.

Analysis of drought tolerance and genetic and epigenetic variations in a somatic hybrid between Ipomoea batatas (L.) Lam. and I. triloba L.

The somatic hybrid KT1 was previously obtained from protoplast fusion between sweetpotato （Ipomoea batatas （L.） Lam.） cv. Kokei No. 14 and its wild relative I. triloba L. However, its genetic and epigenetic variations have not been investigated. This study showed that KT1 exhibited significantly higher drought tolerance compared to the cultivated parent Kokei No. 14. The content of proline and activities of superoxide dismutase （SOD） and photosynthesis were significantly increased, while malonaldehyde （MDA） content was significantly decreased compared to Kokei No. 14 under drought stress. KT1 also showed higher expression level of well-known drought stress-responsive genes compared to Kokei No. 14 under drought stress. Amplified fragment length polymorphism （AFLP） and methylation-sensitive amplified polymorphism （MSAP） analyses indicated that KT1 had AFLP and MSAP band patterns consisting of both parent specific bands and changed bands. Fur- ther analysis demonstrated that in KT1. the proportions of Kokei No. 14 specific genome components and methylation sites were much greater than those of I. triloba. KT1 had the same chloroplast and mitochondrial genomes as Kokei No. 14. These results will aid in developing the useful genes ofI. triloba and understanding the evolution and phylogeny of the cultivated sweetpotato.

Genetic variations in the SMAD4 gene and gastric cancer susceptibility

AIM:To explore the association between mothers against decapentaplegic homolog 4 (SMAD4) gene polymorphisms and gastric cancer risk.METHODS:Five tagging single nucleotide polymor-phisms (tSNPs) in the SMAD4 gene were selected and genotyped in 322 gastric cancer cases and 351 cancerfree controls in a Chinese population by using the polymerase chain reactionrestriction fragment length polymorphism method.Immunohistochemistry was used to examine SMAD4 protein expression in 10 normal gastric tissues adjacent to tumors.RESULTS:In the single-locus analysis,two significantly decreased risk polymorphisms for gastric cancer were observed:the SNP3 rs17663887 TC genotype (adjusted odds ratio=0.38,95% confidence interval:0.21-0.71),compared with the wild-type TT genotype and the SNP5 rs12456284 GG genotype (0.31,0.16-0.60),and with the wild-type AA genotype.In the combined analyses of these two tSNPs,the combined genotypes with 2-3 protective alleles (SNP3 C and SNP5 G allele) had a significantly decreased risk of gastric cancer (0.28,0.16-0.49) than those with 0-1 protective allele.Furthermore,individuals with 0-1 protective allele had significantly decreased SMAD4 protein expression levels in the norma tissues adjacent to tumors than those with 2-3 protective alleles (P=0.025).CONCLUSION:These results suggest that genetic variants in the SMAD4 gene play a protective role in gastric cancer in a Chinese population.

Association of genetic variations of the prostasin gene with essential hypertension in the Xinjiang Kazakh population

Background Transgenic overexpression of human prostasin in rats disturbs salt balance and causes hypertension. We investigated whether genetic variations in prostasin were implicated in hypertension or related phenotypes in the Xinjiang Kazakh population.Methods We sequenced all exons and the promoter regions of the prostasin gene in 94 hypertensive individuals, and the genotype identification was performed by the TaqMan polymerase chain reaction method. Case-control studies were conducted in 938 Kazakh subjects.Results E342K and 2827G＞A, which are novel variants, were successfully genotyped in the general Xinjiang Kazakh population with a sample size of 938 individuals （406 men and 532 women）. Only one hypertensive patient was identified with the E342K mutation. No significant association was observed between 2827G＞A and hypertension. However,quantitative traits of hypertensive intermediate phenotypes were significantly associated with the A allele; P=-0.041 and 0.034 for body mass index （BMI） in the additive and recessive models, P=0.042 and 0.018 for OGTT-2h glucose in the additive and recessive models, P=0.031 for IRT-3h insulin in the recessive model, and P=0.038 for serum potassium in the dominant model.Conclusions This study does not provide evidence of a major role of prostasin variation in blood pressure modulation.However, association of prostasin polymorphisms with hypertension and metabolic effects can be observed in our population. Further investigation is warranted to clarify the relevance of prostasin polymorphisms to blood pressure regulation.

Genetic variation and selection of 10-year-old Eucalyptus camaldulensis based on wind damage index and wood properties

Typhoons are becoming frequent and intense with ongoing climate change,threatening ecological security and healthy forest development in coastal areas.Eucalyptus of a predominant introduced species in southern China,faces significant growth challenges because of typhoon.Therefore,it is vital to investigate the variation of related traits and select superior breeding materials for genetic improvement.Variance,genetic parameter,and correlation analyses were carried out on wind damage indices and eight wood proper-ties in 88 families from 11 provenances of 10-year-old Euca-lyptus camaldulensis.The selection index equation was used for evaluating multiple traits and selecting superior prov-enances and family lines as future breeding material.The results show that all traits were highly significantly differ-ent at provenance and family levels,with the wind damage index having the highest coefficient of genetic variation.The heritability of each trait ranged from 0.48 to 0.87,with the wind damage index,lignin and hemicellulose contents,and microfibril angle having the highest heritabilities.The wind damage index had a positive genetic correlation with wood density,a negative correlation with lignin content,a negative phenotypic correlation and a negative genetic correlation with microfibril angle.Wind damage index and genetic progress in the selection of eight wood traits varied from 7.2%to 614.8%.Three provenances and 12 superior families were selected.The genetic gains of the wind damage index were 10.2%and 33.9%for provenances and families,and these may be starting material for genetic modification for wind resistance in eucalyptus and for their dissemination to typhoon-prone coastal areas of southern China.

Progress in clinical diagnosis and treatment of colorectal cancer with rare genetic variants

Targeted therapy is crucial for advanced colorectal cancer(CRC) positive for genetic drivers. With advances in deep sequencing technology and new targeted drugs, existing standard molecular pathological detection systems and therapeutic strategies can no longer meet the requirements for careful management of patients with advanced CRC. Thus, rare genetic variations require diagnosis and targeted therapy in clinical practice. Rare gene mutations, amplifications, and rearrangements are usually associated with poor prognosis and poor response to conventional therapy. This review summarizes the clinical diagnosis and treatment of rare genetic variations, in genes including erb-b2 receptor tyrosine kinase 2(ERBB2), B-Raf proto-oncogene, serine/threonine kinase(BRAF), ALK receptor tyrosine kinase/ROS proto-oncogene 1, receptor tyrosine kinase(ALK/ROS1), neurotrophic receptor tyrosine kinases(NTRKs), ret proto-oncogene(RET), fibroblast growth factor receptor 2(FGFR2), and epidermal growth factor receptor(EGFR), to enhance understanding and identify more accurate personalized treatments for patients with rare genetic variations.

Genetic Structure of the Oriental River Prawn (Macrobrachium nipponense) from the Yangtze and Lancang Rivers, Inferred from COI Gene Sequence

This study analyzed nueleotide sequences from the mitochondrial eytochrome oxidase submit （COI） gene region （450 bp） to investigate the genetic structure of the oriental river prawn （ Macrobrachium nipponense ） among nine populations from the Yangtze and Lancang Rivers. A total of 79 individuals were collected for this work. Eighty-nine nucleotides were found to be variable, resulting in 46 haplotypes. Among the nine populations, the population from Kunming shows the greatest level of variability （h = 1.000, π = 0.028）, whereas the population from Cbongqing exhibits the lowest level of variability （h = 0.700,π = 0.008）. Analysis of molecular variance suggested that of the total genetic diversity, 9.66% was attributable to inter-population diversity and the remainder （90.34%） to differences within populations. A molecular phylogenetic tree constructed using the Neighbor-joining （N J） method showed that the 46 haplotypes were assigned to two clades associated with geographic regions. These results provide basic information for the conservation and sustainable exploitation of this species.

Genetic Variation of Wild and Hatchery Populations of the Pacific Oyster Crassostrea gigas Assessed by Microsatellite Markers

Microsatellite DNA technique was used to detect the genetic variation between five hatchery populations of the Pacific oyster from China and two wild populations from Japan. Seven microsatellite loci screened in this study showed high polymorphism in both hatchery and wild populations, as observed in an average number of allele per locus （19.1-29.9） and average expected heterozygosity （0.916-0.958）. No significant difference in average allelic richness or expected heterozygosity was observed between Chinese hatchery populations and Japanese wild populations. Pairwise Fsr values and heterogeneity tests of allele frequencies showed significant genetic differentiation between all populations. According to the neighbor-joining tree constructed on the basis of the Dc distance, the seven populations fell into three groups showing a clear division between hatchery and wild populations, and between the northern and southern hatchery populations. Assignment tests correctry assigned high percentages （97%-100%） of individuals to their original populations and demonstrated the feasibility of microsatellite analysis for discrimination between populations. The information obtained in this study is useful for designing suitable management guidelines and selective breeding programs for the Pacific oyster in China.

A Preliminary Study on Genetic Variation of g E Gene of an Epidemic Pseudorabies Virus Strain and Its Pathogenicity to Piglets

[Objective] This study aimed to investigate the genetic variation of g E gene of an epidemic pseudorabies virus（PRV） strain and its pathogenicity to piglets. [Method] By serial passage in Vero cells, a PRV strain was isolated from the brain tissues of stillborn fetuses delivered by sows with suspected PRV infection and preliminarily identified by PCR. g E gene of the isolated PRV strain was amplified and sequenced for phylogenetic analysis. In addition, the pathogenicity of the isolated PRV strain to 6-week-old piglets was evaluated. [Result] A PRV strain was successfully isolated and named PRV N5 B strain, which could proliferate in Vero cells and TCID50 of the 15 thgeneration virus liquid reached 10^7.125/0.1 ml. Specific bands could be amplified by PCR. g E gene in the isolated PRV strain was 1 740 bp in length. A phylogenetic tree was constructed based on full-length g E sequences, which showed that PRV N5 B strain and PRV strains isolated since 2012 were clustered into the same independent category and shared 99.7%-100% homology of nucleotide sequences. Compared with related sequences published previously, there were insertions of three consecutive bases at two loci. Animal experiments showed that intranasal inoculation of 6-week-old piglets with 2 ml of PRV N5 B strain（10^6/0.1 ml） led to a mortality rate of 100%. [Conclusion] In this study,genetic variability of g E gene in PRV N5 B isolate and its pathogenicity to piglets were analyzed, which provided a theoretical basis for the development of new vaccines to prevent and control porcine pseudorabies.

Genetic Diversity of Wild and Cultivated Populations of Castanopsis hystrix in China

[Objective] This study aimed to investigate the genetic variation of wild and cultivated populations of Castanopsis hystrix. [Method] Genetic variation of five wild populations and three cultivated populations of Castanopsis hystrix, was investigated with ISSR-PCR amplification. Totally, 151 individuals were selected and analyzed by amplification using nine pairs of ISSR primers screened. [Result] Each primer pair produced 7-20 bands and 122 polymorphic bands were obtained. At population level, ISSR diversity in the wild populations (P=59.84%, HPOP=0.182 7, I=0.285 6) was higher than which in cultivated ones (P=54.87%, HPOP=0.136 6, and I=0.219 8). The genetic differentiation coefficient among wild populations (GST) was 0.99. The similar population structure was found in three cultivated populations (GST=0.127 5). According to the UPGMA cluster analysis, the genetic distance among wild populations became larger with the increase of geographical distance. [Conclusion] Compared with other seed plants, with either a similar life history or various breeding system attributes, relatively low level of genetic diversity was observed in these five wild populations, which was caused by population size reduction and habitat fragmentation related to human activities. The formation of population structure may be explained by the species’ breeding system.

Analysis of Genetic Variation and Population Structure of Starch Synthesis-related Genes in Indica Rice Cultivars

In this study, 34 molecular markers of starch synthesis-related genes were used to evaluate the genetic variation and population structure of 87 indica rice cultivars from different countries and regions. The results showed that a total of 80 alleles were amplified using 34 primer pairs, with an average of 2.5 alleles per locus. The allele number varied from 2 to 6 among various cultivars. Shannon＇s diversity index of molecular markers varied from 0.303 to 0.796, with an average of 0.539. Polymorphism information content （PIC） varied from 0.084 to 0.658, with an average of 0.295. The genetic similarity coefficients of 87 indica rice cultivars ranged from 0.265 to 0.990, indicating significant genetic differences of starch synthesis-related genes among different cultivars, but the variation frequency of alleles varied among different cultivars. Population structure analysis showed that these 87 indica rice cultivars were divided into three categories. Genetic differences were small within the same category but great among different categories. Moreover, indica rice cultivars with simple genetic components accounted for 39.1% and those with complex genetic background accounted for 60.9%. This study may not only provide theoretical basis for genetic improvement of rice starch quality, but also lay a solid foundation for subsequent association analysis of rice quality-related traits.

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 Variation of the ORF5 Gene of Porcine Reproductive and Respiratory Syndrome Virus in East China during 2008-2010

[Objective] A total of 260 swine samples of dead or sick pigs collected from 7 provinces （municipalities） Jiangsu, Anhui, Shanghai, Shandong, Zhejiang, Fujian and Jiangxi of China during 2008-2010 were detected for porcine reproductive and respiratory syndrome virus （PRRSV）. And the ORF5 genes of some isolates were amplified and sequenced for understanding the molecule epidemiology and the genetic evolution of PRRSV in East China. [Method] Using RT-PCR method, PRRSV was detected by RT-PCR from samples. The complete ORF5 genes of 36 PRRSV positive samples was amplified, sequenced and analyzed with other 15 strains available on GenBank. [Result] PRRSV was detected in 118/260 of the clinical samples, with a positive rate was 45.4%. Sequence analysis showed that the 36 isolates of this study belonged to the North American-type PRRSV strains and were closely related to the highly pathogenic PRRSV （HP-PRRSV） with 94.6%-100% amino acid sequence identities. The sequence analysis combined with the phylogenetic analysis indicated that all these North American-type PRRSV strains in East China were further divided into five subgenotypes, subgenotype Ⅲ showed closer identity with HPPRRSV; almost all subgenotypes were found to be variable in the primary neutralizing epitope; subgenotypes Ⅲ and IV had more glycosylation sites than others. Although these 36 isolates were collected from different provinces in East China, there were no obvious relations between the distribution of PRRSV and the region. [Conclusion] The PRRSV infection was widespread and HP-PRRSV was the popular strain in East China during 2008-2010. However some different genetic characteristics appeared in the genomes, the genetic evolution was relatively stable. There exists a cross-cutting phenomenon on the genetic relationship of PRRSV isolates obtained from different provinces. Subgenotypes IV and V only appeared in some provinces, but the distribution of PRRSV did not show apparent geographical characteristics.

Genetic Control of Air-Dried Wood Density, Mechanical Properties and Its Implication for Veneer Timber Breeding of New Triploid Clones in Populus tomentosa Carr

The wood samples of 9 triploid clones of Populus tomentosa Carr. taken from a 9 year old clonal test site were analyzed in order to investigate the genetic variation of wood properties, including air dried wood density and some mechanical properties. The results showed that significant or extremely significant difference in air dried wood density and the mechanical properties existed among the clones, this means these wood properties were under moderate or strong genetic controls and could be improved by genetic manipulations. The radial and vertical variation patterns of air dried wood density were also studied and the results were found to coordinate with other previous research results. The vertical variation patterns of most mechanical properties within the individual tree also conformed to the general wood theories except the modulus of elasticity and cross section hardness. Among the mechanical properties, modulus of elasticity (MOE) and tangent section hardness were under strong genetic control, with the clonal repeatabilities being 0 90 and 0 80, respectively. However, the clonal repeatabilities of other mechanical properties under study were a little lower than above two indexes. Genetic correlation analysis indicated that super clonal selection and breeding for veneer timber could be realized through indirect selection of wood density and form indexes.

Genetic Variation of Porcine Circovirus Type 2 Isolate 201105ZJ

[Objective] This study aimed to investigate the genetic variation of porcine circovirus type 2 （PCV2） in China. [Method] The strain was isolated from infected samples by cel passage and preliminarily identified by PCR and IFA. Ful-length genome of the isolated strain was obtained by specific amplification for homology and phylogenetic analysis. [Result] A PCV2 strain was successful y isolated and named 201105ZJ, which could proliferate in PK15 cel lines. Specific fragments could be amplified by specific PCR assay. According to results of IFA assay, specif-ic immunofluorescence was observed; the TCID50 was low （102.67）; the ful-length genome sequence of the isolated strain was 1 768 bp, sharing 94.1%-96.8% ho-mology with 13 reference strains; to be specific, the isolated strain exhibited the highest homology of 96.8% with AF055392PCV2a; the isolated strain 201105ZJ and reference strain AF055392 belonged to genotype PCV2a, exhibiting a distant genetic relationship with genotype PCV2c. [Conclusion] Characteristics of genetic variation of PCV2 isolate 201105ZJ provided theoretical basis for vaccine development, investi-gation of PCV2 pathogenesis, and prevention and control of porcine circovirus-as-sociated diseases （PCVAD） in East China.

Assessment of Genetic Variation in Soybean (<i>Glycine max</i>) Accessions from International Gene Pools Using RAPD Markers: Comparison with the ISSR System

Soybean (Glycine max) is one of the most important crops in the world in terms of total production and usage. It is also among the least diverse species. The main objectives of the present study were to 1) assess the level of genetic variation among soybean (G. max) accessions from different countries using Random Amplified Polymorphic DNA (RAPD) markers and 2) compare Inter Simple Sequence Repeats (ISSR) and RAPD marker systems in detecting polymorphic loci in soybeans (G. max). Genomic DNAs from 108 soybeans (G. max) accessions from 11 different gene pools were analyzed using several ISSR and RAPD primers. The average level of polymorphic loci detected with the RAPD primers was 35%. The soybean accessions from the China, Netherlands, and Canada gene pools were the least genetically variable with 25%, 26%, and 30% of polymorphic loci, respectively. Accessions from Hungary (43%) and France (48%) showed the highest level of polymorphism based on the RAPD analysis. Overall, RAPD data revealed that the accessions from different countries are closely related with 64% genetic distance values below 0.40. The levels of polymorphic loci detected with the RAPD and ISSR marker systems were in general moderate and similar even if they target different regions of the genome. A combination of different marker systems that include RAPD/ISSR, microsatellites (SSR), and SNPs should provide the most accurate information on genetic variation of soybean (G. max) accessions.

Genetic variation of Laminaria japonica (Phaeophyta) populations in China as revealed by RAPD markers

For the population genetics analysis of the naturally grown brown seaweed Laminaria japonica （Laminariales,Phaeophyta） sampled from Dalian,Yantai,Weihai,Rongcheng and Qingdao in China,ten primers were employed to produce 88 bands as revealed by randomly amplified polymorphic DNA （RAPD） markers,and all these bands were polymorphic.According to these band patterns,there were 94 distinct phenotypes occurred in 100 samples indicating the high heterozygosity of this kelp.Dalian population samples showed the highest percentage of polymorphism （71.67%）,and also the higher diversity estimated on the basis of the Shannon’s index （8.498）,suggesting that this population could be chosen as the best resource for genetic breeding.The highest diversity of Yantai population possibly resulted from the introduction of L.longissima used for interspecific cross breeding with L.japonica cultivated in China.From Dalian southwards to Qingdao,the genetic variation of the five populations became less with a decrease in latitude,possibly due to the natural selection especially of high temperature.The genetic distance （Φ ST values） of the five populations was a little significantly correlated with the geographical distance （r=0.496） at P =0.05 by Mantel’s test.Weihai,Rongcheng and Yantai populations were closely grouped genetically together by Neighbor-joining cluster analysis probably in that the dispersal of the kelp by propagules more easily occurring in the range of relatively short distance.The analysis of molecular variance （AMOVA） also demonstrated that the relatively higher variation occurred among populations （71.49%） at an extremely significant level （P 0.000 1）.All these evidence showed that there was a relatively distinct genetic differentiation among the sampled kelp populations,and L.japonica grown in China was also rather heterozygous in heredity.

Advances in salinity tolerance of soybean: Genetic diversity, heredity, and gene identification contribute to improving salinity tolerance

Salt stress is one of the major abiotic stresses affecting soybean growth. Genetic improvement for salt tolerance is an effective way to protect soybean yield under salt stress conditions. Successful improvement of salt tolerance in soybean relies on identifying genetic variation that confers tolerance in soybean germplasm and subsequently incorporating these genetic resources into cultivars. In this review, we summarize the progress in genetic diversity and genetics of salt tolerance in soybean, which includes identifying genetic diversity for salt tolerant germplasm; mapping QTLs conferring salt tolerance; map-based cloning; and conducting genome-wide association study（GWAS） analysis in soybean. Future research avenues are also discussed, including high throughput phenotyping technology, the CRISPR/Cas9 Genome-Editing System, and genomic selection technology for molecular breeding of salt tolerance.

Genetic Variation in Triticum turgidum L. ssp. turgidum Landraces from China Assessed by EST-SSR Markers

It was helpful for the wheat improvement to evaluate the genetic resources of Triticum turgidum L. ssp. turgidum landraces. In this study, 68 turgidum landraces accessions, belonging to four geographic populations in China, were investigated by using EST-SSR markers. A total of 63 alleles were detected on 22 EST-SSR loci, and the number of alleles on each locus ranged from 1 to 5, with an average of 2.9. The results of the analysis of molecular variance （AMOVA） indicated that 92.5% of the total variations was attributed to the genetic variations within population, whereas only 7.5% variations among populations. Although the four populations had similar genetic diversity parameters, Sichuan population was yet distinguished from other populations when comparing the population samples in pairs. Significant correlations were detected by the statistic analysis among six genetic diversity parameters among each other. The selection difference between heterozygosty and homozygosty was also observed among different EST-SSR locus. The genetic similarity （GS） ranged from 0.18 to 0.98, with the mean of 0.72, and all accessions could be clustered into 7 groups. The dendrogram suggested that the genetic relationships among turgidum accessions evaluated by EST-SSR markers were unrelated to their geographic distributions. These results implied that turgidum landraces from China had the unique characters of genetic diversity.

Genetic variation and division of Pinus sylvestris provenances by ISSR markers

Inter Simple Sequence Repeat （ISSR） was used to detect genetic variation among nine provenances, including 135 individuals. A total of 108 loci were amplified using 10 random primers. The differentiation of the percentage of polymorphic bands （PPB） among different provenances was evident, ranging from 27% to 54%. of which Honghuaerji provenance had the highest PPB and Kalunshan provenance had the lowest PPB. Shannon＇s Information index （1） at species level was 0.1581 and Nei＇s gene diversity （h） was 0.2393. Coefficient of gene differentiation （Gsr） calculated by Popgene was 0.3965, these results indicated that majority of genetic variation （60.35%） was found within provenances. According to dendrogram among pinus sylvestriv provenances, nine provenances were divided into two provenance areas. namely Daxing＇an and Xiaoxing＇an Mountains provenance area and Hulunbeier provenance area.