Identification,Isolation and Genomic Characterization of Porcine Astrovirus in Shandong Province,China in 2021-2023

[Objective]The paper was to identify,isolate,and characterize porcine astrovirus in Shandong Province between 2021 and 2023.[Method]A total of 1025 samples of porcine diarrhea samples were collected from various regions of Shandong Province between January 2021 and October 2023.The samples were tested by RT-PCR,followed by sequencing and phylogenetic analyses of the polymerase.[Result]The total positive rate of PAstV was 34.6%(355/1025).The respective proportions of individuals infected with PAstV-1,PAstV-2,PAstV-4 and PAstV-5 were 25.4%(90/355),28.2%(100/355),35.2%(125/355)and 22.5%(80/355),respectively.Additionally,mixed infection was observed.Meanwhile,849 samples of healthy pigs were tested by RT-PCR,and the results demonstrated that the total positive rate of PAstV was 8.13%(69/849).Of these,the proportion of PAstV-1,PAstV-2 and PAstV-4 infection was 27.5%(19/69),37.7%(26/69)and 40.6%(28/69),and a mixed infection also existed.Further sequencing and characterization of some the selected isolates revealed low sequence identities(56.2%)with known PAstV strains,indicating the presence of novel types or genotypes of PAstVs.Furthermore,the isolation conditions of porcine astrovirus were optimized,resulting in the purification of a pure PAstV-4 strain(designated PAstV-4-GRF1).The virus was found to exhibit typical astroviral morphology,with nucleotide identity ranging from 89.9 to 95.4%with previously published PAstV-4 strains.Then,macrovirus transcriptome sequencing showed that 88.30%of the CRF1 samples were mammalian astroviruses.By species classification,PAstV 4 and PAstV 2 accounted for 21.79%and 0.32%,respectively.Phylogenetic tree analysis showed that the c15050 fragment was identical to the GRF-1 sequencing fragment of the isolated strain,and exhibited the highest homology with the Hunan PAstV-4 sequence MK460231 in China.[Conclusion]As the inaugural isolated PAstV-4 strain,it furnishes pivotal materialfor the investigation ofthe biological and pathogenic properties of this virus as well as for the prospectivedevelopment of relevant biological and diagnostic reagents.

Analysis of genotype differences of rice response to low Zn^(2+) activity and some morphological characteristics

Zinc deficiency is one of the most widespreadmicro-nutritional disorder for rice. To solve the problem, screening Zn-efficient cultivars isan available method and understanding geno-

The complete genomic sequence analysis of genotype 4 human astrovirus HASTVgz01 strain in Guangzhou

To analyze the genomic molecular structure and genotype of human astrovirus isolated from infant in Guangzhou of China, the primers were designed based on the genomic sequence of astrovirus from the C, enBank and the target sequence were amplified by RT-PCR. Then the PCR-products were cloned to T vector and sequenced. The genomic nucleotide sequences were analyzed by the programs CLUSTAL W and DNASTAR. It was found that the full genomic length of HASTVgz01 strain was 6721 bp and the ORFs were 6558 bp. The 5＇ and 3＇UTR were 82 and 81 nucleotides. The genome included 3 open reading frames （ORFs） ： ORFla, ORFlb and ORF2. The 5＇-terminal ORFla started at nueleotide 83 and extended to nucleotide 2845. ORFlb （nt 2785 to nt 4332） overlaped ORFla by 61 nueleotides. The 3＇-terminal ORF2 began at nucleotide 4325 and terminated at nucleotide 6640. ORF2 had 2316 nucleotides. Compared with other astrovirus sequences in GenBank, the homology of the amino acid sequence of ORF2 of HASTVgz01 strain with that of serotype 4 was 93%. Homology with other serotypes ranged from 61% to 70%. The complete nucleotide sequence of astrovirus HASTVgz01 strain isolated from Guangzhou in China was 6721 bp in length, GenBank accession NO. DQ344027. Comparing the ORF2 of astrovirus HASTVgz01 with the known sequences of types 1-8 the highest homology was serotype 4 （93%）. Comparative sequence analysis of the HASTVgz01 ORF2 with the reported human astrovirus sequences revealed that the isolated astrovirus belongs to genotype （serotype） 4.

AMMI analysis of interaction of genotype and environment in chalkiness of indica rice

Chalkiness is an unpleasant trait for rice con-sumer,which is known to be controlled geneti-cally and affected by environment during grainmaturing.We used the model of Additive Main

Genome-wide association studies reveal the genetic basis of amino acid content variation in tea plants

Tea is one of the most popular non-alcoholic beverages in the world,and free amino acids,especially theanine,make a major contribution to the umami taste of tea.However,the genetic basis of the variation in amino acid content in tea plants remains largely unknown.Here,we measured the free amino acid content in fresh leaves of 174 tea accessions over two years using a targeted metabolomics approach and obtained genotype data via RNA sequencing.Genome-wide association studies were conducted to investigate loci affecting the content of free amino acids.A total of 69 quantitative trait loci(–log10(P-value)>5)were identified.Functional annotation revealed that branched-chain amino acid aminotransferase,glutamine synthetase,nitrate transporter,and glutamate decarboxylase might be important for amino acid metabolism.Two significant loci,glutamine synthetase(Glu1,P=3.71×10^(−4);Arg1,P=4.61×10^(−5))and branched-chain amino acid aminotransferase(Val1,P=4.67×10^(−5);I_Leu1,P=3.56×10^(−6)),were identified,respectively.Based on the genotyping result,two alleles of CsGS(CsGS-L and CsGS-H)and CsBCAT(CsBCAT-L and CsBCAT-H)were selected to perform function verification.Overexpression of CsGS-L and CsGS-H enhanced the contents of glutamate and arginine in transgenic plants,and overexpression of CsBCAT-L and CsBCAT-H promoted the accumulation of valine,isoleucine and leucine.Enzyme activity assay uncovered that SNP1054 is important for CsGS catalyzing glutamate into glutamine.Furthermore,CsGS-L and CsGS-H differentially regulated the accumulation of glutamine,and CsBCAT-L and CsBCAT-H differentially regulated the accumulation of branched-chain amino acids.In summary,the findings in our study would provide new insights into the genetic basis of amino acids contents variation in tea plants and facilitate the identification of elite genes to enhance amino acids content.

The Inheritance of Early Heading in the Rice Variety USSR5

USSR5, a japonica rice variety from the former Soviet Union, is an extremely early maturing rice variety. To elucidate the genetic basis for its early heading, genetic analysis was carried out by crossing it with a set of major gene nearly isogenic lines （NIL） and QTL-isogenic lines. The early heading of USSR5 was attributed to the presence of photoperiod-insensitive alleles at E1 and Se-1 gene, the photoperiod-sensitive inhibitor gene i-Se-1, and the dominant earliness gene Ef-1. Analysis of a backcrossed population （BCIF1） derived from the cross USSR5 x N22 indicated that two quantitative trait loci （QTL） for early heading were located on chromosomes 7 and 8, accounting for 27.4% and 11.2% of the phenotypic variance, respectively, with both early alleles originating from USSRS. From an F2 population of the same cross, early heading QTLs were detected on chromosomes 1, 2, 7, 9, and 10, with individual QTL accounting for between 4.1% and 15.4% of the phenotypic variance. Early heading alleles at four of these five QTLs originated from USSRS. A comparison of chromosomal locations suggests that one of these QTLs may be identical with the known gene Hd4 （E1）. The relationship between the other QTLs and known genes for heading date are not clear. USSR5 is a promising source for propagating earliness for the development of improved early heading rice varieties.

Parental Selection in Rice Cultivar Improvement

The evaluation of rice （Oryza safiva L.） cultivars assists breeders in identifying useful trait relationships and in selecting parents as donors of specific traits. This study was conducted to compare long-grain rice cultivars using genotype x trait （GT） biplot analysis and determine potential donors of traits related to grain yield and quality. Seventeen cultivars in the 2005 and 2006 Uniform Regional Rice Nursery in Beaumont, Texas, USA were analyzed for 20 traits using GT biplot analysis. The GT biplots showed the diversity among cultivars with regards to yield-related traits. Cultivars recommended as donor parents were： Trenasse, Spring, Presidio, and Cocodrie for high grain yield and head rice rate Trenasse and Presidio for semi-dwarfness; Banks for tall plant height; Wells for high flag leaf area, panicle weight, and number and mass of filled grains per panicle; Hidalgo for high tiller density; Francis for high number of spikelets per panicle; Spring and Trenasse for short flowering duration; Cheniere for more days to heading and maturity and Spring for less days; and Spring and Hidalgo for high grain weiqht. Breeders can use these cultivars with specific traits to increase qrain yield and quality.

DNA sequence analysis of the triose phosphate isomerase gene from isolates of Giardia lamblia

Objective To confirm the genetic relation between Giardia lamblia (G. lamblia) isolates from different geographic regions of China and other countries.Methods Genomic DNA were extracted from the trophozoites or cysts of Giardia lamblia. The triose phosphate isomerase (tim) gene was amplified using polymerase chain reaction (PCR) technique. PCR products were digested with endonuclease and sequenced. The data of sequencing were analyzed with the DNAstar software and compared with that of the isolates acquired from GenBank.Results Of nine isolates of Giardia lamblia from China (C1, C2, CH2 and CH3), Cambodia (CAM), Australia (A1 and A2) and America (BP and CDC), respectively, 3 (A1, A2 and CAM) fit into Group 1 (WB), 2 (CH2 and CH3)) into Group 2, and 4 (C1, C2, BP and CDC) into Group 3 (GS). The results confirmed the genetic relatedness of G. lamblia isolates from all over the world.Conclusion Genotyping isolates of G. Lamblia provides important information for establishing the phylogenetic relationship or for the epidemiological evaluation of the spreading of this organism.