A review of the pangenome: how it affects our understanding of genomic variation, selection and breeding in domestic animals?

As large-scale genomic studies have progressed, it has been revealed that a single reference genome pattern cannot represent genetic diversity at the species level. While domestic animals tend to have complex routes of origin and migration, suggesting a possible omission of some population-specific sequences in the current reference genome. Conversely, the pangenome is a collection of all DNA sequences of a species that contains sequences shared by all individuals (core genome) and is also able to display sequence information unique to each individual (variable genome). The progress of pangenome research in humans, plants and domestic animals has proved that the missing genetic components and the identification of large structural variants (SVs) can be explored through pangenomic studies. Many individual specific sequences have been shown to be related to biological adaptability, phenotype and important economic traits. The maturity of technologies and methods such as third-generation sequencing, Telomere-to-telomere genomes, graphic genomes, and reference-free assembly will further promote the development of pangenome. In the future, pangenome combined with long-read data and multi-omics will help to resolve large SVs and their relationship with the main economic traits of interest in domesticated animals, providing better insights into animal domestication, evolution and breeding. In this review, we mainly discuss how pangenome analysis reveals genetic variations in domestic animals (sheep, cattle, pigs, chickens) and their impacts on phenotypes and how this can contribute to the understanding of species diversity. Additionally, we also go through potential issues and the future perspectives of pangenome research in livestock and poultry.

Analysis of Family Structure and Paternity Test of Tan Sheep in Yanchi Area, China.

Tan sheep is a special breed of locally protected sheep in China, one of the best quality meat sheep in the world. Due to the unclear pedigree of the rams on the Ningxia Tan sheep breeding farm, we investigated 74 rams in the field and explored a new method for family division. Genomic DNA was extracted from the blood of breeding rams. Using Plink software, GCTA tools and R language, we analyzed the genetic structure, kinship, and inbreeding coefficient of the breeding sheep, which revealed the genetic relationship between the individuals. The results showed that there was no obvious clustering phenomenon in the PCA, and the genetic background of the samples was similar. The G matrix and IBS distance matrix indicated that most individuals were far away from each other. Paternity testing identified 24 pairs of unknown parent-child pairs, and all the Tan sheep could be divided into 12 families, which provided a reference for sheep breeding. The average inbreeding coefficient based on the ROH of this population was 0.049, so there was a low degree of inbreeding and the rams in the field were able to maintain high genetic diversity. Overall, we explored a more accurate method through paternity and kinship analysis; it provides a scientific basis for pedigree construction, which has an important application value for Tan sheep breeding.

A deletion variant within the FGF5 gene in goats is associated with gene expression levels and cashmere growth.

The FGF5 gene has been associated with the regulation of fibre length in mammals, including cashmere goats. A deletion variant at ~14 kb downstream of the FGF5 gene showed significant divergence between cashmere and non-cashmere goats in previous studies. In this study, we designed specific primers to genotype the deletion variant. The results of gel electrophoresis and Sanger sequencing revealed that a 507-bp deletion mutation is located at 95 454 685-95 455 191 of chromosome 6 in goats. Genotyping data from a large panel of 288 goats showed that the deletion at the FGF5 gene locus appeared to be associated with cashmere length. The deletion variant was close to fixation (frequency 0.97) in cashmere goats. Furthermore, electrophoretic mobility shift assays for evaluating DNA-protein interaction and mRNA expression levels of FGF5 suggested that the deletion variant may serve as a cis-acting element by specifically binding transcription factors to mediate quantitative changes in FGF5 mRNA expression. Our study illustrates how a structural mutation of the FGF5 gene has contributed to the cashmere growth phenotype in domestic goats. The deletion mutation within the FGF5 gene could potentially serve as a molecular marker of cashmere growth in cashmere goat breeding.

A single-nucleotide mutation within the TBX3 enhancer increased body size in Chinese horses.

Chinese ponies are endemic to the mountainous areas of southwestern China and were first reported in the archaeological record at the Royal Tomb of Zhongshan King, Mancheng, dated to approximately ∼2,100 YBP.1 Previous work has started uncovering the genetic basis of size variation in western ponies and horses, revealing a limited number of loci, including HMGA2,2LCORL/NCAPG,3ZFAT, and LASP1.4,5 Whether the same genetic pathways also drive the small body size of Chinese ponies, which show striking anatomical differences to Shetland ponies,6 remains unclear.2,7 To test this, we combined whole-genome sequences of 187 horses across China. Statistical analyses revealed top association between genetic variation at the T-box transcription factor 3 (TBX3) and the body size. Fine-scale analysis across an extended population of 189 ponies and 574 horses narrowed down the association to one A/G SNP at an enhancer region upstream of the TBX3 (ECA8:20,644,555, p = 2.34e-39). Luciferase assays confirmed the single-nucleotide G mutation upregulating TBX3 expression, and enhancer-knockout mice exhibited shorter limbs than wild-type littermates (p < 0.01). Re-analysis of ancient DNA data showed that the G allele, which is most frequent in modern horses, first occurred some ∼2,300 years ago and rose in frequency since. This supports selection for larger size in Asia from approximately the beginning of the Chinese Empire. Overall, this study characterized the causal regulatory mutation underlying small body size in Chinese ponies and revealed size as one of the main selection targets of past Chinese breeders.

Comprehensive analysis of lncRNAs involved in skeletal muscle development in ZBED6-knockout Bama pigs.

BACKGROUND: The mutation of insulin-like growth factor 2 (IGF2 mutation) that a single-nucleotide substitution (G→A) in the third intron of IGF2 abrogates the interaction with zinc finger BED-type containing 6 (ZBED6) and leads to increased muscle mass in pigs. IGF2 mutation knock-in (IGF2 KI) and ZBED6 knockout (ZBED6 KO) lead to changes in IGF2 expression and increase muscle mass in mice and pigs. Long noncoding RNAs (lncRNAs) may participate in numerous biological processes, including skeletal muscle development. However, the role of the ZBED6-lncRNA axis in skeletal muscle development is poorly characterized. RESULTS: In this study, we assembled transcriptomes using RNA-seq data published in previous studies by our group and identified 11,408 known lncRNAs and 2269 potential lncRNAs in seven tissues, heart, longissimus dorsi, gastrocnemius muscle, liver, spleen, lung and kidney, of ZBED6 KO (lean mass model) and WT Bama pigs. ZBED6 affected the expression of 1570 lncRNAs (differentially expressed lncRNAs [DE-lncRNAs]; log2-fold change ≥ 1, nominal p-value ≤ 0.05) in the seven examined tissues. The expressed lncRNAs (FPKM > 0.1) exhibited tissue-specific patterns in WT pigs. Specifically, 3410 lncRNAs were expressed exclusively in only one tissue. Potential functions of lncRNAs were indirectly predicted by searching their target cis- and trans-regulated protein-coding genes. LncRNAs with tissue-specific expression influence numerous genes related to tissue functions. Weighted gene coexpression network analysis (WGCNA) of 1570 DE-lncRNAs between WT and ZBED6 KO pigs was used to define the following six lncRNA modules specific to different tissues: skeletal muscle, heart, lung, spleen, kidney and liver modules. Furthermore, by conjoint analysis of longissimus dorsi data (tissue-specific expression, muscle module and DE-lncRNAs) and ChIP-PCR revealed NONSUSG002145.1 (adjusted p-values = 0.044), which is coexpressed with the IGF2 gene and binding with ZBED6, may play important roles in ZBED6 KO pig skeletal muscle development. CONCLUSIONS: These findings indicate that the identified lncRNAs may play essential roles in tissue function and regulate the mechanism of ZBED6 action in skeletal muscle development in pigs. To our knowledge, this is the first study describing lncRNAs in ZBED6 KO pigs. These results may open new research directions leading to a better understanding of the global functions of ZBED6 and of lncRNA functions in skeletal muscle development in pigs.

Characterization of the complete chloroplast genome of a hybrid species Cymbidium tracyanum var 'huanghua' × Cymbidium faberi cv 'huanghui'.

Cymbidium tracyanumvar 'huanghua' × Cymbidium fabericv 'huanghui' is a hybrid species with important ornamental value. In the research, Illumina high-throughput sequencing technologies was used to sequence the chloroplastic genome of Cymbidium tracyanumvar 'huanghua' × C. fabericv 'huanghui'. The genome features of Cymbidium tracyanumvar 'huanghua' × C. fabericv 'huanghui' and the phylogenetic relationships were reported and established. The total length of the complete chloroplast genome is 154,741 bp, consisting of a pair of inverse duplication regions 26,968 bp, a large single-copy region 84,410 bp and a small single-copy region 16,395 bp. The complete genome contains 73 protein-coding genes (PCGs), The entire genome contains 73 genes that encode proteins, 30 tRNA genes and 4 rRNA genes. The phylogenetic tree revealed that Cymbidium tracyanumvar 'huanghua' × C. fabericv 'huanghui' is more closely related to Cymbidium erythraeum.

Conservation Assessment of the State Goat Farms by Using SNP Genotyping Data.

Conservation of genetic resources is of great concern globally to maintain genetic diversity for sustainable food security. Comprehensive identification of the breed composition, estimation of inbreeding and effective population size are essential for the effective management of farm animal genetic resources and to prevent the animals from genetic erosion. The Zhongwei male (ZWM), Arbas Cashmere male (ACM) and Jining Grey male (JGM) goats are conserved in three different state goat farms in China but their family information, level of inbreeding and effective population size are unknown. We investigated the genomic relationship, inbreeding coefficient and effective population size in these three breeds from three state goat farms using the Illumina goat SNP50 BeadChip. Genomic relationships and phylogenetic analysis revealed that the breeds are clearly separated and formed separate clusters based on their genetic relationship. We obtained a high proportion of informative SNPs, ranging from 91.8% in the Arbas Cashmere male to 96.2% in the Jining Grey male goat breeds with an average mean of 96.8%. Inbreeding, as measured by FROH, ranged from 1.79% in ZWM to 8.62% in ACM goat populations. High FROH values, elevated genomic coverage of very long ROH (>30 Mb) and severe decline in effective population size were recorded in ACM goat farm. The existence of a high correlation between FHOM and FROH indicates that FROH can be used as an alternative to inbreeding estimates in the absence of pedigree records. The Ne estimates 13 generations ago were 166, 69 and 79 for ZWM, ACM and JGM goat farm, respectively indicating that these goat breeds were strongly affected by selection pressure or genetic drift. This study provides insight into the genomic relationship, levels of inbreeding and effective population size in the studied goat populations conserved in the state goat farms which will be valuable in prioritizing populations for conservation and for developing suitable management practices for further genetic improvement of these Chinese male goats.

Characterization of the complete chloroplast genome of a Chinese endangered species Cymbidium mannii.

Cymbidium mannii is an endangered species belonging to the first ranking in protection category in China with important ornamental value and breeding value. This study used Illumina high-throughput sequencing technologies to sequence and analyze the complete chloroplast genome of C. mannii. The genome features of C. mannii and the phylogenetic relationships among Orchidaceae species were reported and established. The complete chloroplast genome is 152,544 bp in length, consisting of a pair of inverse duplication regions 25,357 bp, a large single-copy region 86,014 bp and a small single-copy region 15,816 bp. The entire genome contains 74 mRNA genes, 30 tRNA genes and 4 rRNA genes. The phylogenetic tree of 23 Orchidaceae species revealed C. mannii is more closely related to Cymbidium aloifolium.

Characterization of the complete chloroplast genome of the endangered Chinese species Cymbidium lowianum (Rchb.f.) Rchb.f.

Cymbidium lowianum (Rchb.f.) Rchb.f. is a Class I endangered species in China with important ornamental, economic, and breeding value, especially wild C. lowianum. This study used Illumina high-throughput sequencing technologies to sequence and analyze the complete chloroplast genome of C. lowianum. The genome features of C. lowianum and the phylogenetic relationships among Orchidaceae species were reported and established. The complete chloroplast genome is 155,447 bp long, consisting of a pair of inverse duplication regions that are 26,710 bp long, a large single-copy region of 84,184 bp, and a small single-copy region of 17,843 bp. The entire genome contains 74 mRNA genes, 30 tRNA genes, and 4 rRNA genes. The phylogenetic tree of 24 Orchidaceae species revealed Cymbidium lowianum is more closely related to Cymbidium erythraeum.

Whole Genome Resequencing Reveals Selection Signatures Associated With Important Traits in Ethiopian Indigenous Goat Populations.

Ethiopia is considered as the main gateway for the introduction of livestock species, including goat, to the African continent. Ethiopian goats are characterized by their unique adaptive ability, and different physical characteristics in terms of morphology, body size, coat colors, and other important traits. The comparative population genomic analysis provides useful genomic information associated with important traits. Whole-genome resequencing of 44 Ethiopian indigenous goats produced 16 million single-nucleotide polymorphisms (SNPs) as well as 123,577 insertions and deletions. Specifically, 11,137,576, 10,760,581, 10,833,847, 12,229,657 and 10,749,996 putative SNPs were detected in Abergelle, Afar, Begait, Central Highland and Meafure goat populations, respectively. In this study, we used population differentiation (F ST) and pooled heterozygosity (HP ) Cbased approaches. From the F ST analysis, we identified 480 outlier windows. The HP approach detected 108 and 205 outlier windows for Abergelle, and Begait, respectively. About 11 and 5 genes under selective signals were common for both approaches that were associated with important traits. After genome annotation, we found 41 Gene ontology (GO) terms (12 in biological processes, 8 in cellular components and 11 in the molecular function) and 10 Kyoto Encyclopedia of Genes and Genomes pathways. Several of the candidate genes are involved in the reproduction, body weight, fatty acids, and disease related traits. Our investigation contributes to deliver valuable genetic information and paves the way to design conservation strategy, breed management, genetic improvement, and utilization programs. The genomic resources generated in the study will offer an opportunity for further investigations.

Genome-Wide Runs of Homozygosity, Effective Population Size, and Detection of Positive Selection Signatures in Six Chinese Goat Breeds.

: Detection of selection footprints provides insight into the evolution process and the underlying mechanisms controlling the phenotypic diversity of traits that have been exposed to selection. Selection focused on certain characters, mapping certain genomic regions often shows a loss of genetic diversity with an increased level of homozygosity. Therefore, the runs of homozygosity (ROHs), homozygosity by descent (HBD), and effective population size (Ne) are effective tools for exploring the genetic diversity, understanding the demographic history, foretelling the signature of directional selection, and improving the breeding strategies to use and conserve genetic resources. We characterized the ROH, HBD, Ne, and signature of selection of six Chinese goat populations using single nucleotide polymorphism (SNP) 50K Illumina beadchips. Our results show an inverse relationship between the length and frequency of ROH. A long ROH length, higher level of inbreeding, long HBD segment, and smaller Ne in Guangfeng (GF) goats suggested intensive selection pressure and recent inbreeding in this breed. We identified six reproduction-related genes within the genomic regions with a high ROH frequency, of which two genes overlapped with a putative selection signature. The estimated pair-wise genetic differentiation (FST) among the populations is 9.60% and the inter- and intra-population molecular variations are 9.68% and 89.6%, respectively, indicating low to moderate genetic differentiation. Our selection signatures analysis revealed 54 loci harboring 86 putative candidate genes, with a strong signature of selection. Further analysis showed that several candidate genes, including MARF1, SYCP2,TMEM200C,SF1,ADCY1, and BMP5, are involved in goat fecundity. We identified 11 candidate genes by using cross-population extended haplotype homozygosity (XP-EHH) estimates, of which MARF1 and SF1 are under strong positive selection, as they are differentiated in high and low reproduction groups according to the three approaches used. Gene ontology enrichment analysis revealed that different biological pathways could be involved in the variation of fecundity in female goats. This study provides a new insight into the ROHs patterns for maintenance of within breed diversity and suggests a role of positive selection for genetic variation influencing fecundity in Chinese goat.

EPAS1 Gain-of-Function Mutation Contributes to High-Altitude Adaptation in Tibetan Horses.

High altitude represents some of the most extreme environments worldwide. The genetic changes underlying adaptation to such environments have been recently identified in multiple animals but remain unknown in horses. Here, we sequence the complete genome of 138 domestic horses encompassing a whole altitudinal range across China to uncover the genetic basis for adaptation to high-altitude hypoxia. Our genome data set includes 65 lowland animals across ten Chinese native breeds, 61 horses living at least 3,300 m above sea level across seven locations along Qinghai-Tibetan Plateau, as well as 7 Thoroughbred and 5 Przewalski's horses added for comparison. We find that Tibetan horses do not descend from Przewalski's horses but were most likely introduced from a distinct horse lineage, following the emergence of pastoral nomadism in Northwestern China ∼3,700 years ago. We identify that the endothelial PAS domain protein 1 gene (EPAS1, also HIF2A) shows the strongest signature for positive selection in the Tibetan horse genome. Two missense mutations at this locus appear strongly associated with blood physiological parameters facilitating blood circulation as well as oxygen transportation and consumption in hypoxic conditions. Functional validation through protein mutagenesis shows that these mutations increase EPAS1 stability and its hetero dimerization affinity to ARNT (HIF1B). Our study demonstrates that missense mutations in the EPAS1 gene provided key evolutionary molecular adaptation to Tibetan horses living in high-altitude hypoxic environments. It reveals possible targets for genomic selection programs aimed at increasing hypoxia tolerance in livestock and provides a textbook example of evolutionary convergence across independent mammal lineages.

Genome-wide discovery of lincRNAs with spatiotemporal expression patterns in the skin of goat during the cashmere growth cycle.

BACKGROUND: Long intergenic noncoding RNAs (lincRNAs) have been recognized in recent years as key regulators of biological processes. However, lincRNAs in goat remain poorly characterized both across various tissues and during different developmental stages in goat (Capra hircus). RESULTS: We performed the genome-wide discovery of the lincRNAs in goat by combining the RNA-seq dataset that were generated from 28 cashmere goat skin samples and the 12 datasets of goat tissues downloaded from the NCBI database. We identified a total of 5546 potential lincRNA transcripts that overlapped 3641 lincRNA genes. These lincRNAs exhibited a tissue-specific pattern. Specifically, there are 584 lincRNAs expressed exclusively in only one tissue, and 91 were highly expressed in hair follicle (HF). In addition, 2350 protein-coding genes and 492 lincRNAs were differentially expressed in the skin of goat. The majority exhibited the remarkable differential expression during the transition of the goat skin from the May-June to August-October time point, which covered the different seasons. Fundamental biological processes, such as skin development, were significantly enriched in these genes. Furthermore, we identified several lincRNAs highly expressed in the HF, which exhibited not only the co-expression pattern with the key factors to the HF development but also the activated expression in the August to October time point. Intriguingly, one of spatiotemporal lincRNAs, linc-chig1598 could be a potential regulator of distal-less homeobox 3 expression during the secondary hair follicle growth. CONCLUSIONS: This study will facilitate future studies aimed at unravelling the function of lincRNAs in hair follicle development.

[Effect of mid- and long-term schistosomiasis control plan and discussion of consolidation strategy in marshland endemic regions].

OBJECTIVE: To evaluate the effectiveness of mid- and long-term schistosomiasis control plan and explore the consolidation strategy in marshland endemic regions, so as to provide an effective approach for interrupting and eliminating schistosomiasis in the regions. METHODS: A prospective field study was designed. Dantu District of Zhenjiang City, a marshland schistosomiasis endemic region, was selected, and the "key village, key environment, and key water regions" comprehensive control strategy was implemented according to the endemic level of schistosomiasis. The morbidity due to schistosomiasis in humans and domestic animals, and Oncomelania hupensis snails were surveyed, and the data of the implementation of control measures were collected. The schistosomiasis morbidity and snail status were compared before and after the implementation of the mid- and long-term plan for schistosomiasis prevention and control, and the changing trends of human, domestic animal and snail infections were plotted. RESULTS: During the implementation of the plan from 2005 to 2014, 16.84 km concrete and bank protection and 9 snail sinks were built, 10 culverts re-built, 3.85 hm2 fences were constructed, 29.5 thousand domestic animals were examined and treated, 170 cattle were eliminated, 4930 hm2 fishing farms were built for snail control, 1 560.00 hM2 land were improved, and 376.00 hm2 forests were built for snail control. In addition, 19,364.80 hm2 snail areas were surveyed, 4694.6 hm2 area received molluscicide, 207.9 thousand of people (person-times) received the examination and treatment, 69.1 thousand of harmless toilets were built, 282.2 thousand health education materials and protection materials were allocated, 958 warning signs were established, and 5435 slogans were pasted or hung. After the implementation of the mid- and long-term plan, the percentages of human, bovine and snail infections appeared decline tendencies year by year, and reduced from 0.08%, 1.28% and 0.13% in 2005 to 0 in 2014, respectively, while the areas with snails and infected snails reduced from 284.34 hm2 and 55.10 hm2 in 2005 to 73.60 hm2 and 0 hm2 in 2014, with reduction rates of 74.12% and 100%, respectively. The infection rate of sheep appeared a fluctuation between 2005 and 2014, with the rate of 1.13% in 2005, 0 in 2007 and 2008, rising in 2009 and then between 0.25% and 0.95% from 2009 to 2012, and reducing to 0 in 2013 and 2014. During the 10-year period, the number of cattle reduced year by year from 2005 to 2010, and slightly increased after 2011, showing an overall stable level, while the number of sheep increased year by year after 2006, peaked in 2010, and appeared a decline tendency since 2011, which was almost consistent with the fluctuation of schistosome infection rate in sheep. CONCLUSIONS: The sustainable comprehensive control strategy with the "key village, key environments, and key water regions" is an effective approach for schistosomiasis control in marshland endemic regions. However, the endemic situation of schistosomiasis is extremely easy to repeat. The prevention and control of the impact of sheep and wild animals on schistosomiasis transmission should be strengthened in order to consolidate the schistosomiasis control achievements gained.

[Effect of water storage and aquaculture on Oncomelania hupensis control in tidal flats wetlands of islet-beach type area of Dantu section of lower reaches of Yangtze River].

OBJECTIVE: To evaluate the effect and the benefits of the projects of water storage and aquaculture on Oncomelania hupensis snail control in the tidal flats wetlands of islet-beach type area of lower reaches of the Yangtze River. METHODS: The projects of water storage and aquaculture on 0. hupensis snail control were implemented in the tidal flats wetlands of islet-beach type of lower reaches of the Yangtze River. The breed situation of the snails was investigated by the conventional method before and after the project implementation and the effect of control and elimination of the snails by the projects were evaluated. At the same time, the cost-benefit analysis of two projects among them was performed by the static benefit-cost ratio method. RESULTS: All of 0. hupensis snails were eliminated in the first year after the implementation of seven water storage and aquaculture projects. The costs of detection and control of snails saved by each project was 69.20 thousand yuan a year on average. The annual net benefits of the "Nanhao Group 10 beach" project and "Wutao Group 6-14 beach" project were 2 039.40 thousand yuan and 955.00 thousand yuan respectively, and the annual net benefit-cost ratios were 1.09: 1 and 1.07: 1 respectively. CONCLUSION: The O. hupensis snails could be rapidly eliminated by the water storage and aquaculture, and the economic benefit is obvious, but the wetland ecological protection and flood control safety should be considered in the tidal flats wetlands of islet-beach type area of lower reaches of the Yangtze River.

[Surveillance of schistosomiasis in national surveillance sites of Zhenjiang City, 2005-2010].

OBJECTIVE: To master the changes of schistosomiasis epidemic situation in national surveillance sites of Zhenjiang City, Jiangsu Province. METHODS: According to the scheme of the national schistosomiasis surveillance, the Shicheng Village of Yangzhong County and Sanzhou Village of Dantu District were selected as the national schistosomiasis surveillance sites, and from 2005 to 2010, the schistosomiasis morbidity and Oncomelania hupensis status were surveyed and the results were analyzed statistically. RESULTS: In 2010, in the Shicheng Village, the reduction rates of mean living snail density, infected snail density, area with infected snails, and positive blood tests in residents were 98.4%, 0, 0, 71.8% respectively, and in the Sanzhou Village, the reduction rates were 70.4%, 100%, 100% and 81.5%, respectively compared with those in 2005. No acute infections were found in the 2 villages during the period of 6 consecutive years. CONCLUSION: In the national surveillance sites of Zhenjiang City, the schistosomiasis morbidity has been effectively controlled. However, the areas with snails change little. Therefore, the comprehensive management of snail environment in the marshland should be strengthened in the future.

[Effect of mass chemotherapy in late stage of soil-borne nematodiasis control].

OBJECTIVE: To evaluate the effects and influencing factors of mass chemotherapy in the late stage of soil-borne nematodiasis control so as to provide the evidence for the development of control programs. METHODS: Six villages were divided into three groups: the target chemotherapy, the selective chemotherapy and the control. By observation in three consecutive years, the indexes, mass infection rates, infection degrees and re-infections of soil-borne nematodes, were compared among the 3 groups. The influencing factors were also analyzed. RESULTS: The population infection rates of soil- borne nematodes decreased by 85.94%, 43.10% and 20.87%, respectively, in the three groups after chemotherapy compared with those before the intervention. A higher hookworm infection rate appeared and the chemotherapy effect was impacted in the target chemotherapy group, as some key population applied fresh human waste in vegetable plots. The re-infection rate was 16.65 times of the new infection rate. CONCLUSIONS: Chemotherapy is still useful in the late stage of soil-borne nematode control. It is more important to enhance management of using manure and health education on focus population.

[Surveillance of schistosomiasis in a national, surveillance site of Dantu District, Zhenjiang City, 2005-2009].

The surveillance of schistosomiasis in Sanzhou Village, a national schistosomiasis surveillance site, in Gaoqiao Town of Dantu District, Zhenjiang City from 2005 to 2009 showed that the schistosomiasis morbidity remained in a low level in the surveillance site; however, the Oncomelania snails and infected snail areas remained high. It is suggested that, in addition to snail control, comprehensive control measures should be strengthened, and the causes of infected snails in marshland should be investigated, so as to clarify the roles of various hosts in transmission of schistosomiasis.