Identifying the unique characteristics of the Chinese indigenous pig breeds in the Yangtze River Delta region for precise conservation.

BACKGROUND: China is the country with the most abundant swine genetic resources in the world. Through thousands of years of domestication and natural selection, most of pigs in China have developed unique genetic characteristics. Finding the unique genetic characteristics and modules of each breed is an essential part of their precise conservation. RESULTS: In this study, we used the partial least squares method to identify the significant specific SNPs of 19 local Chinese pig breeds and 5 Western pig breeds. A total of 37,514 significant specific SNPs (p < 0.01) were obtained from these breeds, and the Chinese local pig breed with the most significant SNPs was Hongdenglong (HD), followed by Jiaxing black (JX), Huaibei (HB), Bihu (BH), small Meishan (SMS), Shengxian Hua (SH), Jiangquhai (JQ), Mi (MI), Chunan (CA), Chalu (CL), Jinhualiangtouwu (JHL), Fengjing (FJ), middle Meishan (MMS), Shanzhu (SZ), Pudong white (PD), Dongchuan (DC), Erhualian (EH), Shawutou (SW) and Lanxi Hua (LX) pig. Furthermore, we identified the breeds with the most significant genes, GO terms, pathways, and networks using KOBAS and IPA and then ranked them separately. The results showed that the breeds with the highest number of interaction networks were Hongdenglong (12) and Huaibei (12) pigs. In contrast, the breeds with the lowest interaction networks were Shawutou (4) and Lanxi Hua pigs (3), indicating that Hongdenglong and Huaibei pigs might have the most significant genetic modules in their genome, whereas Shawutou and Lanxi Hua pigs may have the least unique characteristics. To some degree, the identified specific pathways and networks are related to the number of genes and SNPs linked to the specific breeds, but they do not appear to be the same. Most importantly, more significant modules were found to be related to the development and function of the digestive system, regulation of diseases, and metabolism of amino acids in the local Chinese pig breeds, whereas more significant modules were found to be related to the growth rate in the Western pig breeds. CONCLUSION: Our results show that each breed has some relatively unique structural modules and functional characteristics. These modules allow us to better understand the genetic differences among local Chinese and Western pig breeds and therefore implement precise conservation methods. This study could provide a basis for formulating more effective strategies for managing and protecting these genetic resources in the future.

Selection signature reveals genes associated with susceptibility loci affecting respiratory disease due to pleiotropic and hitchhiking effect in Chinese indigenous pigs.

BACKGROUND: Porcine respiratory disease is one of the most important health problems which causes significant economic losses. OBJECTIVE: To understand the genetic basis for susceptibility to swine enzootic pneumonia (EP) in pigs, we detected 102,809 SNPs in a total of 249 individuals based on genome-wide sequencing data. METHODS: Genome comparison of three susceptibility to swine EP pig breeds (Jinhua, Erhualian and Meishan) with two western lines that are considered more resistant (Duroc and Landrace) using XP-EHH and FST statistical approaches identified 691 positively selected genes. Based on QTLs, GO terms and literature search, we selected 14 candidate genes that have convincible biological functions associated with swine EP or human asthma. RESULTS: Most of these genes were tested by several methods including transcription analysis and candidated genes association study. Among these genes: CYP1A1 and CTNNB1 are involved in fertility; TGFBR3 plays a role in meat quality traits; WNT2, CTNNB1 and TCF7 take part in adipogenesis and fat deposition simultaneously; PLAUR (completely linked to AXL, r2=1) plays an essential role in the successful ovulation of matured oocytes in pigs; CLPSL2 (strongly linked to SPDEF, r2=0.848) is involved in male fertility. CONCLUSION: These adverse genes susceptible to swine EP may be selected while selecting for economic traits (especially reproduction traits) due to pleiotropic and hitchhiking effect of linked genes. Our study provided a completely new point of view to understand the genetic basis for susceptibility or resistance to swine EP in pigs thereby, provide insight for designing sustainable breed selection programs. Finally, the candidate genes are crucial due to their potential roles in respiratory diseases in a large number of species, including human.

[Two novel TSC2 frameshift mutations in tuberous sclerosis complex].

High-throughput sequencing was performed for the peripheral blood DNA from two probands in the family with tuberous sclerosis complex (TSC) to determine the sequences of TSC-related genes TSC1 and TSC2 and their splicing regions and identify mutation sites. Amplification primers were designed for the mutation sites and polymerase chain reaction and Sanger sequencing were used to verify the sequences of peripheral blood DNA from the probands and their parents. The two probands had c.3981-3982 insA (p.Asp1327AspfsX87) and c.4013-4014 delCA (p.Ser1338Cysfs) heterozygous mutations, respectively, in the TSC2 gene. The parents of proband 1 had no abnormalities at these two loci; the mother of proband 2 had c.4013-4014 delCA heterozygous mutation in the TSC2 gene, while the father and the grandparents of proband 2 had no abnormalities. c.3981-3982 insA mutation may cause early coding termination of amino acid sequence at the 1413th site, and c.4013-4014 delCA mutation may cause early coding termination of amino acid sequence at the 1412th site. These two mutations are the pathogenic mutations for families 1 and 2, respectively, and both of them are novel frameshift mutations, but their association with the disease needs to be further verified by mutant protein function cell model and animal model.

[Gene mutation analysis and prenatal diagnosis of four pedigrees with methymalonic aciduria].

OBJECTIVE: To study gene mutations in four pedigrees with methymalonic aciduria, as well as the feasibility of prenatal diagnosis of methymalonic aciduria. METHODS: High-throughput sequencing was performed for related genes in the peripheral blood of children or parents who were diagnosed with methymalonic aciduria to identify the loci with mutations. Then amplification primers were designed for each locus, and PCR and direct sequencing were performed to validate the sequencing in the first generation in the four pedigrees. Whether the mutations were pathogenic were determined with reference to literature review and medical history. In the pedigrees 1, 3, and 4, ultrasound-guided chorionic villi biopsy was performed at weeks 11-13 of pregnancy to perform early prenatal diagnosis. RESULTS: In pedigree 1, c.656A>T and c.729-730insTT heterozygous mutations in the MUT gene were detected in the proband's father and mother, respectively. Early prenatal diagnosis showed c.656A>T and c.729-730insTT double heterozygous mutations in the fetus. The couple decided to terminate pregnancy. In pedigree 2, c.1106G>A and c.755-756insA double heterozygous mutations in the MUT gene were detected in the proband. c.1106G>A came from the father and c.755-756insA came from the mother. In pedigree 3, c.217C>T and c.609G>A double heterozygous mutations in the MMACHC gene were detected in the proband. c.217C>T came from the father and c.609G>A came from the mother. Prenatal diagnosis showed c.609G>A heterozygous mutation in the fetus. The baby was successfully delivered, and the result of umbilical cord blood testing was consistent with the prenatal diagnosis. In pedigree 4, c.609G>A and c.567dupT double heterozygous mutations in the MMACHC gene were detected in the proband. c.609G>A came from the father and c.567dupT came from the mother. Prenatal diagnosis showed c.567dupT heterozygous mutation in the fetus. The baby was successfully delivered, and the result of umbilical cord blood testing was consistent with the prenatal diagnosis. CONCLUSIONS: Identification of gene mutations helps with prenatal diagnosis in pedigrees with methymalonic aciduria.

[Multi-objective Identification Method for Influencing Factors of Soil Heavy Metal Content Change].

Identifying the influencing factors of soil heavy metal content changes is the basis for reducing or preventing soil heavy metal pollution. Taking an agricultural experimental field in Changping District of Beijing as an example, the heavy metal content changes in As, Cr, Cu, Ni, Pb, and Zn from 2012 to 2022 were firstly analyzed. Secondly, the influencing factors of the heavy metal content changes were detected based on the geographical detector at the single-target and multi-target levels, respectively. Finally, comparative experiments with the correlation analysis method and existing studies were set up to evaluate the effectiveness of the identification method of influencing factors developed in this study. The results showed that human activity factors have exacerbated the changes in soil heavy metal content in the study area as follows： ① At the single-target level, the land use type was the main influencing factor on the changes in Cr, Cu, and Zn contents, and the annual deposition flux influenced the changes in As. The results of the interaction detection showed that there was an enhancement effect among the factors, and the interaction of the human activity factors dominated for the factor identification. ② The results of the multi-target level detection covered the results of the single-target level detection, which could identify more influencing factors. The land use type affected the changes in Cu, Zn, Cr, Ni, and As, and the changes in As and Zn were influenced by the annual deposition fluxes. ③ The multi-target identification method coupled with geographical detector and principal component analysis could effectively identify the influencing factors of soil heavy metal content changes, which was much more effective than the single soil heavy metal correlation method. The developed multi-target identification method for influencing factors of heavy metal content changes can provide technical support for the regional pollution monitoring and macro-management of soil heavy metals.

[Spatio-temporal Variation in Net Primary Productivity of Different Vegetation Types and Its Influencing Factors Exploration in Southwest China].

Studying the spatiotemporal variation in vegetation net primary productivity (NPP) and exploring its influencing factors are of considerable practical significance for understanding the spatiotemporal variation in vegetation and for guiding ecological restoration and management projects based on local conditions. Based on MODIS NPP data, combined with in situ meteorological data, land use data, and vegetation type data, this study explores the spatiotemporal variation in different types of vegetation NPP in southwest China via the Mann-Kendall significance test and Theil-Sen Median slope estimator. It reveals the influencing factors of spatial differentiation of different types of vegetation NPP and the interaction between influencing factors in combination with stability analysis and Geo Detectors. The results revealed that on the temporal scale, from 2000 to 2021, vegetation NPP, NPPPre (vegetation NPP exclusively under the influence of climate change), and NPPRes (vegetation NPP exclusively under the influence of human activities) in southwest China showed a fluctuating upward trend. Among different vegetation types, NPP, NPPPre, and NPPRes exhibited an upward trend, except for a minor decline in NPPRes of tree vegetation at a rate of -0.183 g·(m2·a)-1. Among them, NPP, NPPPre, and NPPRes of economic vegetation showed the most significant upward rates, 5.96, 3.09, and 2.94 g·(m2·a)-1, respectively. On the spatial scale, the tree vegetation NPP with the most significant downward trend was mainly distributed in Tibet and southern Yunnan, while the economic vegetation NPP with the highest upward trend was primarily distributed in eastern Sichuan Province. The stability of vegetation NPP in southwest China presented a spatial distribution pattern of "low in the south and high in the north," and the average value of the correlation coefficient increased in the ascending order of arbor vegetation (0.101), shrub vegetation (0.105), herb vegetation (0.110), and economic vegetation (0.114). The interaction between surface temperature and relative humidity was the main influencing factor for spatial differentiation of vegetation NPP, while the interaction between sunshine duration and warmth index had the most significant impact on vegetation in southwest China, with an increasing percentage of 30.91%. Different types of vegetation had different requirements for different climatic factors, but their requirements for surface temperature and warmth index were significantly consistent. When the surface temperature was 21.03-28.49℃, and the warmth index was 106.46-167.2, the NPP of different vegetation types peaked. Under natural succession, the impact of climate change on vegetation was inversely proportional to the stability of the vegetation community. The arbor vegetation community with high stability was less affected, while the herb vegetation community with low stability was highly affected by climate. In contrast, the stability of economic vegetation was directly proportional to the impact of climate due to the influence of human activities. This study establishes a theoretical foundation for evaluating the impact of regional climate on the growth of different vegetation types and can be crucial for formulating ecological restoration and management strategies in southwest China that are adapted to the local conditions.

[Quantitative Assessment of the Impact of Climate Change on the Growing Season of Vegetation Gross Primary Productivity in the Middle and Lower Reaches of the Yangtze River].

Quantitatively determining the direct, indirect, and comprehensive effects of climatic factors on the growing season of the vegetation GPP (GPPGS) in the middle and lower reaches of the Yangtze River at the regional and vegetation type scales can provide a scientific basis for the management and restoration of regional vegetation resources under the background of global climate change. Using MODIS GPP data, meteorological data, and vegetation type data, combined with Theil-Sen Median trend analysis and the Mann-Kendall significance test, the spatiotemporal characteristics of the GPPGS in the middle and lower reaches of the Yangtze River were investigated at different temporal and spatial scales. Path analysis was used to further reveal the direct, indirect, and comprehensive effects of climate factors on GPPGS variation in different vegetation types. The results showed that:① from 2000 to 2021, the vegetation GPPGS in the middle and lower reaches of the Yangtze River showed a fluctuating upward trend, with a rising rate (in terms of C, same below) of 2.70 g·(m2·a)-1 (P<0.01). The GPPGS of different vegetation types all showed a significant upward trend (P<0.01), with shrubs having the highest upward rate of 3.31 g·(m2·a)-1 and cultivated vegetation having the lowest upward rate of 2.54 g·(m2·a)-1. ② The proportion of the area with an upward trend in GPPGS in the middle and lower reaches of the Yangtze River was 88.11%. The proportion of the area with an upward trend in GPPGS was greater than 84% for all different vegetation types, with shrubs (49.76%) and cultivated vegetation (44.36%) having significantly higher proportions of the area with an upward trend than that in other vegetation types. ③ The path analysis results showed that precipitation and the maximum temperature had a significant positive direct effect on vegetation GPPGS (P<0.05), whereas solar radiation had a non-significant positive effect (P ≥ 0.05). The indirect effects of maximum temperature, precipitation, and solar radiation on vegetation GPPGS were all non-significantly negative (P ≥ 0.05). Under the combined effects of direct and indirect influences, precipitation and maximum temperature had a non-significant positive effect on vegetation GPPGS (P ≥ 0.05), whereas solar radiation had a non-significant negative effect on vegetation GPPGS (P ≥ 0.05). Among different vegetation types, precipitation was the main climate factor affecting the changes in GPPGS of cultivated vegetation, whereas the maximum temperature was the main climate factor affecting the changes in GPPGS of coniferous forests, broad-leaved forests, shrubs, and grasslands. ④ The changes in vegetation GPPGS in the middle and lower reaches of the Yangtze River were mainly influenced by the direct effects of maximum temperature, precipitation, and solar radiation, with the direct effect of precipitation dominating 56.72% of the changes in GPPGS. The research results can provide a reference for quantifying the carbon sequestration potential of vegetation in the middle and lower reaches of the Yangtze River and formulating ecological restoration governance policies tailored to local conditions under the background of global climate change.

[Spatio-temporal Variation in Vegetation Cover and Its Driving Mechanism Exploration in Southwest China from 2000 to 2020].

Using the MOD13A3 NDVI time series from 2000 to 2020, climate date from 1999 to 2020, and land use type data in 2000 and 2020, the spatio-temporal variation in vegetation cover and the driving mechanisms of climate change and human activities to vegetation variation were analyzed based on Theil-Sen Median analysis, the Mann-Kendall significance test, the multi-collinearity test, residual analysis, and relative analysis. The results showed that the vegetation cover exhibited a fluctuating and increasing trend with a magnitude of 0.0016 a-1 in southwest China from 2000 to 2020. The increasing trend of vegetation cover was mostly significant in the Guangxi Hills and Yunnan-Guizhou Plateau and slightly significant in the Tibet Plateau. The vegetation cover had increased in the context of climate change and human activities, with an increasing rate of 0.0010 a-1 and 0.0006 a-1, respectively. The vegetation improvement was mostly dominated by the combination effects of climate change and human activities. The vegetation improvement was dominated by climate change, and the relative role of climate change reached 61.86%. What is more, the vegetation degradation was dominated by human activities, and the relative role of human activities reached 58.39%. Vegetation cover was positively related to minimum temperature, precipitation, maximum temperature, potential evapotranspiration rate, and relative humidity and negatively related to mean temperature, atmosphere pressure, sunshine duration, warmth index, and humidity index. As a whole, the minimum temperature, sunshine duration, and precipitation were the dominant climate factors affecting the vegetation variation in southwest China. Furthermore, the land use and land cover change were significantly related to vegetation variation in southwest China. The implementation of ecological afforestation projects could be beneficial to regional vegetation improvement, whereas the vegetation degradation was mostly conducted by the built-up land expansion.

[Spatio-temporal Variation in PM2.5 Concentration and Its Relationship with Vegetation Landscape Patterns in Typical Economic Zones in China from 2000 to 2020].

This study explored the temporal and spatial variation in PM2.5 concentration and its relationship with the vegetation landscape pattern in three typical economic zones in China, which is of great significance for regional PM2.5pollution control and atmospheric environmental protection. In this study, the pixel binary model, Getis-Ord Gi* analysis, Theil-Sen Median analysis, Mann-Kendall significance test, Pearson correlation analysis, and multiple correlation analysis were used to explore the spatial cluster and spatio-temporal variation in PM2.5 and its correlation with the vegetation landscape index in the three economic zones of China on the basis of PM2.5 concentration data and MODIS NDVI data set. The results showed that PM2.5 in the Bohai Economic Rim was mainly dominated by the expansion of hot spots and the reduction in cold spots from 2000 to 2020. The proportion of cold spots and hot spots in the Yangtze River Delta showed insignificant changes. Both cold and hot spots in the Pearl River Delta had expanded. PM2.5 showed a downward trend in the three major economic zones from 2000 to 2020, and the magnitudes of increasing rates were higher in the Pearl River Delta, followed by those in the Yangtze River Delta and Bohai Economic Rim. From 2000 to 2020, PM2.5 exhibited a downward trend in the context of all vegetation coverage grades, and PM2.5 had most significantly improved within extremely low vegetation coverage in the three economic zones. On the landscape scale, PM2.5 values were mostly correlated with aggregation index in the Bohai Economic Rim, with the largest patch index in the Yangtze River Delta and Shannon's diversity in the Pearl River Delta, respectively. Under the context of different vegetation coverage levels, PM2.5showed the highest correlation with aggregation index in the Bohai Economic Rim, landscape shape index in the Yangtze River Delta, and percent of landscape in the Pearl River Delta, respectively. PM2.5 showed significant differences with vegetation landscape indices in the three economic zones. The combined effect of multiple vegetation landscape pattern indices on PM2.5 was stronger than that of the single vegetation landscape pattern index. The above results indicated that the spatial cluster of PM2.5 in the three major economic zones had changed, and PM2.5 showed a decreasing trend in the three economic zones during the study period. The relationship between PM2.5 and vegetation landscape indices exhibited obvious spatial heterogeneity in the three economic zones.

[Spatial-temporal Variation in Net Primary Productivity in Terrestrial Vegetation Ecosystems and Its Driving Forces in Southwest China].

Studying the spatial-temporal variation in net primary productivity (NPP) in terrestrial vegetation ecosystems and its driving forces in southwest China is of great importance for regional eco-environmental protection. The spatial and temporal changes in net primary productivity (NPP) in terrestrial vegetation ecosystems and its responding characteristics to climate change and human activities were explored in this study on the basis of the Moderate Resolution Imaging Spectroradiometer (MODIS) NPP from 2000 to 2021, in situ meteorological data from 1999 to 2021, and land use type datasets from 2000 to 2020 using principal component analysis, residual analysis, Theil-Sen Median analysis, and partial correlation analysis. The results showed that on a temporal scale, the vegetation NPP showed a fluctuating upward trend, with a rate of 3.54 g·(m2·a)-1in southwest China from 2000 to 2021. Meanwhile, under the influence of climate change and human activities, NPP of farmland, grassland, and forests all showed an upward trend, but the magnitude of the increasing trends of farmland NPP was the most significant. On the spatial scale, the areas with an upward trend in vegetation NPP accounted for 89.06% in southwest China, and the areas with significant and extremely significant increases were mainly distributed in southern Guangxi, eastern Sichuan, western Chongqing, and the junction areas of Yunnan and Guizhou. Climate change and human activities had dual effects on vegetation growth in southwest China, and the proportions of the areas with upward trends in farmland NPP were higher than that of grassland and forests both under the influences of climate change and human activities. The correlations between vegetation NPP and climate factors showed obvious regional differences in southwest China. On the regional scale, the areas with a positive correlation between vegetation NPP and temperature, precipitation, and sunshine duration were greater than that of the areas with a negative correlation. However, an opposite relationship could be found between vegetation NPP and biological aridity/humidity index. Among them, the areas with a positive correlation between vegetation NPP and temperature were greater than that with other climate factors. In terms of different vegetation ecosystems, temperature, precipitation, and sunshine duration had a stronger role in promoting NPP variation in the grassland ecosystem than in farmland and forest ecosystems. The transformation of other land use types to forest land had contributed to vegetation improvement in southwest China.

[Association between gene polymorphisms of propanoate metabolism pathway and meat quality as well as carcass traits in pigs].

In order to gain more extensive insight into detailed genetic control mechanisms of porcine meat quality and mine novel candidate genes, this study focused on the relationship between the genes of propanpate metabolism pathway and porcine meat quality as well as carcass traits based on the candidate gene set approach. Thirty-seven DLY pigs were tested in this study. A total of 36 SNPs within 7 candidate genes of propanoate metabolism pathway were genotyped and association analysis was conducted via Least Squares method, Multivariate multiple regression model, and a model-based multifactor dimensionality reduction method (MB-MDR). As a result, four SNPs in genes PCCB, MUT, MCEE, and ACSS1 were significantly associated with DLY pig meat quality or carcass traits (P<0.05). Results of MB-MDR analysis demonstrated that the interactions between multiple SNPs were significantly associated with the backfat thickness, water content, and fat content (P<0.05). ACSS2 was significantly associated with fat content; MCEE and MUT significantly influenced backfat thickness; and PCCB was related to fat weight. Moreover, the interactions between the genes in the propanoate metabolism pathway had remarkable influence in porcine meat quality and carcass traits.

[Temporal and Spatial Variation Characteristics of Heavy Metal in Atmospheric Deposition in China from 2000 to 2018].

Owing to the significant impact of heavy metals in atmospheric deposition on soil, clear knowledge on the present situation and temporal and spatial variation in fluxes of heavy metals in atmospheric deposition all around China is urgently needed. In this study, we collected 99 published papers on deposition fluxes of heavy metals from 2001 to 2021 based on the CNKI and Web of Science database and extracted 718 to 1672 monitoring points from these papers. The Meta-analysis method was used to calculate the weighted average of deposition fluxes of heavy metals, and the spatial-temporal characteristics in different periods from 2000 to 2018 were studied by subgroup analysis, which compared the differences between different types of areas, such as agricultural and rural areas and urban and industrial areas. The results showed that the annual fluxes of heavy metals in atmospheric deposition[mg·(m2·a)-1] in China were as follows:Zn (96.75)>Pb (23.37)>Cu (12.77)>Cr (11.04)>Ni (6.61)>As (2.97)>Cd (0.48)>Hg (0.05). Overall, the estimated value of deposition fluxes in China from 2000 to 2018 was higher than that of rural areas in England from 1995 to 1998. The deposition fluxes in industrial areas and urban areas were much higher than those in the agricultural and rural areas, especially the industrial areas where the heavy metal pollution was more serious. The deposition fluxes of As and Cd in the Changsha-Zhuzhou-Xiangtan area were relatively high, whereas the atmospheric deposition of heavy metals in Northeast China, the Pearl River Delta, and North China Plain was more serious than that in the other areas. In the past 20 years, the annual deposition fluxes of Cd fluctuated around the overall average, without an obviously declining trend, whereas the deposition fluxes of Cd in the urban, agricultural, and rural areas showed a trend of growth. These results suggested that precise and risk control measures of atmospheric emissions should be established based on the characteristics of regional industrial structure, which should cover all levels, all types, and all regions. In addition, more restrictive measures should be taken to solve the current problem caused by the higher deposition flux of Cd in atmospheric deposition.

[Progress of transcription factor CCAAT enhancer binding protein ß].

CCAAT enhancer binding protein ß (C/EBP ß) belongs to CCAAT enhancer binding protein (C/EBP) family, which is a subfamily of basic leucine zipper (bZIP) protein family. C/EBP family plays important roles in many processes such as cell differentiation, metabolism, and development. In this paper, the structure, expression regulation, and function of C/EBP ß were reviewed.

Conservation Priorities Analysis of Chinese Indigenous Pig Breeds in the Taihu Lake Region.

Most indigenous pig resources are known to originate from China. Thus, establishing conservation priorities for these local breeds is very essential, especially in the case of limited conservation funds. Therefore, in this study, we analyzed 445 individuals belonging to six indigenous breeds from the Taihu Lake Region, using a total of 131,300 SNPs. In order to determine the long-term guidelines for the management of these breeds, we analyzed the level of diversity in the metapopulation following a partition of diversity within and between breed subpopulations, using both measures of genic and allelic diversity. From the study, we found that the middle Meishan (MMS) pig population contributes the most (22%) to the total gene diversity while the Jiaxing black (JX) pig population contributes the most (27%) to the gene diversity between subpopulations. Most importantly, when we consider one breed is removed from the meta-population, the first two breeds prioritized should be JX pig breed and Fengjing pig breed followed by small Meishan (SMS), Mizhu (MI), and Erhualian (EH) if we pay more attention to the gene diversity between subpopulations. However, if the priority focus is on the total gene diversity, then the first breed to be prioritized would be the Shawutou (SW) pig breed followed by JX, MI, EH, and Fengjing (FJ). Furthermore, we noted that if conservation priority is to be based on the allelic diversity between subpopulations, then the MI breed should be the most prioritized breed followed by SW, Erhuanlian, and MMS. Summarily, our data show that different breeds have different contributions to the gene and allelic diversity within subpopulations as well as between subpopulations. Our study provides a basis for setting conservation priorities for indigenous pig breeds with a focus on different priority criteria.

[Study on regulatory mechanism of bovine early embryos development based on the analysis of gene expression data].

The death of early embryo development will bring huge economic losses in animal husbandry, especially for dairy production of cattle. Thus, it has an extremely important value to study the process of early embryonic development. In our study, one dataset of gene expression was chosen from the public database of GEO, which was related to bovine preimplantation development. Significance and clustering analyses were used to study the genome expression patterns of each stage during bovine preimplantation development. The whole process was assigned to three main groups. The waves of significant gene expression in each stage indicated that both 8-cell and 16-cell stages played an important role during the process of bovine preimplantation development. Further functional analysis and pathway analysis revealed that some major factors and related pathways are required for distinctive developmental stages.

[Effects of H-FABP gene polymorphisms and nutritional factors on pork quality].

Pork quality is affected by both genetic and nutritional factors. However, few researches focused simultaneously on the effects of these two kinds of factors. In order to study the co-effects of these two kinds of factors simultaneously, we implemented this experiment, 136 PIC hybrid pigs with about 65 kg body weight were randomly divided into 4 groups; each group was fed with a different kind of rations. After 35 days of feeding, the pigs were slaughtered at about 95 kg body weight and the pork quality was evaluated. Then the polymorphism of H-FABP gene was analyzed and an association analysis was conducted. The results are as follows: (1) feed ingredient has very significant effect on meat color (MC), pH24, intramuscular fat (IMF, %), and intramuscular protein (IMP, %); (2) H-FABP gene polymorphism has very significant effect on IMF (%) and IMP (%); (3) the interaction between gene and feed ingredient has significant effect on pH and IMF (%), and pH and IMF (%) were the highest for AA genotype in group 0 and group 1, respectively. These results suggest that both genetic and nutritional factors should be concerned in the improvement of pork quality.

Exploring the Structure of Haplotype Blocks and Genetic Diversity in Chinese Indigenous Pig Populations for Conservation Purpose.

Chinese indigenous pigs in the Taihu Lake region are well known for their high fecundity and other excellent characteristics. To better understand the characteristics of these breeds in this area as well as to provide the government and breeders the molecular basis for formulating a reasonable conservation policy, we explored the structure of haplotype blocks and genetic diversity of the 7 populations which is relevant for the management and conservation of these important genetic resources using next-generation sequencing data. In this study, a total of 131 300 single-nucleotide polymorphisms with minor allele frequencies ⩾0.05 were obtained for further analysis. In general, there are similar within-breed genetic diversities (He, Ho, Pn, Ar) among these 7 pig populations in the Taihu Lake region. Average values for the inbreeding coefficients estimates in the 7 populations are 0.110 (F1), 0.056 (F2), and 0.078 (F3). All the breeds have seen a continuous decline in Ne estimates over time with FJ and SW populations having a very similar curve. Moreover, the Ne of SMS pig breeds were smaller than other Chinese pig breeds, indicating that SMS pig breeds underwent stronger selection pressure than other Chinese pig breeds. The average genetic distances among the 7 populations in the Taihu Lake region were 0.235 (MMS), 0.240 (SMS), 0.269 (EH), 0.248 (MI), 0.221 (FJ), 0.254 (JX), and 0.212 (SW). A summary of the number of haplotype blocks and haplotype diversity was also presented. This study provide a deep understanding of the current situation of conservation in this region, thereby uncovering the pertinent insight to better formulate more reasonable preservation policies for the government departments and breeding planners to follow-up.

The genetic connectedness calculated from genomic information and its effect on the accuracy of genomic prediction.

The magnitude of connectedness among management units (e.g., flocks and herds) gives a reliable estimate of genetic evaluation across these units. Traditionally, pedigree-based methods have been used to evaluate the genetic connectedness in China. However, these methods have not been able to yield a substantial outcome due to the lack of accuracy and integrity of pedigree data. Therefore, it is necessary to ascertain genetic connectedness using genomic information (i.e., genome-based genetic connectedness). Moreover, the effects of various levels of genome-based genetic connectedness on the accuracy of genomic prediction still remain poorly understood. A simulation study was performed to evaluate the genome-based genetic connectedness across herds by applying prediction error variance of difference (PEVD), coefficient of determination (CD) and prediction error correlation (r). Genomic estimated breeding values (GEBV) were predicted using a GBLUP model from a single and joint reference population. Overall, a continued increase in CD and r with a corresponding decrease in PEVD was observed as the number of common sires varies from 0 to 19 regardless of heritability levels, indicating increasing genetic connectedness between herds. Higher heritability tends to obtain stronger genetic connectedness. Compared to pedigree information, genomic relatedness inferred from genomic information increased the estimates of genetic connectedness across herds. Genomic prediction using the joint versus single reference population increased the accuracy of genomic prediction by 25% and lower heritability benefited more. Moreover, the largest benefits were observed as the number of common sires equals 0, and the gain of accuracy decreased as the number of common sires increased. We confirmed that genome-based genetic connectedness enhanced the estimates of genetic connectedness across management units. Additionally, using the combined reference population substantially increased accuracy of genomic prediction. However, care should be taken when combining reference data for closely related populations, which may give less reliable prediction results.

Identifying Genetic Differences Between Dongxiang Blue-Shelled and White Leghorn Chickens Using Sequencing Data.

The Dongxiang Blue-shelled chicken is one of the most valuable Chinese indigenous poultry breeds. However, compared to the Italian native White Leghorn, although this Chinese breed possesses numerous favorable characteristics, it also exhibits lower growth performance and fertility. Here, we utilized genotyping sequencing data obtained via genome reduction on a sequencing platform to detect 100,114 single nucleotide polymorphisms and perform further biological analysis and functional annotation. We employed cross-population extended haplotype homozygosity, eigenvector decomposition combined with genome-wide association studies (EigenGWAS), and efficient mixed-model association expedited methods to detect areas of the genome that are potential selected regions (PSR) in both chicken breeds, and performed gene ontology (GO) enrichment and quantitative trait loci (QTL) analyses annotating using the Kyoto Encyclopedia of Genes and Genomes. The results of this study revealed a total of 2424 outlier loci (p-value <0.01), of which 2144 occur in the White Leghorn breed and 280 occur in the Dongxiang Blue-shelled chicken. These correspond to 327 and 94 PSRs containing 297 and 54 genes, respectively. The most significantly selected genes in Blue-shelled chicken are TMEM141 and CLIC3, while the SLCO1B3 gene, related to eggshell color, was identified via EigenGWAS. We show that the White Leghorn genes JARID2, RBMS3, GPC3, TRIB2, ROBO1, SAMSN1, OSBP2, and IGFALS are involved in immunity, reproduction, and growth, and thus might represent footprints of the selection process. In contrast, we identified six significantly enriched pathways in the Dongxiang Blue-shelled chicken that are related to amino acid and lipid metabolism as well as signal transduction. Our results also reveal the presence of a GO term associated with cell metabolism that occurs mainly in the White Leghorn breed, while the most significant QTL regions mapped to the Chicken QTL Database (GG_4.0) for the Dongxiang Blue-shelled breed are predominantly related to lesions, bone mineral content, and other related traits compared to tibia length and body weight (i.e., at 14, 28, 42, and 70 d) in the White Leghorn. The results of this study highlight differences in growth, immunity, and egg quality traits between the two breeds, and provide a foundation for the exploration of their genetic mechanisms.

Genomic analysis reveals genes affecting distinct phenotypes among different Chinese and western pig breeds.

The differences in artificial and natural selection have been some of the factors contributing to phenotypic diversity between Chinese and western pigs. Here, 830 individuals from western and Chinese pig breeds were genotyped using the reduced-representation genotyping method. First, we identified the selection signatures for different pig breeds. By comparing Chinese pigs and western pigs along the first principal component, the growth gene IGF1R; the immune genes IL1R1, IL1RL1, DUSP10, RAC3 and SWAP70; the meat quality-related gene SNORA50 and the olfactory gene OR1F1 were identified as candidate differentiated targets. Further, along a principal component separating Pudong White pigs from others, a potential causal gene for coat colour (EDNRB) was discovered. In addition, the divergent signatures evaluated by Fst within Chinese pig breeds found genes associated with the phenotypic features of coat colour, meat quality and feed efficiency among these indigenous pigs. Second, admixture and genomic introgression analysis were performed. Shan pigs have introgressed genes from Berkshire, Yorkshire and Hongdenglong pigs. The results of introgression mapping showed that this introgression conferred adaption to the local environment and coat colour of Chinese pigs and the superior productivity of western pigs.