Genome-wide association study for cashmere traits in Inner Mongolia cashmere goat population reveals new candidate genes and haplotypes.

BACKGROUND: The cashmere goat industry is one of the main pillars of animal husbandry in Inner Mongolia Autonomous Region, and plays an irreplaceable role in local economic development. With the change in feeding methods and environment, the cashmere produced by Inner Mongolia cashmere goats shows a tendency of coarser, and the cashmere yield can not meet the consumption demand of people. However, the genetic basis behind these changes is not fully understood. We measured cashmere traits, including cashmere yield (CY), cashmere diameter (CD), cashmere thickness (CT), and fleece length (FL) traits for four consecutive years, and utilized Genome-wide association study of four cashmere traits in Inner Mongolia cashmere goats was carried out using new genomics tools to infer genomic regions and functional loci associated with cashmere traits and to construct haplotypes that significantly affect cashmere traits. RESULTS: We estimated the genetic parameters of cashmere traits in Inner Mongolia cashmere goats. The heritability of cashmere yield, cashmere diameter, and fleece length traits of Inner Mongolia cashmere goats were 0.229, 0.359, and 0.250, which belonged to the medium heritability traits (0.2 ~ 0.4). The cashmere thickness trait has a low heritability of 0.053. We detected 151 genome-wide significantly associated SNPs with four cashmere traits on different chromosomes, which were very close to the chromosomes of 392 genes (located within the gene or within ± 500 kb). Notch3, BMPR1B, and CCNA2 have direct functional associations with fibroblasts and follicle stem cells, which play important roles in hair follicle growth and development. Based on GO functional annotation and KEGG enrichment analysis, potential candidate genes were associated with pathways of hair follicle genesis and development (Notch, P13K-Akt, TGF-beta, Cell cycle, Wnt, MAPK). We calculated the effective allele number of the Inner Mongolia cashmere goat population to be 1.109-1.998, the dominant genotypes of most SNPs were wild-type, the polymorphic information content of 57 SNPs were low polymorphism (0 < PIC < 0.25), and the polymorphic information content of 79 SNPs were moderate polymorphism (0.25 < PIC < 0.50). We analyzed the association of SNPs with phenotypes and found that the homozygous mutant type of SNP1 and SNP3 was associated with the highest cashmere yield, the heterozygous mutant type of SNP30 was associated with the lowest cashmere thickness, the wild type of SNP76, SNP77, SNP78, SNP80, and SNP81 was associated with the highest cashmere thickness, and the wild type type of SNP137 was associated with the highest fleece length. 21 haplotype blocks and 68 haplotype combinations were constructed. Haplotypes A2A2, B2B2, C2C2, and D4D4 were associated with increased cashmere yield, haplotypes E2E2, F1F1, G5G5, and G1G5 were associated with decreased cashmere fineness, haplotypes H2H2 was associated with increased cashmere thickness, haplotypes I1I1, I1I2, J1J4, L5L3, N3N2, N3N3, O2O1, P2P2, and Q3Q3 were associated with increased cashmere length. We verified the polymorphism of 8 SNPs by KASP, and found that chr7_g.102631194A > G, chr10_g.82715068 T > C, chr1_g.124483769C > T, chr24_g.12811352C > T, chr6_g.114111249A > G, and chr6_g.115606026 T > C were significantly genotyped in verified populations (P < 0.05). CONCLUSIONS: In conclusion, the genetic effect of single SNP on phenotypes is small, and SNPs are more inclined to be inherited as a whole. By constructing haplotypes from SNPs that are significantly associated with cashmere traits, it will help to reveal the complex and potential causal variations in cashmere traits of Inner Mongolia cashmere goats. This will be a valuable resource for genomics and breeding of the cashmere goat.

Benefits and costs: Understanding the influence of heavy metal pollution on environmental adaptability in Strauchbufo raddei tadpoles through an energy budget perspective.

Understanding the impact of environmental pollution on organismal energy budgets is crucial for predicting adaptive responses and potential maladaptation to stressors. However, the regulatory mechanism governing the trade-off between energy intake and consumption remains largely unknown, particularly considering the diverse adaptations influenced by exposure history in realistic field conditions. In the present study, we conducted a simulated field reciprocal transplant experiment to compare the energy budget strategies of Strauchbufo raddei tadpoles exposed to heavy metal. The simulated heavy metal concentrations (0.29 mg/L Cu, 1.17 mg/L Zn, 0.47 mg/L Pb, 0.16 mg/L Cd) mirrored the actual environmental exposure concentrations observed in the field habitat. This allowed for a comparison between tadpoles with parental chronic exposure to heavy metal pollutants in their habitat and those without such exposure. Results revealed that under heavy metal exposure, tadpoles originating from unpolluted areas exhibited heightened vulnerability, characterized by reduced food intake, diminished nutrient absorption, increased metabolism cost, reduced energy reserves, and increased mortality rates. In contrast, tadpoles originating from areas with long-term heavy metal pollution demonstrated adaptive strategies, manifested through adjustments in liver and small intestine phenotypes, optimizing energy allocation, and reducing energy consumption to preserve energy, thus sustaining survival. However, tadpoles from polluted areas exhibited certain maladaptive such as growth inhibition, metabolic suppression, and immune compromise due to heavy metal exposure. In conclusion, while conserving energy consumption has proven to be an effective way to deal with long-term heavy metal stress, it poses a threat to individual survival and population development in the long run.

GDSL Lipase Gene HTA1 Negatively Regulates Heat Tolerance in Rice Seedlings by Regulating Reactive Oxygen Species Accumulation.

High temperature is a significant environmental stress that limits plant growth and agricultural productivity. GDSL lipase is a hydrolytic enzyme with a conserved GDSL sequence at the N-terminus, which has various biological functions, such as participating in plant growth, development, lipid metabolism, and stress resistance. However, little is known about the function of the GDSL lipase gene in the heat tolerance of rice. Here, we characterized a lipase family protein coding gene HTA1, which was significantly induced by high temperature in rice. Rice seedlings in which the mutant hta1 was knocked out showed enhanced heat tolerance, whereas the overexpressing HTA1 showed more sensitivity to heat stress. Under heat stress, hta1 could reduce plant membrane damage and reactive oxygen species (ROS) levels and elevate the activity of antioxidant enzymes. Moreover, real-time quantitative PCR (RT-qPCR) analysis showed that mutant hta1 significantly activated gene expression in antioxidant enzymes, heat response, and defense. In conclusion, our results suggest that HTA1 negatively regulates heat stress tolerance by modulating the ROS accumulation and the expression of heat-responsive and defense-related genes in rice seedlings. This research will provide a valuable resource for utilizing HTA1 to improve crop heat tolerance.

Research on the estimation and spatial pattern of net tourism carbon emissions in the Yellow River Basin from 2009 to 2019.

Based on panel data and remote sensing data of cities in the Yellow River Basin in China from 2009 to 2019, and using the tourism carbon footprint and tourism carbon carrying capacity models, the tourism carbon emissions, tourism carbon carrying capacity, and net tourism carbon of 65 cities in the Yellow River Basin were calculated. The balance and dynamic changes in carbon emissions and carbon fixation of urban tourism in the past ten years were compared. The results show that (1) tourism carbon emissions in the Yellow River Basin are generally on the rise, along with a distribution characteristic of downstream > middle reaches > upstream with obvious characteristics of urban agglomeration centrality within the basin; (2) the carbon carrying capacity of tourism is higher than that of tourism. The growth of carbon emissions is relatively slow, showing a spatial distribution pattern of high in the west and low in the east, which is mainly related to the geographical environment and economic development of the city; (3) the tourism carbon emissions and tourism carbon carrying capacity in the upstream areas can basically maintain a balance, but in the middle and lower reaches of the region, they show a carbon surplus. There is a significant positive spatial correlation in urban net tourism carbon emissions, and the clusters are mainly H-H and L-L.

Accuracy of Genomic Selection for Important Economic Traits of Cashmere and Meat Goats Assessed by Simulation Study.

Genomic selection in plants and animals has become a standard tool for breeding because of the advantages of high accuracy and short generation intervals. Implementation of this technology is hindered by the high cost of genotyping and other factors. The aim of this study was to determine an optional marker density panel and reference population size for using genomic selection of goats, with speculation on the number of QTLs that affect the important economic traits of goats. In addition, the effect of buck population size in the reference population on the accuracy of genomic estimated breeding value (GEBV) was discussed. Based on the previous genetic evaluation results of Inner Mongolia White Cashmere Goats, live body weight (LBW, h 2 = 0.11) and fiber diameter (FD, h 2 = 0.34) were chosen to perform genomic selection in this study. Reasonable genome parameters and generation transmission processes were set, and phenotypic and genotype data of the two traits were simulated. Then, different sizes of the reference population and validation population were selected from progeny. The GEBVs were obtained by six methods, including GBLUP (Genomic Best Linear Unbiased Prediction), ssGBLUP (Single Step Genomic Best Linear Unbiased Prediction), BayesA, BayesB, Bayesian ridge regression, and Bayesian LASSO. The correlation coefficient between the predicted and realized phenotypes from simulation was calculated and used as a measure of the accuracy of GEBV in each trait. The results showed that the medium marker density Panel (45 K) could be used for genomic selection in goats, which can ensure the accuracy of the GEBV. The reference population size of 1,500 can achieve greater genetic progress in genomic selection for fiber diameter and live body weight in goats by comparing with the population size below this level. The accuracy of the GEBV for live body weight and fiber diameter was better when the number of QTLs was 100 and 50, respectively. Additionally, the accuracy of GEBV was discovered to be good when the buck population size was up to 200. Meanwhile, the accuracy of the GEBV for medium heritability traits (FDs) was found to be higher than the accuracy of the GEBV for low heritability traits (LBWs). These findings will provide theoretical guidance for genomic selection in goats by using real data.

Assessing Genetic Diversity and Estimating the Inbreeding Effect on Economic Traits of Inner Mongolia White Cashmere Goats Through Pedigree Analysis.

Objective: The purpose of this study was to discover the population structure and genetic diversity of Inner Mongolia White Cashmere goats (IMCGs) and demonstrate the effect of inbreeding on the live body weight (LBW), cashmere yield (CY), fiber length (FL), and fiber diameter (FD) of IMCGs. Materials and Methods: All data were collected from pedigree information and production performance records of IMCGs from 1983 to 2019. The population structure and genetic diversity were analyzed by Endog 4.8 software. Inbreeding coefficients were obtained by the pedigree package in R. Then, a linear regression model was used to analyze how inbreeding influences economic traits in IMCGs. Four levels of inbreeding coefficients (F i ) were classified in this study, including F i = 0, 0< F i ≤ 6.25, 6.25< F i ≤ 12.5 and F i ≥12.5. Variance analysis was performed to determine whether inbreeding levels had a significant effect on economic traits in IMCGs. Results: The proportions of rams and dams in IMCGs for breeding were relatively small, with values of 0.8 and 20.5%, respectively. The proportion of inbred animals in the entire population was high, with values up to 68.6%; however, the average inbreeding coefficient and relatedness coefficient were 4.50 and 8.48%, respectively. To date, the population has experienced 12 generations. The average generation interval obtained in the present study was 4.11 ± 0.01 years. The ram-to-son pathway was lowest (3.97 years), and the ewe-to-daughter pathway was highest (4.24 years). It was discovered that the LBW, CY, and FL increased by 3.88 kg, 208.7 g, and 1.151 cm, respectively, with every 1% increase in the inbreeding coefficient, and the FD decreased by 0.819 µm with every 1% increase in the inbreeding coefficient. Additionally, multiple comparison analysis indicated that when the inbreeding coefficient was higher than 6.25%, the LBW showed an obvious decreasing trend. The threshold value of inbreeding depression in the CY is 12.5%. However, inbreeding depression has not been observed in the FL and FD. Conclusion: Pedigree completeness needs to be further strengthened. The degree of inbreeding in this flock should be properly controlled when designing breeding programs.

Perception of Health Conditions and Test Availability as Predictors of Adults' Mental Health during the COVID-19 Pandemic: A Survey Study of Adults in Malaysia.

Research identifying adults' mental health during the coronavirus disease 2019 (COVID-19) pandemic relies solely on demographic predictors without examining adults' health condition as a potential predictor. This study aims to examine individuals' perception of health conditions and test availability as potential predictors of mental health-insomnia, anxiety, depression, and distress-during the COVID-19 pandemic. An online survey of 669 adults in Malaysia was conducted during 2-8 May 2020, six weeks after the Movement Control Order (MCO) was issued. We found adults' perception of health conditions had curvilinear relationships (horizontally reversed J-shaped) with insomnia, anxiety, depression, and distress. Perceived test availability for COVID-19 also had curvilinear relationships (horizontally reversed J-shaped) with anxiety and depression. Younger adults reported worse mental health, but people from various religions and ethnic groups did not differ significantly in reported mental health. The results indicated that adults with worse health conditions had more mental health problems, and the worse degree deepened for unhealthy people. Perceived test availability negatively predicted anxiety and depression, especially for adults perceiving COVID-19 test unavailability. The significant predictions of perceived health condition and perceived COVID-19 test availability suggest a new direction for the literature to identify the psychiatric risk factors directly from health-related variables during a pandemic.

Co-sensitization of the HD-2 complex with low-cost cyanoacetanilides for highly efficient DSSCs.

The photophysical and electrochemical properties of new targeted 2-cyanoacetanilide-based dyes are illustrated. New cyanoacetanilides SA7-10 were synthesized and employed as co-sensitizers in DSSCs. The chemical structures of these 2-cyanoacetanilides differ according to the substituent at the benzene ring (-H, -Me, -OMe and -NEt2), with the anchoring moiety being the same, a -COOH group. Furthermore, a density functional theory (DFT) calculation has shown an effective intermolecular charge transfer character, the HOMOs of SA7-10 are mainly located on the corresponding donor part, and their LUMOs are located on carboxylic acid moieties as the acceptor. Interestingly, using photosensitizers SA7-10 as co-sensitizers with HD-2 dye causes an improvement in their photovoltaic performances. Among the dyes, SA10 co-sensitized with HD-2 displayed an overall efficiency of 8.25%, a JSC of 19.5 mA cm-2, a VOC of 0.65 V and an FF of 64.35 compared to 7.46%, 19 mA cm-2, 0.64 V and 60.54, respectively, of HD-2 only. Moreover, the electrochemical impedance spectroscopy (EIS) data of SA7-10 and HD-2 were found to be in accordance with the obtained photovoltaic parameters. Finally, the results indicated that 2-cyanoacetanilide-based dyes were utilized as promising co-sensitizers due to their easy preparation methods and their relatively small size.