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.

Gibberellin-mediated far-red light-induced leaf expansion in cucumber seedlings.

Our experiments explored the effects of far-red (FR) light on cucumber (Cucumis sativus L. 'Zhongnong No. 26') seedling growth. Our results indicated that FR light significantly promoted the growth of cucumber seedlings. Specifically, it promoted the accumulation of shoot biomass and the elongation of internodes and leaves (except the first leaf at the bottom). Further analysis showed that FR light had no effect on the accumulation contents of abscisic acid (ABA) and auxin (IAA) in seedling leaves. Still, it significantly caused the increase of the gibberellin (GA3, GA4, and GA7) contents and the decrease of GA1 content, which suggested that the leaf expansion progress under FR light may be primarily related to GA. Therefore, the cucumber seedling leaf expansion response to GA was evaluated under different light sources. The exogenous spraying of different GA4/7 contents significantly promoted the leaf expansion of cucumber seedlings under white light, while the GA biosynthesis inhibitor paclobutrazol (PAC) significantly promoted the expression of GA hydrolytic genes (GA2ox2 and GA2ox4) and decreased the content of endogenous active GA, which inhibited the leaf expansion induced by FR light. As expected, the combination of exogenous GA4/7 and PAC restored the growth promotion effect of FR light on cucumber seedling leaves. It increased the contents of endogenous active GA (GA1, GA3, GA4, and GA7), and the expression trend in GA synthetic/hydrolytic-related genes was the opposite of that of PAC was applied alone. All of the above results indicated that FR light regulates leaf expansion progress in cucumber seedlings through GA.

Safe range of femoral neck system insertion and the risk of perforation.

BACKGROUND: Internal fixation of the femoral neck carries a risk of perforation due to the presence of the isthmus of the femoral neck. At present, there are few studies on the safe and risk zones of the femoral neck system (FNS) implantation. This study aimed to recommend the safe range of injection of FNS in the lateral wall of the proximal femur, parallel to the axis of the femoral neck, during FNS treatment of femoral neck fracture (FNF). METHODS: Femoral computed tomography (CT) data of 80 patients (male: 40; female: 40) who met the inclusion criteria were collected. Mimics 21.0 software was used to complete the modeling. 3-Matic 13.0 software was used to establish the axis of the femoral neck and its vertical plane, perform the cutting of the femoral neck, and project it on the vertical plane of the femoral neck axis. After matching a rectangle for each projection map, all sample sizes (80 cases) were standardized and superimposed to obtain gradient maps of the safe zone (SZ) and dangerous zone (RZ), thereby securing edge key points and safe FNS insertion range. RESULTS: In the 80 samples, the mean diameter of the smallest femoral neck section was 33.87 ± 2.32 mm for men and 29.36 ± 1.92 mm for women. All 80 femoral necks had safe and risky areas. The SZ/S × 100% was 77.59 (± 2.22%), and the RS/S × 100% was 22.39% (± 2.22%). The risk area was composed of four parts: (1), (2), (3), and (4), respectively, corresponding to 3.45 ± 1.74%, 5.51 ± 2.63%, 6.22 ± 1.41%, and 7.22 ± 1.39%. Four marginal key points, perforation risk, and safe ranges (SR) of FNS were analyzed on the lateral wall of the femoral neck. CONCLUSIONS: The SR of FNS placement was recommended by digital simulation. In addition, Regions (3) and (4) posed a higher risk of penetrating the cortex. Using the gradient map of RZ for preoperative evaluation is recommended to avoid iatrogenic perforation.

The analysis of the characteristics of imported COVID-19 cases from January to April in 2020: a cross-sectional study.

Background: Since the first case reported in December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused an outbreak of coronavirus disease 2019 (COVID-19) worldwide. The global case count continued to rise and the WHO declared a Public Health Emergency of International Concern (PHEIC), causing a growing risk of imported COVID-19 infection. This study aimed to provide descriptive and quantitative epidemiological characteristics of imported COVID-19 cases in China. Methods: This cross-sectional study examined all imported COVID-19 cases in Mainland China from 22 January to 21 April 2020. Ratios, Median and percentile were used for descriptive analysis. Spearman's correlation analysis was performed between daily new imported cases in Mainland China and the country of origin. The chi-square test was used to evaluate the difference between home quarantine and compulsory centralized quarantine on native transmission. Results: A total of 1,610 cases of COVID-19 were imported from 49 countries to 27 provincial administrative regions in China; 79.8% were from European countries and the United States of America (the USA). Before 29 March 2020, the imported cases were mainly from the USA (27.7%) and United Kingdom (UK; 42.6%). After 29 March 2020, the daily newly imported cases from Russia rapidly grew. After 12 April 2020, the number of daily newly imported cases gradually decreased and remained at a low level (12±7 cases per day). Airport entry was encouraged, and ground border crossing was limited. Among the 1,610 cases, 54.0% were in the asymptomatic incubation period on arrival in Mainland China. Conclusions: The transmissions by imported COVID-19 were gradually and effectively curbed in Mainland China, despite a disproportionally high number of cases worldwide. Entry screening measures must be implemented universally to all inbound travelers at a point of entry or targeted to specific travel routes or to specific travelers. Compulsory centralized quarantine should be recommended in the prevention of the imported COVID-19 epidemic.

Genome-Wide Identification and Characterization of Long Non-Coding RNAs in Longissimus dorsi Skeletal Muscle of Shandong Black Cattle and Luxi Cattle.

There is an increasing understanding of the possible regulatory role of long non-coding RNAs (LncRNA). Studies on livestock have mainly focused on the regulation of cell differentiation, fat synthesis, and embryonic development. However, there has been little study of skeletal muscle of domestic animals and the potential role of lncRNA. In this study, the transcriptome numbers of longissimus muscle of different beef cattle (Shandong black catle and Luxi catlle) were used to construct muscle related lncRNAs-miRNA-mRNA interaction network through bioinformatics analysis. This is helpful to clarify the molecular mechanism of bovine muscle development, and can be used to promote animal husbandry and improve animal husbandry production. According to the screening criteria of |FC|≧2 and q < 0.05, a total of 1,415 transcripts (of which 480 were LncRNAs) were differentially expressed (q < 0.05) in the different breeds. Further, we found that the most differentially expressed LncRNAs were found on chromosome 9, in which the differentially expressed LncRNAs targeted 1,164 protein coding genes (MYORG, Wnt4, PAK1, ADCY7,etc) (upstream and downstream<50 Kb). In addition, Pearson's correlation coefficients of co-expression levels indicated a potential trans regulatory relationship between the differentially expressed LncRNAs and 43844 mRNAs (r > 0.9). The identified co-expressed mRNAs (MYORG, Dll1, EFNB2, SOX6, MYOCD, and MYLK3) are related to the formation of muscle structure, and enriched in muscle system process, strained muscle cell differentiation, muscle cell development, striated muscle tissue development, calcium signaling, and AMPK signaling. Additionally, we also found that some LncRNAs (LOC112444238, LOC101903367, LOC104975788, LOC112441863, LOC112449549, and LOC101907194) may interact with miRNAs related to cattle muscle growth and development. Based on this, we constructed a LncRNAs-miRNA-mRNA interaction network as the putative basis for biological regulation in cattle skeletal muscle. Interestingly, a candidate differential LncRNA (LOC104975788) and a protein-coding gene (Pax7) contain miR-133a binding sites and binding was confirmed by luciferase reporter assay. LOC104975788 may combined miR-133a competitively with Pax7, thus relieving the inhibitory effect of miR-133a on Pax7 to regulate skeletal muscle development. These results will provide the theoretical basis for further study of LncRNA regulation and activity in different cattle breeds.