Genetic parameters and genome-wide association analyses for lifetime productivity in Chinese Holstein cattle.

Lifetime productivity is a trait of great importance to dairy cattle populations as it combines information from production and longevity variables. Therefore, we investigated the genetic background of lifetime productivity in high-producing dairy cattle by integrating genomics and transcriptomics data sets. A total of 3,365,612 test-day milk yield records from 134,029 Chinese Holstein cows were used to define 6 lifetime productivity traits, including lifetime milk yield covering full lifespan and 5 cumulative milk yield traits covering partial lifespan. Genetic parameters were estimated based on univariate and bivariate linear animal models and the Restricted Maximum Likelihood (REML) method. Genome-wide association studies (GWAS) and weighted gene co-expression network analyses (WGCNA) were performed to identify candidate genes associated with lifetime productivity based on genomic data from 3,424 cows and peripheral blood RNA-seq data from 23 cows, respectively. Lifetime milk yield averaged 24,800.8 ± 14,396.6 kg (mean ± SD) across an average of 2.4 parities in Chinese Holstein population. The heritability estimates for lifetime productivity traits ranged from 0.05 (±0.01 for SE) to 0.10 (±0.02 for SE). The estimate of genetic correlation between lifetime milk yield and productive life is 0.88 (±0.3 for SE) while the genetic correlation with 305d milk yield in the first lactation was 0.49 (±0.08 for SE). Absolute values for most genetic correlation estimates between lifetime productivity and type traits were lower than 0.30. Moderate genetic correlations were found between udder related traits and lifetime productivity, such as with udder depth (0.33), rear udder attachment height (0.33), and udder system (0.34). Some single nucleotide polymorphisms and gene co-expression modules significantly associated with lifetime milk yield were identified based on GWAS and WGCNA analyses, respectively. Functional enrichment analyses of the candidate genes identified revealed important pathways related to immune system, longevity, energy utilization and metabolism, and FoxO signaling. The genes NTMT1, FNBP1, and S1PR1 were considered to be the most important candidate genes influencing lifetime productivity in Holstein cows. Overall, our findings indicate that lifetime productivity is heritable in Chinese Holstein cattle and important candidate genes were identified by integrating genomic and transcriptomic data sets.

Estimation of genomic inbreeding coefficients based on high-density SNP markers in Chinese Holstein cattle.

In livestock, inbreeding coefficient based on pedigree information is usually used to evaluate the level of inbreeding. Recently, with cost reduction of high-density SNP genotyping, it's possible to analyze real genomic inbreeding degree using genomic information. In this study, utilizing high-density SNP chip data, we analyzed the frequency and distribution of runs of homozygosity (ROH) in 2107 Chinese Holstein cattle in Beijing area, and calculated 2 genomic inbreeding coefficients, i.e., 1) the proportion of ROH length in the total length of autosomal genome (Froh), and 2) the percentage of homozygous SNPs (Fhom). Then we analyzed the correlation between 2 genomic inbreeding coefficients and the correlation between genomic and pedigree inbreeding coefficients. We totally detected 44 676 ROHs that mainly ranged from 1 to 10 Mb. Various lengths of ROHs existed in the genome. There were more short ROHs than long ROHs. ROHs aren't evenly distributed in chromosomes. The area with most ROHs is in the middle part of chromosome 10. Strong correlation (r > 0.90) existed between 2 kinds of genomic inbreeding coefficients, but the correlation between pedigree and genomic inbreeding coefficients were much lower (r < 0.50). Our finding suggests that pedigree completeness influences the correlation between genomic and pedigree inbreeding. Genomic inbreeding measures may reflect individuals' real inbreeding, which could be a useful tool to evaluate population inbreeding.

Metalenses phase characterization by multi-distance phase retrieval.

Metalens, characterized by their unique functions and distinctive physical properties, have gained significant attention for their potential applications. To further optimize the performance of metalens, it is necessary to characterize the phase modulation of the metalens. In this study, we present a multi-distance phase retrieval system based on optical field scanning and discuss its convergence and robustness. Our findings indicate that the system is capable of retrieving the phase distribution of the metalens as long as the measurement noise is low and the total length of the scanned light field is sufficiently long. This system enables the analysis of focal length and aberration by utilizing the computed phase distribution. We extend our investigation to measure the phase distribution of the metalens operating in the near-infrared (NIR) spectrum and identify the impact of defects in the sample on the phase. Additionally, we conduct a comparative analysis of the phase distribution of the metalens in air and ethanol and observe the variations in the phase modulation of the metalens in different working mediums. Our system provides a straightforward method for the phase characterization of metalens, aiding in optimizing the metalens design and functionality.

Prevalence of nine genetic defects in Chinese Holstein cattle.

Worldwide use of elite sires has caused inbreeding accumulation and high frequencies of genetic defects in dairy cattle populations. In recent years, several genetic defect genes or haplotypes have been identified in Holstein cattle. A rapid and reliable microfluidic chip with Kompetitive allele-specific PCR (KASP) assay was developed in our previous study for the detection of heterozygotes at eight genetic defect loci of bovine leukocyte adhesion deficiency (BLAD), Brachyspina syndrome (BS), complex vertebral malformation (CVM), Holstein haplotype 1 (HH1), Holstein haplotype 3 (HH3), Holstein haplotype 4 (HH4), Holstein haplotype 5 (HH5) and haplotype for cholesterol deficiency (HCD). This study aimed to extend that assay to include a newly identified genetic defect of Holstein haplotype 6 (HH6) and to estimate the frequencies of carriers for each of the nine genetic defects in six Chinese Holstein herds. Of the 1633 cows, carrier frequencies of the genetic defects were 6.92%, 5.76%, 4.46%, 4.30%, 3.62%, 2.94%, 1.86% and 0.37% for HH1, HH3, CVM, HH5, HCD, BS, HH6 and BLAD, respectively. No carrier was found for HH4. Notably, 27.43% of cows carried at least one genetic defect, while 2.27% and 0.12% of cows carried double and triple genetic defect alleles, respectively. The existence of genetic defects calls for routine molecular testing and effective management of genetic defects by avoiding carrier-to-carrier mating in production herds and eliminating or at least reducing the frequency of the defective alleles through marker-assisted selection in breeding herds.

[Clinical study of lymph node metastatic pattern of thoracic esophageal squamous carcinoma].

OBJECTIVE: To analyze the patterns of lymph node metastases of thoracic esophageal carcinoma and define the adequate range of lymph node dissection. METHODS: The clinical data of 217 patients with esophageal carcinoma undergoing radical surgical resection of the lymph nodes in three regions were retrospectively analyzed. RESULTS: Lymph node metastases were found in 136 of the 217 patients (62.6%) and skip metastases of the lymph nodes in 12 patients (5.5%). In 3 989 lymph nodes desected, metastases were identified in 454 lymph nodes (11.38%). The rates of lymph node metastasis were 31.7%, 21.2% and 12.1% in the neck, thoracic mediastinum and abdominal cavity, respectively, in upper thoracic esophageal carcinoma, 21.9%, 30.5% and 15.6% in middle thoracic carcinoma, and 9.75%, 12.7% and 34.5% in lower thoracic carcinoma. The degree of tumor differentiation, depth of tumor invasion and lymphatic vessel invasion were factors influencing lymph node metastases (P<0.05). CONCLUSION: Because of the upward, downward and skip metastasis of esophageal carcinoma cells to the lymph nodes, the operable patients with thoracic esophagus carcinoma should receive radical desection of the lymph nodes in the 3 regions to promote the patients' survival.

[A prospective study of combined chemoradiotherapy followed by surgery in the treatment of esophageal carcinoma].

OBJECTIVE: To evaluate the effect of combined chemoradiotherapy followed by surgery for patients with esophageal carcinoma. METHODS: Ninety-seven patients with stage II or III esophageal carcinoma without contraindication against operation and chemoradiotherapy, were randomly divided into two groups: combined group (Group A) 48 and control group (Group B) 49. Patients in group A were given neoadjuvant treatment consisted of chemotherapy with 5-fluorouracil and cisplatin for 2 cycles and radiotherapy of DT36 Gy/12 f/17 d. Three weeks later, operation was performed. Patients in group B were given operation alone. Survival rate was calculated with Kaplan-Meier method. Chi and Log-rank test was used to assess the difference between the two groups. RESULTS: The radical resectability of group A and group B were 85.4% and 65.3% (P = 0.018 1). The lymph node metastasis rate of the two groups were 21.7% and 45.7% (P = 0.019 4). The T stage of group A was significantly lowered (P = 0.003 6). The local and regional recurrence rate of two groups were 34.8% and 58.7% (P = 0.023 6), while there was no significant difference in operative complications between the two groups. Significant improvement in the long-term survival rate was observed in group A, especially in patients who achieved partial and complete response with high 5-year survival rate of 56.5%. CONCLUSION: Preoperative neoadjuvant chemoradiotherapy is able to reduce the tumor and tumor stage, lower the lymph node metastasis rate and local or regional recurrence rate, also it can improve radical resectability and long-term survival without increasing the operative complications.

[Analysis of lymph node metastases of 217 cases of thoracic esophageal carcinoma and its impact on prognosis].

BACKGROUND & OBJECTIVE: At present, the range of lymph node dissection in treatment of thoracic esophageal cancer is still controversial. This study was designed to explore the status of lymph node metastases of thoracic esophageal carcinoma and its influence on the prognosis and to seek reasonable dissecting range of lymph nodes. METHODS: A retrospective study was performed on the clinical data of 217 patients who had underwent radical operation through three-field lymphadenectomy. Nine distinguishing clinicopathological factors possibly influencing survival rate were chosen. A multivariate analysis of these factors was performed by the computerized Cox proportional hazards model. RESULTS: The 1-, 3-, and 5-year survival rates of all patients were 82.6%, 59.8%, and 48.8%, respectively. The lymph node metastasis rate was 62.6% and the leaping metastasis rate of lymph nodes was 5.5%. In 3989 lymph nodes dissected, metastases were detected in 454 (11.38%). The lymph node metastasis rates present in neck, thoracic mediastinum, and abdominal cavity were 31.7%, 21.2%, and 12.1% in upper-thoracic esophageal carcinoma, 21.9%, 30.5%, and 15.6% in middle-thoracic carcinoma, 9.75%, 12.7%, and 34.5% in lower-thoracic carcinoma, respectively. Degree of tumor differentiation, depth of tumor invasion, and lymphatic vessels invasion were the factors influencing lymph nodes metastases, but the length of tumor was not. According to multivariate analysis, depth of tumor invasion, tumor differentiation, the number of lymph nodes metastatic field, and tumor location were of prognostic significance. With the increasing of the number of lymph nodes metastatic field, the survival rate of the patients dropped gradually(P = 0.0284). CONCLUSION: Lymph node metastasis especially the number of lymph node metastatic field is one of key factors affecting the prognosis of patients. Because of the upward, downward, and leaping spreading of esophageal carcinoma cells to the lymph nodes, the patients with thoracic esophageal carcinoma should be given radical operation through three-field lymphadenectomy to promote the 5-years survival rate.