Predicting nitrogen use efficiency,nitrogen loss and dry matter intake of individual dairy cows in late lactation by including mid‑infrared spectra of milk samples

Background Nitrate leaching to groundwater and surface water and ammonia volatilization from dairy farms have negative impacts on the environment.Meanwhile,the increasing demand for dairy products will result in more pollution if N losses are not controlled.Therefore,a more efficient,and environmentally friendly production system is needed,in which nitrogen use efficiency(NUE)of dairy cows plays a key role.To genetically improve NUE,extensively recorded and cost-effective proxies are essential,which can be obtained by including mid-infrared(MIR)spectra of milk in prediction models for NUE.This study aimed to develop and validate the best prediction model of NUE,nitrogen loss(NL)and dry matter intake(DMI)for individual dairy cows in China.Results A total of 86 lactating Chinese Holstein cows were used in this study.After data editing,704 records were obtained for calibration and validation.Six prediction models with three different machine learning algorithms and three kinds of pre-processed MIR spectra were developed for each trait.Results showed that the coefficient of determination(R2)of the best model in within-herd validation was 0.66 for NUE,0.58 for NL and 0.63 for DMI.For external validation,reasonable prediction results were only observed for NUE,with R2 ranging from 0.58 to 0.63,while the R2 of the other two traits was below 0.50.The infrared waves from 973.54 to 988.46 cm−1 and daily milk yield were the most important variables for prediction.Conclusion The results showed that individual NUE can be predicted with a moderate accuracy in both within-herd and external validations.The model of NUE could be used for the datasets that are similar to the calibration dataset.The prediction models for NL and 3-day moving average of DMI(DMI_a)generated lower accuracies in within-herd validation.Results also indicated that information of MIR spectra variables increased the predictive ability of models.Additionally,pre-processed MIR spectra do not result in higher accuracy than original MIR spectra in the external validation.These models will be applied to large-scale data to further investigate the genetic architecture of N efficiency and further reduce the adverse impacts on the environment after more data is collected.

利用SNP芯片信息评估新疆近交牛基因组纯合度

新疆近交牛是经45年近亲繁育形成的近交群体,但由于繁育记录缺失,其原始亲本品种未知。为了明确新疆近交牛的遗传背景,并探索利用基因组信息评价牛群近交水平的可行性,本研究利用该群体及荷斯坦牛、新疆褐牛和哈萨克牛等16个国内外牛品种的SNP芯片数据,应用主成分分析和Admixture方法对塔城地区新疆近交牛的群体结构进行分析;通过进一步计算新疆近交牛、荷斯坦牛、新疆褐牛和哈萨克牛的群体遗传学参数以及基因组近交指标评估各群体近交程度;结合新疆近交牛的体型分类和基因组近交指标信息,探讨了个体近交程度与体型表现的关系;最后,基于对新疆近交牛和哈萨克牛高频长纯合片段区域的筛选,鉴定了新疆近交牛基因组特征区域。研究结果显示,新疆近交牛的遗传背景与哈萨克牛基本一致,近交牛基因组纯合程度明显高于其他群体,且基因纯合率越高的近交牛其体型越小,在一定程度上呈现了近交衰退对体型的影响。本研究还鉴定到与新疆近交牛基因组特征区域相关的6个基本生物学通路以及与重要经济性状相关的32个数量基因座(quantitative trait loci,QTL)。本研究结果为新疆近交牛这一特殊遗传资源的育种规划及未来该群体的开发利用提供了科学依据。

Variance components and correlations of female fertility traits in Chinese Holstein population

Background: The objective of the present study was to estimate(co)variance components of female fertility traits in Chinese Holsteins, considering fertility traits in different parities as different traits. Data on 88,647 females with 215,632 records(parities) were collected during 2000 to 2014 from 32 herds in the Sanyuan Lvhe Dairy Cattle Center, Beijing, China. The analyzed female fertility traits included interval from calving to first insemination, interval from first to last insemination, days open, conception rate at first insemination, number of inseminations per conception and non-return rates within 56 days after first insemination.Results: The descriptive statistics showed that the average fertility of heifers was superior to that of cows. Moreover,the genetic correlations between the performances of a trait in heifers and in cows were all moderate to high but far from one, which suggested that the performances of a trait in heifers and cows should be considered as different but genetically correlated traits in genetic evaluations. On the other hand, genetic correlations between performances of a trait in different parities of cows were greater than 0.87, with only a few exceptions, but variances were not homogeneous across parities for some traits. The estimated heritabilities of female fertility traits were low; all were below 0.049(except for interval from calving to first insemination). Additionally, the heritabilities of the heifer interval traits were lower than those of the corresponding cow interval traits. Moreover, the heritabilities of the interval traits were higher than those of the threshold traits when measuring similar fertility functions. In general, estimated genetic correlations between traits were highly consistent with the biological categories of the female fertility traits.Conclusions: Interval from calving to first insemination, interval from first to last insemination and non-return rates within 56 days after first insemination are recommended to be included in the selection index of the Chinese Holstein population. The parameters estimated in the present study will facilitate the development of a genetic evaluation system for female fertility traits to improve the reproduction efficiency of Chinese Holsteins.

Identification of novel molecular markers of mastitis caused by Staphylococcus aureus using gene expression profiling in two consecutive generations of Chinese Holstein dairy cattle

Background: Mastitis in dairy cows caused by Staphylococcus aureus is a major problem hindering economic growth in dairy farms worldwide. It is difficult to prevent or eliminate due to its asymptomatic nature and long persistence of infection. Although transcriptomic responses of bovine mammary gland cells to pathogens that cause mastitis have been studied, the common responses of peripheral blood leukocytes to S. aureus infection across two consecutive generations of dairy cattle have not been investigated.Methods: In the current study, RNA-Seq was used to profile the transcriptomes of peripheral blood leukocytes sampled from S. aureus-infected mothers and their S. aureus-infected daughters, and also healthy non-infected mothers and their healthy daughters. Differential gene expression was evaluated as follows: 1) S. aureus-infected cows versus healthy non-infected cows(S vs. H, which include all the mothers and daughters), 2) S. aureus-infected mothers versus healthy non-infected mothers(SM vs. HM), and 3) S. aureus-infected daughters versus healthy noninfected daughters(SMD vs. HMD).Results: Analysis of all identified expressed genes in the four groups(SM, SMD, HM, and HMD) showed that EPOR,IL9, IFNL3, CCL26, IL26 were exclusively expressed in both the HM and HMD groups, and that they were significantly(P < 0.05) enriched for the cytokine-cytokine receptor interaction pathway. A total of 17, 13 and 10 differentially expressed genes(DEGs)(FDR Padj. < 0.1 and |FC| > 1.2) were detected in the three comparisons, respectively. DEGs with P < 0.05 and |FC| > 2 were used for functional enrichment analyses. For the S vs. H comparison, DEGs detected included CCL20, IL13 and MMP3, which are associated with the IL-17 signaling pathway. In the SM vs. HM and SMD vs. HMD comparisons, five(BLA-DQB, C1 R, C2, FCGR1 A, and KRT10) and six(BLA-DQB, C3 AR1, CFI, FCAR, FCGR3 A, and LOC10498484) genes, respectively, were involved in the S. aureus infection pathway.Conclusions: Our study provides insights into the transcriptomic responses of bovine peripheral blood leukocytes across two generations of cattle naturally infected with S. aureus. The genes highlighted in this study could serve as expression biomarkers for mastitis and may also contain sequence variation that can be used for genetic improvement of dairy cattle for resilience to mastitis.

Novel SNPs in IL-17F and IL-17A genes associated with somatic cell count in Chinese Holstein and Inner-Mongolia Sanhe cattle

Background： Bovine mastitis is the most common and costly disease of lactating cattle worldwide. Apart from milk somatic cell count（SCC） and somatic cell score（SCS）, serum cytokines such as interleukin-17（IL-17） and interleukin-4（IL-4） may also be potential indicators for bovine mastitis. The present study was designed to investigate the effects of single nucleotide polymorphisms（SNPs） in bovine IL-17 F and IL-17 A genes on SCC, SCS and serum cytokines in Chinese Holstein and Inner-Mongolia Sanhe cattle, and to compare the m RNA expression variations of the cows with different genotypes.Results： A total of 464 lactating cows（337 Holstein and 127 Inner-Mongolia Sanhe cattle） were screened for SNPs identification and the data were analyzed using fixed effects of herd, parity, season and year of calving by general linear model procedure. The results revealed that SNP g.24392436 C ＆gt; T in IL-17 F and SNP g.24345410 A ＆gt; G in IL-17 A showed significant effects on SCC and IL-4 in Holstein（n = 337） and on IL-17 and IL-4 in Sanhe cattle（n = 127）. The homozygous GG genotype of SNP g.24345410 A ＆gt; G had significantly higher m RNA expression compared with the heterozygous AG genotype.Conclusions： The results indicate that IL-17 F and IL-17 A could be powerful candidate genes of mastitis resistance and the significant SNPs might be useful genetic markers against mastitis in both dairy and dual purpose cattle.

A novel method for rapid and reliable detection of complex vertebral malformation and bovine leukocyte adhesion deficiency in Holstein cattle

Background： Complex vertebral malformation （CVM） and bovine leukocyte adhesion deficiency （BLAD） are two autosomal recessive lethal genetic defects frequently occurring in Holstein cattle, identifiable by single nucleotide polymorphisms. The objective of this study is to develop a rapid and reliable genotyping assay to screen the active Holstein sires and determine the carrier frequency of CVM and BLAD in Chinese dairy cattle population. Results： We developed real-time PCR-based assays for discrimination of wild-type and defective alleles, so that carriers can be detected. Only one step was required after the DNA extraction from the sample and time consumption was about 2 hours. A total of 587 Chinese Holstein bulls were assayed, and fifty-six CVM-carriers and eight BLAD-carriers were identified, corresponding to heterozygote carrier frequencies of 9.54% and 1.36%, respectively. The pedigree analysis showed that most of the carriers could be traced back to the common ancestry, Osborndale Ivanhoe for BLAD and Pennstate Ivanhoe Star for CVM. Conclusions： These results demonstrate that real-time PCR is a simple, rapid and reliable assay for BLAD and CVM defective allele detection. The high frequency of the CVM allele suggests that implementing a routine testing system is necessary to gradually eradicate the deleterious gene from the Chinese Holstein population.

Weighted single-step GWAS and RNA sequencing reveals key candidate genes associated with physiological indicators of heat stress in Holstein cattle

Background: The study of molecular processes regulating heat stress response in dairy cattle is paramount for developing mitigation strategies to improve heat tolerance and animal welfare. Therefore, we aimed to identify quantitative trait loci(QTL) regions associated with three physiological indicators of heat stress response in Holstein cattle, including rectal temperature(RT), respiration rate score(RS), and drooling score(DS). We estimated genetic parameters for all three traits. Subsequently, a weighted single-step genome-wide association study(WssGWAS) was performed based on 3200 genotypes, 151,486 phenotypic records, and 38,101 animals in the pedigree file. The candidate genes located within the identified QTL regions were further investigated through RNA sequencing(RNA-seq) analyses of blood samples for four cows collected in April(non-heat stress group) and four cows collected in July(heat stress group).Results: The heritability estimates for RT, RS, and DS were 0.06, 0.04, and 0.03, respectively. Fourteen, 19, and 20 genomic regions explained 2.94%, 3.74%, and 4.01% of the total additive genetic variance of RT, RS, and DS, respectively. Most of these genomic regions are located in the Bos taurus autosome(BTA) BTA3, BTA6, BTA8, BTA12, BTA14, BTA21, and BTA24. No genomic regions overlapped between the three indicators of heat stress, indicating the polygenic nature of heat tolerance and the complementary mechanisms involved in heat stress response. For the RNA-seq analyses, 2627 genes were significantly upregulated and 369 downregulated in the heat stress group in comparison to the control group. When integrating the WssGWAS, RNA-seq results, and existing literature, the key candidate genes associated with physiological indicators of heat stress in Holstein cattle are: PMAIP1, SBK1, TMEM33, GATB, CHORDC1, RTN4IP1, and BTBD7.Conclusions: Physiological indicators of heat stress are heritable and can be improved through direct selection. Fifty-three QTL regions associated with heat stress indicators confirm the polygenic nature and complex genetic determinism of heat tolerance in dairy cattle. The identified candidate genes will contribute for optimizing genomic evaluation models by assigning higher weights to genetic markers located in these regions as well as to the design of SNP panels containing polymorphisms located within these candidate genes.

Evaluation of heat stress effects on cellular and transcriptional adaptation of bovine granulosa cells

Background:Heat stress is known to affect follicular dynamics,oocyte maturation,and fertilization by impairing steroidogenic ability and viability of bovine granulosa cell(bGCs).The present study explored the physiological and molecular response of bGCs to different heat stress intensities in-vitro.We exposed the primary bGCs to heat stress(HS)at 39℃,40℃ and 41℃ along with control samples(38℃)for 2 h.To evaluate the impact of heat stress on bGCs,several in vitro cellular parameters including cell apoptosis,intracellular reactive oxygen species(ROS)accumulation and HSP70 kinetics were assessed by flow cytometry,florescence microscopy and western blot,respectively.Furthermore,the ELISA was performed to confirm the 17β-estradiol(E2)and progesterone(P4)levels.In addition,the RNA sequencing(RNA-Seq)method was used to get the molecular based response of bGCs to different heat treatments.Results:Our findings revealed that the HS significantly decreased the cell viability,E2 and P4 levels in bGCs,whereas,increased the cellular apoptosis and ROS.Moreover,the RNA-Seq experiments showed that all the treatments(39℃,40℃ and 41℃)significantly regulated many differentially expressed genes(DEGs)i.e.BCL2L1,STAR,CYP11A1,CASP3,SOD2,HSPA13,and MAPK8IP1 and pathways associated with heat stress,apoptosis,steroidogenesis,and oxidative stress.Conclusively,our data demonstrated that the impact of 40°C treatment was comparatively detrimental for cell viability,apoptosis and ROS accumulation.Notably,a similar trend of gene expression was reported by RT-qPCR for RNA-seq data.Conclusions:Our study presented a worthy strategy for the first time to characterize the cellular and transcriptomic adaptation of bGCs to heat stress(39,40 and 41°C)in-vitro.The results infer that these genes and pathways reported in present study could be useful candidates/indicators for heat stress research in dairy cattle.Moreover,the established model of bGCs to heat stress in the current study provides an appropriate platform to understand the mechanism of how heat-stressed bGCs can affect the quality of oocytes and developing embryo.

Estimation of Genetic Parameters for 305 Days Milk Yields and Calving Interval in Xinjiang Brown Cattle

This study was conducted to estimate variance components and genetic parameters for 305 days mature equivalent milk yields (MEM) and calving interval (CAI) of registered Xinjiang Brown cattle. The total records were 3940 including 2579 for 305-day MEM and 1970 for CAI, which were collected from Xinjiang Urumqi Cattle Breeding farm in China with calving records from 1990 to 2008. Genetic parameters were obtained by multiple trait derivative-free restricted maximum likelihood (MTDFREML) using animal model. The model included year, season, parity and calving interval of calving for 305 days MEM, and year, season and parity of birth for CAI as fixed effects. Heritability for 305 days MEM was moderate (0.39) and in the same range of parameters estimated in management systems with medium production levels. Heritability of calving interval was small (0.02) as fertility traits for Xinjiang Brown cattle. Estimates of genetic and environmental correlations between 305 days MEM and CAI were 0.47 and 0.37, respectively. Estimates of genetic variation and heritability indicated that selection would result in genetic improvement of production traits. Estimates of both heritability and genetic variation for CAI were small, which indicates that genetic improvement would be difficult.

Genomic and transcriptomic analyses enable the identification of important genes associated with subcutaneous fat deposition in Holstein cows

Subcutaneous fat deposition has many important roles in dairy cattle,including immunological defense and mechanical protection.The main objectives of this study are to identify key candidate genes regulating subcutaneous fat deposition in high-producing dairy cows by integrating genomic and transcriptomic datasets.A total of 1654 genotyped Holstein cows are used to perform a genome-wide association study(GWAS)aiming to identify genes associated with subcutaneous fat deposition.Subsequently,weighted gene co-expression network analyses(WGCNA)are conducted based on RNA-sequencing data of 34 cows and cow yield deviations of subcutaneous fat deposition.Lastly,differentially expressed(DE)m RNA,lnc RNA,and differentially alternative splicing genes are obtained for 12 Holstein cows with extreme and divergent phenotypes for subcutaneous fat deposition.Forty-six protein-coding genes are identified as candidate genes regulating subcutaneous fat deposition in Holstein cattle based on GWAS.Eleven overlapping genes are identified based on the analyses of DE genes and WGCNA.Furthermore,the candidate genes identified based on GWAS,WGCNA,and analyses of DE genes are significantly enriched for pathways involved in metabolism,oxidative phosphorylation,thermogenesis,fatty acid degradation,and glycolysis/gluconeogenesis pathways.Integrating all findings,the NID2,STARD3,UFC1,DEDD,PPP1R1B,and USP21 genes are considered to be the most important candidate genes influencing subcutaneous fat deposition traits in Holstein cows.This study provides novel insights into the regulation mechanism underlying fat deposition in high-producing dairy cows,which will be useful when designing management and breeding strategies.

Cs_(3)Bi_(2)l_(9)-hydroxyapatite composite waste forms for cesium and iodine immobilization

Perovskite-based ceramic composites were developed as potential waste form materials for immobilizing cesium(Cs)and iodine(I)with high waste loadings and chemical durability.The perovskite Cs_(3)Bi_(2)I_(9)has high Cs(22 wt%)and I(58 wt%)content,and thus can be used as a potential host phase to immobilize these critical radionuclides.In this work,the perovskite Cs_(3)Bi_(2)I_(9)phase was synthesized by a cost effective solution-based approach,and was embedded into a highly durable hydroxyapatite matrix by spark plasma sintering to form dense ceramic composite waste forms.The chemical durabilities of the monolithic Cs_(3)Bi_(2)I_(9)and Cs_(3)Bi_(2)I_(9)-hydroxyapatite composite pellets were investigated by static and semi-dynamic leaching tests,respectively.Cs and I are incongruently released from the matrix for both pure Cs_(3)Bi_(2)I_(9)and composite structures.The normalized Cs release rate is faster than that of I,which can be explained by the difference in the strengths between Cs-I and Bi-I bonds as well as the formation of insoluble micrometer-sized BiOI precipitates.The activation energies of elemental releases based on dissolution and diffusion-controlled mechanisms are determined with significantly higher energy barriers for dissolution from the composite versus that of the monolithic Cs_(3)Bi_(2)I_(9).The ceramic-based composite waste forms exhibit excellent chemical durabilities and waste loadings,commensurate with the state-of-the-art glass-bonded perovskite composites for I and Cs immobilization.