A note on QTL detecting for censored traits

Fang, Yixin

doi:10.1051/gse:2005037

Cited by 3 publications

(3 citation statements)

References 12 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The effects of saponins on in vitro rumen fermentation and the microbial composition are influenced by diet composition (Patra and Yu, 2015). Growing cattle need fiber for rumen development, and soybean hulls and alfalfa hay are two fiber sources that are widely used in cattle production (Richards et al, 2006; Jahani-Moghadam et al, 2015). In this study, we hypothesized that the effects of tea saponins on the rumen microbiota might be influenced by the dietary fiber source and that an interaction between the rumen microbiota and rumen metabolites exists, which would demonstrate a regulatory role of saponins on rumen metabolism.…”

Section: Introductionmentioning

confidence: 99%

Saponin-Induced Shifts in the Rumen Microbiome and Metabolome of Young Cattle

et al. 2019

View full text Add to dashboard Cite

The aim of this study was to explore the effects of saponins on the rumen microbiota and the ruminal metabolome. Alfalfa hay (AH) and soybean hulls (SH) were used as fiber sources for the control diets. The AH and SH diets were supplemented with tea saponins resulting in two additional diets named AHS and SHS, respectively. These 4 diets were fed to 24 young male Holstein cattle ( n = 6 per diet). After 28 days of feeding, the rumen fluid from these cattle was collected using an oral stomach tube. Illumina MiSeq sequencing and ultrahigh-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (UHPLC-QTOF/MS) were used to investigate the changes in the ruminal microbes and their metabolites. The relative abundance of Prevotellaceae_YAB2003 increased, while Ruminococcaceae_NK4A214 and Lachnospiraceae_NK3A20 decreased in SHS and AHS compared to SH and AHS, respectively. Feeding SHS resulted in higher ruminal concentrations of squalene, lanosterol, 3-phenylpropanoic acid, and citrulline compared to SH. The different microbial genes predicted by Tax4Fun were involved in amino sugar and nucleotide sugar metabolism. The pathways of arginine and proline metabolism, purine metabolism, and pyrimidine metabolism were enriched by different metabolites. Moreover, in the SH group, a positive correlation was observed between Prevotella_1 ( Bacteroidetes ), Prevotellaceae_YAB2003 ( Bacteroidetes ), and Christensenellaceae_R.7 ( Firmicutes ), and the metabolites, including citrulline, lanosterol, and squalene. The increased abundances of Prevotella_1 , Ruminococcaceae_UCG.002 , and Prevotellaceae_YAB2003 might result in increased fiber digestion and nutrient utilization but nutrient digestion was not measured in the current study. In summary, saponins have the ability to modulate the ruminal microbial community and ruminal metabolites and thus affect the rumen environment. However, the response seems to be dependent on the composition of the basal diet. This study provides a comprehensive overview of the microbial and biochemical changes in the rumen of cattle fed saponins.

show abstract

Section: Introductionmentioning

confidence: 99%

Saponin-Induced Shifts in the Rumen Microbiome and Metabolome of Young Cattle

et al. 2019

View full text Add to dashboard Cite

show abstract

“…While the purpose of candidate gene studies is to confirm a biological hypothesis, the aim of GWAS is to uncover novel genes that were not known before to be associated with a given biomarker. Although the issue of dealing with censored data in these contexts has been extensively investigated in the last decade (Epstein et al., ; Diao et al., ; Diao and Lin, ; Fang, ; Li et al., ), the omission of ND values from the analyses is still common although it has been demonstrated that this may lead to biased estimates (Schafer, ; Little and Rubin, ), particularly when the proportion of ND values is above 10% (Lubin et al., ).…”

Section: Introductionmentioning

confidence: 99%

Bayesian analysis of censored response data in family‐based genetic association studies

Pattaro

Minelli

et al. 2016

Biometrical J

View full text Add to dashboard Cite

Biomarkers are subject to censoring whenever some measurements are not quantifiable given a laboratory detection limit. Methods for handling censoring have received less attention in genetic epidemiology, and censored data are still often replaced with a fixed value. We compared different strategies for handling a left-censored continuous biomarker in a family-based study, where the biomarker is tested for association with a genetic variant, S, adjusting for a covariate, X. Allowing different correlations between X and S, we compared: simple substitution of censored observations with the detection limit followed by a linear mixed effect model (LMM); Bayesian model with non-informative priors; Tobit model with robust standard errors; the mutiple imputation (MI) with and without S in the imputation followed by a LMM. Our comparison was based on real and simulated data in which 20% and 40% censoring were artificially induced. The complete data was also analysed with a LMM. In the MICROS study, the Bayesian model gave results closer to those obtained with the complete data. In the simulations, simple substitution was always the most biased method; the Tobit approach gave the least biased estimates at all censoring levels and correlation values; the Bayesian model and both MI approaches gave slightly biased estimates but smaller root mean square errors. On the basis of these results the Bayesian approach is highly recommended for candidate gene studies; however, the computationally simpler Tobit and the MI without S are both good options for genome-wide studies.

show abstract

“…

…”

mentioning

confidence: 99%

The anti–heat stress effects of Chinese herbal medicine prescriptions and rumen‐protected γ‐aminobutyric acid on growth performance, apparent nutrient digestibility, and health status in beef cattle

Chen

Guo

Song

et al. 2020

Animal Science Journal

View full text Add to dashboard Cite

The high temperature and humid weathers coupled with low wind speed can induce heat stress in animal, resulting in reduced growth performance, compromised health status, or even death (Mader, Davis, & Brown-Brandl, 2006). Heat stress is known to disturb metabolic and physiological processes required for optimal cattle productivity, as well as cattle immunity (Collier, Collier, Rhoads, & Baumgard, 2008; Rhoads et al., 2009; West, 2003). Previous studies demonstrated that heat stress lowers average daily feed intake (ADFI) and average daily gain (ADG), which significantly increases breeding cost and compromises production profit (Piotr, Sabina, & Jacek, 2018; Polsky & Von Keyserlingk, 2017). Therefore, it is necessary to develop anti-heat stress therapy to improve the cattle production efficiency. Natural products, such as traditional Chinese herbal medicine (CHM) and γ-aminobutyric acid (GABA), have received remarkable attention due to their anti-heat stress potential (Song, Xu, Wang, &

show abstract

A note on QTL detecting for censored traits

Cited by 3 publications

References 12 publications

Saponin-Induced Shifts in the Rumen Microbiome and Metabolome of Young Cattle

Saponin-Induced Shifts in the Rumen Microbiome and Metabolome of Young Cattle

Bayesian analysis of censored response data in family‐based genetic association studies

The anti–heat stress effects of Chinese herbal medicine prescriptions and rumen‐protected γ‐aminobutyric acid on growth performance, apparent nutrient digestibility, and health status in beef cattle

Contact Info

Product

Resources

About