The R-package MoBPS provides a computationally efficient and flexible framework to simulate complex breeding programs and compare their economic and genetic impact. Simulations are performed on the base of individuals. MoBPS utilizes a highly efficient implementation with bit-wise data storage and matrix multiplications from the associated R-package miraculix allowing to handle large scale populations. Individual haplotypes are not stored but instead automatically derived based on points of recombination and mutations. The modular structure of MoBPS allows to combine rather coarse simulations, as needed to generate founder populations, with a very detailed modeling of todays' complex breeding programs, making use of all available biotechnologies. MoBPS provides pre-implemented functions for common breeding practices such as optimum genetic contributions and single-step GBLUP but also allows the user to replace certain steps with personalized and/or self-written solutions.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7263682 | PMC |
| http://dx.doi.org/10.1534/g3.120.401193 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Understanding the triacylglycerol-based carbon anabolic differentiation in Cyperus esculentus and Cyperus rotundus developing tubers via transcriptomic and metabolomic approaches.
BMC Plant Biol
December 2024
College of Agronomy and Biotechnology, Key Laboratory for Crop Production and Smart Agriculture of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China.
Background: Yellow nutsedge (Cyperus esculentus, known as 'YouShaDou' in China, YSD) and purple nutsedge (Cyperus rotundus, known as 'XiangFuZi' in China, XFZ), closely related Cyperaceae species, exhibit significant differences in triacylglycerol (TAG) accumulation within their tubers, a key factor in carbon flux repartitioning that highly impact the total lipid, carbohydrate and protein metabolisms. Previous studies have attempted to elucidate the carbon anabolic discrepancies between these two species, however, a lack of comprehensive genome-wide annotation has hindered a detailed understanding of the underlying molecular mechanisms.
Results: This study utilizes transcriptomic analyses, supported by a comprehensive YSD reference genome, and metabolomic profiling to uncover the mechanisms underlying the major carbon perturbations between the developing tubers of YSD and XFZ germplasms harvested in Yunnan province, China, where the plant biodiveristy is renowned worldwide and may contain more genetic variations relative to their counterparts in other places.
A complex acoustical environment during development enhances auditory perception and coding efficiency in the zebra finch.
J Neurosci
December 2024
Department of Psychology, University of Virginia, Charlottesville VA 22904, USA
Sensory experience during development has lasting effects on perception and neural processing. Exposing juvenile animals to artificial stimuli influences the tuning and functional organization of the auditory cortex, but less is known about how the rich acoustical environments experienced by vocal communicators affect the processing of complex vocalizations. Here, we show that in zebra finches (), a colonial-breeding songbird species, exposure to a naturalistic social-acoustical environment during development has a profound impact on auditory perceptual behavior and on cortical-level auditory responses to conspecific song.
View Article and Find Full Text PDFFat-tail allele-specific expression genes may affect fat deposition in tail of sheep.
PLoS One
December 2024
Embrapa Southeast Livestock, São Carlos, Brazil.
Different sheep breeds show distinct phenotypic plasticity in fat deposition in the tails. The genetic background underlying fat deposition in the tail of sheep is complex, multifactorial, and may involve allele-specific expression (ASE) mechanism to modulate allelic expression. ASE is a common phenomenon in mammals and refers to allelic imbalanced expression modified by cis-regulatory genetic variants that can be observed at heterozygous loci.
View Article and Find Full Text PDFExploring Gene Expression and Alternative Splicing in Duck Embryonic Myoblasts via Full-Length Transcriptome Sequencing.
Vet Sci
November 2024
College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China.
The duck industry is vital for supplying high-quality protein, making research into the development of duck skeletal muscle critical for improving meat and egg production. In this study, we leveraged Oxford Nanopore Technologies (ONT) sequencing to perform full-length transcriptome sequencing of myoblasts harvested from the leg muscles of duck embryos at embryonic day 13 (E13), specifically examining both the proliferative (GM) and differentiation (DM) phases. Our analysis identified a total of 5797 novel transcripts along with 2332 long non-coding RNAs (lncRNAs), revealing substantial changes in gene expression linked to muscle development.
View Article and Find Full Text PDFMulti-Omics Analysis Provides Insights into Green Soybean in Response to Cold Stress.
Metabolites
December 2024
Hainan Key Laboratory of Crop Genetics and Breeding, Institute of Food Crops, Hainan Academy of Agricultural Sciences, Haikou 571100, China.
Green soybean ( (L.) Merrill) is a highly nutritious food that is a good source of protein and fiber. However, it is sensitive to low temperatures during the growing season, and enhancing cold tolerance has become a research hotspot for breeding improvement.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!