Software applications for providing comprehensive computing capabilities to problems related to mixed models in animal breeding

Several computer packages have been developed to accomplish improved programs for animal breeding and genetic selection. This paper described most of the currant software and provided suggestions for improved software. Khon Kaen University, Thailand, will provide free of charge the new software developed at Khon Kaen University by the author of this paper. The contact for requesting the software is listed: monchai@kku.ac.th.

Development of Genome-Wide Scan for Selection Signature in Farm Animals

Identifying targets of positive selection in farm animals has, until recently, been frustratingly slow, relying on the analysis of individual candidate genes. Genomics, however, has provided the necessary resources to systematically interrogate the entire genome for signatures of selection. This review described important recent results derived from the application of genome-wide scan to the study of genetic changes in farm animals. These included findings of regions of the genome that showed breed differentiation, evidence of selective sweeps within individual genomes and signatures of demographic events. Particular attention is focused on the study of the implications for domestication. To date, sixteen genome-wide scans for recent or ongoing positive selection have been performed in farm animals. A key challenge is to begin synthesizing these newly constructed maps of selection into a coherent narrative of animal breed evolutionary history and derive a deeper mechanistic understanding of how animal populations improve or evolve. The major insights from the surveyed studies are highlighted and directions for future study are suggested.

Candidate genes for male and female reproductive traits in Canchim beef cattle

Background： Beef cattle breeding programs in Brazil have placed greater emphasis on the genomic study of reproductive traits of males and females due to their economic importance. In this study, genome-wide associations were assessed for scrotal circumference at 210 d of age, scrotal circumference at 420 d of age, age at first calving, and age at second calving, in Canchim beef cattle. Data quality control was conducted resulting in 672,778 SNPs and 392 animals.Results： Associated SNPs were observed for scrotal circumference at 420 d of age（435 SNPs）, followed by scrotal circumference at 210 d of age（12 SNPs）, age at first calving（six SNPs）, and age at second calving（four SNPs）. We investigated whether significant SNPs were within genic or surrounding regions. Biological processes of genes were associated with immune system, multicellular organismal process, response to stimulus, apoptotic process, cellular component organization or biogenesis, biological adhesion, and reproduction.Conclusions： Few associations were observed for scrotal circumference at 210 d of age, age at first calving, and age at second calving, reinforcing their polygenic inheritance and the complexity of understanding the genetic architecture of reproductive traits. Finding many associations for scrotal circumference at 420 d of age in various regions of the Canchim genome also reveals the difficulty of targeting specific candidate genes that could act on fertility; nonetheless,the high linkage disequilibrium between loci herein estimated could aid to overcome this issue. Therefore, al relevant information about genomic regions influencing reproductive traits may contribute to target candidate genes for further investigation of causal mutations and aid in future genomic studies in Canchim cattle to improve the breeding program.

Animal Molecular Breeding(AMB)

Animal Molecular Breeding(ISSN 1927-5609)is an open access,peer reviewed journal published online by Bio Publisher.The journal is publishing all the latest and outstanding research articles,letters and reviews in all areas of animal molecular breeding,containing transgenic breeding and marker assisted breeding,particularly publishing innovative

Animal Molecular Breeding(AMB)

Animal Molecular Breeding(ISSN 1927-5609)is an open access,peer reviewed journal published online by Bio Publisher.The journal is publishing all the latest and outstanding research articles,letters and reviews in all areas of animal molecular breeding,containing transgenic breeding and marker assisted breeding,

Embryo-mediated genome editing for accelerated genetic improvement of livestock

Selecting beneficial DNA variants is the main goal of animal breeding.However,this process is inherently inefficient because each animal only carries a fraction of all desirable variants.Genome editing technology with its ability to directly introduce beneficial sequence variants offers new opportunities to modernize animal breeding by overcoming this biological limitation and accelerating genetic gains.To realize rapid genetic gain,precise edits need to be introduced into genomicallyselected embryos,which minimizes the genetic lag.However,embryo-mediated precision editing by homology-directed repair(HDR)mechanisms is currently an inefficient process that often produces mosaic embryos and greatly limits the numbers of available edited embryos.This review provides a summary of genome editing in bovine embryos and proposes an embryo-mediated accelerated breeding scheme that overcomes the present efficiency limitations of HDR editing in bovine embryos.It integrates embryo-based genomic selection with precise multi-editing and uses embryonic cloning with elite edited blastomeres or embryonic pluripotent stem cells to resolve mosaicism,enable multiplex editing and multiply rare elite genotypes.Such a breeding strategy would enable a more targeted,accelerated approach for livestock improvement that allows stacking of beneficial variants,even including novel traits from outside the breeding population,in the most recent elite genetic background,essentially within a single generation.