In the developing world, rural farmers rely on local breeds to play crucial roles
aimed at ameliorating the effects of adverse environments and resources shortages
in sustaining their livelihoods. The local breeds appear to be adapted to numerous
unfavorable environmental stressors that include worsening droughts characterized
by extreme temperatures and debilitating disease challenges, the epitome of low input
production systems. Breeding and genetics research programs are striving to develop
robust animals that are adapted to local conditions and can produce at optimal and
sustainable levels under constrained environments. Elucidating the intertwined relationship
between production environments and the genetics of animals, with the aim of establishing
selection priorities and developing suitable improvement strategies, is critical.
Previously, livestock improvement programs have failed to realize expected gains due
to the lack of performance data, pedigree records and funding, and worsened by such
factors as uncontrolled livestock breeding practices on communal pastures. Advances
in livestock genomics have facilitated the generation of “big data” in genetics through
the advent of whole genome/transcriptome sequencing, genome assemblies and genome-wide
SNP genotyping. Regardless of the room for genetic gains in local breeds and the anticipated
higher impact of genomics assisted breeding and selection, developing countries still
lag behind in the uptake of genomic technologies. This Research Topic addresses the
need for livestock genomics for developing countries through review articles, original
research articles and considerations of future opportunities.
The Research Topic yielded 23 articles that are either review (five papers) or original
research articles (18 papers) covering major livestock species kept in developing
countries including cattle (seven papers), sheep (five papers), goats (three papers),
and chickens (three papers). The manuscripts cover a broad range of genomic applications
such as genomic selection/assisted breeding, genome-wide association analysis, diversity
studies with a particular emphasis on adaptive genetic variation and signatures of
selection analysis, and some elements of functional genomics using RNA sequencing
and differential gene expression profiling. Whilst a broad range of genomic applications
are covered, there is a bias toward genomic diversity studies, indicating the limited
utility of other genomic applications due to inherent limitations to data collection
and funding that characterize most developing countries, and are highlighted in some
of the review articles.
The reviews provide an overview of the current and potential applications of genomics
in developing countries, the opportunities that can be used from other supporting
technologies such as reproductive technologies and the challenges and possible solutions
of applying genomics in a developing country context. According to Mrode et al., genotypic
data can provide solutions for parent verification, breed composition determination
and genetic evaluation for smallholder farmers. The review by Mrode et al., also highlights
the major problem of small reference populations, which could be overcome by across
regional genomic prediction programs that pull together data from multiple countries.
The review by Ducrocq et al. explores challenges facing developing countries, including
limited capacity to genotype, poor data management, multiple breeding goals emanating
from exposure to unfavorable conditions such as heat and diseases, requirement of
special attention on fitness traits and limited expertise to drive genomics programs.
Marshall et al. present case studies from Africa on the application of livestock genomics
which included the identification and development of unique breeds in the region.
This review also looks at the role of genomic studies on African livestock to understand
the genetics of particular diseases and in the potential of technologies such as gene
editing in disease management. The review by Van Marle-Kőster and Visser highlight
the benefits of a dual system of a highly developed commercial sector using the most
recent technologies vs. a small holder and communal sector in South Africa, and how
resources can be harnessed to advance both sectors. This review also highlights the
importance of national animal recording schemes and government funding to ensure progress
in driving the application of genomics across the two sectors. In line with this,
Ibeagha-Awemu et al. discuss the importance of leveraging available resources and
stakeholder involvement for coordinated improvement of livestock production in Africa.
The review further highlights in-depth approaches that can enable the application
of genomic technologies for rapid improvement of livestock traits of economic importance
in the era of genomic breeding.
The first set of original research papers present case studies of genomic selection
and genome-wide association analysis. Hosseini-Vardanjani et al. evaluate the gain
in accuracy of genomic evaluations using multi-breed reference populations and demonstrates
the utility of incorporating prior knowledge of principal components in genomic prediction
as well as the potential of a multi-breed reference population to contribute to enhanced
prediction accuracies. In the absence of conventional genetic evaluations and selection,
Mujibi et al. and Cheruiyot et al. use genomic data to understand breed composition
and associate it to production performance. Genome-wide association studies are often
challenging because of the need of very large number of experimental units with good
phenotypes. A genome-wide association study (GWAS) by Xu et al. highlights the potential
for different genetic mechanisms for litter size among sheep breeds. Nazari-Ghadikolaei
et al. identify candidate genes for coat color and mohair traits in the Iranian Markhoz
goats through a GWAS. Bhuiyan et al. use imputed sequence level SNP data in a GWAS
to identify variants in genic and exon regions significantly associated to carcass
traits in Korean Hanwoo cattle.
The second set of original research articles describes the common application of genomics
in smallholder livestock systems of developing countries such as analysis of the level
of admixture and investigation of signatures of selection in cattle (Chagunda et al.;
Alshawi et al.); sheep (Ahbara et al.; Al-Atiyat et al.; Edea et al.); goats (Onzima
et al.; Cui et al.) and in native chickens (Elbeltagy et al.; Walugembe et al.; Lawal
et al.). Finally, Pierce et al. investigate copy number variations (CNVs), which have
recently gained prominence, as a genomic tool, to ascertain genetic diversity and
population structure in South African cattle.
Only one study focuses on functional genomics, using RNA-Seq and differential gene
expression studies to investigate genetic and molecular mechanisms underlying traits
of importance in sheep (Ma et al.). This probably reflects the complexities of setting
up transcriptome experiments in largely uncontrolled smallholder farming systems of
Overall, the topic demonstrates the utility of genomics in diverse application across
species and geographical regions of the developing countries and the opportunities
that exist in the future.
FM and JS initiated the Research Topic and invited MR, EI-A, AJ, GG, and JM as topic
co-editors. FM drafted the Research Topic editorial. All authors participated in the
editorial process of this Research Topic, revised, and approved the final draft of
Conflict of Interest
The authors declare that the research was conducted in the absence of any commercial
or financial relationships that could be construed as a potential conflict of interest.