Genomic Selection and Use of Molecular Tools in Breeding Programs for Indigenous and Crossbred Cattle in Developing Countries: Current Status and Future Prospects

Abstract

Genomic selection (GS) has resulted in rapid rates of genetic gains especially in dairy cattle in developed countries resulting in a higher proportion of genomically proven young bulls being used in breeding. This success has been undergirded by well-established conventional genetic evaluation systems. Here, the status of GS in terms of the structure of the reference and validation populations, response variables, genomic prediction models, validation methods, and imputation efficiency in breeding programs of developing countries, where smallholder systems predominate and the basic components for conventional breeding are mostly lacking is examined. Also, the application of genomic tools and identification of genome-wide signatures of selection is reviewed. The studies on genomic prediction in developing countries are mostly in dairy and beef cattle usually with small reference populations (500–3,000 animals) and are mostly cows. The input variables tended to be pre-corrected phenotypic records and the small reference populations has made implementation of various Bayesian methods feasible in addition to GBLUP. Multi-trait single-step has been used to incorporate genomic information from foreign bulls, thus GS in developing countries would benefit from collaborations with developed countries, as many dairy sires used are from developed countries where they may have been genotyped and phenotyped. Cross validation approaches have been implemented in most studies resulting in accuracies of 0.20–0.60. Genotyping animals with a mixture of HD and LD chips, followed by imputation to the HD have been implemented with imputation accuracies of 0.74–0.99 reported. This increases the prospects of reducing genotyping costs and hence the cost-effectiveness of GS. Next-generation sequencing and associated technologies have allowed the determination of breed composition, parent verification, genome diversity, and genome-wide selection sweeps. This information can be incorporated into breeding programs aiming to utilize GS. Cost-effective GS in beef cattle in developing countries may involve usage of reproductive technologies (AI and in-vitro fertilization) to efficiently propagate superior genetics from the genomics pipeline. For dairy cattle, sexed semen of genomically proven young bulls could substantially improve profitability thus increase prospects of small holder farmers buying-in into genomic breeding programs.

Accelerating Genetic Gain in Sugarcane Breeding Using Genomic Selection

“…Interestingly, genetic gains were also reported for low-heritability traits such as disease resistance and fertility [73]. Consequently, GS has been implemented on a very large scale in other animal species such as beef cattle, pigs, sheep, and chicken [96,97].…”

Developments in genetic modification of cattle and implications for regulation, safety and traceability

“…These developments have revolutionized the sector. Advantages include, among others, time savings as progeny testing would normally require seven or more years, and a greater number of genetic markers beyond the individual ones (such as for milk casein) previously used [5,6] .…”

Effect of composition and size of the reference population in genotype imputation efficiency of INDUSCHIP in HF Crossbred cattle

“…To implement genomic selection in India for indicus breeds and their taurine crosses a medium-density customized chip i.e INDUSCHIP v1 consisting of 45700 SNPs sampled from HD genotype of the mostly four indicus breeds (Gir, Sahiwal, Kankrej, Redsindhi) and their taurine crosses (HF cross & Jersey cross) have been developed. (Mrode et al 2019). The genotyping chip contained around 41000 SNPs from HD data having high MAF (0.25), uniformly distributed across the genome for all the breeds under study with an average distance between two consecutive SNPs around 65 kbps.…”