Economic evaluation of progeny-testing and genomic selection schemes for small-sized nucleus dairy cattle breeding programs in developing countries

Breeding strategies for improving smallholder dairy cattle productivity in Sub-Saharan Africa

Breeding strategies for smallholder dairy farming systems in Sub-Saharan Africa (SSA) were simulated and evaluated considering cow traits identified as priorities by farmers in different agro-ecological zones. These traits were related to cow milk yield, fertility, temperament, feed intake and disease resistance. The first breeding strategy was based on continuous importation of genetically superior exotic dairy sire semen to SSA and crossing with local females leading to a gradual upgrade of the indigenous population. The second strategy assumed that semen from elite exotic bulls would be imported to SSA and used on indigenous cows to produce F1 animals. Thereafter, elite animals would be selected from within the F1 and each subsequent generation to establish a new synthetic breed. The third strategy was to improve the indigenous population by genetically selecting the best sires available domestically. Results showed positive genetic progress for all breeding goal traits. After 15 generations of selection, the genetic response of the importation strategy exceeded the corresponding genetic response of the synthetic breed strategy by 20%-60%. The former also exceeded the genetic response of the indigenous breed improvement strategy by 43%-75%. Potentially there is an opportunity for breeders to choose an appropriate breeding strategy that fits a specific need of smallholder dairy farmers.

Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other Two Bos Species Adapted to Divergent Climatic Conditions

Understanding the biological mechanisms of climatic adaptation is of paramount importance for the optimization of breeding programs and conservation of genetic resources. The aim of this study was to investigate genetic diversity and unravel genomic regions potentially under selection for heat and/or cold tolerance in thirty-two worldwide cattle breeds, with a focus on Chinese local cattle breeds adapted to divergent climatic conditions, Datong yak (Bos grunniens; YAK), and Bali (Bos javanicus) based on dense SNP data. In general, moderate genetic diversity levels were observed in most cattle populations. The proportion of polymorphic SNP ranged from 0.197 (YAK) to 0.992 (Mongolian cattle). Observed and expected heterozygosity ranged from 0.023 (YAK) to 0.366 (Sanhe cattle; SH), and from 0.021 (YAK) to 0.358 (SH), respectively. The overall average inbreeding (±SD) was: 0.118 ± 0.028, 0.228 ± 0.059, 0.194 ± 0.041, and 0.021 ± 0.004 based on the observed versus expected number of homozygous genotypes, excess of homozygosity, correlation between uniting gametes, and runs of homozygosity (ROH), respectively. Signatures of selection based on multiple scenarios and methods (F ST, HapFLK, and ROH) revealed important genomic regions and candidate genes. The candidate genes identified are related to various biological processes and pathways such as heat-shock proteins, oxygen transport, anatomical traits, mitochondrial DNA maintenance, metabolic activity, feed intake, carcass conformation, fertility, and reproduction. This highlights the large number of biological processes involved in thermal tolerance and thus, the polygenic nature of climatic resilience. A comprehensive description of genetic diversity measures in Chinese cattle and YAK was carried out and compared to 24 worldwide cattle breeds to avoid potential biases. Numerous genomic regions under positive selection were detected using three signature of selection methods and candidate genes potentially under positive selection were identified. Enriched function analyses pinpointed important biological pathways, molecular function and cellular components, which contribute to a better understanding of the biological mechanisms underlying thermal tolerance in cattle. Based on the large number of genomic regions identified, thermal tolerance has a complex polygenic inheritance nature, which was expected considering the various mechanisms involved in thermal stress response.

Enhancing Genetic Gain through Genomic Selection: From Livestock to Plants

Although long-term genetic gain has been achieved through increasing use of modern breeding methods and technologies, the rate of genetic gain needs to be accelerated to meet humanity's demand for agricultural products. In this regard, genomic selection (GS) has been considered most promising for genetic improvement of the complex traits controlled by many genes each with minor effects. Livestock scientists pioneered GS application largely due to livestock's significantly higher individual values and the greater reduction in generation interval that can be achieved in GS. Large-scale application of GS in plants can be achieved by refining field management to improve heritability estimation and prediction accuracy and developing optimum GS models with the consideration of genotype-by-environment interaction and non-additive effects, along with significant cost reduction. Moreover, it would be more effective to integrate GS with other breeding tools and platforms for accelerating the breeding process and thereby further enhancing genetic gain. In addition, establishing an open-source breeding network and developing transdisciplinary approaches would be essential in enhancing breeding efficiency for small- and medium-sized enterprises and agricultural research systems in developing countries. New strategies centered on GS for enhancing genetic gain need to be developed.

Genetic benefits of genomic selection breeding programmes considering foreign sire contributions

Background

In modern dairy breeding programmes, high contributions from foreign sires are nearly always present. Genotyping, and therefore genomic selection (GS), concern only a subpopulation of the breeding programme’s wider dairy population. These features of a breeding programme contribute in different ways to the rate of genetic gain for the wider industry.

Methods

A deterministic recursive gene flow model across subpopulations of animals in a dairy industry was created to predict the commercial performance of replacement heifers and future artificial insemination bulls. Various breeding strategies were assessed by varying the reliability of breeding values, the genetic contributions from subpopulations, and the genetic trend and merit of the foreign subpopulation.

Results

A higher response in the true breeding goal measured in standard deviations (SD) of true merit (G) after 20 years of selection can be achieved when genetic contributions shift towards higher merit alternatives compared to keeping them fixed. A foreign annual genetic trend of 0.08 SD of the breeding goal, while the domestic genetic trend is 0.10 SD, results in the overall net present value of genetic gain increasing by 1.2, 2.3, and 3.4% after 20 years as the reliability of GS in the domestic population increased from 0.3 to 0.45, 0.60 and 0.75. With a foreign genetic trend of 0.10 SD, these increases are more modest; 0.9, 1.7, and 2.4%. Increasing the foreign genetic trend so that it is higher than the domestic trend erodes the benefits of increasing the reliability of domestic GS further.

Conclusions

Having a foreign source of genetic material with a high rate of genetic progress contributes substantially to the benefits of domestic genetic progress while at the same time reducing the expected returns from investments to improve the accuracy of genomic prediction in the home country.

Leveraging Available Resources and Stakeholder Involvement for Improved Productivity of African Livestock in the Era of Genomic Breeding

The African continent is home to diverse populations of livestock breeds adapted to harsh environmental conditions with more than 70% under traditional systems of management. Animal productivity is less than optimal in most cases and is faced with numerous challenges including limited access to adequate nutrition and disease management, poor institutional capacities and lack of adequate government policies and funding to develop the livestock sector. Africa is home to about 1.3 billion people and with increasing demand for animal proteins by an ever growing human population, the current state of livestock productivity creates a significant yield gap for animal products. Although a greater section of the population, especially those living in rural areas depend largely on livestock for their livelihoods; the potential of the sector remains underutilized and therefore unable to contribute significantly to economic development and social wellbeing of the people. With current advances in livestock management practices, breeding technologies and health management, and with inclusion of all stakeholders, African livestock populations can be sustainably developed to close the animal protein gap that exists in the continent. In particular, advances in gene technologies, and application of genomic breeding in many Western countries has resulted in tremendous gains in traits like milk production with the potential that, implementation of genomic selection and other improved practices (nutrition, healthcare, etc.) can lead to rapid improvement in traits of economic importance in African livestock populations. The African livestock populations in the context of this review are limited to cattle, goat, pig, poultry, and sheep, which are mainly exploited for meat, milk, and eggs. This review examines the current state of livestock productivity in Africa, the main challenges faced by the sector, the role of various stakeholders and discusses in-depth strategies that can enable the application of genomic technologies for rapid improvement of livestock traits of economic importance.