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The delivery of genomic sequences for most livestock species over the past 10–15 years has generated the potential to revolutionize livestock production globally, by providing farmers with the ability to match individual animals to the requirements of rapidly changing climates, production systems and markets. The technology which has had the greatest impact to date is genomic selection [1]. Genomic selection uses information from a large number of genetic markers or single nucleotide polymorphisms (SNPs) in conjunction with measurements (phenotypes) of important traits in livestock and plants to estimate breeding values, without requiring precise knowledge of where specific genes are located in the genome. Since the principles of genomic selection were initially proposed in 2001, genomic selection has been widely adopted in animal and plant breeding programs globally because of its ability to improve selection accuracy, reduce phenotyping and generation intervals and increase genetic gains. It has transformed the livestock and plant industries, as well as delivered human health diagnostic applications, adding billions of dollars and strong social and environmental benefits, particularly across the world's higher income countries.

However, genomic selection also requires improvements to the discovery of causal variations and genomic selection methodologies, greater efforts to overcome limitations associated with lack of essential phenotypes for expensive or difficult-to-measure traits, and the ongoing challenges with implementing genomic selection by smallholder livestock farmers in low–middle income countries. This Special Issue examines some of these issues to identify successes and ongoing limitations that must be overcome to achieve practical applications and social, economic and environmental benefits for all livestock producers in the future.

Genomic selection has transformed animal and plant breeding in advanced economies globally, resulting in economic, social and environmental benefits worth billions of dollars annually. Although genomic selection offers great potential in low- to middle-income countries because detailed pedigrees are not required to estimate breeding values with useful accuracy, the difficulty of effective phenotype recording, complex funding arrangements for a limited number of essential reference populations in only a handful of countries, questions around the sustainability of those livestock-resource populations, lack of on-farm, laboratory and computing infrastructure and lack of human capacity remain barriers to implementation. This paper examines those challenges and explores opportunities to mitigate or reduce the problems, with the aim of enabling smallholder livestock-keepers and their associated value chains in low- to middle-income countries to also benefit directly from genomic selection.

The world’s population is expected to increase significantly by 2050, leading to significantly increased demands for meat and dairy products. However, cattle are major emitters of greenhouse gases that speed up climate change. To achieve food security by 2050, livestock enterprises need to double their outputs from constant resources, in the face of increased competition for inputs such as land, water, grain and labour. To cope with climate change, the livestock need to be productive under hotter and drier climates and be able to tolerate increased challenges from parasites and vector-borne diseases. The best way for smallholder cattle farmers in tropical low-medium income countries to overcome these multiple challenges is to focus on improving the productivity of their herds. This paper discusses a range of simple and cost-effective options already available to smallholder farmers to significantly improve the productivity and profitability of their herds and by doing so, they will indirectly reduce greenhouse gas emissions from their cattle and improve the natural resource base on which their cattle graze. Improved herd productivity will in turn deliver significant social, environmental, economic and livelihood benefits to the smallholder farmers themselves and the communities and value chains in which they operate.

This paper reviews the literature relevant to the breeding of cattle grazed in tropical environments and particularly Indonesia. The aim is to identify new breeding opportunities for cattle owned by Indonesia’s smallholder farmers, whilst also conserving unique local cattle beef breeds. Crossbreeding has been practiced extensively in Indonesia, but to date there have been no well-designed programs, resulting in many mixed-breed animals and no ability to determine their genetic composition, productive capabilities or adaptation to environmental stressors. An example of within-breed selection of Bali cattle based on measured live weight has similarly disregarded other productive and adaptive traits. It is unlikely that smallholder farmers could manage effective crossbreeding programs due to the complexities of management required. However, a tropically adapted composite breed(s) could perhaps be developed and improved using within-breed selection. Establishing reference population(s) of local breeds or composites and using within-breed selection to genetically improve those herds may be feasible, particularly if international collaborations can be established to allow data-pooling across countries. The use of genomic information and a strong focus on all economically important traits in practical breeding objectives is critical to enable genetic improvement and conservation of unique Indonesian cattle breeds.

Integrated cattle and dryland farming systems in Indonesia use a range of crop residues and by products to feed cattle through intensive and extensive production systems. Intensive systems use stalls to house cattle and cut and carry feeding systems, primarily for fattening cattle. Under extensive systems, cattle are free-grazing,and the systems apply only where greater land areas exist and they are used for breeding and fattening cattle. This paper therefore specifically focuses on the opportunities that exist to improve beef production in dryland farming systems in Indonesia. The best strategies for smallholder farmers in Indonesia to improve beef production require farmers to focus on profitability and use proven management strategies, including a) using adapted cattle breeds resistant/tolerant to environmental stressor, b) understanding the market preference; c) managing cattle breeding herds based on rainfall patterns, d) keeping good records on all aspects of breeding and fattening activities and e) adjusting stocking rates in extensive system to match the carrying capacity of the land.