11 sustainable plant breeding

Plant Breeding 132, 1–9 (2013) © 2012 Blackwell Verlag GmbH doi:10.1111/pbr.12026 Review Sustainable plant breeding W A L L A C E A C O W L I N G 1, The UWA Institute of Agriculture M082, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; Canola Breeders Western Australia Pty Ltd, Locked Bag 888, Como, WA 6952, Australia; Corresponding author, E-mail: wallace cowling@uwa.edu.au With figure Received August 1, 2012/Accepted October 18, 2012 Communicated by J Leon Abstract Plant breeders disrupt Hardy–Weinberg equilibrium through selection, non-random mating, drift, migration and mutation Sustainable plant breeding can be defined as productive and competitive breeding that is achieved without loss of genetic diversity in the elite breeding population during the professional career of the breeder Breeding is often productive but not sustainable From 1974 to 2000, the animal breeding programme Meatlinc in the United Kingdom had effective population size of 95, population inbreeding of 0.19% per year and generation interval of 2.15 years Genetic progress in Meatlinc tripled in the years following introduction of best linear unbiased prediction (BLUP) selection (based on the information from relatives) in 1992 Canola breeding in Australia from 1970 to 2000 had longer generation interval (6 years), smaller effective population size (0.7% per year) BLUP selection in canola was first reported in 2010 Neither programme replaced genetic diversity lost through selection and drift Most breeding programmes violate conditions of the infinitesimal model, thereby reducing predictability of selection, but breeders can minimize these limitations to sustainable plant breeding Key words: genetic improvement — BLUP selection — genetic selection — pedigree selection — genomic selection — evolutionary forces — animal model — genotype environment interaction This review considers the impact of evolutionary forces that disrupt Hardy–Weinberg equilibrium in plant breeding programmes and affect the competitiveness and sustainability of plant breeding Plant breeders influence evolutionary processes to develop superior varieties from their elite breeding pools through selection, migration, mutation, random genetic drift (effective population size) and designed mating systems In practice, either with or without planned intervention, plant breeders add or gain new alleles through migration and mutation, re-arrange alleles through intermating and genetic recombination, and remove or lose alleles through selection and random genetic drift How this is done affects the competitiveness and sustainability of plant breeding in the long term Sustainable plant breeding can be defined as productive and competitive breeding that is achieved without loss of genetic diversity in the elite breeding population during the professional career of the breeder A sustainable plant breeding programme will maintain or increase genetic diversity in the elite breeding pool through migration and mutation The question that many breeders (or their bosses) ask is ‘will a genetically diverse breeding programme be competitive?’ Breeders are reluctant to cross outside of elite pools, because migration from exotic germplasm into elite breeding pools is almost always accompanied by negative impacts on quantitative trait performance (Rasmusson and Phillips 1997) This does not have to be the case A two-phase process of migration from wild or exotic germplasm into elite crop breeding pools was proposed to avoid such negative impacts (Cowling et al 2009), and this two-phase process forms an integral part of the successful recurrent introgression population enrichment (RIPE) barley breeding system (Falk 2010) Migration from 2-row to 6-row barley through cycles of crossing and selection improved yield in the elite 6-row breeding pool (Peel and Rasmusson 2000), and a back-crossing process (combined with markerassisted selection) was used to successfully migrate alleles for grain yield from wild into cultivated rice (McCouch et al 2007) Clearly, valuable alleles exist in wild and exotic germplasm for complex traits such as yield and methods exist to assist migration of these alleles while minimizing the negative impacts of linkage drag ‘Prebreeding’ is a term often used in relation to plant breeding activities dedicated to enlarging genetic diversity and enhancing genetic knowledge Often prebreeding is physically and genetically isolated from commercial breeding The focus of prebreeders is normally on the identification of major gene traits and molecular markers, while commercial breeders focus on introgression of these major genes into elite breeding pools by marker-assisted backcrossing Potentially valuable minor alleles for economic traits require special methods for incorporation into elite breeding populations from prebreeding or exotic sources, and such methods (discussed later in this review) are predicated on a direct link between prebreeding and commercial breeding Plant breeders have powerful selection tools to improve response to selection, such as best linear unbiased prediction (BLUP) selection based on the information from relatives in the pedigree, or whole-genome marker data in the case of genomic selection Ironically, the cumulative effect of selection reduces effective population size because of fewer parents and also because parents tend to be close relatives (Walsh and Lynch 2012c) Therefore, breeders must find ways to replenish genetic diversity in elite breeding pools, as replenishment of genetic diversity at the elite level will be even more important as we wileyonlinelibrary.com W A COWLING move towards BLUP and genomic selection (Cowling et al 2011) Genetic Diversity – The Impact of Small Effective Population Size and Random Genetic Drift Successful crop genetic improvement is demonstrated by corn breeding in the USA Corn hybrids released around 2000 yielded 10 tonnes per hectare, more than twice the yield of hybrids released in 1930s and 1940s, when tested in historical variety trials (Duvick et al 2004) Modern corn varieties in the USA are based on six founder genotypes, which contributed on average 90% of the pedigrees of maize hybrids developed for the westcentral USA corn belt around 2000 (Duvick et al 2004) Allelic diversity, measured by the average number of alleles per locus at 298 simple sequence repeat (SSR) loci, was