In order to develop new varieties which for example respond to changing biotic and abiotic pressures, or have a commercial value such as improved nutritious values or new colours, the tools breeders use developed over time:
• Traditionally, breeding is based on the principle of crossing and selecting the naturally existing diversity of plants. Since the rediscovery of Mendel’s rules around 1900, breeders experimented with intentional crossing between selected parent plants to obtain desirable traits. If offspring had a highly beneficial trait, it was preserved and propagated for further breeding over generations.
• Tissue culture is among the earliest techniques used for growing plant cells (Haberlandt 1902). Further developments led to the application of tissue culture to five broad areas, namely, cell behaviour, plant modification and improvement, pathogen-free plants angermplasm storage, clonal propagation, and product formation, starting in the mid-1960s.
• In the mid 20th century, the development of hybrid varieties led to dramatic increases in yield in maize, followed by a range of crops. A hybrid variety is comprised of a population originating from a cross and is directly used as the commercial variety to be cultivated. Hybrids present enhanced performance and uniformity compared to either parent. Due to their hybrid nature, their offspring will segregate and result in a heterogenous population that will not perform as well as the hybrid parents.
• Internationally coordinated mutation breeding became popular in the 1960s, mainly radiation and the use of chemicals created genetic variation. It led to numerous new cultivated varieties of many species such as broccoli, nectarines, or rapeseed.
• The discovery of molecular markers since the early 1980s enabled breeders to track traits at the genetic level without waiting for the plant to mature. This marker assisted selection (MAS) technique made selection faster, cheaper and more precise.
• Genetic engineering tools were developed in the 1980s and 1990s. The decision in the U.S. to allow patents on genetically modified microorganisms (Chakrabarty vs Diamond 1980) and the patent on the rDNA technology (Stanford University and the University of California System) led to an uptake of genetic engineering. The available technique allows introducing transgenes into crops to obtain traits such as herbicide tolerance or insect resistance. Bt maize and Bt cotton, which are resistant to certain pests, are primary examples. In 1987, the U.S. start-up Calgene obtained a patent in the U.S. on a tomato with a trait for longer shelf life.
• The genomic sequencing of crop genomes provides understanding complex traits. The first full genome sequencing of the model plant Arabidopsis thaliana in the year 2000, is hailed as the turning point for the modern plant breeding research. Since then, hundreds of plant species, including all major agronomically relevant crops (such as rice (2002/2005), maize (2009), soybean (2010), millet (2017), wheat (2018), and oat (2022)), root crops (potato (2011)), vegetables (chickpea (2013), brassica (2014), cassava (2016), pea (2019)), or fruits (papaya (2005), apple (2010), peach (2013)), have been sequenced.
• Since around 2010, CRISPR/Cas and other genome editing technologies allow breeders to target modifications without introducing foreign genes. In particular CRISPR/Cas9 has been in the focus and is a key patented technology with applications in plants since 2014. The system has been continuously developed since its discovery and a broader range of tools are available such as base editing or prime editing. These use different tools such as Cpf1 (now called Cas12a).
• Speed breeding – combination of techniques used under controlled environments to accelerate the plant growth cycle while machine learning and genomic data analysis provides breeders with tools to optimise breeding decisions (precision breeding). Various companies – in particular in the U.S. - offer platforms to develop the envisaged plant as service providers (e.g. GreenVenus, Pairwise).
• Integrated approaches for ‘next-generation plant breeding’ – increasingly breeders can use integrated pipelines (platforms) that offer convergence of multiple advanced methods to optimise the development of improved plant varieties. Genomic selection, speed breeding, genome editing and pangenomics, high-throughput phenotyping are combined with machine learning and the integration of -omics – to name currently available tools. • Other tools including high-throughput phenotyping and genotyping expanded the array of tools and enabled the rapid analysis of large numbers of plants and their genomes.
