Conventional and Molecular Techniques from Simple Breeding to Speed Breeding in Crop Plants: Recent Advances and Future Outlook

Abstract

In most crop breeding programs, the rate of yield increment is insufficient to cope with the increased food demand caused by a rapidly expanding global population. In plant breeding, the development of improved crop varieties is limited by the very long crop duration. Given the many phases of crossing, selection, and testing involved in the production of new plant varieties, it can take one or two decades to create a new cultivar. One possible way of alleviating food scarcity problems and increasing food security is to develop improved plant varieties rapidly. Traditional farming methods practiced since quite some time have decreased the genetic variability of crops. To improve agronomic traits associated with yield, quality, and resistance to biotic and abiotic stresses in crop plants, several conventional and molecular approaches have been used, including genetic selection, mutagenic breeding, somaclonal variations, whole-genome sequence-based approaches, physical maps, and functional genomic tools. However, recent advances in genome editing technology using programmable nucleases, clustered regularly interspaced short palindromic repeats (CRISPR), and CRISPR-associated (Cas) proteins have opened the door to a new plant breeding era. Therefore, to increase the efficiency of crop breeding, plant breeders and researchers around the world are using novel strategies such as speed breeding, genome editing tools, and high-throughput phenotyping. In this review, we summarize recent findings on several aspects of crop breeding to describe the evolution of plant breeding practices, from traditional to modern speed breeding combined with genome editing tools, which aim to produce crop generations with desired traits annually.

Keywords: CRISPR/Cas9; CRISPR/Cpf1; conventional breeding; food scarcity; food security; high-throughput phenotyping; speed breeding.

Figure 1

Historical milestones in plant breeding. For 10,000 years, farmers and breeders have been developing and improving crops. Presently, farmers feed 10 times more people using the same amount of land as 100 years ago.

Figure 2

Improvement of agronomic traits using traditional breeding and chemical or physical mutagenic approaches. (A) Improving a trait (e.g., disease resistance) by the traditional breeding and for the introduction of the desired donor trait into the ‘chosen’ recipient line by selecting the progeny with the desired traits from the recipient line and crossing it with the donor line. (B) This process uses chemical or physical mutagens to generate mutants via random mutagenesis.

Figure 3

The plant breeding innovation cycle.

Figure 4

CRISPR–Cas9-based genome editing. CRISPR/Cas9 system uses Cas9 and sgRNA to cleave foreign DNA. It works in three steps: (1) the expression of the nuclear-localized Cas9 protein, (2) the generation of gRNA containing first 20-nt complementary to the target gene, and (3) the NGG PAM site recognition located nearly at the 3’ end of the target site. This process is followed by three additional steps: (1) design target and construction of a gene-specific sgRNA (vector), (2) CRISPR–Cas9 sgRNA can be transfected into the plant protoplast through Agrobacterium-mediated transformation, and (3) regenerated plants are screened for mutation via PCR-assay and sequencing. The estimated time needed is indicated for most steps.

Figure 5

Graphical presentation of the elite line development procedure. Comparison of time (in months) required to develop elite lines from selected parents of some crops. Extended photoperiods induced earlier flowering and created 4 generations annually. The optimal temperature regime (maximum and minimum temperatures) should be applied for each crop. A higher temperature should be maintained during the photoperiod, whereas a fall in temperature during the dark period can aid in stress recovery. At the University of Queensland; (UQ), a 12-h 22 °C/17 °C temperature cycling regime with 2 h of darkness occurring within 12 h of 17 °C has proven successful. The figure is briefly modified from Watson et al. (2018).