On the road to breeding 4.0: unraveling the good, the bad, and the boring of crop quantitative genomics

Authors: WALLACE, JASON - University Of Georgia; RODGERS-MELNICK, ELI - Corteva Agriscience; Buckler, Edward - Ed

Submitted to: Annual Review of Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/4/2018
Publication Date: 11/23/2018
Citation: Wallace, J.G., Rodgers-Melnick, E., Buckler IV, E.S. 2018. On the road to breeding 4.0: unraveling the good, the bad, and the boring of crop quantitative genomics. Annual Review of Genetics. 52(1)421-444. https://doi.org/10.1146/annurev-genet-120116-024846.
DOI: https://doi.org/10.1146/annurev-genet-120116-024846

Interpretive Summary: The history of plant breeding can be divided into four stages based on available technology: (1) Breeding 1.0 comprises the first 10,000 years and is characterized by incidental selection. (2) Breeding 2.0 began in the late nineteenth century and focused on statistical and experimental design to improve selection efforts. (3) Roughly 30 years ago, the present stage of Breeding 3.0 introduced the integration of genetic and genomic data. (4) The next phase of breeding, Breeding 4.0, has the goal of combining any known alleles (variant forms of a gene) into optimal combinations to improve crop production. As plant breeding transitions to Breeding 4.0, this paper identifies and addresses three questions: (a) How do we adapt crops to better fit agricultural environments? (b) What is the nature of genetic variation that exists in plants? (c) How do we deal with harmful alleles that can be detrimental to crop production? In responding to the above questions, this paper determines that (a) crops are still only partly adapted to agriculture and can be improved by breeding them to better fit modern growing environments; (b) variation that is relevant to agriculture is not randomly spread through the genome, so finding the relevant portions can improve the focus of breeding efforts; (c) much of Breeding 4.0 probably revolves around identifying and purging deleterious variants. As current and future breeding technologies are developed, more should be done to make these technologies accessible to large and small plant breeders so that they benefit all of global agriculture.

Technical Abstract: Understanding the quantitative genetics of crops has been and will continue to be central to maintaining and improving global food security. We outline four stages that plant breeding either has already achieved or will probably soon achieve. Top-of-the-line breeding programs are currently in Breeding 3.0, where inexpensive, genome-wide data coupled with powerful algorithms allow us to start breeding on predicted instead of measured phenotypes. We focus on three major questions that must be answered to move from current Breeding 3.0 practices to Breeding 4.0: (a) How do we adapt crops to better fit agricultural environments? (b) What is the nature of the diversity upon which breeding can act? (c) How do we deal with deleterious variants? Answering these questions and then translating them to actual gains for farmers will be a significant part of achieving global food security in the twenty-first century.