Pallavi Sinha, Vikas K. Singh, Abhishek Bohra, Arvind Kumar, Jochen C. Reif & Rajeev K. Varshney

Theoretical and Applied Genetics June 2021; vol. 134:1829–1843

Key message

Integrating genomics technologies and breeding methods to tweak core parameters of the breeder’s equation could accelerate delivery of climate-resilient and nutrient rich crops for future food security.

Abstract

Accelerating genetic gain in crop improvement programs with respect to climate resilience and nutrition traits, and the realization of the improved gain in farmers’ fields require integration of several approaches. This article focuses on innovative approaches to address core components of the breeder’s equation. A prerequisite to enhancing genetic variance (σ²g) is the identification or creation of favorable alleles/haplotypes and their deployment for improving key traits. Novel alleles for new and existing target traits need to be accessed and added to the breeding population while maintaining genetic diversity. Selection intensity (i) in the breeding program can be improved by testing a larger population size, enabled by the statistical designs with minimal replications and high-throughput phenotyping. Selection priorities and criteria to select appropriate portion of the population too assume an important role. The most important component of breeder′s equation is heritability (h²). Heritability estimates depend on several factors including the size and the type of population and the statistical methods. The present article starts with a brief discussion on the potential ways to enhance σ²g in the population. We highlight statistical methods and experimental designs that could improve trait heritability estimation. We also offer a perspective on reducing the breeding cycle time (t), which could be achieved through the selection of appropriate parents, optimizing the breeding scheme, rapid fixation of target alleles, and combining speed breeding with breeding programs to optimize trials for release. Finally, we summarize knowledge from multiple disciplines for enhancing genetic gains for climate resilience and nutritional traits.

See: https://link.springer.com/article/10.1007/s00122-021-03847-6

Figure 1: Enhancing genetic variation through identifying/ creating and utilizing favorable alleles/haplotypes. Genetic variance (σ²_g) is estimated with genetic parameters including phenotypic variance composed by genotypic and environmental variance (not inheritable). Genetic variance allows an understanding of the genetic structure involved in the progenies, determined by additive and non-additive effects. (1) Genome to phenome deals with the connection and causation between the genetic makeup of an accession and the observed physical or physiological traits or characteristics (phenome). This can be achieved by characterizing germplasm collections at the phenotypic and genotypic level. (2) Trait associated genes can be identified through NGS based trait mapping (extreme pools- based and complete population-based) and/or through systems biology approaches. (3) Genetic variations can be assayed using germplasm characterization or can be created by through genome editing, multiparent advanced generation intercross (MAGIC), targeting induced local lesions in genomes (TILLING) and Eco-TILLING populations. (4) Genomic breeding to combine superior/ novel alleles/ haplotypes in elite backgrounds. The identified genetic variations can be introduced in a crop improvement programs through genomics-assisted breeding (GAB) approaches including marker- assisted backcrossing (MABC), marker- assisted recurrent selection (MARS), haplotype-based breeding (HBB), forward breeding (FB) and genomic selection (GS).