Emerging paradigms in genomics-based crop improvement

Abstract

Next generation sequencing platforms and high-throughput genotyping assays have remarkably expedited the pace of development of genomic tools and resources for several crops. Complementing the technological developments, conceptual shifts have also been witnessed in designing experimental populations. Availability of second generation mapping populations encompassing multiple alleles, multiple traits, and extensive recombination events is radically changing the phenomenon of classical QTL mapping. Additionally, the rising molecular breeding approaches like marker assisted recurrent selection (MARS) that are able to harness several QTLs are of particular importance in obtaining a "designed" genotype carrying the most desirable combinations of favourable alleles. Furthermore, rapid generation of genome-wide marker data coupled with easy access to precise and accurate phenotypic screens enable large-scale exploitation of LD not only to discover novel QTLs via whole genome association scans but also to practise genomic estimated breeding value (GEBV)-based selection of genotypes. Given refinements being experienced in analytical methods and software tools, the multiparent populations will be the resource of choice to undertake genome wide association studies (GWAS), multiparent MARS, and genomic selection (GS). With this, it is envisioned that these high-throughput and high-power molecular breeding methods would greatly assist in exploiting the enormous potential underlying breeding by design approach to facilitate accelerated crop improvement.

Figure 1

Schematic representation of genomics assisted crop improvement. ∗DH: Double haploid; BC: Backcross population; RIL: Recombinant inbred line; AIL: Advanced intercross line; HIF: Heterogeneous inbred family; NIL: Near isogenic line; BIL: Backcross inbred line; IL: Introgression line; CSSL: Chromosome segment substitution line; HS: Heterogeneous stocks; NAM: Nested association mapping; MAGIC: Multiparent advanced generation intercross; MAS: Marker assisted selection; MABC: Marker assisted backcrossing; MARS: Marker assisted recurrent selection; GWAS: Genome-wide association study; GS: Genomic selection.