Sequence-Based Breeding for Plant Improvement

This book chapter discusses the significant improvement in breeding programs’ utilizing modern genomic tools and technologies. Next-generation sequencing technologies have enabled the availability of genome sequence assemblies, high-density genetic maps, various marker genotyping platforms, and the identification of markers associated with numerous agronomic traits in several economically important crops. While marker-assisted backcrossing and selection approaches have been employed to develop improved lines, there is a need for continuous population improvement after every breeding cycle to hasten the genetic gains in crops. This book chapter proposes a sequencing-based breeding approach involving parental selection, enhancement of genetic diversity of breeding programs, forward breeding for early generation selection, and genomic selection using sequencing/genotyping technologies. Additionally, we discussed the speed breeding technology, which allows for 4–6 generations per year and can accelerate genetic gain much faster. The book chapter is described in two sections: the first focuses on sequencing-based trait mapping, and the second is geared toward sequencing-based breeding for crop improvement. The potential of sequence-based breeding applications, including trait discovery, is immense and could revolutionize crop improvement programs.