For instance, next-generation sequencing technologies have facilitated availability of genome sequence assemblies, re-sequencing of several hundred lines, development of HapMaps, high-density genetic maps, a range of marker genotyping platforms and identification of markers associated with a number of agronomic traits in these legume crops. Although marker-assisted backcrossing and marker-assisted selection approaches have been used to develop superior lines in several cases, it is the need of the hour for continuous population improvement after every breeding cycle to accelerate genetic gain in the breeding programs. In this context, we propose a sequence-based breeding approach which includes use of independent or combination of parental selection, enhancing genetic diversity of breeding programs, forward breeding for early generation selection, and genomic selection using sequencing/genotyping technologies. Also, adoption of speed breeding technology by generating 4–6 generations per year will be contributing to accelerate genetic gain. While we see a huge potential of the sequence-based breeding to revolutionize crop improvement programs in these legumes, we anticipate several challenges especially associated with high-quality and precise phenotyping at affordable costs, data analysis and management related to improving breeding operation efficiency. Finally, integration of improved seed systems and better agronomic packages with the development of improved varieties by using sequence-based breeding will ensure higher genetic gains in farmers’ fields.
Figure 1: Flowchart for developing improved legume varieties through sequence-based breeding. The next-generation genomic tools and high-throughput phenotyping systems enable harnessing the superior alleles harbored within vast genetic resources of grain legume crops. Genotyping-based techniques have yielded promising results with the delivery of a variety of molecular breeding products in these crops. In this post genomics era, a shift from genotyping- to sequencing-based assays coupled with our enhanced capacity to integrate multi-omics science or a systems biology approach promises to accelerate the genetic gains. Breeder’s decisions greatly informed by such modern advances will reflect in higher productivity gains with fewer resources and in less time