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.
Highlights
Plant breeding aims at tailoring the genetic architecture of a genotype in an artistic and scientific way, and its success is largely attributable to the extent of genetic variation present in the germplasm
Among several methods being used for trait introgression, backcrossing is a well-established method routinely used for introgression or defect elimination, but its progress as well as accuracy is hampered by (i) slow decrease rate of undesirable donor genome or linkage drag and (ii) time taken for the maximum recovery of the recurrent parent (RP) genome
Decreasing genotyping and sequencing costs are dramatically changing the scenario of genomics-assisted breeding
Summary
Plant breeding aims at tailoring the genetic architecture of a genotype in an artistic and scientific way, and its success is largely attributable to the extent of genetic variation present in the germplasm. The traits controlled by a large number of smaller effects and epistatic QTLs and displaying significant genotype × environment (G × E) interactions could not be addressed appropriately through phenotypic selection (PS) based breeding methods [1, 2]. A wide array of marker systems has become available since the introduction of restriction fragment length polymorphism (RFLP) as the first genetic marker by Grodzicker and colleagues [3] This progress has been driven by generation sequencing- (NGS-) based technologies and high-throughput (HTP) marker genotyping systems that have truly revolutionized the plant genomics [4]. Keeping all these developments in view, this article provides a comprehensive review on these emerging molecular breeding approaches including their current status, impediments, and perspectives
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