eChapter Name: Harnessing the Wealth of Haplotypes in Crop Breeding
9789372191417
eBook Name: NEXT GENERATION PLANT BREEDING
Introduction
Plant being sessile are subjected to a myriad of biotic and abiotic stresses that impede growth and resulting significant losses in crop productivity globally (Bhat et al., 2019; Ganie & Reddy, 2021). In this context, there is an immediate need to develop high yielding climate-resilient crop varieties for ensuring food security in the face of increasing population growth. Although conventional breeding has achieved notable success in the development of high-yielding crop varieties (Bhat et al., 2020), but this approach is slow to maintain pace with ever increasing population. In this regard, more recent approach of genomics-assisted breeding (GAB) has emerged as a pivotal approach to develop the high-yielding climate resilient crop varieties (Bhat et al. 2021). Although, low-throughput sequencebased markers like simple sequence repeats (SSRs) have been extensively utilized in molecular breeding programs, but they have the limitations of reduced genomic coverage and high cost (Varshney et al., 2014; Zargar et al., 2015). In this context, the emergence of second-generation DNA marker systems has provided higher genomic coverage and low cost in marker-assisted breeding. For example, recent advancements in next-generation sequencing (NGS) and genotyping platforms have substantially enhanced marker density and genomic coverage while reducing costs (Przewieslik-Allen et al., 2019); thus rendering them commercially available for both model and non-model crop species (Huang & Han, 2014; Rasheed et al., 2017). These high-throughput genotyping platforms provides millions of DNA polymorphisms (Bassi et al., 2016; Ganal et al., 2012), thereby enhancing gene mapping resolution and prediction accuracy in genomic selection (GS) (Robertsen et al., 2019; Yu et al., 2019). Most of the agriculturally important crop traits, such as yield, quality, and stress tolerance, possess complex inheritance i.e., governed by multiple genes with minor effect on trait of interest as well as are highly influenced by genotype-by-environment (G × E) interactions (Voss-Fels & Snowdon, 2016). The conventional linkage mapping approach has elucidated the genetic basis of agriculturally important complex traits but this approach involves the use of bi-parental mapping populations which are constrained by the limited genetic diversity, low resolution, and restricted recombination events (Brachi et al., 2011; Collard et al., 2005). Consequently, the genome-wide association study (GWAS) has emerged as a powerful approach for dissecting the genetic basis of complex quantitative traits in crop plants, resulting higher resolution and allelic diversity (Varshney et al., 2020; Zhu et al., 2008). Moreover, owing to the availability of cost-effective and high-density genotyping platforms, has allowed the routine use of GS in the crop breeding which is more recent approach of GAB (Crossa et al., 2017). In recent years, the advent of next-generation sequencing (NGS)-based genotyping techniques has significantly allowed the genotyping of extensive germplasm collections, enabling comprehensive GWAS and GS analyses (Annicchiarico et al., 2017; Zargar et al., 2015). Nonetheless, the predominant limitations impeding the utilization of SNPs in the GWAS and GS approaches encompass their inherently biallelic nature, the occurrence of rare alleles, and the prevalence of linkage drag (Voss-Fels & Snowdon, 2016; Wray et al., 2013). In
