ABSTRACT

Introduction ................................................................................................................................. 188 Why resequencing of genome? ............................................................................................ 188

Resolving evolution and domestication trajectories in crop plant ...................................... 189 Unfolding the hidden genetic diversity at genome level in crop plant .............................. 190 Genome-wide discovery of markers to expedite genomics-assisted breeding ..................200 Uncovering gene/QTLs of agronomic importance................................................................ 201 Exploring linkage disequilibrium pattern for GWAS ............................................................ 203

Rare mutation mapping via whole-genome sequencing .................................................. 203 Major QTL delineation via whole-genome sequencing ........................................................ 204 Conclusion and future prospects .............................................................................................. 205 Acknowledgment .......................................................................................................................205 References ..................................................................................................................................... 205

Introduction The paradigm shift in next-generation sequencing (NGS)-driven sequencing technology has resulted in remarkable progress in plant genome sequencing, leading to decode more than two dozens of plant genome sequences till date (Deschamps and Campbell 2010, Jackson et  al. 2011, Edwards et  al. 2012, Michael and Jackson 2013). Importantly, this technology has beneted plant scientists thereby deciphering the structural genome variations either by enabling in de novo sequencing or by resequencing of plant genome species with the available “reference genome” sequence (Bhat 2011, Jackson et  al. 2011). Subsequently, dramatic evolvement of “second-generation sequencing technologies,” the two most commercially used NGS platforms Illumina Genome Analyzer (Illumina-GA) and Roche Genome Sequencer FLX (GS-FLX) have gained much popularity, propelling genome-sequencing research at a greater height in biological science in post-Sanger sequencing era (Mardis 2008, Shendure and Ji 2008, Imelfort and Edwards 2009, Metzke 2010). Interestingly, dropping down in sequencing cost followed by capability in generating longer and high-quality reads, coupled with advancement in short-read assembler tools and algorithms by introducing third-generation sequencing platforms, can further increase the quality of genome assembly at a higher magnitude (Imelfort and Edwards 2009, Schatz et al. 2010, 2012, Thudi et al. 2012). Till date, genome sequences of more than 50 plants belonging to different species have been cracked (Michael and Jackson 2013), thus allowing identication and characterization of genes of interest mostly used in genomicsassisted crop improvement program. Despite the availability of the complete “reference genome” sequence of a specic crop genotype, this is not sufcient to give the complete landscape of all the complex traits and existing structural genome variations causing specic phenotypic variants in crop plants (Kim et al. 2010, Schatz et al. 2014). Evidences of existing genomic variations both between and within the cultivars of crops have been decoded (Springer et al. 2009, Lai et al. 2010, Swanson-Wagner et al. 2010, Haun et al. 2011, Zheng et al. 2011, Lin et al. 2012, McHale et al. 2012). Therefore, understanding of complex traits, genomic diversity, much in-depth study of geographic origin of crop plants in connection with its domestication-related processes and speciation, resequencing of wild species, or crop accessions is necessary (Kim et al. 2010, Sakai et al. 2014).