**4.2 NGS-based genotyping for soybean design breeding**

In recent decades, the total dependence on phenotypic selection has gradually shifted to a greater use of genotypic-based approaches for plant selection, facilitated by NGS-based genotyping platforms [99–101]. NGS technology has boosted throughput, speeed of genome-wide genotyping, and cost-effectiveness [109] (**Table 3**). NGS-based genotyping technologies have tremendously aided in enhancing the resolution of gene mapping and tagging the gene/QTL extremely closer to the neighboring maker. In GWAS analysis, for example, the use of NGS has made it feasible to genotype huge populations of plants with a greater density of markers than was previously possible, which directly leads to better mapping resolution [110, 111]. In GWAS analysis, using a varied and big population allows for the discovery of more recombination break sites, which aids in the identification of candidate genes with greater precision [112]. Many studies have used NGS-based genotyping for GWAS analysis in soybean for various traits, and these studies have shown significant success in identifying candidate genes for specific traits of interest. For instance, previous study used the RAD-seq method to find a candidate gene underlying the main QTL controlling flooding tolerance in soybean [113]. Many other studies have shown that NGS-based genotyping facilitated candidate gene identification in areas such as nitrogen fixation [114], soybean plant height and primary branches [115], agronomic traits [116], disease resistance [117], and protein content [118]. The NGS-based WGRS has greatly improved the power of bulk segregant analysis (BSA) and its modified techniques, and it is now extensively employed in a variety of plant species, including soybean. For example, in another study, WGRS was employed to resequence different DNA pools

#### *Soybean Molecular Design Breeding DOI: http://dx.doi.org/10.5772/intechopen.105422*


**Table 3.**

*Tools of design breeding in soybean using high-throughput SNP genotyping platforms.*

in the BSA study, and they discovered two significant genes that regulate cotyledon color in soybeans at the same time. Furthermore, many studies have used NGS-based techniques in the BSA approach to identify candidate genes for various soybean traits, including soybean mosaic virus [119], charcoal rot resistance [120], flowering time [121], phytophthora resistance [122], and powdery mildew resistance [123].
