Molecular Plant Breeding 2024, Vol.15, No.6, 371-378 http://genbreedpublisher.com/index.php/mpb 374 4 Case Study: GWAS for Identifying Yield-Related QTLs in Soybean 4.1 Research area, environmental conditions, and soybean germplasm The study was conducted across multiple environments to capture the genotype by environment interactions that significantly influence soybean yield. For instance, one study evaluated 227 soybean genotypes across four different environments (Figure 2) (Yoosefzadeh-Najafabadi et al., 2021), while another assessed 541 genotypes in four environments in Kansas, U.S. (Ayalew et al., 2022). These diverse environmental conditions help in identifying stable QTLs that are consistent across different settings. The germplasm used in these studies included a wide range of soybean genotypes. For example, a panel of 541 soybean genotypes from three maturity groups was used (Ayalew et al., 2022), and another study utilized 200 genotypes derived from Canadian × Chinese crosses (Priyanatha et al., 2022). This diversity in germplasm ensures a broad genetic base, which is crucial for identifying yield-related QTLs. Figure 2 The structure and kinship plots for the 227 soybean genotypes (Adopted from Yoosefzadeh-Najafabadi et al., 2021) Image caption: The x-axis is the number of genotypes used in this GWAS panel, and the y-axis is the membership of each subgroup. G1-G7 stands for the subpopulation (Adopted from Yoosefzadeh-Najafabadi et al., 2021) 4.2 Genotyping process and measurement of phenotypic traits Genotyping was performed using high-density SNP arrays and sequencing methods. The SoySNP50K iSelect BeadChip was used to genotype 541 soybean genotypes, identifying 19 significant SNPs associated with seed yield (Izquierdo et al., 2023). Another study employed genotyping-by-sequencing (GBS) to yield almost 32K high-quality SNPs for 200 genotypes. These high-density markers provide comprehensive coverage of the soybean genome, facilitating the identification of QTLs. Phenotypic traits measured included seed yield, seed weight, pod number, and other yield components. For instance, seed yield, seed weight, shattering resistance, days to maturity, and plant height were measured in a diverse panel of soybean genotypes. Another study focused on seed yield, seed protein concentration, seed oil concentration, plant height, 100-seed weight, days to maturity, and lodging score (Shook et al., 2021). These measurements are critical for associating phenotypic traits with genetic markers.
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