SbGBST47K: A high-resolution genotyping-by-target-sequencing liquid chip in sorghum

1. Developed the first high-density sorghum GBTS liquid chip (SbGBST47K) with 47,040 SNPs, incorporating genome-wide background markers, liquor-sorghum diagnostic markers, and trait-associated loci for versatile applications. 2. Demonstrated its utility in high-resolution population structure analysis, GWAS for key agronomic and quality traits, and haplotype-based mining of favorable alleles, providing a robust platform for sorghum functional genomics and precision breeding. Sorghum ( Sorghum bicolor L. Moench) is essential for global food security, yet its genetic improvement has been hindered by the limited exploitation of genomic resources. To address this gap, we developed the SbGBST47K liquid chip, a high-throughput genotyping-by-target-sequencing (GBTS) platform with 47,040 SNPs, using whole-genome resequencing data from 1,025 diverse accessions. This chip integrates 45,506 genome-wide background SNPs, 1,278 liquor-sorghum diagnostic markers, and 268 trait-associated loci, enabling cost-effective, high-resolution genotyping. Validation across 434 accessions revealed a distinct population structure comprising four genetic groups (Foreign, Chinese north, Chinese south, and Chinese southwest). Genome-wide association studies (GWAS) detected 160 significant SNPs for eight agronomic traits, highlighting chromosomes 1, and 2 (pigmentation, tannin content), 7 (plant height), and 10 (starch metabolism) as genomic hotspots. Haplotype analysis of Wx and Tan2 revealed that their population distribution reflects regional preferences in sorghum usage. Furthermore, a important candidate gene for grain pigmentation was predicated at the major locus on chromosome 4. The SbGBST47K platform bridges functional genomics and precision breeding, accelerating the development of multi-purpose sorghum varieties.