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Journal of Integrative Agriculture
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SbGBST47K: A high-resolution genotyping-by-target-sequencing liquid chip in sorghum

Qiaoling Zhang1*, Yanqing Ding2*, Yinlin Wang1, Jianxia Xu2, Feng Jiang1, Ning Cao2, Fan Yang1#, Liyi Zhang2#

1 Kweichow Moutai Co., Ltd., Maotai Town, Renhuai 564501, China

2 Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China

 Highlights 

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.

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摘要  

高粱(Sorghum bicolor L. Moench)对保障全球粮食安全具有重要意义,然而其基因组资源的挖掘与利用尚不充分,制约了遗传改良进程。为填补这一空白,本研究利用1025份全球代表性高粱种质的全基因组重测序数据,开发了一款包含47040SNP的高通量靶向测序基因分型液相芯片——SbGBST47K。该芯片整合了45506个全基因组背景SNP1278个酿酒高粱特异性诊断标记以及268个已报道的农艺性状关联位点,可兼顾检测通量与成本效益,实现高分辨率基因分型。利用该芯片对434份高粱种质进行基因分型,揭示了其群体遗传结构可划分为四大类群(国外群体、中国北方群体、中国南方群体及中国西南群体)。针对8个农艺性状的全基因组关联分析共检测到160个显著关联SNP,并鉴定出多个基因组热点区域,包括控制籽粒颜色与单宁含量的1号和2号染色体、调控株高的7号染色体以及参与淀粉代谢的10号染色体。对WxTan2基因的单倍型分析表明,其单倍型分布模式反映了不同地区对高粱用途的偏好。此外,在4号染色体上定位到一个控制籽粒颜色的主效位点,并预测到了关键候选基因。SbGBST47K平台的建立将有效推动功能基因组学与精准育种的深度融合,加速多用途高粱品种的选育进程。



Abstract  

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.

Keywords:  sorghum (Sorghum bicolor)       SNP liquid chip                    genotyping-by-target-sequencing (GBTS)                    genome-wide association study (GWAS)  
Online: 11 March 2026  
Fund: 

This study was supported by the Guizhou Provincial Basic Research Program (Natural Science), China (QKHJC[2024]QN382), the National Natural Science Foundation of China (32572425), the Scientific Research Project of Kweichow Moutai Liquor Co., Ltd., China (MTGF2023007) and the Guizhou Provincial Key Laboratory of Biotechnology Breeding for Special Minor Cereals, China (QKHPT[2025]026).

About author:  #Correspondence Liyi Zhang, E-mail: lyzhang1997@hotmail.com; Fan Yang E-mail: yangfanmoutai@163.com *These authors contributed equally to this work.

Cite this article: 

Qiaoling Zhang, Yanqing Ding, Yinlin Wang, Jianxia Xu, Feng Jiang, Ning Cao, Fan Yang, Liyi Zhang. 2026.

SbGBST47K: A high-resolution genotyping-by-target-sequencing liquid chip in sorghum . Journal of Integrative Agriculture, Doi:10.1016/j.jia.2026.03.031

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