Development and validation of novel MD-100K liquid-phase chip: Advancing genetic research and breeding in dairy and dual-purpose cattle

doi:10.1016/j.jia.2026.09.022

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Development and validation of novel MD-100K liquid-phase chip: Advancing genetic research and breeding in dairy and dual-purpose cattle

Yatong Wang¹*, Siqian Chen¹*, Hao Zhong¹*, Quanzhen Chen¹, Yongjie Tang¹, Xiao Feng¹, Songyan An¹, Shanyuan Chen², Kerong Shi³, Xixia Huang⁴, Yachun Wang¹, Qin Zhang³, Ying Yu¹^#

¹State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China

² School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China

³ College of Animal Science and Technology, Shandong Agricultural University, Tai’an 271018, China

⁴College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China

Highlights:

l A 101,565-SNP liquid-phase chip was developed for seven Chinese dairy and dual-purpose cattle breeds.

l The chip provides balanced genome-wide coverage with mean call rates exceeding 99.8%.

l Breed-specific and conserved candidate loci were identified for milk production (DGAT1) and immune-related traits (WT1) via GWAS.

Abstract
References

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摘要

乳用及乳肉兼用牛在现代畜牧业中占据重要地位，其遗传改良对于保障畜产品供应和促进产业可持续发展至关重要，而这一过程高度依赖高性能、低成本的基因分型工具。然而，现有商业化基因芯片多针对西方商业品种开发，对中国饲养品种的适用性存在不足，导致中国乳用及乳肉兼用牛的遗传评估与基因组选择长期缺乏合适的工具。因此，本研究针对7个中国乳用及乳肉兼用牛品种，开发了MD-100K （Milk and Dual-Purpose Cattle 100K）单核苷酸多态性（SNP）液相芯片。该芯片包含101,565个高质量SNP标记，覆盖泌乳性能、乳房健康、个体健康、繁殖、热应激、冷应激、体况、长寿性、乳成分、分子QTL、品种鉴定及亲子鉴定等12类经济与功能性状。候选位点通过多来源收集，并在包含7个品种的599个个体的参考群体中进行严格过滤（最小等位基因频率≥0.05，检出率≥0.9），最终实现了全基因组的均衡覆盖。在基因分型性能验证方面，该芯片在1,454头荷斯坦牛（乳用牛）和三河牛（乳肉兼用牛）的独立验证群体中平均检出率超过99.8%；在43头多品种验证群体中，与全基因组测序数据的一致性达99.90%，技术重复一致性达99.85%，展现出高度的准确性和可重复性。群体遗传结构分析清晰区分了上述两个品种，其基因组平均固定指数（Fst）为0.066。利用该芯片进行的全基因组关联分析（GWAS）在荷斯坦牛、三河牛及两者荟萃分析中分别鉴定出121、9和52个候选位点。例如，对于产奶性状，14号染色体上检测到显著影响平均日产奶量（ADMY）的全基因组信号，其Lead SNP位于DGAT1基因外显子中，该基因是调控乳脂合成的关键基因。综上所述，MD-100K液相芯片在乳用及乳肉兼用牛中均表现出优异的基因分型性能和广泛的应用潜力。该芯片能够有效捕获群体结构、基因组多样性与功能性状变异，为中国乳用及乳肉兼用牛的遗传研究和分子育种提供了可靠且高性价比的基因分型工具。

Abstract

Dairy and dual-purpose cattle play an important role in modern livestock production. However, genetic evaluation and improvement in Chinese dual-purpose cattle have been constrained by the lack of efficient and cost-effective genotyping tools. We developed the MD-100K (Milk and Dual-Purpose Cattle 100K) single-nucleotide polymorphism (SNP) liquid‑phase chip for seven dairy and dual-purpose breeds. The chip comprises 101,565 high-quality markers spanning 12 economic and functional traits, selected through multiple approaches and filtered against a reference population of 599 individuals. The chip provides balanced genome-wide coverage. Validation in 1,454 Holstein and Sanhe cattle achieved mean call rates exceeding 99.8%. Genetic structure analysis revealed clear differentiation between the two breeds. The genome-wide average fixation index (Fst) was 0.066, with strong differentiation observed on chromosome 18 (peak Fst=0.864). Genome-wide association study (GWAS) identified 121, 9, and 52 candidate loci in Holstein, Sanhe, and the meta‑analysis, respectively. A prominent genome-wide significant signal was detected for average daily milk yield (ADMY) on chromosome 14, with the lead SNP located in the exon of DGAT1. For immune‑related traits, five suggestive loci were identified, including 15_63147124_G_A, an intronic variant in WT1, which was consistently detected as a candidate association in both granulocyte-to-monocyte ratio (GMR) and lymphocyte-to-monocyte ratio (LMR) meta-GWAS. In consequence, the MD-100K SNP liquid-phase chip serves as a reliable tool for capturing population structure, genomic diversity, and functional trait variation for dairy and dual-purpose cattle populations evaluated in this study, Holstein and Sanhe cattle.

Keywords: dairy and dual-purpose cattle liquid-phase chip genetic structure genome-wide association study (GWAS) molecular breeding tool

Online: 14 September 2026

Fund:

This work was supported by the National Key Research and Development Program of China (2021YFD1200903 and 2023YFF1000902), the National Natural Science Foundation of China (32302706), the Young Scientists Fund, China (Category C, Grant No. 32502864), and the earmarked fund for CARS-35, China (Beijing, China).

About author: # Correspondence Ying Yu, E-mail: yuying@cau.edu.cn * These authors contributed equally to this study

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Yatong Wang, Siqian Chen, Hao Zhong, Quanzhen Chen, Yongjie Tang, Xiao Feng, Songyan An, Shanyuan Chen, Kerong Shi, Xixia Huang, Yachun Wang, Qin Zhang, Ying Yu. 2026.

Development and validation of novel MD-100K liquid-phase chip: Advancing genetic research and breeding in dairy and dual-purpose cattle . Journal of Integrative Agriculture, Doi:10.1016/j.jia.2026.09.022

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