Xian Zhang , Pingping Yang , Jin Zhang

Hainan Provincial Key Laboratory of Crop Molecular Breeding, Sanya, 572025, Hainan, China
Author    Correspondence author
Cotton Genomics and Genetics, 2025, Vol. 16, No. 5   doi: 10.5376/cgg.2025.16.0025
Received: 13 Aug., 2025    Accepted: 25 Sep., 2025    Published: 18 Oct., 2025

This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Zhang X., Yang P.P., and Zhang J., 2025, High-throughput genotyping and its role in accelerating cotton breeding, Cotton Genomics and Genetics, 16(5): 249-258 (doi: 10.5376/cgg.2025.16.0025)

 

Cotton, as a globally significant economic crop, has long been the core goal of breeding improvement in terms of its yield and fiber quality. However, traditional breeding methods are characterized by long cycles and low efficiency, making it difficult to meet the increasingly complex breeding demands. The rise of High-Throughput Genotyping (HTG) technology has provided strong technical support for cotton molecular breeding, especially showing broad application prospects in quantitative trait localization, molecular marker development, genomic selection, etc. This study systematically reviews the characteristics and applicability of the current mainstream HTG technology platforms (such as SNP chips, GBS, RAD-seq, DArT, etc.), and analyzes their application progress in the genetic basis research of important agronomic traits such as yield, quality, and resistance. The practical role of HTG in QTL localization, GWAS analysis, marker-assisted selection and other links was discussed. Through typical breeding practice cases, evaluate its breeding acceleration efficiency in the context of multiple environments and varieties, and further look forward to the prospects of its deep integration with phenomics, genomic selection and intelligent decision-making platforms. This research provides theoretical basis and technical support for accelerating the genetic improvement and molecular breeding of cotton.

Cotton breeding; High-throughput genotyping; Molecular marker; Genomic selection; QTL positioning