Reconciliation of wheat 660K and 90K SNP arrays and their utilization in dough rheological properties of bread wheat

Congwei Sun; Zhenhai Jing; Xiaoqian Chen; Jiahui Chen; Qiaoqiao Shang; Hui Jin; Jizeng Jia; Yan Ren; Lei Zhao; Lifeng Gao; Zhonghu He; Feng Chen

doi:10.1016/j.jare.2025.01.011

Reconciliation of wheat 660K and 90K SNP arrays and their utilization in dough rheological properties of bread wheat

J Adv Res. 2025 Jan 5:S2090-1232(25)00030-X. doi: 10.1016/j.jare.2025.01.011. Online ahead of print.

Authors

Congwei Sun¹, Zhenhai Jing¹, Xiaoqian Chen¹, Jiahui Chen¹, Qiaoqiao Shang¹, Hui Jin², Jizeng Jia², Yan Ren¹, Lei Zhao¹, Lifeng Gao³, Zhonghu He⁴, Feng Chen⁵

Affiliations

¹ Agronomy College / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046 China.
² State Key Laboratory of Crop Gene Resources and Breeding / Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081 China.
³ State Key Laboratory of Crop Gene Resources and Breeding / Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081 China. Electronic address: [email protected].
⁴ State Key Laboratory of Crop Gene Resources and Breeding / Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081 China. Electronic address: [email protected].
⁵ Agronomy College / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046 China. Electronic address: [email protected].

PMID: 39765327
DOI: 10.1016/j.jare.2025.01.011

Abstract

Introduction: High-density Wheat 660K and 90K SNP arrays are powerful tools for understanding the genetic basis of wheat traits. However, their inconsistantly physical positions that were caused by different versions of Chinese Spring genome during developing arrays are confused and inconvenient for further application.

Objective: With the repid development of wheat geonome sequencing, we aim to reconciliate Wheat 660K and 90K SNP arrays in modern cultivar and reveal the genetic basis of dough rheological properties in bread wheat.

Methods: We refined physical positions of Wheat 660K and 90K SNP arrays in the currently popular wheat cultivar AK58 genome that was released more recently. We next performed genome-wide association studies (GWAS) and linkage analysis to identify important genetic loci related to quality traits using updated and un-updated arrays, respectively.

Results: Refining results showed that 92.3% and 83% of SNPs in the Wheat 660K and 90K SNP arrays were precisely mapped to the AK58 genome, respective. GWAS results by the updated 660K and 90K arrays indicated that 26 intervals composed of 1032 significant SNPs were associated with 9 quality traits in multiple environments. The significant interval for stability time on 1D was narrowed into an 8.4-Mb region using the updated arrays, whereas the interval is 405 Mb using the un-updated arrays. Linkage analysis revealed an important QTL QST.henau-1D.2 for stability time with 1.64 Mb. Integration of GWAS and QTL results narrowed the significant interval into 6.46 Mb containing 35 annotation genes by collinearity analysis. After T-test, gene expression analysis, seven of them are potential candidate genes and thus favorable haplotypes are identified to benefit marker-assisted selection.

Conclusion: A reconciliation of Wheat 660K and 90K arrays promote their efficient applications. Important genetic loci and favorable haplotypes identified in this study provided valuable information for wheat quality breeding.

Keywords: Bread wheat; Dough rheological properties; GWAS; Stability time; Wheat SNP array.