Genome-wide association analysis of wheat stem traits using 55K microarrays

Wei Wang¹Na Sun²Kai Zhao¹Jikun Song³Hui Fang⁴Fan Guiqiang⁴Yonghong Gao⁴Tianrong Huang⁴Yindeng Ding^4*

• ¹School of Computer Science and Information Engineering, Anyang Institute of Technology, Anyang, China
• ²Yili Prefecture Institute of Agricultural Science, Yili, China
• ³Cotton Research Institute, Chinese Academy of Agricultural Sciences, AnYang 455000, China;, anyang, China
• ⁴Xinjiang Academy of Agricultural Sciences Institute of Microbiology, Urumqi, China

Wheat lodging poses a severe threat to yield and quality, with the morphological and structural traits of the basal second internode being critical determinants of stem strength and lodging resistance. We conducted phenotypic analysis on 239 wheat varieties (lines) collected from around the world. This analysis was complemented by genotyping using the wheat 55K SNP chip. Genome-wide association analysis (GWAS) was executed employing the MLM (Q+K) algorithm within the TASSLE software suite. The findings unveiled pronounced phenotypic variability in the stem diameter of the second internode across disparate temporal intervals, characterized by a coefficient of variation spanning from 11.31% to 13.95%, alongside robust inter-year correlations. Furthermore, the genome-wide linkage disequilibrium (LD) decay distance was ascertained to 3 Mb. Analyses of population structure, phylogenetic dendrograms, and principal components revealed that the intrinsic population structure of the 239 wheat varieties (lines) was markedly simplified, segregating into three discernible subgroups. GWAS analysis identified 118 SNPs significantly associated with the stem diameter of the second internode (P ≤ 0.001). Notably, among these loci, three SNPs (AX-111557672, AX-94584919, and AX-109819835) overlapped with previously reported associations, while the remaining 115 SNPs represented novel discoveries distributed across chromosomes 1A, 1B,