Genome-wide association study and selective sweep analyses identify loci associated with plant height and spike number in a Chinese micro-core collection of common wheat (Triticum aestivum L.)

Plant height (PH) and spike number per plant (SN) are important components of wheat architecture and adaptation. However, the extent to which loci underlying these traits overlap genomic regions targeted during modern breeding remains incompletely understood. We combined genome-wide association analysis with selective sweep scans to identify quantitative trait loci (QTLs) and positional candidate genes for these traits in common wheat. A panel of 280 accessions, comprising 133 landraces and 147 modern cultivars, was genotyped with a single-nucleotide polymorphism array, retaining 319,986 markers after quality control. Population analyses separated most landraces from modern cultivars and inferred migration edges from several landrace groups toward corresponding cultivar groups. Genome-wide association analyses of the two environments and best linear unbiased predictions identified 53 QTLs, comprising 18 for PH and 35 for SN. Of these, eight QTLs were detected in at least two datasets. Selective sweep scans based on nucleotide diversity, population differentiation, and the cross-population composite likelihood ratio identified genomic regions showing signatures of breeding selection. Three QTLs, QPH.ynau-5B.1 , QSN.ynau-1A.4 , and QSN.ynau-6B.3 , overlapped these regions. Genes encoding a NAC domain-containing transcription factor, beta-glucanase, and diacylglycerol kinase were prioritized as positional candidates within the overlapping regions. These findings connect trait-associated loci with genomic signatures of breeding selection and provide candidate loci and genes for understanding and improving wheat architecture.