Genome-wide association analysis of fiber-related traits and identification of diagnostic SNP markers differentiating spelt wheat (Triticum spelta L.) from bread wheat

Abstract

Introduction Spelt wheat (Triticum spelta L.) represents a valuable genetic resource within hexaploid wheat due to its high genetic diversity and adaptation to low-input agricultural systems; however, the genetic basis of its dietary fiber composition remains poorly understood. This study aimed to identify genomic regions associated with key soluble fiber components, including water-extractable pentosans (arabinoxylans), β-glucan, and fructans, and to detect diagnostic SNP markers that may support targeted breeding for improved nutritional quality. Methods A diverse panel of 255 genotypes, including spelt, bread wheat, and wild hexaploid accessions, was genotyped using a 25K SNP array and phenotyped over two consecutive years. Genome-wide association studies (GWAS) were performed with correction for population structure, and candidate genes were identified within ±1 Mb intervals surrounding significant SNPs based on functional annotations. Results Significant phenotypic differences were observed between spelt and bread wheat, with spelt consistently exhibiting lower levels of soluble fiber components, whereas total pentosan content remained comparable between the groups. GWAS identified 24, 10, 17, and 20 significant marker-trait associations for total pentosan, water-extractable pentosan, β-glucan, and fructan content, respectively. Major genomic regions associated with fiber-related traits were detected on chromosomes 1B, 2A, 2B, 5A, 5B, 5D, 6B, and 7A. Several stable SNP markers exhibited consistent phenotypic effects across years and distinguished allele variants characteristic of spelt. Notably, one spelt-specific marker was associated with β-glucan content, highlighting potentially valuable allelic variation in spelt that could be exploited to improve grain quality. Candidate genes involved in carbohydrate metabolism and cell wall biosynthesis, including glycosyltransferases, cellulose synthase-like proteins, and fructan-related enzymes, were identified in the vicinity of associated loci. In addition, 16 diagnostic spelt-specific SNP markers enabled reliable discrimination between homogeneous spelt and bread wheat lines. Discussion Overall, this study provides new insights into the genetic architecture of fiber-related quality traits in wheat and delivers molecular resources for marker-assisted breeding and the genetic identification of spelt germplasm.