Single Nucleotide Polymorphisms in the Wheat Genome Associated with Tolerance of Acidic Soils and Aluminum Toxicity

Aluminum toxicity is a major yield constraint of wheat (Triticum aestivum L.) in acidic soils, which compose a significant area of Earth's arable land. There is natural variation in wheat's Al tolerance and a tolerance gene on chromosome 4D named ALMT1 has been cloned and characterized. Some wheat populations, however, show much variation in acidic field tolerance that is not explained by known major Al tolerance loci. This study was conducted to discover new loci that condition wheat's tolerance of low soil pH with the ultimate goal of DNA marker development for expedited tolerance breeding and selection. To this end, two diverse populations of the US Pacific Northwest (PNW)-adapted winter wheat were genotyped on recently developed 9K and 90K single nucleotide polymorphism (SNP) genetic marker platforms and phenotyped in three low-pH, Al-toxic field settings. The first population consisted of 459 accessions of soft white wheat. The second population, which was further phenotyped hydroponically, consisted of 401 accessions, some of which were soft white and some hard red. Genome-wide association studies (GWAS) uncovered a total of 55 loci, 15 of which were common to both populations. The molecular marker wmc331, linked to ALMT1, was analyzed in both populations, revealing only eight individuals with the favorable allele. We found that the unique germplasm examined in this study has novel sources of low-pH tolerance that could be exploitable in the development of wheat cultivars that are tolerant of soil acidity and Al toxicity.