Variability in predicted deleterious mutations among barley accessions conserved ex situ

Abstract

Understanding the genetic cost for long-term conservation of more than 7 million plant germplasm accessions in 1750 genebanks worldwide requires knowledge about the extent and variation of deleterious mutations within and among conserved germplasm collections. Our recent study revealed a wide range of mutations predicted to be deleterious to gene function and averaged sample-wise mutation burden per deleterious locus across barley, wheat, oat, soybean, maize, rapa, and sunflower germplasm collections. Here we report the extent and variation of predicted deleterious mutations among nine accessions of a barley (Hordeum vulgare L.) collection from an RNA-Seq analysis of 16 individual samples of each accession. The assayed accessions were found to vary significantly in the number and proportion of single nucleotide polymorphisms (SNPs) predicted to be deleterious mutations (ranging from 242 to 314 with a mean of 270 and from 0.00073 to 0.00099 with a mean of 0.00086, respectively). Similarly, a significant variation was also observed in the averaged sample-wise mutation burden estimates per deleterious locus, ranging from 0.541 to 0.747 with a mean of 0.681. Cultivar accessions had higher averages in the proportions of the predicted deleterious SNPs and in the averaged sample-wise mutation burden estimates than landrace accessions (0.00090 vs. 0.00082 and 0.695 vs. 0.663, respectively). The estimates of deleterious base-substitution mutations (×10⁻⁸) for the nine accessions varied from 0.313 to 0.406 with a mean of 0.349. These within-collection findings are useful for understanding the genetic cost in conserved germplasm and have implications for long-term germplasm management and conservation.