Environmental isolation explains Iberian genetic diversity in the highly homozygous model grass Brachypodium distachyon

Abstract

Background Brachypodium distachyon (Poaceae), an annual Mediterranean Aluminum (Al)-sensitive grass, is currently being used as a model species to provide new information on cereals and biofuel crops. The plant has a short life cycle and one of the smallest genomes in the grasses being well suited to experimental manipulation. Its genome has been fully sequenced and several genomic resources are being developed to elucidate key traits and gene functions. A reliable germplasm collection that reflects the natural diversity of this species is therefore needed for all these genomic resources. However, despite being a model plant, we still know very little about its genetic diversity. As a first step to overcome this gap, we used nuclear Simple Sequence Repeats (nSSR) to study the patterns of genetic diversity and population structure of B. distachyon in 14 populations sampled across the Iberian Peninsula (Spain), one of its best known areas.ResultsWe found very low levels of genetic diversity, allelic number and heterozygosity in B. distachyon, congruent with a highly selfing system. Our results indicate the existence of at least three genetic clusters providing additional evidence for the existence of a significant genetic structure in the Iberian Peninsula and supporting this geographical area as an important genetic reservoir. Several hotspots of genetic diversity were detected and populations growing on basic soils were significantly more diverse than those growing in acidic soils. A partial Mantel test confirmed a statistically significant Isolation-By-Distance (IBD) among all studied populations, as well as a statistically significant Isolation-By-Environment (IBE) revealing the presence of environmental-driven isolation as one explanation for the genetic patterns found in the Iberian Peninsula.ConclusionsThe finding of higher genetic diversity in eastern Iberian populations occurring in basic soils suggests that these populations can be better adapted than those occurring in western areas of the Iberian Peninsula where the soils are more acidic and accumulate toxic Al ions. This suggests that the western Iberian acidic soils might prevent the establishment of Al-sensitive B. distachyon populations, potentially causing the existence of more genetically depauperated individuals.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-017-0996-x) contains supplementary material, which is available to authorized users.

Neutral molecular markers support common origin of aluminium tolerance in three congeneric grass species growing in acidic soils

“…The average number of alleles per locus calculated using SSR markers was also higher in Al-sensitive (2.3) B. hybridum than in Al-tolerant (1.4) B. hybridum accessions. This result agrees with data obtained by Marques et al (2017) in B. distachyon populations from the Iberian Peninsula. Similarly to B. distachyon , the acidic soils might prevent the establishment of Al-sensitive B. hybridum populations, probably causing the existence of more genetically depauperate individuals.…”

“…All accessions of B. distachyon were homozygotes in the 17 loci studied, each SSR locus showing only one allele in each accession. A high homozygosity was also obtained by Vogel et al (2009) using 43 SSR loci and 187 diploid accessions of B. distachyon and by Marques et al (2017) using 10 SSR loci and 14 populations of B. distachyon sampled across the Iberian Peninsula. This suggests a high homozygosity and reflects that B. distachyon is mainly a selfing species.…”

“…Contrastingly, B. hybridum grows across the Iberian Peninsula at low to mid-elevations, in NE and NW Spain (all places except the very humid North) inhabiting dry environments in which a predictable summer drought period exists ( Manzaneda et al 2012 ; López-Álvarez et al 2012 , 2015 ). Recently, Marques et al (2017) have found a higher genetic diversity in eastern Iberian populations of B. distachyon occurring in basic soils suggesting that these populations could be less constrained than those occurring in western areas of the Iberian Peninsula where the soils are more acidic and accumulate toxic Al ions. This result suggests that the western Iberian acidic soils might prevent the establishment of Al-sensitive B. distachyon populations, potentially causing the existence of more genetically depauperate individuals.…”

Cryptic species in an ancient flowering‐plant lineage (Hydatellaceae, Nymphaeales) revealed by molecular and micromorphological data

“…occurs in ephemeral aquatic ponds probably further reduces the probability of gene flow between them. The absence of genetic variation within populations observed in this study is not uncommon in highly autogamous plants (e.g., Shiposha & al., ; Marques & al., ).…”

Genetic diversity of Herpetospermum caudigerum (Ser.) Baill using AFLP and chloroplast microsatellites

“…To assess the genetic diversity of H. caudigerum Baill., the genetic parameters, including the number of total bands, the number of polymorphic bands, polymorphic rates, number of alleles (Na), effective number of alleles (Ne), Nei's gene The burn-in steps and the number of replicates were 10,000 and 50,000 for each K, respectively. The optimum K was estimated by the DK according to Structure Harvester [29]. Sequences were viewed and overlapping fragments were assembled using DNAStar.…”