Abstract
BackgroundBrachypodium 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.
Highlights
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
Individual plants from Northeast (NE) Iberian populations LUM, PER, BAN, ARE, YAS, ABI, SAR, CAN and MUR were sampled in the wild, whereas individuals from Northwest (NW) Iberian populations SOB, CMH and ISC and South (S) Iberian populations PLA and GRAZ are first generation seed-germinated selfed plants (S1), each of them obtained from a different wild mother plant
Results from Bayesian analyses implemented in INEst revealed that only inbreeding contributed to the excessive homozogosity since this model (DICnfb: 2578.593) was preferred over the model that included only null alleles (DICnb: 3683.439) based on the Deviance Information Criterion (DIC) criterion
Summary
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. Has become one of the most important model systems for functional genomic studies of temperate cereals and forage grasses and for bioenergy crops [1, 2]. The diploid Brachypodium distachyon shows a short generation time (annual life cycle), one of the smallest genomes among grass species (272 Mbp in five chromosomes) and it is a highly selfing plant that can be grown under controlled conditions [2]. A high-quality reference genome of B. distachyon (based on the diploid inbred line Bd21) is already available [2] and significant investments have been further made in developing and using Brachypodium as a model system to learn the genetic mechanisms controlling relevant traits such as cell wall composition, biomass yield, abiotic and biotic stress tolerance, grain development and other features relevant to biomass crop development [3, 5,6,7,8,9,10]. Candidate genes identified from C4 grasses that are emerging biomass crops (e.g., maize, sorghum) are being introduced into the temperate C3-plant B. distachyon with the aim of changing its photosynthetic characteristics since the C4 photosynthetic pathway is generally more efficient under hot and dry conditions [11]
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