Genetic characterization of Setaria (Poaceae) populations: cytogenomic and molecular diversity

Abstract

Grasses are considered the most important angiosperm group in economic terms, being widely distributed worldwide and with great adaptability. The advanced in studies of genome size, cytogenetics next-generation sequencing and bioinformatics have been providing relevant information in genomic studies. Repetitive DNA, especially retrotransposons (TEs), contribute significantly to plant genome size, evolution, and adaptation. Setaria Beauv. (Poaceae) is a reference genus in forage production and has been explored especially due to its great adaptability under climate changes. Setaria sphacelata has different ploidy levels, being a resilient cereal crop, with good yields in dry and marginal land. However, little is known about its genome constitution. The study aimed to characterize germplasm populations of S. sphacelata. We analyzed 72 populations that were collected in different regions of the world. Flow cytometry was used for genome size detection, followed by chromosome counting, fluorescent in situ hybridization and meiotic analysis. In addition, we analysed the constitution of DNA repetitive sequences in S. sphacelata for the first time. Given the importance of transposable elements in different cellular process, we taken advanced of the genetic resources available for model plants to quantify the proportion of active elements in Setaria viridis, using bioinformatics tools. Most populations showed mainly tetraploids individuals (2n=36) with DNA content ranging from 3 to 3.7 picograms. Additionally, diploids (~ 1.6 to 2pg, 2n=18), pentaploids (~4 pg, 2n=45), hexaploids (~ 4,5 pg, 2n=54) and octaploids (~6pg, 2n= 72ca) were also detected, but in low number of populations. The highest variation was found in populations of South Africa. The mapping of 5S and 18S rDNA sites varied among and within the ploidy levels. Regular meiosis suggests that allopolyploidy was probably one of the steps in evolutionary history. The genetic diversity analysis revealed that S. sphacelata is a complex with intra and mainly inter populational variation. Diploids seem to be a distinct group based on SSR markers. Analysing two diploid cultivars of S. sphacelata, we found that Ty3/Gypsy retrotransposons were the most abundant repeat sequences. However, variations in the proportion of sublineages Athila and Ogre suggest a different amplification process of repeats during the species complex evolution. Some satellites probes showed a conserved pattern observed in pericentromeric regions. Concerning the expression of TE in S. viridis, repeats were more abundant in ribo-depleted RNA libraries (analysed in stem and crown tissues) than in poly-A RNA libraries (analysed in leaf and inflorescence tissues). The expression of TEs was influenced by their type (Ty1/copia more active than Ty3/gypsy), genome proportion, GC ratio and reads similarity. In summary, these findings provide a better understanding of the genome organization, evolutionary history and transcription dynamics of repetitive elements in Setaria.