RESUMO

Allopolyploidy is widely present across plant lineages. Though estimating the correct phylogenetic relationships and origin of allopolyploids may sometimes become a hard task. In the genus Stylosanthes Sw. (Leguminosae), an important legume crop, allopolyploidy is a key speciation force. This makes difficult adequate species recognition and breeding efforts on the genus. Based on comparative analysis of nine high-throughput sequencing (HTS) samples, including three allopolyploids (S. capitata Vogel cv. "Campo Grande," S. capitata "RS024" and S. scabra Vogel) and six diploids (S. hamata Taub, S. viscosa (L.) Sw., S. macrocephala M. B. Ferreira and Sousa Costa, S. guianensis (Aubl.) Sw., S. pilosa M. B. Ferreira and Sousa Costa and S. seabrana B. L. Maass & 't Mannetje) we provide a working pipeline to identify organelle and nuclear genome signatures that allowed us to trace the origin and parental genome recognition of allopolyploids. First, organelle genomes were de novo assembled and used to identify maternal genome donors by alignment-based phylogenies and synteny analysis. Second, nuclear-derived reads were subjected to repetitive DNA identification with RepeatExplorer2. Identified repeats were compared based on abundance and presence on diploids in relation to allopolyploids by comparative repeat analysis. Third, reads were extracted and grouped based on the following groups: chloroplast, mitochondrial, satellite DNA, ribosomal DNA, repeat clustered- and total genomic reads. These sets of reads were then subjected to alignment and assembly free phylogenetic analyses and were compared to classical alignment-based phylogenetic methods. Comparative analysis of shared and unique satellite repeats also allowed the tracing of allopolyploid origin in Stylosanthes, especially those with high abundance such as the StyloSat1 in the Scabra complex. This satellite was in situ mapped in the proximal region of the chromosomes and made it possible to identify its previously proposed parents. Hence, with simple genome skimming data we were able to provide evidence for the recognition of parental genomes and understand genome evolution of two Stylosanthes allopolyploids.

RESUMO

Wild species are important sources of genetic variability and may be exploited by breeding programs. Crosses between teosinte and maize occur freely and teosinte serves as genetic source of agronomic traits for introduction in maize. The objective of this study was to estimate genetic variability among and within maize and teosinte populations (Zea mays mexicana). Two sweet maize populations (BR400 and BR402), two common maize populations (Suwan and Pampa) and one teosinte population were analyzed using microsatellites markers. Results indicated that 64,5 percent of the variation was detected within the populations, suggesting the possibility of obtaining genetic progress by selection within each population. The analysis with 25 microsatellites loci enabled the identification of 92 alleles with a mean of 3.7 alleles per locus. The average Polymorphism Information Content (PIC) was 0.52. The percentage of polymorphic loci varied from 64 percent in the BR400 and Pampa populations to 80 percent in the teosinte population. The estimated genetic distance confirmed the genomic similarity of maize and teosinte.

Espécies silvestres são fontes importantes de variabilidade genética e podem ser exploradas pelos programas de melhoramento. Cruzamentos entre teosinto e milho ocorrem naturalmente, e o teosinto pode ser utilizado como fonte de caracteres agronômicos para introdução em milho. O objetivo deste estudo foi estimar a variabilidade genética entre e dentro de populações de milho e teosinto (Zea mays mexicana). Duas populações de milho doce (BR400 e BR402), duas de milho comum (Suwan e Pampa) e uma de teosinto foram analisadas utilizando-se marcadores microssatélites. Os resultados indicaram que 64,5 por cento da variação foi detectada dentro das populações, sugerindo a possibilidade de obtenção de progresso genético através da seleção dentro de cada população. A análise de 25 locos microssatélites permitiu identificar 92 alelos, com uma média de 3,7 alelos por loco. O percentual de locos polimórficos variou de 64 por cento nas populações BR400 e Pampa a 80 por cento na população de teosinto. A distância genética estimada confirmou a similaridade genética entre milho e teosinto.