Gene Duplication in the Sugarcane Genome: A Case Study of Allele Interactions and Evolutionary Patterns in Two Genic Regions.

Sugarcane (Saccharum spp.) is highly polyploid and aneuploid. Modern cultivars are derived from hybridization between S. officinarum and S. spontaneum. This combination results in a genome exhibiting variable ploidy among different loci, a huge genome size (~10 Gb) and a high content of repetitive regions. An approach using genomic, transcriptomic, and genetic mapping can improve our knowledge of the behavior of genetics in sugarcane. The hypothetical HP600 and Centromere Protein C (CENP-C) genes from sugarcane were used to elucidate the allelic expression and genomic and genetic behaviors of this complex polyploid. The physically linked side-by-side genes HP600 and CENP-C were found in two different homeologous chromosome groups with ploidies of eight and ten. The first region (Region01) was a Sorghum bicolor ortholog region with all haplotypes of HP600 and CENP-C expressed, but HP600 exhibited an unbalanced haplotype expression. The second region (Region02) was a scrambled sugarcane sequence formed from different noncollinear genes containing partial duplications of HP600 and CENP-C (paralogs). This duplication resulted in a non-expressed HP600 pseudogene and a recombined fusion version of CENP-C and the orthologous gene Sobic.003G299500 with at least two chimeric gene haplotypes expressed. It was also determined that it occurred before Saccharum genus formation and after the separation of sorghum and sugarcane. A linkage map was constructed using markers from nonduplicated Region01 and for the duplication (Region01 and Region02). We compare the physical and linkage maps, demonstrating the possibility of mapping markers located in duplicated regions with markers in nonduplicated region. Our results contribute directly to the improvement of linkage mapping in complex polyploids and improve the integration of physical and genetic data for sugarcane breeding programs. Thus, we describe the complexity involved in sugarcane genetics and genomics and allelic dynamics, which can be useful for understanding complex polyploid genomes.

Genetic diversity assessed by microsatellite markers in the amphicarpic species Trifolium polymorphum Poir.

Trifolium polymorphum Poir. is an amphicarpic forage legume from southern Brazil, Uruguay, Argentina, Paraguay and Chile. Information on the genetic diversity of natural populations in natural grasslands in southern Brazil is limited. In order to increase the knowledge about this species, an analysis of the genetic diversity was carried out in 10 natural populations of T. polymorphum with the use of 20 microsatellite markers. The expected heterozygosity in T. polymorphum populations ranged from 0.40 to 0.43, with a mean of 0.42. A total of 193 alleles were detected with a mean of 9.3 alleles per locus and polymorphic information content (PIC) for these markers of 0.62 to 0.89 with a mean of 0.84.The grouping based on the Jaccard's coefficient of similarity classified populations, regardless of their regions of origin, into two groups with a mean similarity coefficient of 0.32, reflecting the high genetic variability of the populations, especially those located in the Campanha phytogeographic region. This information on diversity can be used to plan future germplasm collection strategies for conservation purposes and also for the breeding of the species.

Cytogenetic data for Paspalum notatum Flügge accessions

Several species of the genus Paspalum L. are important forages, due their to quality, productivity and tolerance to environmental stresses. Chromosome numbers, meiotic configurations and pollen fertility were evaluated in a collection of 85 accessions of Paspalum notatum Flügge and in seven accessions of Pensacola (P. notatum var saurae). All P. notatum accessions were tetraploid, with 2n = 4x = 40, except one diploid accession, considered as an escape of Pensacola. All Pensacola plants had 2n = 2x = 20. Meiotic configurations at diakinesis and metaphase I varied among tetraploid accessions, from plants with only bivalents to plants with high frequency of quadrivalents. Pollen fertility varied from 82.5 to 95.9% among diploid accessions and from 72.4 to 97.9% among the tetraploids. Due to the apomictic mode of reproduction of tetraploid P. notatum, meiotic irregularities can be maintained by plants without harming their propagation. At the same time, pollen fertility should be high enough to assure endosperm development, since the species is pseudogamous. Wild diploid P. notatum populations, apart from the endemic P. notatum var saurae, are very rare. From a plant breeding point of view, all the examined tetraploid accessions are potentially male-fertile and could be used as males in crosses.

Muitas espécies do genus Paspalum L. são importantes forragens, devido à qualidade, produtividade e tolerância para o stress ambiental. Números cromossômicos, configurações meióticas e fertilidade do pólen foram analisados em uma coleção de 85 acessos de Paspalum notatum Flügge e sete acessos de Pensacola (P. notatum var saurae). Todos os acessos de P. notatum eram tetraplóides, com 2n = 4x = 40, com exceção de um diplóide, considerado como escape de Pensacola. Todas as plantas de Pensacola examinadas tinham 2n = 2x = 20. Foi verificada variação entre os acessos tetraplóides quanto às configurações cromossômicas em diacinese e metáfase I, desde plantas com apenas bivalentes até aquelas com alta freqüência de quadrivalentes. A fertilidade do pólen variou de 82,5 a 95,9% entre os acessos diplóides e de 72,4 a 97,9% entre os tetraplóides. Devido ao modo de reprodução apomítico de P. notatum tetraplóide, irregularidades meióticas podem ser mantidas sem prejuízo da propagação. Ao mesmo tempo, a fertilidade do pólen deve ser suficientemente alta para assegurar a formação do endosperma, já que a espécie é pseudogâmica. Diplóides silvestres de P. notatum, além do endêmico P. notatum var saurae são muito raros. Do ponto de vista do melhoramento, todos os tetraplóides são potencialmente macho-férteis e poderiam ser utilizados como genitores masculinos em cruzamentos.

Cytogenetic data for Paspalum notatum Flügge accessions

Several species of the genus Paspalum L. are important forages, due their to quality, productivity and tolerance to environmental stresses. Chromosome numbers, meiotic configurations and pollen fertility were evaluated in a collection of 85 accessions of Paspalum notatum Flügge and in seven accessions of Pensacola (P. notatum var saurae). All P. notatum accessions were tetraploid, with 2n = 4x = 40, except one diploid accession, considered as an escape of Pensacola. All Pensacola plants had 2n = 2x = 20. Meiotic configurations at diakinesis and metaphase I varied among tetraploid accessions, from plants with only bivalents to plants with high frequency of quadrivalents. Pollen fertility varied from 82.5 to 95.9% among diploid accessions and from 72.4 to 97.9% among the tetraploids. Due to the apomictic mode of reproduction of tetraploid P. notatum, meiotic irregularities can be maintained by plants without harming their propagation. At the same time, pollen fertility should be high enough to assure endosperm development, since the species is pseudogamous. Wild diploid P. notatum populations, apart from the endemic P. notatum var saurae, are very rare. From a plant breeding point of view, all the examined tetraploid accessions are potentially male-fertile and could be used as males in crosses.

Muitas espécies do genus Paspalum L. são importantes forragens, devido à qualidade, produtividade e tolerância para o stress ambiental. Números cromossômicos, configurações meióticas e fertilidade do pólen foram analisados em uma coleção de 85 acessos de Paspalum notatum Flügge e sete acessos de Pensacola (P. notatum var saurae). Todos os acessos de P. notatum eram tetraplóides, com 2n = 4x = 40, com exceção de um diplóide, considerado como escape de Pensacola. Todas as plantas de Pensacola examinadas tinham 2n = 2x = 20. Foi verificada variação entre os acessos tetraplóides quanto às configurações cromossômicas em diacinese e metáfase I, desde plantas com apenas bivalentes até aquelas com alta freqüência de quadrivalentes. A fertilidade do pólen variou de 82,5 a 95,9% entre os acessos diplóides e de 72,4 a 97,9% entre os tetraplóides. Devido ao modo de reprodução apomítico de P. notatum tetraplóide, irregularidades meióticas podem ser mantidas sem prejuízo da propagação. Ao mesmo tempo, a fertilidade do pólen deve ser suficientemente alta para assegurar a formação do endosperma, já que a espécie é pseudogâmica. Diplóides silvestres de P. notatum, além do endêmico P. notatum var saurae são muito raros. Do ponto de vista do melhoramento, todos os tetraplóides são potencialmente macho-férteis e poderiam ser utilizados como genitores masculinos em cruzamentos.