Haplotype analysis of sucrose synthase gene family in three Saccharumspecies

Abstract

BackgroundSugarcane is an economically important crop contributing about 80% and 40% to the world sugar and ethanol production, respectively. The complicated genetics consequential to its complex polyploid genome, however, have impeded efforts to improve sugar yield and related important agronomic traits. Modern sugarcane cultivars are complex hybrids derived mainly from crosses among its progenitor species, S. officinarum and S. spontanuem, and to a lesser degree, S. robustom. Atypical of higher plants, sugarcane stores its photoassimilates as sucrose rather than as starch in its parenchymous stalk cells. In the sugar biosynthesis pathway, sucrose synthase (SuSy, UDP-glucose: D-fructose 2-a-D-glucosyltransferase, EC 2.4.1.13) is a key enzyme in the regulation of sucrose accumulation and partitioning by catalyzing the reversible conversion of sucrose and UDP into UDP-glucose and fructose. However, little is known about the sugarcane SuSy gene family members and hence no definitive studies have been reported regarding allelic diversity of SuSy gene families in Saccharum species.ResultsWe identified and characterized a total of five sucrose synthase genes in the three sugarcane progenitor species through gene annotation and PCR haplotype analysis by analyzing 70 to 119 PCR fragments amplified from intron-containing target regions. We detected all but one (i.e. ScSuSy5) of ScSuSy transcripts in five tissue types of three Saccharum species. The average SNP frequency was one SNP per 108 bp, 81 bp, and 72 bp in S. officinarum, S. robustom, and S. spontanuem respectively. The average shared SNP is 15 between S. officinarum and S. robustom, 7 between S. officinarum and S. spontanuem , and 11 between S. robustom and S. spontanuem. We identified 27, 35, and 32 haplotypes from the five ScSuSy genes in S. officinarum, S. robustom, and S. spontanuem respectively. Also, 12, 11, and 9 protein sequences were translated from the haplotypes in S. officinarum, S. robustom, S. spontanuem, respectively. Phylogenetic analysis showed three separate clusters composed of SbSuSy1 and SbSuSy2, SbSuSy3 and SbSuSy5, and SbSuSy4.ConclusionsThe five members of the SuSy gene family evolved before the divergence of the genera in the tribe Andropogoneae at least 12 MYA. Each ScSuSy gene showed at least one non-synonymous substitution in SNP haplotypes. The SNP frequency is the lowest in S. officinarum, intermediate in S. robustum, and the highest in S. spontaneum, which may reflect the timing of the two rounds of whole genome duplication in these octoploids. The higher rate of shared SNP frequency between S. officinarum and S. robustum than between S. officinarum and in S. spontaneum confirmed that the speciation event separating S. officinarum and S. robustum occurred after their common ancestor diverged from S. spontaneum. The SNP and haplotype frequencies in three Saccharum species provide fundamental information for designing strategies to sequence these autopolyploid genomes.

Recent polyploidization events in three Saccharum founding species

“…The reduction in basic chromosome number from 10 to 8 could result from either chromosome fusion or chromosome fission followed by integration of chromosome segments into different chromosomes after the speciation event separating S. spontaneum from the common ancestor of S. officinarum and S. robustum, because S. spontaneum linkage groups aligned to all 10 sorghum chromosomes (Ming et al, 1998). The two rounds of WGD via autopolyploidization occurred after these chromosome reduction events, likely earlier than the two rounds of WGD events in S. officinarum and S. robustum, because higher SNP rate was detected among orthologous haplotypes in S. spontaeum than those in S. officinarum and S. robustum (Zhang et al, 2013). The genic highdensity genetic maps provided large-scale collinearity analysis and allowed detection of more interchromosomal rearrangements between Saccharum and sorghum chromosomes.…”

Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum

“…After a 100 years of sugarcane breeding, the increase in sucrose production per hectare is still a major goal (Smith, 2008). However, only a few genes present in the sucrose metabolic pathway have been identified in sugarcane (Papini-Terzi et al, 2009;Zhang et al, 2013). In this context, MF scaffolds offer the possibility to identify complete pathways such as the genes for the metabolism of sucrose and starch.…”

Caracterização do relógio biológico e seu impacto no metabolismo da cana-de-açúcar

“…No caso do homólogo PPD-H1 (ou HvPRR37), o efeito da baixa temperatura é semelhante ao observado em Arabidopsis (Calixto et al, 2016 Estas isoformas alternativas foram observadas em experimentos de HR RT-PCR (James et al, 2012;Calixto et al, 2016) (Zhang et al, 2013) e para transportadores de sacarose (Zhang et al, 2016 Realizar esta análise é importante para acessar a influência conjunta do relógio biológico com o ambiente natural sobre a fisiologia e o metabolismo das plantas em campo. As variações ambientais (luz e temperatura, por exemplo) são percebidas pelas vias de entrada do relógio biológico, incorporadas ao seu oscilador central e resultam em respostas fisiológicas e metabólicas organizadas temporalmente (Filichkin et al, 2011;Izawa et al, 2011).…”

“…As estimativas mais recentes dão conta de uma variação de ploidia de 6 a 14 cromossomos (Garcia et al, 2013). Além disso, dados de expressão gênica apontam para a expressão de múltiplos haplótipos em cultivares comerciais de cana- de-açúcar e também em espécies de cana-de-açúcar ancestrais (Zhang et al, 2013;Zhang et al, 2016). Ou seja, a poliploidia da cana parece não estar restrita ao genoma, ela se manifesta na expressão dos genes, abrindo possibilidades para especulação sobre a complexidade do relógio biológico da cana-de-açúcar.…”

“…A partir da presença de SNPs nos transcritos destes genes, foi possível detectar possíveis alelos diferentes sendo expressos no órgão F1 da cana-de-açúcar, mesmo sabendo que a frequência de SNPs não necessariamente aponta para uma diversidade de haplótipos (Zhang et al, 2013 A análise de SNPs e alelos para os genes do relógio destes dois ancestrais aliada a uma comparação com os SNPs e alelos expressos encontrados nos cultivares modernos, como SP80-3280, seria uma estratégia interessante para mapear diferenças e semelhanças entre os genes do relógio biológico dos ancestrais e a frequência de cada um deles dentro do genoma dos cultivares modernos. A heterozigosidade ainda está relacionada ao ganho de biomassa pelo cultivar (Li et al, 2016).…”