Evolution and Expression Analysis of Starch Synthase Gene Families in Saccharum spontaneum

Starch is one of two crucial products of photosynthetic carbon-assimilation and mainly functions as the unit of energy storage in most crops such as rice, maize and sorghum, whereas interestingly in sugarcane that unit of energy storage is sucrose. Mature sugarcane stalk tissue has a very large apoplastic volume and contains nearly 700 mM sucrose-which is among the highest recorded sucrose concentrations in plant tissue. We identified 9 genes of starch synthases (SSs) related to the starch synthesis pathway in the genome of S. spontaneum. Based on gene structure and phylogenetic analysis, SSs genes were clustered into five clades and were relatively conserved. In S. spontaneum, the SS is a very ancient gene family, in which, SSIIIa and SSIIIb originated from the rho-whole genome duplications (WGDs), SSIIb and SsIIc originated from gene duplication after the split of monocots and dicots; GBSSI and GBSSII in Clade V and SSIIa in Clade II were retained from the epsilon-WGD, and the remaining two SSs (SSI and SSIV) were retained from the very ancient gene duplication event about 355-389 million year ago (Mya). In addition, we found all SS genes were under the influence of strong purification with a Ka/Ks ratio of less than 0.5 in S. spontaneum. In the 5 families, SSIIIa, SSIIb and GBSSII had relatively predominant expression levels in all the examined tissues from the two Saccharum species, indicating the three genes were the fundamental members in the non-storage tissues, leaf or stem, which is in agreement with previous studies. Interestingly, the expression levels of SSs in stems showed significantly higher values in S. spontenum than in S. officinarum at pre-mature and mature stages. These results were negatively correlated with the sucrose levels between the two Saccharum species. At the pre-mature and mature stages, the sucrose contents in stems from S. officinarum were much higher than in stems from S. spontenum, suggesting that SSs involved in the differential of carbohydrate metabolism between the two Saccharum species. Besides, the expression of SSs displayed a clearly consistent trend in line with normal distribution under the diurnal rhythms of S. spontaneum. Moreover, the expression pattern of SSIIIa, SSIIb and GBSSII displayed a clearly consistent trend in both Saccharum species and in maize, rice, which was in accordance with photosynthetic intensity across leaf gradients. This result suggested the functional constraints for the SSs gene family in Gramineae. Our results are valuable for further functional analysis of SSs genes and provided the foundation for carbohydrate metabolism in sugarcane.