Structure, phylogeny, allelic haplotypes and expression of sucrose transporter gene families in Saccharum. (December 2016)

• Record Type: Journal Article
• Authors: Zhang, Qing; Hu, Weichang; Zhu, Fan; Wang, Liming; Yu, Qingyi; Ming, Ray; Zhang, Jisen
• Is Part Of: BMC genomics. Volume 17:Number 1(2016)
• Page Start: 1
• Page End: 18
• Publication Date: 2016-12
• Subjects: Saccharum species -- Sucrose transporter -- Gene family -- Allelic haplotype -- Polyploidy; Genomes -- Periodicals; Gene mapping -- Periodicals; Genomics -- Periodicals; Base Sequence -- Periodicals; Chromosome Mapping -- Periodicals; Genetic Techniques -- Periodicals; Sequence Analysis, DNA -- Periodicals; 572.8605
• DOI: 10.1186/s12864-016-2419-6
• Languages: English
• ISSNs: 1471-2164

Abstract

Abstract Background Sugarcane is an economically important crop contributing to about 80 % of the world sugar production. Increasing efforts in molecular biological studies have been performed for improving the sugar yield and other relevant important agronomic traits. However, due to sugarcane's complicated genomes, it is still challenging to study the genetic basis of traits, such as sucrose accumulation. Sucrose transporters (SUTs) are critical for both phloem loading in source tissue and sucrose uptaking in sink tissue, and are considered to be the control points for regulating sucrose storage. However, no genomic study for sugarcane sucrose transporter (SsSUT) families has been reported up to date. Results By using comparative genomics and bacterial artificial chromosomes (BACs), six SUT genes were identified and characterized inS. spontaenum . Phylogenetic analyses revealed that the two pairsSsSUTs (SsSUT1 /SsSUT3 andSsSUT5 /SsSUT6 ) could be clustered together into two separate monocot specific SUT groups, whileSsSUT2 andSsSUT4 were separated into the other two groups, with members from both dicot and monocot species. Gene structure comparison demonstrated that the number and position of exons/introns inSUTs were highly conserved among the close orthologs; in contrast, there were variations among the paralogousSUTs inSacchuarm . Though with the high polyploidy level, gene allelic haplotype comparative analysis showed that the examined fourSsSUT members exhibited conservations of gene structures and amino acid sequences among the allelic haplotypes accompanied by variations of intron sizes. Gene expression analyses were performed for tissues from seedlings under drought stress and mature plants of threeSaccharum species (S.officinarnum, S.spotaneum andS.robustum ). BothSUT1 andSUT4 expressed abundantly at different conditions.SUT2 had similar expression level in all of the examined tissues, butSUT3 was undetectable. Both ofSUT5 andSUT6 had lower expression level than other gene member, and expressed stronger in source leaves and are likely to play roles in phloem loading. In the seeding plant leave under water stress, four genesSUT1, SUT2, SUT4 andSUT5 were detectable. In these detectable genes, SUT1 andSUT4 were down regulated, while, SUT2 andSUT5 were up regulated. Conclusions In this study, we presented the first comprehensive genomic study for a whole gene family, the SUT family, inSaccharum . We speculated that there were sixSUT members in theS. spotaneum genome. Out of the six members, SsSUTs, SsSUT5 andSsSUT6 were recent duplication genes accompanied by rapid evolution, while, SsSUT2 andSsSUT4 were the ancient members in the families. Despite the high polypoidy genome, functional redundancy may not exist among the SUTs allelic haplotypes supported by the evidence of strong purifying selection of the gene allele.SUT3 could be a low active member in the family because it is undetectable in our study, but it might not be a pseudogene because it harbored integrated gene structure.SUT1 andSUT4 were the main members for the sucrose transporter, while, theseSUTs had sub-functional divergence in response to sucrose accumulation and plant development inSaccharum .