title: Soybean (Glycine max) SWEET gene family: insights through comparative genomics, transcriptome profiling and whole genome re-sequence analysis.
abstract: BACKGROUND
  SWEET (MtN3_saliva) domain proteins, a recently identified group of efflux transporters, play an indispensable role in sugar efflux, phloem loading, plant-pathogen interaction and reproductive tissue development. The SWEET gene family is predominantly studied in Arabidopsis and members of the family are being investigated in rice. To date, no transcriptome or genomics analysis of soybean SWEET genes has been reported.
  
  
  RESULTS
  In the present investigation, we explored the evolutionary aspect of the SWEET gene family in diverse plant species including primitive single cell algae to angiosperms with a major emphasis on Glycine max. Evolutionary features showed expansion and duplication of the SWEET gene family in land plants. Homology searches with BLAST tools and Hidden Markov Model-directed sequence alignments identified 52 SWEET genes that were mapped to 15 chromosomes in the soybean genome as tandem duplication events. Soybean SWEET (GmSWEET) genes showed a wide range of expression profiles in different tissues and developmental stages. Analysis of public transcriptome data and expression profiling using quantitative real time PCR (qRT-PCR) showed that a majority of the GmSWEET genes were confined to reproductive tissue development. Several natural genetic variants (non-synonymous SNPs, premature stop codons and haplotype) were identified in the GmSWEET genes using whole genome re-sequencing data analysis of 106 soybean genotypes. A significant association was observed between SNP-haplogroup and seed sucrose content in three gene clusters on chromosome 6.
  
  
  CONCLUSIONS
  Present investigation utilized comparative genomics, transcriptome profiling and whole genome re-sequencing approaches and provided a systematic description of soybean SWEET genes and identified putative candidates with probable roles in the reproductive tissue development. Gene expression profiling at different developmental stages and genomic variation data will aid as an important resource for the soybean research community and can be extremely valuable for understanding sink unloading and enhancing carbohydrate delivery to developing seeds for improving yield.
authors.affiliation: National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA. patilg@missouri.edu.
authors.forename: Gunvant
authors.initials: G
authors.lastname: Patil
authors.affiliation: National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA. valliyodanb@missouri.edu.
authors.forename: Babu
authors.initials: B
authors.lastname: Valliyodan
authors.affiliation: National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA. rupesh0deshmukh@gmail.com.
authors.forename: Rupesh
authors.initials: R
authors.lastname: Deshmukh
authors.affiliation: National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA. princesj@missouri.edu.
authors.forename: Silvas
authors.initials: S
authors.lastname: Prince
authors.affiliation: Department of Plant Biology and Forest Genetics and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden. Bjorn.Nicander@slu.se.
authors.forename: Bjorn
authors.initials: B
authors.lastname: Nicander
authors.affiliation: National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA. soyshen@126.com.|Current address: Agronomy College of Shenyang Agricultural University, Shenyang, China. soyshen@126.com.
authors.forename: Mingzhe
authors.initials: M
authors.lastname: Zhao
authors.affiliation: National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA. biohuma@gmail.com.
authors.forename: Humira
authors.initials: H
authors.lastname: Sonah
authors.affiliation: National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA. songli@missouri.edu.
authors.forename: Li
authors.initials: L
authors.lastname: Song
authors.affiliation: National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA. linl@missouri.edu.
authors.forename: Li
authors.initials: L
authors.lastname: Lin
authors.affiliation: National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA. chaudharyj@missouri.edu.
authors.forename: Juhi
authors.initials: J
authors.lastname: Chaudhary
authors.affiliation: Department of Computer Science, Informatics Institute, and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA. ylmk2@mail.missouri.edu.
authors.forename: Yang
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Department of Computer Science, Informatics Institute, and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA. joshitr@missouri.edu.
authors.forename: Trupti
authors.initials: T
authors.lastname: Joshi
authors.affiliation: Department of Computer Science, Informatics Institute, and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA. xudong@missouri.edu.
authors.forename: Dong
authors.initials: D
authors.lastname: Xu
authors.affiliation: National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA. nguyenhenry@missouri.edu.
authors.forename: Henry T
authors.initials: HT
authors.lastname: Nguyen
mesh_terms: D020816:Amino Acid Motifs / Q000235:genetics; D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods; D032461:Chromosomes, Plant / Q000235:genetics; D019295:Computational Biology; D017124:Conserved Sequence / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics; D012275:Oryza / Q000235:genetics; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods; D013025:Glycine max / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*
chemical_list: D010940:Plant Proteins