Soybean (Glycine max) SWEET gene family: insights through comparative genomics, transcriptome profiling and whole genome re-sequence analysis

BMC Genomics

Research Article

Yang Liu¹  Trupti Joshi¹  Dong Xu¹  Bjorn Nicander²  Juhi Chaudhary³  Silvas Prince³  Rupesh Deshmukh³  Humira Sonah³  Babu Valliyodan³  Henry T. Nguyen³  Gunvant Patil³  Li Song³  Li Lin³  Mingzhe Zhao⁴ 

[1] Department of Computer Science, Informatics Institute, and Christopher S. Bond Life Sciences Center, University of Missouri, 65211, Columbia, MO, USA;Department of Plant Biology and Forest Genetics and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden;National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, 65211, Columbia, MO, USA;National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, 65211, Columbia, MO, USA;Current address: Agronomy College of Shenyang Agricultural University, Shenyang, China;

关键词: SWEET;    Effluxer;    Sugar transport;    Sink;    Whole genome re-sequencing;    Soybean;   

DOI  :  10.1186/s12864-015-1730-y

 received in 2014-12-29, accepted in 2015-06-26,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundSWEET (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.ResultsIn 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.ConclusionPresent 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.

【 授权许可】

Unknown   
© Patil et al. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.