title: Mango (Mangifera indica L.) germplasm diversity based on single nucleotide polymorphisms derived from the transcriptome.
abstract: BACKGROUND
  Germplasm collections are an important source for plant breeding, especially in fruit trees which have a long duration of juvenile period. Thus, efforts have been made to study the diversity of fruit tree collections. Even though mango is an economically important crop, most of the studies on diversity in mango collections have been conducted with a small number of genetic markers.
  
  
  RESULTS
  We describe a de novo transcriptome assembly from mango cultivar 'Keitt'. Variation discovery was performed using Illumina resequencing of 'Keitt' and 'Tommy Atkins' cultivars identified 332,016 single-nucleotide polymorphisms (SNPs) and 1903 simple-sequence repeats (SSRs). Most of the SSRs (70.1%) were of trinucleotide with the preponderance of motif (GGA/AAG)n and only 23.5% were di-nucleotide SSRs with the mostly of (AT/AT)n motif. Further investigation of the diversity in the Israeli mango collection was performed based on a subset of 293 SNPs. Those markers have divided the Israeli mango collection into two major groups: one group included mostly mango accessions from Southeast Asia (Malaysia, Thailand, Indonesia) and India and the other with mainly of Floridian and Israeli mango cultivars. The latter group was more polymorphic (FS=-0.1 on the average) and was more of an admixture than the former group. A slight population differentiation was detected (FST=0.03), suggesting that if the mango accessions of the western world apparently was originated from Southeast Asia, as has been previously suggested, the duration of cultivation was not long enough to develop a distinct genetic background.
  
  
  CONCLUSIONS
  Whole-transcriptome reconstruction was used to significantly broaden the mango's genetic variation resources, i.e., SNPs and SSRs. The set of SNP markers described in this study is novel. A subset of SNPs was sampled to explore the Israeli mango collection and most of them were polymorphic in many mango accessions. Therefore, we believe that these SNPs will be valuable as they recapitulate and strengthen the history of mango diversity.
authors.affiliation: Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel. asherman@volcani.agri.gov.il.
authors.forename: Amir
authors.initials: A
authors.lastname: Sherman
authors.affiliation: Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel. morr@volcani.agri.gov.il.
authors.forename: Mor
authors.initials: M
authors.lastname: Rubinstein
authors.affiliation: Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel. reshed@volcani.agri.gov.il.
authors.forename: Ravit
authors.initials: R
authors.lastname: Eshed
authors.affiliation: Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel. miriamzarbiv@walla.co.il.
authors.forename: Miri
authors.initials: M
authors.lastname: Benita
authors.affiliation: Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel. mazali@volcani.agri.gov.il.
authors.forename: Mazal
authors.initials: M
authors.lastname: Ish-Shalom
authors.affiliation: Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel. michalsha@volcani.agri.gov.il.|The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel. michalsha@volcani.agri.gov.il.
authors.forename: Michal
authors.initials: M
authors.lastname: Sharabi-Schwager
authors.affiliation: Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel. adar@volcani.agri.gov.il.
authors.forename: Ada
authors.initials: A
authors.lastname: Rozen
authors.affiliation: Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel. saada@volcani.agri.gov.il.
authors.forename: David
authors.initials: D
authors.lastname: Saada
authors.affiliation: Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel. vhyuvalc@volcani.agri.gov.il.
authors.forename: Yuval
authors.initials: Y
authors.lastname: Cohen
authors.affiliation: Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel. ron@agri.gov.il.
authors.forename: Ron
authors.initials: R
authors.lastname: Ophir
mesh_terms: D018506:Gene Expression Regulation, Plant; D055993:Germ Cells, Plant / Q000378:metabolism; D007557:Israel; D031022:Mangifera / Q000235:genetics* / Q000378:metabolism; D018895:Microsatellite Repeats; D008969:Molecular Sequence Data; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D059467:Transcriptome