title: Leaf Transcriptome Sequencing for Identifying Genic-SSR Markers and SNP Heterozygosity in Crossbred Mango Variety 'Amrapali' (Mangifera indica L.).
abstract: Mango (Mangifera indica L.) is called "king of fruits" due to its sweetness, richness of taste, diversity, large production volume and a variety of end usage. Despite its huge economic importance genomic resources in mango are scarce and genetics of useful horticultural traits are poorly understood. Here we generated deep coverage leaf RNA sequence data for mango parental varieties 'Neelam', 'Dashehari' and their hybrid 'Amrapali' using next generation sequencing technologies. De-novo sequence assembly generated 27,528, 20,771 and 35,182 transcripts for the three genotypes, respectively. The transcripts were further assembled into a non-redundant set of 70,057 unigenes that were used for SSR and SNP identification and annotation. Total 5,465 SSR loci were identified in 4,912 unigenes with 288 type I SSR (n ≥ 20 bp). One hundred type I SSR markers were randomly selected of which 43 yielded PCR amplicons of expected size in the first round of validation and were designated as validated genic-SSR markers. Further, 22,306 SNPs were identified by aligning high quality sequence reads of the three mango varieties to the reference unigene set, revealing significantly enhanced SNP heterozygosity in the hybrid Amrapali. The present study on leaf RNA sequencing of mango varieties and their hybrid provides useful genomic resource for genetic improvement of mango.
authors.affiliation: ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India.
authors.forename: Ajay Kumar
authors.initials: AK
authors.lastname: Mahato
authors.affiliation: The Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India.
authors.forename: Nimisha
authors.initials: N
authors.lastname: Sharma
authors.affiliation: ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India.
authors.forename: Akshay
authors.initials: A
authors.lastname: Singh
authors.affiliation: The Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India.
authors.forename: Manish
authors.initials: M
authors.lastname: Srivastav
authors.affiliation: The Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India.
authors.lastname: Jaiprakash
authors.affiliation: The Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India.
authors.forename: Sanjay Kumar
authors.initials: SK
authors.lastname: Singh
authors.affiliation: The Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India.
authors.forename: Anand Kumar
authors.initials: AK
authors.lastname: Singh
authors.affiliation: ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India.
authors.forename: Tilak Raj
authors.initials: TR
authors.lastname: Sharma
authors.affiliation: ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India.
authors.forename: Nagendra Kumar
authors.initials: NK
authors.lastname: Singh
mesh_terms: D003433:Crosses, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D006579:Heterozygote; D031022:Mangifera / Q000235:genetics*; D018895:Microsatellite Repeats; D018515:Plant Leaves / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D018749:RNA, Plant / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D018749:RNA, Plant