PineElm_SSRdb: a microsatellite marker database identified from genomic, chloroplast, mitochondrial and EST sequences of pineapple (Ananas comosus (L.) Merrill)

Hereditas, Nov 2016

Background Simple Sequence Repeats or microsatellites are resourceful molecular genetic markers. There are only few reports of SSR identification and development in pineapple. Complete genome sequence of pineapple available in the public domain can be used to develop numerous novel SSRs. Therefore, an attempt was made to identify SSRs from genomic, chloroplast, mitochondrial and EST sequences of pineapple which will help in deciphering genetic makeup of its germplasm resources. Results A total of 359511 SSRs were identified in pineapple (356385 from genome sequence, 45 from chloroplast sequence, 249 in mitochondrial sequence and 2832 from EST sequences). The list of EST-SSR markers and their details are available in the database. Conclusions PineElm_SSRdb is an open source database available for non-commercial academic purpose at http://app.bioelm.com/ with a mapping tool which can develop circular maps of selected marker set. This database will be of immense use to breeders, researchers and graduates working on Ananas spp. and to others working on cross-species transferability of markers, investigating diversity, mapping and DNA fingerprinting.

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PineElm_SSRdb: a microsatellite marker database identified from genomic, chloroplast, mitochondrial and EST sequences of pineapple (Ananas comosus (L.) Merrill)

Chaudhary et al. Hereditas PineElm_SSRdb: a microsatellite marker database identified from genomic, chloroplast, mitochondrial and EST sequences of pineapple (Ananas comosus (L.) Merrill) Sakshi Chaudhary 0 Bharat Kumar Mishra Thiruvettai Vivek Santoshkumar Magadum Jeshima Khan Yasin 0 0 Equal contributors Division of Genomic Resources, ICAR- National Bureau of Plant Genomic Resources , PUSA campus, 110012 New Delhi , India Background: Simple Sequence Repeats or microsatellites are resourceful molecular genetic markers. There are only few reports of SSR identification and development in pineapple. Complete genome sequence of pineapple available in the public domain can be used to develop numerous novel SSRs. Therefore, an attempt was made to identify SSRs from genomic, chloroplast, mitochondrial and EST sequences of pineapple which will help in deciphering genetic makeup of its germplasm resources. Results: A total of 359511 SSRs were identified in pineapple (356385 from genome sequence, 45 from chloroplast sequence, 249 in mitochondrial sequence and 2832 from EST sequences). The list of EST-SSR markers and their details are available in the database. Conclusions: PineElm_SSRdb is an open source database available for non-commercial academic purpose at http://app.bioelm.com/ with a mapping tool which can develop circular maps of selected marker set. This database will be of immense use to breeders, researchers and graduates working on Ananas spp. and to others working on cross-species transferability of markers, investigating diversity, mapping and DNA fingerprinting. Ananas; Genome wide marker analysis; Organelle; Pineapple; Simple sequence repeats - Background The extremely surprising flavour and fragrance of pineapple (Ananas comosus L.) delighted mankind at that time of its discovery by Christopher Columbus and even today. Pineapple, a perennial monocot plant belongs to Bromeliales order, Bromelioideae subfamily and Bromeliaceae family. Pineapple is a tropical plant native to South America, domesticated more than 6000 years ago [1]. At the end of the sixteenth century, pineapple had become pantropical and is the third most economically important tropical fruit crop after banana and mango. Pineapple has become industrial crop during 20th century [2,3]. In addition to fresh fruit consumption, pineapple is used for canned slices, juice and juice concentrate, extraction of bromelain (a meat-tenderizing enzyme), high-quality fibre, animal feed and medicines [2]. At present, gross production value of pineapple is approaching $9 billion due to its cultivation on 1.02 million hectares of land in over 80 countries and annual production of 24.8 million metric tonnes of fruit [4]. Wild varieties of pineapple are self-compatible, whereas cultivated pineapple, A. comosus (L.) Merr., is self-incompatible [5], which provides an opportunity to scrutinize the molecular basis of self-incompatibility in monocots. Over the last few decades, a wide range of molecular markers have been developed and used in crop improvement as molecular markers are helpful in assessing © The Author(s). 2016 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. 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. Fig. 1 Homepage of the web app germplasm diversity, testing of hybridity, trait mapping, marker assisted selection etc. [6]. Among all the markers till date, Simple Sequence Repeats (SSRs) are the most ideal, powerful and reliable markers for molecular plant breeding applications because of their high abundance, co-dominant inheritance and multiple alleles [7]. In addition, BES-SSR markers serve a useful resource for integrating genetic and physical maps [8,9]. SSRs consists of 2–7 base pair tandem repeat motifs of mono-, di-, tri-, tetra and penta-nucleotides (A, T, AT, GA, AGG, AAAG etc.) with different lengths of repeat motifs. These repeats are extensively distributed throughout plants and animal genomes. A high level of genetic variation is observed between and within species due to differences in the number of tandem repeating units at a locus which produces a highly polymorphic banding pattern [10] and is detected by the Polymerase Chain Reaction (PCR) using locus specific flanking primers [11]. Molecular markers are widely recognized as a tool in generating linkage maps [12] as they define specific locations in the genome unambiguously [13,14]. There are few valuable software and tools available for SSRs identification and in-silico marker devel (...truncated)


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Sakshi Chaudhary, Bharat Kumar Mishra, Thiruvettai Vivek, Santoshkumar Magadum, Jeshima Khan Yasin. PineElm_SSRdb: a microsatellite marker database identified from genomic, chloroplast, mitochondrial and EST sequences of pineapple (Ananas comosus (L.) Merrill), Hereditas, 2016, pp. 16, Volume 153, Issue 1, DOI: 10.1186/s41065-016-0019-8