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
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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
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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)