Comparative transcriptomics and comprehensive marker resource development in mulberry
Saeed et al. BMC Genomics
Comparative transcriptomics and comprehensive marker resource development in mulberry
Bushra Saeed 0
Vinay K. Baranwal 0
Paramjit Khurana 0
0 Department of Plant Molecular Biology, University of Delhi South Campus , New Delhi 110021 , India
Background: High potential of Morus laevigata and Morus serrata has been proposed in the breeding programs for Morus sp. However, due to the lack of dense molecular markers this goal is still in its nascent stage and not yet realized. We thus, sequenced the transcriptomes of these two wild Morus species and utilized the data for marker development. Results: We generated 87.0 and 80.3 Mb of transcriptome data from M. laevigata and M. serrata, respectively. The transcriptomes from M. laevigata and M. serrata, were assembled into 95,181 and 85,269 transcripts, respectively, and annotated. We identified around 24,049 Simple Sequence Repeats (SSRs), 1,201,326 Single Nucleotide Polymorphisms (SNPs) and 67,875 Insertion-Deletions (InDels). The variants having a higher impact were also identified and their effect was further investigated. Conclusions: The transcriptome resource from the wildly growing mulberry species developed in this study can find wide applicability in gene identification and/or characterization. It can also contribute immensely in the existing mulberry improvement programs.
Morus spp; Single nucleotide polymorphism; Simple sequence repeats; Transcriptome
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Background
Mulberry plays a crucial role in driving the sericulture
industry as it serves as the sole feed for silkworm. In
India, four species of mulberry have been reported to
occur naturally i.e. M. indica, M. alba, M. laevigata and
M. serrata [1]. M. indica and M. alba are cultivated for
silkworm rearing whereas the other two grow naturally
in the wild. Apart from its uses in sericulture, mulberry
is also cultivated for fruit especially M. laevigata which
produces long sweet fruits, firewood, fodder, and used
in furniture, traditional medicine etc. M. laevigata
grows across the Indian sub-continent and some
collections harbor important traits such as disease and
termite resistance [2]. M. serrata on the other hand, is
restricted to higher altitudes (upto 3000 m above sea
level) particularly northwestern Himalayas and is
known to be tolerant to frost and drought [2, 3]. M.
serrata also possesses several other important traits
such as thicker leaves and higher moisture content and
higher moisture retention [1].
Since the ultimate commercial importance of mulberry
lies as a feedant for the silkworm, leaf palatability is an
important trait directly dependent on leaf water
retention capacity, total biomass, and size and weight which
are considered significant in the present day breeding
programs [4]. Nonetheless, these species possess several
agronomically important traits and to utilize the vast
genetic potential of these species, hybridization
programs between the wild species and cultivated varieties
of Morus sp. are promising [5, 6].
Additionally, owing to the medicinal and commercial
importance of mulberry, a need for developing
comprehensive genomic resource has also been felt. In this
pursuit, our lab has contributed immensely by generating rich
transcriptome-based resources of mature leaf, drought
specific transcriptome [7] and root tissue [8] of M. indica.
The complete chloroplast genome of mulberry was also
sequenced [9]. Additionally, these resources have been
utilized for generation of Simple Sequence Repeat (SSR)
markers for use in mulberry and related species [8, 10].
Recently, though the draft genome of haploid mulberry,
M. notabilis has been sequenced [11], this is far from
complete limiting its practical utility. The growing
concern in mulberry is evident from the recent efforts in the
expansion of genomic resources [12] and its subsequent
utilization in marker development programs [13]. With
recent advancements in sequencing technologies,
prediction of markers from transcribed regions of the genome
has become a method of choice for genotyping
particularly for non-model species with less commercial value.
With the above background, in the present study we
describe sequencing and generation of large-scale
transcriptome based resource for two wild species of
mulberry, M. laevigata and M. serrata, integrated with
available information on haploid mulberry M. notabilis
for DNA based marker development.
Results and discussion
Even with the advent of next generation sequencing
techniques, sequencing whole genomes of ‘less
attractive’ or non-model plants/wild species remains
impracticable. A fundamental need for introducing wild gene pool
in the cultivated varieties of M. indica and M. alba has
been long felt [6]. Thus, two wild species of Morus
growing in different geographical locations in India were
selected for transcriptome sequencing to explore their
novel genetic potential and to undertake a comparative
analysis. Also, transcriptome sequencing data comprisi (...truncated)