Comparative transcriptomics and comprehensive marker resource development in mulberry

BMC Genomics, Feb 2016

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.

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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 - 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)


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Bushra Saeed, Vinay Baranwal, Paramjit Khurana. Comparative transcriptomics and comprehensive marker resource development in mulberry, BMC Genomics, 2016, pp. 98, 17, DOI: 10.1186/s12864-016-2417-8