Comparative transcriptomics and comprehensive marker resource development in mulberry

Saeed, Bushra; Baranwal, Vinay Kumar; Khurana, Paramjit

doi:10.1186/s12864-016-2417-8

Cited by 22 publications

(21 citation statements)

References 45 publications

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“…Sequence variants (InDels, frame shift, stop gained, stop lost and non synormymous coding) that potentially have high impact on transcript/protein were predicted according to the method described by Saeed et al [49]. …”

Section: Methodsmentioning

confidence: 99%

Comparative transcriptome profiling of the fertile and sterile flower buds of a dominant genic male sterile line in sesame (Sesamum indicum L.)

Liu

Ming

et al. 2016

BMC Plant Biol

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BackgroundSesame (Sesamum indicum L.) is a globally important oilseed crop with highly-valued oil. Strong hybrid vigor is frequently observed within this crop, which can be exploited by the means of genic male sterility (GMS). We have previously developed a dominant GMS (DGMS) line W1098A that has great potential for the breeding of F1 hybrids. Although it has been genetically and anatomically characterized, the underlying molecular mechanism for male sterility remains unclear and therefore limits the full utilization of such GMS line. In this study, RNA-seq based transcriptome profiling was carried out in two near-isogenic DGMS lines (W1098A and its fertile counterpart, W1098B) to identify differentially expressed genes (DEGs) related to male sterility.ResultsA total of 1,502 significant DEGs were detected, among which 751 were up-regulated and 751 were down-regulated in sterile flower buds. A number of DEGs were implicated in both ethylene and JA synthesis & signaling pathway; the expression of which were either up- or down-regulated in the sterile buds, respectively. Moreover, the majority of NAC and WRKY transcription factors implicated from the DEGs were up-regulated in sterile buds. By querying the Plant Male Reproduction Database, 49 sesame homologous genes were obtained; several of these encode transcription factors (bHLH089, MYB99, and AMS) that showed reduced expression in sterile buds, thus implying the possible role in specifying or determining tapetal fate and development. The predicted effect of allelic variants on the function of their corresponding DEGs highlighted several Insertions/Deletions (InDels), which might be responsible for the phenotype of sterility/fertility in DGMS lines.ConclusionThe present comparative transcriptome study suggested that both hormone signaling pathway and transcription factors control the male sterility of DGMS in sesame. The results also revealed that several InDels located in DEGs prone to cause loss of function, which might contribute to male sterility. These findings provide valuable genomic resources for a deeper insight into the molecular mechanism underlying DGMS.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0934-x) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Comparative transcriptome profiling of the fertile and sterile flower buds of a dominant genic male sterile line in sesame (Sesamum indicum L.)

Liu

Ming

et al. 2016

BMC Plant Biol

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“…The NCBI SRA accession for the samples is SRX504963, SRX504944, SRX504924, SRX504906 and SRX504893 for leaf, male flower, winter bud, bark and root tissue respectively. Our group has previously sequenced and submitted the raw data [ 22 , 23 , 24 ] for ML and MS with accession numbers SRX1515878 and SRX1506562 respectively. Trinity software version r20140413p1 [ 25 ] with default parameters was used to assemble the sequences of M. serrata , M. laevigata and M. notabilis .…”

Section: Methodsmentioning

confidence: 99%

Auxin Response Factor Genes Repertoire in Mulberry: Identification, and Structural, Functional and Evolutionary Analyses

Baranwal

Negi

Khurana

2017

Genes

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Auxin Response Factors (ARFs) are at the core of the regulation mechanism for auxin-mediated responses, along with AUX/IAA proteins.They are critical in the auxin-mediated control of various biological responses including development and stress. A wild mulberry species genome has been sequenced and offers an opportunity to investigate this important gene family. A total of 17 ARFs have been identified from mulberry (Morus notabilis) which show a wide range of expression patterns. Of these 17 ARFs, 15 have strong acidic isoelectric point (pI) values and a molecular mass ranging from 52 kDa to 101 kDa. The putative promoters of these ARFs harbour cis motifs related to light-dependent responses, various stress responses and hormone regulations suggestive of their multifactorial regulation. The gene ontology terms for ARFs indicate their role in flower development, stress, root morphology and other such development and stress mitigation related activities. Conserved motif analysis showed the presence of all typical domains in all but four members that lack the PB1 domain and thus represent truncated ARFs. Expression analysis of these ARFs suggests their preferential expression in tissues ranging from leaf, root, winter bud, bark and male flowers. These ARFs showed differential expression in the leaf tissue of M. notabilis, Morus laevigata and Morus serrata. Insights gained from this analysis have implications in mulberry improvement programs.

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“…ex Brandis and M. serrata Roxb. (Saeed et al, 2016) were assembled together, and the sequences thus obtained were used for primer designing. The primers were designed by using Primer Express 2.0 software (PE Applied Biosystems) using default parameters and checked by BLAST tool against M. notabilis genome and melting curve analysis following PCR.…”

Section: Methodsmentioning

confidence: 99%

Identification and Expression Profiling of the Lectin Gene Superfamily in Mulberry

2016

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Lectins are a diverse group of ubiquitously present, highly specific sugar-binding proteins. Members of this large gene family have been assigned broad biological functions from defense to acting as storage proteins. Despite possessing several interesting characteristics, their functions remain essentially undefined. Mulberry (Morus spp.) known for its medicinal benefits is also a rich source of lectins. Using an exhaustive hidden Markov model (HMM)-based search, we identified the lectin gene complement in M. notabilis C.K. Schneid with around 197 members. These putative lectin genes were classified into 12 distinct gene families based on the presence of characteristic sugar-binding domains. Members of this superfamily were assigned varied gene ontologies (GOs) to identify putative functions and determine cellular localizations. Interestingly, characteristic expression patterns were observed across the lectin superfamily in response to a variety of environmental cues. This is suggestive of specialized functions under diverse conditions possibly by linking the specificity of sugar recognition with mediating precise stress responses in plants. The identification of putative gene family members from the genus Morus developed in this study can find wide applicability in lectin gene identification and characterization. It can also contribute immensely in the understanding of lectins from mulberry with potential medicinal uses.

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Comparative transcriptomics and comprehensive marker resource development in mulberry

Cited by 22 publications

References 45 publications

Comparative transcriptome profiling of the fertile and sterile flower buds of a dominant genic male sterile line in sesame (Sesamum indicum L.)

Comparative transcriptome profiling of the fertile and sterile flower buds of a dominant genic male sterile line in sesame (Sesamum indicum L.)

Auxin Response Factor Genes Repertoire in Mulberry: Identification, and Structural, Functional and Evolutionary Analyses

Identification and Expression Profiling of the Lectin Gene Superfamily in Mulberry

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