Development and characterization of polymorphic microRNA‐based microsatellite markers in <i>Nelumbo nucifera</i> (Nelumbonaceae)

Wang, Xiaolei; Gui, Songtao; Pan, Lei; Hu, Jihong; Ding, Yi

doi:10.3732/apps.1500091

Cited by 13 publications

(5 citation statements)

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“…However, the consequences of the same in non-coding transcripts are less studied. A very few reports demonstrated the significance of analysis of SSRs in non-coding miRNA [ 12 – 15 , 49 ]. In current study, 13 of 33 total predicted pre-miRNAs had one or more SSR motifs (Table 1 ).…”

Section: Resultsmentioning

confidence: 99%

“…Predominant of such markers like SSR, ISSR, EST-SSR have been effectively utilized in several crop improvement program [ 7 – 11 ]. MicroRNA precursor based SSR markers are very recently incorporated in this chapter and mostly utilized in marker trait association analysis in several species [ 12 – 15 ]. These micro RNAs are short, non-coding RNA molecules, involved in post transcriptional mode of gene regulation and [ 16 ] thus effects on related phenotype [ 17 , 18 ].…”

Section: Introductionmentioning

confidence: 99%

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Extrapolative microRNA precursor based SSR mining from tea EST database in respect to agronomic traits

et al. 2017

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Tea (Camellia sinensis, (L.) Kuntze) is considered as most popular drink across the world and it is widely consumed beverage for its several health-benefit characteristics. These positive traits primarily rely on its regulatory networks of different metabolic pathways. Development of microsatellite markers from the conserved genomic regions are being worthwhile for reviewing the genetic diversity of closely related species or self-pollinated species. Although several SSR markers have been reported, in tea, the trait-specific Simple Sequence Repeat (SSR) markers, leading to be useful in marker assisted breeding technique, are yet to be identified. Micro RNAs are short, non-coding RNA molecules, involved in post transcriptional mode of gene regulation and thus effects on related phenotype. Present study deals with identification of the microsatellite motifs within the reported and predicted miRNA precursors that are effectively followed by designing of primers from SSR flanking regions in order to PCR validation. In addition to the earlier reports, two new miRNAs are predicting here from tea expressed tag sequence database. Furthermore, 18 SSR motifs are found to be in 13 of all 33 predicted miRNAs. Trinucleotide motifs are most abundant among all followed by dinucleotides. Since, miRNA based SSR markers are evidenced to have significant role on genetic fingerprinting study, these outcomes would pave the way in developing novel markers for tagging tea specific agronomic traits as well as substantiating non-conventional breeding program.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Extrapolative microRNA precursor based SSR mining from tea EST database in respect to agronomic traits

et al. 2017

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“…The Bonferroni correction method, which estimates a threshold p-value to control the false positive rate, is based on the assumption that every genetic variant tested is independent of the rest (Kaler and Purcell, 2019). However, this is also considered as the most conservative method and many important loci may not qualify the stringent criterion of significance test (Wang et al, 2016). Hence, each of the markers identified can be utilized later on, for a larger population (especially from a mapping population) to check their true associations and heritability.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide SNP discovery from Darjeeling tea cultivars - their functional impacts and application toward population structure and trait associations

Hazra¹,

Kumar²,

Sengupta³

et al. 2021

Genomics

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Genotyping by sequencing and identification of functionally relevant nucleotide variations in crop accessions are the key steps to unravel genetic control of desirable traits. In the scope of present work, elite cultivars of Darjeeling tea were undergone SNP genotyping by doubledigest restriction site associated DNA sequencing method. This study reports a set of 54,206 high-quality SNP markers discovered from ~10.4 GB sequence data, encompassing 15 chromosomes of reference tea genome. Genetic relatedness among the accessions conforms to the analyses of Bayesian clustering, UPGMA, and PCoA methods. High percent of heterozygous loci in the majority of the cultivars reflect their 'hybrid' ancestry as reported earlier. Genomic positions of the discovered SNPs and their putative effect on annotated genes designated a thoughtful understanding of their functional aspects in tea system biology.A group of 95 genes was identified to be affected by high impact variants, most of them are involved in signal transduction, biosynthesis of secondary metabolite, transcriptional and translational regulation. Genome-wide association analyses of 21 agronomic and biochemical phenotypes resulted in trait-linked polymorphic loci with strong confidence (p < 0.05 and 0.001). The selection of significant marker-trait associations with the Bonferroni correction threshold retained a set of 57 SNPs distributed across 14 chromosomes to be linked with eight phenotypic traits. High impact and trait-associated nucleotide polymorphisms perceived in this study can be exploited in worldwide germplasm of contrasting origin to depict their heritability and to unlock their potentiality in marker-assisted breeding.

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“…Later, the same authors reported identification of 129 miR‐SSRs in conserved miRNA genes; 20 of these SSRs, each had seven or more repeats (Ganie & Mondal, ). In M. truncatula, a total of 169 primer pairs were successfully designed from 130 miRNA genes (Min et al, ); (b) in lotus ( Nelumbo nucifera ), 1,000 bp sequences (500 bp flanking 5′ and 3′ ends) each in 106 pre‐miRNAs were screened for the presence of miR‐SSRs using MISA; 45 miR‐SSRs were identified in 36 genotypes (Wang, Gui, Pan, Hu, & Ding, ). (c) In tea ( Camellia sinensis ), using an online program WebSat, 18 SSRs were identified in 13 of 33 predicted miRNAs that were located in ESTs; primer pairs flanking each SSR were designed with the help of BatchPrimer3 server (Hazra, Dasgupta, Sengupta, & Das, ).…”

Section: Polymorphisms Involving Mirnas and Target Sitesmentioning

confidence: 99%

Sequence variation in genes encoding miRNAs/targets and other related approaches for possible use in crop improvement

Gupta

2019

Plant Breeding

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MicroRNAs (miRNAs) are small non-coding RNAs (ncRNAs), which are involved in regulation of gene expression in almost all plant and animal systems. In crop plants, a large number of miRNAs are now known, which regulate expression of genes controlling a variety of traits including yield and tolerance to biotic and abiotic stresses. Like protein-coding genes, miRNA genes (MIRs) and their products (including pri-miRNAs, pre-miRNAs or miRNAs themselves) also exhibit sequence variation. This variation affects the corresponding miRNAs in a variety of ways including their own transcription, maturation and target specificity. In this review, we summarize the available information on markers based on sequence variations in MIRs and the corresponding target genes. The association of these markers with agronomic traits of value and their possible use in crop improvement is also discussed using suitable examples.

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Development and characterization of polymorphic microRNA‐based microsatellite markers in Nelumbo nucifera (Nelumbonaceae)

Cited by 13 publications

References 12 publications

Extrapolative microRNA precursor based SSR mining from tea EST database in respect to agronomic traits

Extrapolative microRNA precursor based SSR mining from tea EST database in respect to agronomic traits

Genome-wide SNP discovery from Darjeeling tea cultivars - their functional impacts and application toward population structure and trait associations

Sequence variation in genes encoding miRNAs/targets and other related approaches for possible use in crop improvement

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