Transcriptome Characterization and Identification of Molecular Markers (SNP, SSR, and Indels) in the Medicinal Plant Sarcandra glabra spp.

Sarcandra glabra has significant metabolically active bioingredients of pharmaceutical importance. The deficiency of molecular markers for S. glabra is a hindrance in molecular breeding for genetic improvement. In this study, 57.756 million pair-end reads were generated by transcriptome sequencing in S. glabra (Thunb.) Nakai and its subspecies S. glabra ssp. brachystachys. A total of 141,954 unigenes with 646.63 bp average length were assembled. A total of 25,620 simple sequence repeats, 726,476 single nucleotide polymorphisms, and 42,939 insertions and deletions were identified, and the associated unigenes and differentially expressed genes were characterized. This work enhanced the molecular marker resources and will facilitate molecular breeding and gene mining in S. glabra spp.

Download Full-text

Development of Molecular Markers for Predicting Radish (Raphanus sativus) Flesh Color Based on Polymorphisms in the RsTT8 Gene

Plants ◽

10.3390/plants10071386 ◽

2021 ◽

Vol 10 (7) ◽

pp. 1386

Author(s):

Soyun Kim ◽

Keunho Yun ◽

Han Yong Park ◽

Ju Young Ahn ◽

Ju Yeon Yang ◽

...

Keyword(s):

Molecular Markers ◽

Raphanus Sativus ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Cosmetic Industry ◽

Natural Colorants ◽

Health Promoting ◽

Primer Sets ◽

Red Radish ◽

Simple Sequence

Red radish (Raphanus sativus L.) cultivars are a rich source of health-promoting anthocyanins and are considered a potential source of natural colorants used in the cosmetic industry. However, the development of red radish cultivars via conventional breeding is very difficult, given the unusual inheritance of the anthocyanin accumulation trait in radishes. Therefore, molecular markers linked with radish color are needed to facilitate radish breeding. Here, we characterized the RsTT8 gene isolated from four radish genotypes with different skin and flesh colors. Sequence analysis of RsTT8 revealed a large number of polymorphisms, including insertion/deletions (InDels), single nucleotide polymorphisms (SNPs), and simple sequence repeats (SSRs), between the red-fleshed and white-fleshed radish cultivars. To develop molecular markers on the basis of these polymorphisms for discriminating between radish genotypes with different colored flesh tissues, we designed four primer sets specific to the RsTT8 promoter, InDel, SSR, and WD40/acidic domain (WD/AD), and tested these primers on a diverse collection of radish lines. Except for the SSR-specific primer set, all primer sets successfully discriminated between red-fleshed and white-fleshed radish lines. Thus, we developed three molecular markers that can be efficiently used for breeding red-fleshed radish cultivars.

Download Full-text

Single Nucleotide Polymorphisms and Indel Markers from the Transcriptome of Garlic

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.141.1.62 ◽

2016 ◽

Vol 141 (1) ◽

pp. 62-65 ◽

Cited By ~ 6

Author(s):

Michael J. Havey ◽

Yul-Kyun Ahn

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Single Nucleotide Polymorphisms ◽

Nucleotide Polymorphisms ◽

Phenotypic Characteristics ◽

Single Nucleotide ◽

Germplasm Collections ◽

Indel Markers ◽

Production Environments ◽

Culinary Uses

Garlic (Allium sativum) is cultivated worldwide and appreciated for its culinary uses. In spite of primarily being asexually propagated, garlic shows great morphological variation and adaptability to diverse production environments. Molecular markers and phenotypic characteristics have been used to assess the genetic diversity among garlics. In this study, we undertook transcriptome sequencing from a single garlic plant to identify molecular markers in expressed regions of the garlic genome. Garlic sequences were assembled and selected if they were similar to monomorphic sequences from a doubled haploid (DH) of onion (Allium cepa). Single nucleotide polymorphisms (SNPs) and insertion–deletion (indel) events were identified in 4355 independent garlic assemblies. A sample of the indels was verified using the original complementary DNA (cDNA) library and genomics DNAs from diverse garlics, and segregations confirmed by sexual progenies of garlic. These molecular markers from the garlic transcriptome should be useful for estimates of genetic diversity, identification and removal of duplicate accessions from germplasm collections, and the development of a detailed genetic map of this important vegetable crop.

Download Full-text

The effect of linkage disequilibrium on the estimates of Single Nucleotide Polymorphic effects

Proceedings of the British Society of Animal Science ◽

10.1017/s1752756200028830 ◽

2009 ◽

Vol 2009 ◽

pp. 44-44

Author(s):

K Moore ◽

J Gibson ◽

D Johnston

Keyword(s):

Linkage Disequilibrium ◽

Single Nucleotide Polymorphisms ◽

Genetic Improvement ◽

Dairy Herd ◽

Physical Distance ◽

Causative Mutation ◽

Nucleotide Polymorphisms ◽

Production Traits ◽

Single Nucleotide Polymorphic ◽

Single Nucleotide

The identification and exploitation of single nucleotide polymorphisms (SNP) associated with production traits present new opportunities for livestock genetic improvement. Often the identified SNP is not the causative mutation but rather is in some degree of linkage disequilibrium (LD). LD markers within 5cM can be considered as direct markers for the causative mutation because they are located close to the causative mutation (Dekkers, 2004). In a dairy herd, Farnir et al., (2000) estimated that the average LD, measured as D′ was 0.5 for loci pairs positioned within 5cM. Goddard et al., (2006) estimated that LD measured as r2 decreased rapidly as the physical distance between loci increased; at a separating distance of 0.5Mb the LD (r2) was only approximately 0.2. The aim of this work was to use stochastic simulation to investigate the effect that the distance between the SNP and causative mutation had on the accuracy of estimating additive and dominance effects of the causative mutation.

Download Full-text

Inheritance Pattern and Molecular Markers for Resistance to Blackleg Disease in Cabbage

Plants ◽

10.3390/plants8120583 ◽

2019 ◽

Vol 8 (12) ◽

pp. 583

Author(s):

Mostari Jahan Ferdous ◽

Mohammad Rashed Hossain ◽

Jong-In Park ◽

Arif Hasan Khan Robin ◽

Denison Michael Immanuel Jesse ◽

...

Keyword(s):

Molecular Markers ◽

High Resolution Melting ◽

Leptosphaeria Maculans ◽

Inbred Lines ◽

Indel Marker ◽

Detection Accuracy ◽

Nucleotide Polymorphisms ◽

Blackleg Disease ◽

Marker Assisted Breeding ◽

Single Nucleotide

The inheritance and causal loci for resistance to blackleg, a devastating disease of Brassicaceous crops, are yet to be known in cabbage (Brassica oleracea L.). Here, we report the pattern of inheritance and linked molecular marker for this trait. A segregating BC1 population consisting of 253 plants was raised from resistant and susceptible parents, L29 (♀) and L16 (♂), respectively. Cotyledon resistance bioassay of BC1 population, measured based on a scale of 0–9 at 12 days after inoculation with Leptosphaeria maculans isolate 03–02 s, revealed the segregation of resistance and ratio, indicative of dominant monogenic control of the trait. Investigation of potential polymorphism in the previously identified differentially expressed genes within the collinear region of ‘B. napus blackleg resistant loci Rlm1′ in B. oleracea identified two insertion/deletion (InDel) mutations in the intron and numerous single nucleotide polymorphisms (SNPs) throughout the LRR-RLK gene Bol040029, of which six SNPs in the first exon caused the loss of two LRR domains in the susceptible line. An InDel marker, BLR-C-InDel based on the InDel mutations, and a high resolution melting (HRM) marker, BLR-C-2808 based on the SNP C2808T in the second exon were developed, which predicated the resistance status of the BC1 population with 80.24%, and of 24 commercial inbred lines with 100% detection accuracy. This is the first report of inheritance and molecular markers linked with blackleg resistance in cabbage. This study will enhance our understanding of the trait, and will be helpful in marker assisted breeding aiming at developing resistant cabbage varieties.

Download Full-text

Association of Twelve Candidate Gene Polymorphisms with the Intramuscular Fat Content and Average Backfat Thickness of Chinese Suhuai Pigs

Animals ◽

10.3390/ani9110858 ◽

2019 ◽

Vol 9 (11) ◽

pp. 858 ◽

Cited By ~ 5

Author(s):

Wang ◽

Li ◽

Zhou ◽

Gao ◽

Liu ◽

...

Keyword(s):

Molecular Markers ◽

Gene Polymorphisms ◽

Genetic Correlations ◽

Intramuscular Fat ◽

Fat Content ◽

Backfat Thickness ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Coefficients Of Variation ◽

Intramuscular Fat Content

The present study aimed to identify the molecular markers for genes that influence intramuscular fat content (IFC), but not average backfat thickness (ABT). A total of 330 Suhuai pigs were slaughtered, and measurements of IFC and ABT were obtained. Phenotypic and genetic correlations between IFC and ABT were calculated. Thirteen single nucleotide polymorphisms (SNPs) among 12 candidate genes for IFC were analyzed, including FABP3, LIPE, IGF1, IGF2, LEP, LEPR, MC4R, PHKG1, RETN, RYR1, SCD, and UBE3C. Associations of the evaluated SNPs with IFCIFC and ABT were performed. Our results showed that the means of IFC and ABT were 1.99 ± 0.03 % and 26.68 ± 0.28 mm, respectively. The coefficients of variation (CVs) of IFC and ABT were 31.21% and 19.36%, respectively. The phenotypic and genetic correlations between IFC and ABT were moderate. Only the FABP3 (rs1110770079) was associated with IFC (p < 0.05) but not with ABT. Besides, there was a tendency for associations of RYR1 (rs344435545) and SCD (rs80912566) with IFC (p < 0.1). Our results indicated that the FABP3 (rs1110770079) SNP could be used as a marker to improve IFC without changing ABT in the Suhuai pig breeding system.

Download Full-text

Chloroplast genomes elucidate diversity, phylogeny, and taxonomy of Pulsatilla (Ranunculaceae)

Scientific Reports ◽

10.1038/s41598-020-76699-7 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Qiu-jie Li ◽

Na Su ◽

Ling Zhang ◽

Ru-chang Tong ◽

Xiao-hui Zhang ◽

...

Keyword(s):

Molecular Markers ◽

Phylogenetic Trees ◽

Phylogenetic Signal ◽

Data Sets ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Variable Regions ◽

Chloroplast Genomes ◽

Medicinal Value ◽

Cp Genome

AbstractPulsatilla (Ranunculaceae) consists of about 40 species, and many of them have horticultural and/or medicinal value. However, it is difficult to recognize and identify wild Pulsatilla species. Universal molecular markers have been used to identify these species, but insufficient phylogenetic signal was available. Here, we compared the complete chloroplast genomes of seven Pulsatilla species. The chloroplast genomes of Pulsatilla were very similar and their length ranges from 161,501 to 162,669 bp. Eight highly variable regions and potential sources of molecular markers such as simple sequence repeats, large repeat sequences, and single nucleotide polymorphisms were identified, which are valuable for studies of infra- and inter-specific genetic diversity. The SNP number differentiating any two Pulsatilla chloroplast genomes ranged from 112 to 1214, and provided sufficient data for species delimitation. Phylogenetic trees based on different data sets were consistent with one another, with the IR, SSC regions and the barcode combination rbcL + matK + trnH-psbA produced slightly different results. Phylogenetic relationships within Pulsatilla were certainly resolved using the complete cp genome sequences. Overall, this study provides plentiful chloroplast genomic resources, which will be helpful to identify members of this taxonomically challenging group in further investigation.

Download Full-text