Identification of MFLP fingerprint for higher seed zinc accumulation in barley DH population

Selection through molecular markers for seed Zn accumulation might be an efficient complementary breeding tool in barley breeding. To develop a specific molecular markers, 150 DH lines derived from a cross between Clipper (low-Zn-accumulator) and Sahara-3771 (high-Zn-accumulator) were screened under field and glasshouse conditions. Microsatellite-anchored fragment length polymorphism (MFLP) fingerprint generated by SSR-anchor primer MF128 in combination with AFLP primer MseI-AGA (5?-GATGAGTCCTGAGTAAAGA-3?) was identified as a candidate marker for tagging seed Zn accumulation gene. The sequencing of the band showed a marker of 369 bp with the sequence of SSR anchor primer MF128 and MseI-AGA at the two ends as expected. The MFLP marker associated with higher seed Zn accumulation has potential to be converted to a simple, sequence-specific, PCR-based, low-cost marker amenable to large populations, making it potentially viable for marker-assisted selection in barley breeding. This marker might be useful in the improvement of barley productivity and nutritional quality in Zn-deficient environments.

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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.

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Two User-Friendly Molecular Markers Developed for the Identification of Hybrid Lethality Genes in Brassica oleracea

Agronomy ◽

10.3390/agronomy11050982 ◽

2021 ◽

Vol 11 (5) ◽

pp. 982

Author(s):

Zhiliang Xiao ◽

Congcong Kong ◽

Fengqing Han ◽

Limei Yang ◽

Mu Zhuang ◽

...

Keyword(s):

Molecular Markers ◽

Brassica Oleracea ◽

Rapid Identification ◽

Inbred Lines ◽

Hybrid Lethality ◽

Specific Pcr ◽

Allele Specific ◽

User Friendly ◽

Allele Specific Pcr ◽

Kasp Marker

Cabbage (Brassica oleracea) is an important vegetable crop that is cultivated worldwide. Previously, we reported the identification of two dominant complementary hybrid lethality (HL) genes in cabbage that could result in the death of hybrids. To avoid such losses in the breeding process, we attempted to develop molecular markers to identify HL lines. Among 54 previous mapping markers closely linked to BoHL1 or BoHL2, only six markers for BoHL2 were available in eight cabbage lines (two BoHL1 lines; three BoHL2 lines; three lines without BoHL); however, they were neither universal nor user-friendly in more inbred lines. To develop more accurate markers, these cabbage lines were resequenced at an ~20× depth to obtain more nucleotide variations in the mapping regions. Then, an InDel in BoHL1 and a single-nucleotide polymorphism (SNP) in BoHL2 were identified, and the corresponding InDel marker MBoHL1 and the competitive allele-specific PCR (KASP) marker KBoHL2 were developed and showed 100% accuracy in eight inbred lines. Moreover, we identified 138 cabbage lines using the two markers, among which one inbred line carried BoHL1 and 11 inbred lines carried BoHL2. All of the lethal line genotypes obtained with the two markers matched the phenotype. Two markers were highly reliable for the rapid identification of HL genes in cabbage.

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Genotyping of Peach and Nectarine Cultivars with SSR and SRAP Molecular Markers

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.129.2.0204 ◽

2004 ◽

Vol 129 (2) ◽

pp. 204-210 ◽

Cited By ~ 37

Author(s):

Riaz Ahmad ◽

Dan Potter ◽

Stephen M. Southwick

Keyword(s):

Molecular Markers ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Sweet Cherry ◽

Prunus Persica ◽

Sequence Repeat ◽

Srap Markers ◽

Upgma Cluster Analysis ◽

Commercially Important ◽

Simple Sequence

Simple sequence repeat (SSR) and sequence related amplified polymorphism (SRAP) molecular markers were evaluated for detecting intraspecific variation in 38 commercially important peach and nectarine (Prunus persica) cultivars. Out of the 20 SSR primer pairs 17 were previously developed in sweet cherry and three in peach. The number of putative alleles revealed by SSR primer pairs ranged from one to five showing a low level of genetic variability among these cultivars. The average number of alleles per locus was 2.2. About 76% of cherry primers produced amplification products in peach and nectarine, showing a congeneric relationship within Prunus species. Only nine cultivars out of the 38 cultivars could be uniquely identified by the SSR markers. For SRAP, the number of fragments produced was highly variable, ranging from 10 to 33 with an average of 21.8 per primer combination. Ten primer combinations resulted in 49 polymorphic fragments in this closely related set of peaches and nectarines. Thirty out of the 38 peach and nectarine cultivars were identified by unique SRAP fingerprints. UPGMA Cluster analysis based on the SSR and SRAP polymorphic fragments was performed; the relationships inferred are discussed with reference to the pomological characteristics and pedigree of these cultivars. The results indicated that SSR and SRAP markers can be used to distinguish the genetically very close peach and nectarine cultivars as a complement to traditional pomological studies. However, for fingerprinting, SRAP markers appear to be much more effective, quicker and less expensive to develop than are SSR markers.

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Study of Plant Genetic Variation through Molecular Markers: An Overview

Journal of Pharmaceutical Research International ◽

10.9734/jpri/2021/v33i45b32828 ◽

2021 ◽

pp. 464-473

Author(s):

Zeina S. M. Al-Hadeithi ◽

Saade Abdalkareem Jasim

Keyword(s):

Molecular Markers ◽

Simple Sequence Repeat Marker ◽

Fragment Length ◽

Simple Sequence Repeat ◽

Plant Biotechnology ◽

Molecular Techniques ◽

Basic Material ◽

Sequence Repeat ◽

Simple Sequence

This article refers to viewing the role of molecular markers during analyzing the genome of plants and their importance in plant biotechnology. In recent years, we observed the role of molecular techniques in programs for improving plant breeding and preserving genetic resources has been observed, and molecular and biochemical indicators which represent basic material through determining the diversity between genotypes for indicators it is never affected by external surrounding conditions as always in the phenotype features. Molecular markers of DNA have been widely applied to answer a range of questions related to taxonomy, molecular evolution, population genetics, and genetic diversity, as well as monitoring trade in plants and food products , in addition to its having a role in studying gene expression , genetic mapping, and studies of species evolution providing fast and accurate results. In this work, the advantages and limitations of the molecular techniques applied in plant sciences such as: RAPD (Random Amplification Polymorphic DNA Marker); ISSR (Inter Simple Sequence Repeat Marker); SSR (Simple Sequence Repeat Marker); AFLP (Amplified Fragment Length Polymorphic Marker); RFLP (Restriction Fragment Length Polymorphism Marker); SNP (Single Nucleotide Polymorphism) and Real Time PCR.

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SmartKC

Proceedings of the ACM on Interactive Mobile Wearable and Ubiquitous Technologies ◽

10.1145/3494982 ◽

2021 ◽

Vol 5 (4) ◽

pp. 1-27

Author(s):

Siddhartha Gairola ◽

Murtuza Bohra ◽

Nadeem Shaheer ◽

Navya Jayaprakash ◽

Pallavi Joshi ◽

...

Keyword(s):

Low Cost ◽

Pearson Correlation ◽

Step Method ◽

Middle Income ◽

Middle Income Countries ◽

Large Populations ◽

Pixel Location ◽

3D Printed ◽

Working Distance ◽

Fitting In

Keratoconus is a severe eye disease affecting the cornea (the clear, dome-shaped outer surface of the eye), causing it to become thin and develop a conical bulge. The diagnosis of keratoconus requires sophisticated ophthalmic devices which are non-portable and very expensive. This makes early detection of keratoconus inaccessible to large populations in low-and middle-income countries, making it a leading cause for partial/complete blindness among such populations. We propose SmartKC, a low-cost, smartphone-based keratoconus diagnosis system comprising of a 3D-printed placido's disc attachment, an LED light strip, and an intelligent smartphone app to capture the reflection of the placido rings on the cornea. An image processing pipeline analyzes the corneal image and uses the smartphone's camera parameters, the placido rings' 3D location, the pixel location of the reflected placido rings and the setup's working distance to construct the corneal surface, via the Arc-Step method and Zernike polynomials based surface fitting. In a clinical study with 101 distinct eyes, we found that SmartKC achieves a sensitivity of 87.8% and a specificity of 80.4%. Moreover, the quantitative curvature estimates (sim-K) strongly correlate with a gold-standard medical device (Pearson correlation coefficient = 0.77). Our results indicate that SmartKC has the potential to be used as a keratoconus screening tool under real-world medical settings.

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Assessment of Genetic Diversity of Rheum species (Endangered Medicinal Herb of Indian Himalayan Region) using Molecular Markers

Research Journal of Biotechnology ◽

10.25303/1611rjbt147154 ◽

2021 ◽

Vol 16 (11) ◽

pp. 147-154

Author(s):

Anjali Uniyal ◽

Akhilesh Kumar ◽

Sweta Upadhyay ◽

Vijay Kumar ◽

Sanjay Gupta

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Fragment Length Polymorphism ◽

Dna Polymorphisms ◽

Inter Simple Sequence Repeats ◽

Pharmaceutical Industries ◽

Endangered Medicinal Herb ◽

Identification And Characterization ◽

Simple Sequence

The Rheum species are important medicinal plants that are facing extinction due to their unplanned development and overexploitation by pharmaceutical industries. DNA polymorphisms are not prone to environmental modifications, thus they are widely used for the identification and characterization of plants. The use of different molecular markers has enabled the researchers for the valuation of genetic variability and diversity in its natural zone of distribution. The conventional approach may take several years to yield this information. For the estimation of molecular and genetic variations in geographical zone of distribution, various molecular markers technique are available like RAPD (Randomly Amplified Polymorphic DNA), RFLP (Restriction fragment length polymorphism), ISSR (Inter-Simple Sequence Repeats), SSR and AFLP. The uses of different molecular markers for the study of genetic diversity have been discussed in the review.

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Digital histological markers based on routine H&E slides to predict benefit from maintenance immunotherapy in esophagogastric adenocarcinoma.

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.15_suppl.e16074 ◽

2021 ◽

Vol 39 (15_suppl) ◽

pp. e16074-e16074

Author(s):

Quoc Dang Vu ◽

Caroline Fong ◽

Katharina von Loga ◽

Shan E Ahmed Raza ◽

Daniel Nava Rodrigues ◽

...

Keyword(s):

Molecular Markers ◽

Predictive Power ◽

Low Cost ◽

Predictive Biomarkers ◽

Operating Characteristics ◽

Treatment Benefit ◽

Platinum Based Chemotherapy ◽

Slide Image ◽

Tumor Mutational Burden ◽

Hematoxylin And Eosin

e16074 Background: Immune checkpoint inhibition (ICI) is an effective treatment for a subset of patients with inoperable esophagogastric (EG) adenocarcinoma. Robust predictive biomarkers are required to identify these patients and a variety of strategies including immunohistochemical staining of PD-L1 and tumor mutational burden (TMB) assessment have been employed. Here, we explore digital histological (dHis) markers based on routine hematoxylin and eosin (H&E) slides alone or in combination with molecular markers (PD-L1 and TMB) as predictive biomarkers of benefit from maintenance immunotherapy in patients with inoperable EG adenocarcinoma. Methods: We developed a deep learning based algorithm to construct novel digital histological (dHis) markers by summarizing the statistics of all different types of nuclei present in the tumor tissue sections, their morphological features and their colocalization across each of the whole slide image. The dHis markers were then input into a decision-tree based approach to test for prognostic and predictive power alone or in combination with molecular markers. We assessed two cohorts of patients randomized to surveillance (n=38) or maintenance durvalumab (n=35) after 18 weeks of first-line platinum-based chemotherapy in the PLATFORM trial (NCT02678182) according to the 12-week progression-free rate. We measured the accuracy as the area under the receiver operating characteristics curve (AUROC) to determine the prognostic and predictive power of each marker set. We conducted a stratified 3-fold cross-validation, repeated 5 times and report the overall AUROC results. Results: Molecular markers alone yielded an AUROC of 0.5581±0.0939 on the surveillance arm, 0.6671±0.1479 on the treatment arm, and 0.6376±0.0958 for both the arms. Digital histological markers alone yielded an AUROC of 0.8952±0.0638, 0.8995±0.0719 and 0.8488±0.0700 on surveillance, immunotherapy and both arms, respectively. When using these two sets of markers together for both arms, molecular markers offered a limited improvement (around 0.02). Patients with TMB in the highest tertile were associated with lower likelihood of having progressive disease 12 weeks after randomization. Interestingly, dHis markers from morphology of connective and inflammatory nuclei were highly predictive for treatment benefit. Conclusions: Preliminary results suggest digital histological markers offer significant improvement over PD-L1 and TMB markers alone for predicting benefit from immunotherapy in EG adenocarcinoma with the added advantages of scalable, rapid, low-cost and objective quantification on routine histology sections. We are further validating their effectiveness on a larger cohort. Clinical trial information: NCT02678182.

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