scholarly journals Genotyping by RAD Sequencing Analysis Assessed the Genetic Distinctiveness of Experimental Lines and Narrowed down the Genomic Region Responsible for Leaf Shape in Endive (Cichorium endivia L.)

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 462
Author(s):  
Alice Patella ◽  
Fabio Palumbo ◽  
Samathmika Ravi ◽  
Piergiorgio Stevanato ◽  
Gianni Barcaccia
Keyword(s):  
Ssr Markers ◽  
Leaf Shape ◽  
Chromosome 8 ◽  
Experimental Population ◽  
Sequencing Analysis ◽  
Elongator Complex ◽  
Population Structure Analysis ◽  
Cichorium Endivia ◽  
Marker Loci ◽  
Genetic Distinctiveness

The characterization of genetic diversity in elite breeding stocks is crucial for the registration and protection of new varieties. Moreover, experimental population structure analysis and information about the genetic distinctiveness of commercial materials are essential for crop breeding programs. The purpose of our research was to assess the genetic relationships of 32 endive (Cichorium endivia L.) breeding lines, 18 from var. latifolium (escarole) and 14 from var. crispum (curly), using heterologous Cichorium intybus-derived simple sequence repeats (SSR) markers and single-nucleotide polymorphisms (SNP) markers. We found that 14 out of 29 SSR markers were successfully amplified, but only 8 of them were related to polymorphic loci. To overcome the limitation of the low number of informative SSR marker loci, an alternative SNP-based approach was employed. The 4621 SNPs produced by a restriction site-associated DNA marker sequencing approach were able to fully discriminate the 32 endive accessions; most importantly, as many as 50 marker loci were found to distinguish the curly group from the escarole group. Interestingly, 24 of the marker loci mapped within a peripheral segment of chromosome 8 of lettuce (Lactuca sativa L.), spanning a chromosomal region of 49.6 Mb. Following Sanger sequencing-based validation, three genes were determined to carry nonsynonymous SNPs, and one of them matched a putative ortholog of AtELP1, subunit 1 of the Elongator complex. Considering that several previously characterized Elongator complex subunit mutants exhibited elongated and/or curly leaf phenotypes, this gene should be taken into consideration for a better understanding of the underlying mechanism controlling leaf shape in endive.

scholarly journals Cross Species/Genera Transferability of SSR Markers, Genetic Diversity and Population Structure Analysis in Gladiolus (Gladiolus × grandiflorus L.) Genotypes

2021 ◽  
Author(s):  
Varun Hiremath ◽  
Kanwar Pal Singh ◽  
Neelu Jain ◽  
Kishan Swaroop ◽  
Pradeep Kumar Jain ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Structure Analysis ◽  
Genetic Relationships ◽  
Crop Improvement ◽  
Test Analysis ◽  
Average Value ◽  
Population Structure Analysis ◽  
Genetic Diversity And Structure

Abstract Genetic diversity and structure analysis using molecular markers is necessary for efficient utilization and sustainable management of gladiolus germplasm. Genetic analysis of gladiolus germplasm using SSR markers is largely missing due to scarce genomic information. In the present investigation, we report 66.66% cross transferability of Gladiolus palustris SSRs whereas 48% of Iris EST-SSRs were cross transferable across the gladiolus genotypes used in the study. A total of 17 highly polymorphic SSRs revealed a total 58 polymorphic loci ranging from two to six in each locus with an average of 3.41 alleles per marker. PIC values ranged from 0.11 to 0.71 with an average value of 0.48. Four SSRs were selectively neutral based on Ewens-Watterson test. Analysis of genetic structure of 84 gladiolus genotypes divided whole germplasm into two subpopulations. 35 genotypes were assigned to subpopulation 1 whereas 37 to subpopulation 2 and rest of the genotypes recorded as admixture. Analysis of molecular variance indicated maximum variance (53.59%) among individuals within subpopulations whereas 36.55% of variation observed among individuals within total population. Least variation (9.86%) was noticed between two subpopulations. Moderate (FST = 0.10) genetic differentiation of two subpopulations was observed. Grouping pattern of population structure was consistent with UPGMA dendrogram based on simple matching dissimilarity coefficient (ranged from 01.6 to 0.89) and PCoA. Genetic relationships assessed among the genotypes of respective clusters assist the breeders in selecting desirable parents for crossing. SSR markers from present study can be utilized for cultivar identification, conservation and sustainable utilization of gladiolus genotypes for crop improvement.

Genetic diversity of the Bambara groundnut (Vigna subterranea (L.) Verdc.) as assessed by SSR markers

Genome ◽  
2011 ◽  
Vol 54 (11) ◽  
pp. 898-910 ◽  
Author(s):  
P. Somta ◽  
S. Chankaew ◽  
O. Rungnoi ◽  
P. Srinives
Keyword(s):  
Ssr Markers ◽  
Gene Diversity ◽  
Bambara Groundnut ◽  
West African ◽  
Azuki Bean ◽  
Vigna Subterranea ◽  
East African ◽  
The West ◽  
Legume Crop ◽  
Population Structure Analysis

Bambara groundnut ( Vigna subterranea (L.) Verdc.) is an important African legume crop. In this study, a collection consisting of 240 accessions was analyzed using 22 simple sequence repeat (SSR) markers. In total, 166 alleles were detected, with a mean of 7.59 alleles per locus. Allelic and gene diversities were higher in the west African and Cameroon/Nigeria regions with 6.68 and 6.18 alleles per locus, and 0.601 and 0.571, respectively. The genetic distance showed high similarity between west African and Cameroon/Nigeria accessions. Principal coordinate analyses and neighbor-joining analysis consistently revealed that the majority of west African accessions were grouped with Cameroon/Nigeria accessions, but they were differentiated from east African, central African, and southeast Asian accessions. Population structure analysis showed that two subpopulations existed, and most of the east African accessions were restricted to one subpopulation with some Cameroon/Nigeria accessions, whereas most of the west African accessions were associated with most of the Cameroon/Nigeria accessions in the other subpopulation. Comparison with SSR analysis of other Vigna cultigens, i.e., cultivated azuki bean ( Vigna angularis ) and mungbean ( Vigna radiata ), reveals that the mean gene diversity of Bambara groundnut was lower than azuki bean but higher than mungbean.

scholarly journals A Novel ELP2 Compound Heterozygous Mutation in a Boy with Severe Intellectual Disability, Spastic Diplegia, Stereotypic Behavior and Review of the Current Literature

2020 ◽  
Vol 11 (5-6) ◽  
pp. 315-319
Author(s):  
Ayberk Turkyilmaz ◽  
Gunes Sager
Keyword(s):  
Intellectual Disability ◽  
Current Literature ◽  
Stereotypic Behavior ◽  
Compound Heterozygous Mutation ◽  
Heterozygous Mutation ◽  
Spastic Diplegia ◽  
Compound Heterozygous ◽  
Sequencing Analysis ◽  
Severe Intellectual Disability ◽  
Elongator Complex

The elongator complex consists of 6 highly conserved subunit proteins and is indispensable for various cellular functions, such as transcription elongation, histone acetylation, and tRNA modification. The elongator complex contains 2 subunits, each of which consists of 3 different proteins (encoded by the <i>ELP1–3</i> and <i>ELP4–6</i> genes). According to the OMIM database, <i>ELP2</i> gene variations have been reported to be associated with autosomal recessive mental retardation type 58. Here, we report a male patient with severe intellectual disability, spastic diplegia, and stereotypic behavior; in addition, we also provide a review of the current literature. Using whole-exome sequencing analysis, we detected a novel compound heterozygous variation in the <i>ELP2</i> gene. We present this case report to clarify the clinical findings of a very rare neurodevelopmental phenotype and to contribute new information to the current literature on genotype-phenotype correlations.

scholarly journals Genome-Wide Novel Genic Microsatellite Marker Resource Development and Validation for Genetic Diversity and Population Structure Analysis of Banana

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1479
Author(s):  
Manosh Kumar Biswas ◽  
Mita Bagchi ◽  
Dhiman Biswas ◽  
Jennifer Ann Harikrishna ◽  
Yuxuan Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Comparative Mapping ◽  
In Silico ◽  
Large Scale ◽  
Crop Improvement ◽  
Musa Spp ◽  
Population Structure Analysis ◽  
A Genome ◽  
Development And Validation

Trait tagging through molecular markers is an important molecular breeding tool for crop improvement. SSR markers encoded by functionally relevant parts of a genome are well suited for this task because they may be directly related to traits. However, a limited number of these markers are known for Musa spp. Here, we report 35136 novel functionally relevant SSR markers (FRSMs). Among these, 17,561, 15,373 and 16,286 FRSMs were mapped in-silico to the genomes of Musa acuminata, M. balbisiana and M. schizocarpa, respectively. A set of 273 markers was validated using eight accessions of Musa spp., from which 259 markers (95%) produced a PCR product of the expected size and 203 (74%) were polymorphic. In-silico comparative mapping of FRSMs onto Musa and related species indicated sequence-based orthology and synteny relationships among the chromosomes of Musa and other plant species. Fifteen FRSMs were used to estimate the phylogenetic relationships among 50 banana accessions, and the results revealed that all banana accessions group into two major clusters according to their genomic background. Here, we report the first large-scale development and characterization of functionally relevant Musa SSR markers. We demonstrate their utility for germplasm characterization, genetic diversity studies, and comparative mapping in Musa spp. and other monocot species. The sequences for these novel markers are freely available via a searchable web interface called Musa Marker Database.

Congenital Undifferentiated Pure Erythroid Leukemia

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 5231-5231
Author(s):  
Akihiro Tamura ◽  
Daiichiro Hasegawa ◽  
Suguru Uemura ◽  
Atsuro Saito ◽  
Emiko Takeoka ◽  
...  
Keyword(s):  
Tumor Cells ◽  
Chromosome 8 ◽  
Glycophorin A ◽  
Sequencing Analysis ◽  
Flow Cytometric ◽  
Pas Staining ◽  
Wbc Count ◽  
Glycophorin C ◽  
Split Signal ◽  
E Cadherin

Abstract INTRODUCTION: Congenital pure erythroid leukemia (M6b) is exceedingly rare with only a few reported cases to date. Because of the extreme rarity, almost nothing is known about the pathogenesis, appropriate therapy and prognosis. Diagnosis of erythroid leukemia is usually based on the positivity for Glycophorin A, Glycophorin C or PAS staining. We report a first case of congenital pure erythroid leukemia expressing E-cadherin in the absence of Glycophorin A, Glycophorin C and PAS staining. We analyzed the cytogenetic abnormalities of this extremely rare disease. RESULTS: The patient was the first daughter of healthy and non-consanguineous Japanese parents, born at 40 weeks of gestation by emergency cesarean section in non-reassuring fetal state after uncomplicated pregnancy. Apgar score was 8/9. Characteristic facial appearance was not recognized. At birth, she presented with marked hepatomegaly, purpura and disseminated intravascular coagulation. White blood cell (WBC) count was 63.5x109/L with blastic cells with vacuoles. Although congenital leukemia was suspected, flow cytometric analyses using CD45 blast gating failed to demonstrate leukemic cells. Karyotype was 46, XX. Fluorescence in situ hybridization (FISH) for trisomy 21 and MLL split signal were negative. GATA1 mutation was not detected. WBC count has gradually decreased within 3-4 weeks with supportive care.However, liver failure, hemophagocytic lymphohistiocytosis and schistocytosis developed. Although treatment with dexamethasone and etoposide has started, multiple nodules appeared in the liver 11 weeks after birth. Liver biopsy demonstrated small round cell tumor with high N/C ratio and vacuoles infiltrating the liver. The tumor cells were immunohistochemically positive for CD43, CD71, E-cadherin, beta-catenin, Ki-67 and c-Myc and negative for CD45, CD20, CD10, PAX5, CD3, CD4, CD8, TdT, CD1a, CD34, CD56, cyMPO, c-kit, CD42b, CD61, Glycophorin A, Glycophorin C, tyrosine hydroxylase, PGP9.5, myogenin, glypican3, NKX2.2, CAM5.2 and Periodic Acid Schiff (PAS) staining etc. Flow cytometric analysis revealed CD43+ CD71+ CD36+ CD58+ cells within large CD45 negative cell population. These cells expressed almost no other hematopoietic cell markers used to screen for leukemia. These cells were indistinguishable from normal erythroblast based on surface markers only. However, flow cytometric cell sorting revealed these cells are blasts with vacuoles. Karyotype of tumor cells has changed to 50, XX, +7, +8, add(15)(q22), +19, add(19)(q13.1-13.3)×2, +21. Based on these results, she was diagnosed with pure erythroid leukemia. Low dose Cytosine Arabinoside improved her clinical symptoms. She is alive at 5 months of age. DISCUSSION: E-cadherin is a selective marker of immature erythroblast. In our case, E-cadherin was key in erythroid lineage assignment. To our knowledge, this is the first reported case of infantile pure erythroid leukemia expressing E-cadherin in the absence of Glycophorin A, Glycophorin C and PAS staining. These results suggest that the tumor cells originated from undifferentiated erythroblast. This disease entity should be recognized. Immunohistochemical staining of c-Myc showed strong positivity. The c-Myc gene is located on chromosome 8. FISH for c-Myc split signal was negative. G-banding and FISH revealed trisomy 8. Overexpression of c-Myc may be involved in the pathogenesis of this undifferentiated pure erythroid leukemia. At birth, karyotype was 46, XX and blasts in peripheral blood decreased with supportive care only. However, we observed changes in karyotype of blasts. We assume that second hit was added during clinical course. Whole exome sequencing analysis is in progress to reveal somatic and germline mutations underlying this unrecognized disease. Disclosures No relevant conflicts of interest to declare.

Genetic variability of Indonesian landraces of Vigna subterranea: Morphological characteristics and molecular analysis using SSR markers

2020 ◽  
Vol 21 (9) ◽  
Author(s):  
MUHAMMAD FAUZAN FARID ALHAMDI ◽  
Asep Setiawan ◽  
Satriyas Ilyas ◽  
Wai Kuan Ho
Keyword(s):  
Genetic Variability ◽  
Ssr Markers ◽  
Molecular Analysis ◽  
Block Design ◽  
Leaf Shape ◽  
Morphological Characteristics ◽  
Bambara Groundnut ◽  
Vigna Subterranea ◽  
Alternative Source ◽  
Randomized Block Design

Abstract. Alhamdi MFF, Setiawan A, Ilyas S, Ho WK. 2020. Genetic variability of Indonesian landraces of Vigna subterranea: The morphological characteristics and molecular analysis using SSR markers. Biodiversitas 21: 3929-3937. Bambara groundnut (Vigna subterranea (L.) Verdc.) is a potential grain, which can be considered as an alternative source of protein and carbohydrate. Due to unavailability of commercial bambara groundut cultivar in Indonesia, the characterization of bambara groundnut landraces is an important step before developing cultivar with traits of interest. The objective of the research was to access genetic variability of Indonesian landraces of bambara groundnut with different seed coat colors based on morphological and molecular markers. The experiment was arranged as split-plot in a complete randomized block design with the main plot was cultivation methods and the sub plot was landraces. There were differences in leaf shape and pod shape among the landraces. There were two main clusters of Indonesian landraces of bambara groundnut with 88.28% similarity. The first cluster was Cream, Brown Sumedang, Black Sumedang and Black Tasikmalaya, and the second cluster was Black Sukabumi, Brown Gresik, Black Madura, and Black Gresik. The result based on SSR marker with capillary electrophoresis indicated Black Gresik and Black Madura landraces were different from other Indonesian landraces.  Cream Sumedang or Brown Sumedang from the first cluster and Black Gresik or Brown Gresik from the second cluster have the farthest distances for developing improved variety of bambara groundnut.

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