Using soybean pedigrees to identify genomic selection signatures associated with long-term breeding for cultivar improvement

Genetic hitchhiking methods used to uncover selection signatures related to traits of agronomic importance in crops have primarily been used at the level of domestication by comparing groups of wild germplasm to landraces or elite breeding lines. In this study, two groups of cultivars defined by an elite Canadian soybean cultivar, ‘OAC Bayfield’, were compared to identify selection signatures related to long-term breeding within a specific region. Cultivars were assigned to either a pre- or post-OAC Bayfield group. Of the 162 simple sequence repeat markers used to genotype members of the pedigree, 14 were fixed and 19 exhibited a selective signature. An in silico analysis compared the results in this study to quantitative trait loci (QTL) reported in SoyBase and showed that 18 out of the 19 markers with a selective signature were associated with at least one QTL. From the 80 QTL associated with the 18 markers, half were related to plant architecture, yield, or maturity. In addition, the number and type of QTL associated with the fixed versus selected loci differed, particularly for yield. Genomic regions exhibiting a selection signature may contain important loci that either need to be conserved for agronomic performance or be targeted for introgressive breeding and germplasm enrichment.

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Integration of data from the in vitro long-term exposure study on human endothelial cells and the in silico analysis: A case of dibutyl phthalate-induced vascular dysfunction

Toxicology Letters ◽

10.1016/j.toxlet.2021.12.006 ◽

2021 ◽

Author(s):

Bojana Stanic ◽

Dunja Kokai ◽

Biljana Tesic ◽

Svetlana Fa ◽

Dragana Samardzija Nenadov ◽

...

Keyword(s):

Endothelial Cells ◽

In Silico ◽

Dibutyl Phthalate ◽

Vascular Dysfunction ◽

In Silico Analysis ◽

Human Endothelial Cells ◽

Exposure Study ◽

Silico Analysis

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Development of a composite collection for mining germplasm possessing allelic variation for beneficial traits in chickpea

Plant Genetic Resources ◽

10.1079/pgr2005101 ◽

2006 ◽

Vol 4 (1) ◽

pp. 13-19 ◽

Cited By ~ 34

Author(s):

H.D. Upadhyaya ◽

B.J. Furman ◽

S.L. Dwivedi ◽

S.M. Udupa ◽

C.L.L. Gowda ◽

...

Keyword(s):

Agricultural Research ◽

Allelic Variation ◽

Reference Sample ◽

Grain Legume ◽

Breeding Lines ◽

Germplasm Collections ◽

Breeding Populations ◽

Beneficial Traits ◽

Elite Breeding Lines ◽

Simple Sequence

Chickpea is one of the most important grain legume crops in the world. Large collections of genetic resources are maintained in the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) and International Center for Agricultural Research in the Dry Areas (ICARDA) genebanks. Association mapping using neutral markers has been suggested as a means to identify useful alleles in the vast reservoirs of genetic diversity existing in the germplasm collections that could be associated with the phenotypes among the population individuals. ICRISAT in collaboration with ICARDA developed a global composite collection of 3000 accessions that will be profiled using 50 polymorphic simple sequence repeat (SSR) markers. The data generated through this collaborative effort will be used to define the genetic structure of the global composite collection and to select a reference sample of 300 accessions representing the maximum diversity for the isolation of allelic variants of candidate gene associated with beneficial traits. It is then expected that molecular biologists and plant breeders will have opportunities to use diverse lines in functional and comparative genomics, in mapping and cloning gene(s), and in applied plant breeding to diversify the genetic base of the breeding populations which should lead to the development of broad-based elite breeding lines/cultivars with superior yield and enhanced adaptation to diverse environments.

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Unravelling Vitamins as Wonder Molecules for Covid-19 Management via Structure-based Virtual Screening

10.21203/rs.3.rs-144177/v1 ◽

2021 ◽

Author(s):

Medha Pandya ◽

Sejal Shah ◽

Dhanalakshmi Menamadathil ◽

Ayushman Gadnayak ◽

Tanzil Juneja ◽

...

Keyword(s):

Virtual Screening ◽

Vitamin B12 ◽

In Silico Analysis ◽

Host Protein ◽

Therapeutic Management ◽

Clinical Settings ◽

Preparedness Planning ◽

Vitamin B9 ◽

Silico Analysis

Abstract The emergence situation of coronavirus disease 2019 (COVID-19) pandemic has realised the global scientific communities to develop strategies for immediate priorities and long-term approaches for utilization of existing knowledge and resources which can be diverted to pandemic preparedness planning. Lack of proper vaccine candidate and therapeutic management has accelerated the researchers to repurpose the existing drugs with known preclinical and toxicity profiles, which can easily enter Phase 3 or 4 or can be used directly in clinical settings. We focused to justify even exploration of supplements, nutrients and vitamins to dampen the disease burden of the current pandemic may play a crucial role for its management. We have explored structure based virtual screening of 15 vitamins against non-structural (NSP3, NSP5, ORF7a, NSP12, ORF3a), structural (Spike & Hemagglutinin esterase) and host protein furin. The in silico analysis exhibited that vitamin B12, Vitamin B9, Vitamin D3 determined suitable binding while vitamin B15 manifested remarkable H-bond interactions with all targets. Vitamin B12 bestowed the lowest energies with human furin and SARS-COV-2 RNA dependent RNA polymerase. Furin mediated cleavage of the viral spike glycoprotein is directly related to enhanced virulence of SARS-CoV-2. In contrast to these, vitamin B12 showed zero affinity with SARS-CoV-2 spike protein. These upshots intimate that Vitamin B12 could be the wonder molecule to shrink the virulence by hindering the furin mediated entry of spike to host cell. These identified molecules may effectively assist in SARS-CoV-2 therapeutic management to boost the immunity by inhibiting the virus imparting relief in lung inflammation.

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Genetic diversity in three groups of barley germplasm assessed by simple sequence repeats

Genome ◽

10.1139/g02-071 ◽

2002 ◽

Vol 45 (6) ◽

pp. 1095-1106 ◽

Cited By ~ 111

Author(s):

I A Matus ◽

P M Hayes

Keyword(s):

Genetic Diversity ◽

Hordeum Vulgare ◽

Molecular Marker ◽

Mapping Population ◽

Allelic Diversity ◽

Breeding Lines ◽

Barley Germplasm ◽

High Level ◽

Elite Breeding Lines ◽

Simple Sequence

Genetic diversity can be measured by several criteria, including phenotype, pedigree, allelic diversity at marker loci, and allelic diversity at loci controlling phenotypes of interest. Abundance, high level of polymorphism, and ease of genotyping make simple sequence repeats (SSRs) an excellent molecular marker system for genetics diversity analyses. In this study, we used a set of mapped SSRs to survey three representative groups of barley germplasm: a sample of crop progenitor (Hordeum vulgare subsp. spontaneum) accessions, a group of mapping population parents, and a group of varieties and elite breeding lines. The objectives were to determine (i) how informative SSRs are in these three sets of barley germplasm resources and (ii) the utility of SSRs in classifying barley germplasm. A total of 687 alleles were identified at 42 SSR loci in 147 genotypes. The number of alleles per locus ranged from 4 to 31, with an average of 16.3. Crop progenitors averaged 10.3 alleles per SSR locus, mapping population parents 8.3 alleles per SSR locus, and elite breeding lines 5.8 alleles per SSR locus. There were many exclusive (unique) alleles. The polymorphism information content values for the SSRs ranged from 0.08 to 0.94. The cluster analysis indicates a high level of diversity within the crop progenitors accessions and within the mapping population parents. It also shows a lower level of diversity within the elite breeding germplasm. Our results demonstrate that this set of SSRs was highly informative and was useful in generating a meaningful classification of the germplasm that we sampled. Our long-term goal is to determine the utility of molecular marker diversity as a tool for gene discovery and efficient use of germplasm.Key words: Hordeum vulgare subsp. vulgare, Hordeum vulgare subsp. spontaneum, SSR, genetic diversity, germplasm.

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Genomic Scan for Selection Signature Reveals Fat Deposition in Chinese Indigenous Sheep with Extreme Tail Types

Animals ◽

10.3390/ani10050773 ◽

2020 ◽

Vol 10 (5) ◽

pp. 773 ◽

Cited By ~ 1

Author(s):

Fuping Zhao ◽

Tianyu Deng ◽

Liangyu Shi ◽

Wenwen Wang ◽

Qin Zhang ◽

...

Keyword(s):

Candidate Genes ◽

Coat Color ◽

Reproductive Traits ◽

Bioinformatic Analysis ◽

Selection Signatures ◽

Selection Signature ◽

Positional Candidate ◽

Indigenous Sheep ◽

Tibetan Sheep ◽

Genomic Regions

It is a unique feature that fat can be deposited in sheep tails and rumps. To elucidate the genetic mechanism underlying this trait, we collected 120 individuals from three Chinese indigenous sheep breeds with extreme tail types, namely large fat-tailed sheep (n = 40), Altay sheep (n = 40), and Tibetan sheep (n = 40), and genotyped them using the Ovine Infinium HD SNP BeadChip. Then genomic scan for selection signatures was performed using the hapFLK. In total, we identified 25 genomic regions exhibiting evidence of having been under selection. Bioinformatic analysis of the genomic regions showed that selection signatures related to multiple candidate genes had a demonstrated role in phenotypic variation. Nine genes have documented association with sheep tail types, including WDR92, TBX12, WARS2, BMP2, VEGFA, PDGFD, HOXA10, ALX4, and ETAA1. Moreover, a number of genes were of particular interest, including RXFP2 associated with the presence/absence and morphology of horns; MITF involved in coat color; LIN52 and SYNDIG1L related to the number of teats; MSRB3 gene associated with ear sizes; LTBP2 considered as a positional candidate genes for number of ribs; JAZF1 regulating lipid metabolism; PGRMC2, SPAG17, TSHR, GTF2A1, and LARP1B implicated with reproductive traits. Our findings provide insights into fat tail formation and a reference for carrying out molecular breeding and conservation in sheep.

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Novel and known signals of selection for fat deposition in domestic sheep breeds from Africa and Eurasia

10.1101/493940 ◽

2018 ◽

Author(s):

Salvatore Mastrangelo ◽

Hussain Bahbahani ◽

Bianca Moioli ◽

Abulgasim Ahbara ◽

Mohammed Al Abri ◽

...

Keyword(s):

Fat Deposition ◽

Domestic Sheep ◽

Selection Signatures ◽

Selection Signature ◽

Sheep Breeds ◽

Fat Tail ◽

Genome Wide ◽

Geographic Origins ◽

Genomic Regions ◽

Great Complexity

Genomic regions subjected to selection frequently show signatures such as within-population reduced nucleotide diversity and outlier values of differentiation among differentially selected populations. In this study, we analyzed 50K SNP genotype data of 373 animals belonging to 23 sheep breeds of different geographic origins using the Rsb and FST statistical approaches, to identify loci associated with the fat-tail phenotype. We also checked if these putative selection signatures overlapped with regions of high-homozygosity (ROH). The analyses identified novel signals and confirmed the presence of selection signature in genomic regions that harbor candidate genes known to affect fat deposition. Several genomic regions that frequently appeared in ROH were also identified within each breed, but only two ROH islands overlapped with the putative selection signatures. The results reported herein provide the most complete genome-wide study of selection signatures for fat-tail in African and Eurasian sheep breeds; they also contribute insights into the genetic basis for the fat tail phenotype in sheep, and confirm the great complexity of the mechanisms that underlie quantitative traits, such as the fat-tail.

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In silico analysis of Simple Sequence Repeats from chloroplast genomes of Solanaceae species

Cropp Breeding and Applied Biotechnology ◽

10.12702/1984-7033.v09n04a09 ◽

2009 ◽

Vol 9 (4) ◽

pp. 344-352 ◽

Cited By ~ 8

Author(s):

E.V. Tambarussi ◽

D.M. Melotto-Passarin ◽

S.G. Gonzalez ◽

J.B. Brigati ◽

F.A. Jesus ◽

...

Keyword(s):

Simple Sequence Repeats ◽

In Silico ◽

In Silico Analysis ◽

Chloroplast Genomes ◽

Solanaceae Species ◽

Silico Analysis ◽

Simple Sequence

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Simple-sequence Repeat Marker Analysis of Genetic Relationships within Hydrangea paniculata

HortScience ◽

10.21273/hortsci.44.1.27 ◽

2009 ◽

Vol 44 (1) ◽

pp. 27-31 ◽

Cited By ~ 4

Author(s):

Sandra M. Reed ◽

Timothy A. Rinehart

Keyword(s):

Ssr Markers ◽

Simple Sequence Repeat ◽

Genetic Similarity ◽

Genetic Relationships ◽

Early Flowering ◽

Sequence Repeat ◽

Breeding Lines ◽

Diversity Studies ◽

Simple Sequence

Genetic diversity studies using 26 simple-sequence repeat (SSR) markers were conducted with 36 cultivars, breeding lines, and wild-collected accessions of Hydrangea paniculata Sieb. The SSR markers were highly variable among the genotypes, producing a mean of 5.8 alleles per marker. Three cultivars (Boskoop, Compact Grandiflora, and Webb) were either identical to or sports of the popular cultivar Grandiflora. The name ‘Pee Wee’ appears to have been applied to two phenotypically different compact forms of H. paniculata, one of which seems to be a sport of ‘Tardiva’, whereas the other is likely derived from ‘Grandiflora’. No close genetic similarity was observed among several cultivars from a long-term Belgium breeding program, although many had one parent in common. Early-flowering genotypes clustered separately from genotypes that flower in midsummer, but close genetic relationships were not observed among early-flowering cultivars. Two genotypes from Taiwan were genetically similar but were distinctly different from the Japanese genotypes. These, along with the early-flowering genotypes and a new collection from Japan, may represent unexploited sources of germplasm for improvement of H. paniculata.

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MBRS-13. MiR-1253 POTENTIATES CISPLATIN RESPONSE IN PEDIATRIC MEDULLOBLASTOMA BY REGULATING FERROPTOSIS

Neuro-Oncology ◽

10.1093/neuonc/noaa222.530 ◽

2020 ◽

Vol 22 (Supplement_3) ◽

pp. iii400-iii400

Author(s):

Ranjana K Kanchan ◽

Naveenkumar Perumal ◽

Pranita Atri ◽

Ramakanth Chirravuri Venkata ◽

Ishwor Thapa ◽

...

Keyword(s):

High Risk ◽

Cell Lines ◽

In Silico Analysis ◽

Poor Overall Survival ◽

Cancer Cell Death ◽

Pediatric Medulloblastoma ◽

Mitochondrial Ros ◽

Group 3 ◽

Silico Analysis

Abstract Despite improvements in targeted therapies, few group 3 medulloblastoma patients survive long-term. Haploinsufficiency of 17p13.3 is a hallmark of these high-risk tumors; included within this locus is miR-1253, which has tumor suppressive properties in medulloblastoma. Therapeutic strategies capitalizing on the anti-neoplastic properties of miRNAs can provide promising adjuncts to chemotherapy. In this study, we explored the potentiation of miR-1253 on cisplatin cytotoxicity in group 3 MB. Overexpression of miR-1253 sensitized group 3 MB cell lines to cisplatin, leading to a pronounced downregulation in cell viability and induction of apoptosis. Cisplatin is reported as an inducer of both apoptosis and ferroptosis-mediated cancer cell death. In silico analysis revealed an upregulation of several ABC transporters in high-risk MB tumors. When compared to cell lines overexpressing miR-1253, the ABC transporter ABCB7, which regulates both apoptosis and ferroptosis, was revealed as a putative target of miR-1253 with poor survival that may facilitate its chemosensitizing effects by modulating mitochondrial ROS and HIF1α-driven NFκB signaling. We observed high expression of ABCB7 and GPX4, ferroptosis regulators, in MB patients with poor overall survival. MiR-1253 negatively regulated the expression of ABCB7 in Group 3 MB cell lines and induced cytoplasmic ROS and mitochondrial O2-, suggesting ROS-mediated induction of ferroptosis through regulation of ABCB7 and GPX4. Treatment with ROS and ferroptosis inhibitors rescued miR-1253 transfected cells treated with cisplatin. We conclude that miR-1253 induced ROS and potentiated the ferroptotic effects of cisplatin via targeting miR-1253/ABCB7/GPX4/mtROS axis.

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