scholarly journals PopAmaranth: A population genetic genome browser for grain amaranths and their wild relatives

2020 ◽  
Author(s):  
José Gonçalves-Dias ◽  
Markus G Stetter
Keyword(s):  
Genetic Diversity ◽  
Genome Sequencing ◽  
Interdisciplinary Research ◽  
Genetic Information ◽  
Population Genetic ◽  
Wild Relatives ◽  
Genome Browser ◽  
Reference Sequence ◽  
Grain Amaranth ◽  
Amaranth Species

The last decades of genomic, physiological, and population genetic research have accelerated the understanding and improvement of a numerous crops. The transfer of methods to minor crops could accelerate their improvement if knowledge is effectively shared between disciplines. Grain amaranth is an ancient nutritious pseudocereal from the Americas that is regaining importance due to its high protein content and favorable amino acid and micronutrient composition. To effectively combine genomic and population genetic information with molecular genetics, plant physiology, and use it for interdisciplinary research and crop improvement, an intuitive interaction for scientists across disciplines is essential. Here, we present PopAmaranth, a population genetic genome browser, which provides an accessible representation of the genetic variation of the three grain amaranth species (A. hypochondriacus, A. cruentus, and A. caudatus) and two wild relatives (A. hybridus and A. quitensis) along the A. hypochondriacus reference sequence. We performed population-scale diversity and selection analysis from whole-genome sequencing data of 88 curated genetically and taxonomically unambiguously classified accessions. We incorporate the domestication history of the three grain amaranths to make an evolutionary perspective for candidate genes and regions available. We employ the platform to show that genetic diversity in the water stress-related MIF1 gene declined during amaranth domestication and provide evidence for convergent saponin reduction between amaranth and quinoa. These examples show that our tool enables the detailed study of individual genes, provides target regions for breeding efforts and can enhance the interdisciplinary integration of population genomic findings across species. PopAmaranth is available through amaranthGDB at amaranthgdb.org/popamaranth.htmlSignificanceSharing population genetic results between disciplines can facilitate interdisciplinary research and accelerate the improvement of crops. Since the onset of genome sequencing online genome browser platforms have provide access to features of an organisms genetic information. Rarely this has been extended to population-wide summary statistics for evolutionary hypothesis testing. We implemented a population genetic genome browser PopAmaranth for three grain amaranth species and their two wild relatives. The intuitive and user-friendly interface of PopA-maranth makes the genetic diversity of the species complex available to broad audience of biologists across disciplines. We show how our tool can be used to study convergence across distant genera and find signals of past selection in domestication and stress related genes. Community platforms and genome browsers are an integrative element of numerous study systems. PopAmaranth can serve as template for other research communities to integrate and share their results.

scholarly journals PopAmaranth: A population genetic genome browser for grain amaranths and their wild relatives

2021 ◽  
Author(s):  
José Gonçalves-Dias ◽  
Markus G Stetter
Keyword(s):  
Interdisciplinary Research ◽  
Population Genetic ◽  
Genetic Research ◽  
Wild Relatives ◽  
Genome Browser ◽  
Reference Sequence ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
Grain Amaranth ◽  
Amaranth Species

Abstract The combination of genomic, physiological, and population genetic research has accelerated the understanding and improvement of numerous crops. For non-model crops the lack of interdisciplinary research hinders their improvement. Grain amaranth is an ancient nutritious pseudocereal that has been domesticated three times in different regions of the Americas. We present and employ PopAmaranth, a population genetic genome browser, which provides an accessible representation of the genetic variation of the three grain amaranth species (A. hypochondriacus, A. cruentus, and A. caudatus) and two wild relatives (A. hybridus and A. quitensis) along the A. hypochondriacus reference sequence. We performed population-scale diversity and selection analysis from whole-genome sequencing data of 88 curated genetically and taxonomically unambiguously classified accessions. We employ the platform to show that genetic diversity in the water stress-related MIF1 gene declined during amaranth domestication and provide evidence for convergent saponin reduction between amaranth and quinoa. PopAmaranth is available through amaranthGDB at amaranthgdb.org/popamaranth.html.

KERAGAMAN GENETIK INDUK UDANG WINDU DI PERAIRAN SELATAN PANGANDARAN DAN BINUANGEUN, JAWABARAT

2018 ◽  
Vol 5 (3) ◽  
Author(s):  
Ratu Siti Aliah
Keyword(s):  
Genetic Diversity ◽  
Population Genetic ◽  
Gene Locus ◽  
Penaeus Monodon ◽  
12S Rrna ◽  
Brood Stock ◽  
Population Genetic Diversity ◽  
Result Show ◽  
Mtdna Diversity

An evaluation of the Black Tiger Brood Stock (Penaeus monodon) genetic diversity of Pangandaran and Binuangeun was conducted by using the mtDNA diversity of two gene locus of CO I and 12S rRNA to understand their population genetic diversity. The result show that the brood stock of Pangandaran has 17 haplotipe, while from Binuangeun has 13 haplotipe. The result indicated that the genetic diversity of the Balck Tiger brood stock of Pangandaran was higher than thatBinuangeun.Key words : Genetic diversity, Black Tiger brood stock, Pangandaran, Binuangeun

Microsatellite analysis of population genetic diversity in Triplophysa xiangxiensis

2013 ◽  
Vol 37 (1) ◽  
pp. 26 ◽  
Author(s):  
Yanhong YAO ◽  
Lingfu KONG ◽  
Dengqiang WANG ◽  
Wenhui HE ◽  
Li HE ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Genetic ◽  
Microsatellite Analysis ◽  
Population Genetic Diversity

Allozyme variation and an estimate of the inbreeding coefficient in the coffee berry borer, Hypothenemus hampei (Coleoptera: Scolytidae)

1995 ◽  
Vol 85 (1) ◽  
pp. 21-28 ◽  
Author(s):  
Philippe Borsa ◽  
D. Pierre Gingerich
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Population Genetic ◽  
New Caledonia ◽  
Allozyme Variation ◽  
Inbreeding Coefficient ◽  
Hypothenemus Hampei ◽  
Coffee Berry ◽  
Biological Features ◽  
High Degree

AbstractSeven presumed Mendelian enzyme loci (Est-2, Est-3, Gpi, Idh-l, Idh-2, Mdh-2 and Mpi) were characterized and tested for polymorphism in coffee berry borers, Hypothenemus hampei (Ferrari), sampled in Côte d′Ivoire, Mexico and New Caledonia. The average genetic diversity was H = 0.080. Two loci, Mdh-2 and Mpi were polymorphic, and thus usable as genetic markers. The population structure of H. hampei was analysed using Weir & Cockerham's estimators of Wright's F-statistics. A high degree of inbreeding (f = 0.298) characterized the elementary geographic sampling unit, the coffee field. The estimate of gene flow between fields within a country was Nm = 10.6 and that between countries was Nm = 2. The population genetic structure in H. hampei could be related to its known population biological features and history.

scholarly journals Whole genome sequencing reveals high differentiation, low levels of genetic diversity and short runs of homozygosity among Swedish wels catfish

Heredity ◽  
2021 ◽  
Author(s):  
Axel Jensen ◽  
Mette Lillie ◽  
Kristofer Bergström ◽  
Per Larsson ◽  
Jacob Höglund
Keyword(s):  
Genetic Diversity ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome Sequencing Data ◽  
Peripheral Populations ◽  
Whole Genome ◽  
Runs Of Homozygosity ◽  
Sequencing Data ◽  
Isolated Populations ◽  
Native Populations

AbstractThe use of genetic markers in the context of conservation is largely being outcompeted by whole-genome data. Comparative studies between the two are sparse, and the knowledge about potential effects of this methodology shift is limited. Here, we used whole-genome sequencing data to assess the genetic status of peripheral populations of the wels catfish (Silurus glanis), and discuss the results in light of a recent microsatellite study of the same populations. The Swedish populations of the wels catfish have suffered from severe declines during the last centuries and persists in only a few isolated water systems. Fragmented populations generally are at greater risk of extinction, for example due to loss of genetic diversity, and may thus require conservation actions. We sequenced individuals from the three remaining native populations (Båven, Emån, and Möckeln) and one reintroduced population of admixed origin (Helge å), and found that genetic diversity was highest in Emån but low overall, with strong differentiation among the populations. No signature of recent inbreeding was found, but a considerable number of short runs of homozygosity were present in all populations, likely linked to historically small population sizes and bottleneck events. Genetic substructure within any of the native populations was at best weak. Individuals from the admixed population Helge å shared most genetic ancestry with the Båven population (72%). Our results are largely in agreement with the microsatellite study, and stresses the need to protect these isolated populations at the northern edge of the distribution of the species.

scholarly journals Molecular diversity analysis in hexaploid wheat (Triticum aestivum L.) and two Aegilops species (Aegilops crassa and Aegilops cylindrica) using CBDP and SCoT markers

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Ghazal Ghobadi ◽  
Alireza Etminan ◽  
Ali Mehras Mehrabi ◽  
Lia Shooshtari
Keyword(s):  
Genetic Diversity ◽  
Triticum Aestivum ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Crop Improvement ◽  
Wild Relatives ◽  
Resolving Power ◽  
Start Codon ◽  
Aegilops Cylindrica ◽  
Aegilops Crassa

Abstract Background Evaluation of genetic diversity and relationships among crop wild relatives is an important task in crop improvement. The main objective of the current study was to estimate molecular variability within the set of 91 samples from Triticum aestivum, Aegilops cylindrica, and Aegilops crassa species using 30 CAAT box–derived polymorphism (CBDP) and start codon targeted (SCoT) markers. Results Fifteen SCoT and Fifteen CBDP primers produced 262 and 298 fragments which all of them were polymorphic, respectively. The number of polymorphic bands (NPB), polymorphic information content (PIC), resolving power (Rp), and marker index (MI) for SCoT primers ranged from 14 to 23, 0.31 to 0.39, 2.55 to 7.49, and 7.56 to 14.46 with an average of 17.47, 0.34, 10.44, and 5.69, respectively, whereas these values for CBDP primers were 15 to 26, 0.28 to 0.36, 3.82 to 6.94, and 4.74 to 7.96 with a mean of 19.87, 0.31, 5.35, and 6.24, respectively. Based on both marker systems, analysis of molecular variance (AMOVA) indicated that the portion of genetic diversity within species was more than among them. In both analyses, the highest values of the number of observed (Na) and effective alleles (Ne), Nei’s gene diversity (He), and Shannon’s information index (I) were estimated for Ae. cylindrica species. Conclusion The results of cluster analysis and population structure showed that SCoT and CBDP markers grouped all samples based on their genomic constitutions. In conclusion, the used markers are very effective techniques for the evaluation of the genetic diversity in wild relatives of wheat.

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