scholarly journals Worldwide phylogeography and history of wheat genetic diversity

2019 ◽  
Vol 5 (5) ◽  
pp. eaav0536 ◽  
Author(s):  
François Balfourier ◽  
Sophie Bouchet ◽  
Sandra Robert ◽  
Romain De Oliveira ◽  
Hélène Rimbert ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism Array ◽  
Human Migration ◽  
Structural Variations ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Allele Distribution ◽  
Fertile Crescent ◽  
History Of ◽  
New Alleles

Since its domestication in the Fertile Crescent ~8000 to 10,000 years ago, wheat has undergone a complex history of spread, adaptation, and selection. To get better insights into the wheat phylogeography and genetic diversity, we describe allele distribution through time using a set of 4506 landraces and cultivars originating from 105 different countries genotyped with a high-density single-nucleotide polymorphism array. Although the genetic structure of landraces is collinear to ancient human migration roads, we observe a reshuffling through time, related to breeding programs, with the appearance of new alleles enriched with structural variations that may be the signature of introgressions from wild relatives after 1960.

scholarly journals Worldwide phylogeography and history of wheat genetic diversity

2018 ◽  
Author(s):  
François Balfourier ◽  
Sophie Bouchet ◽  
Sandra Robert ◽  
Romain De Oliveira ◽  
Hélène Rimbert ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Snp Array ◽  
Wild Relatives ◽  
Human Migration ◽  
Structural Variations ◽  
Breeding Programs ◽  
Allele Distribution ◽  
Fertile Crescent ◽  
History Of ◽  
New Alleles

AbstractSince its domestication in the Fertile Crescent ~8,000 to 10,000 years ago, wheat has undergone a complex history of spread, adaptation and selection. To get better insights into the wheat phylogeography and genetic diversity, we describe allele distribution through time using a set of 4,506 landraces and cultivars originating from 105 different countries genotyped with a high-density SNP array. Although the genetic structure of landraces is collinear to ancient human migration roads, we observe a reshuffling through time, related to breeding programs, with the apparition of new alleles enriched with structural variations that may be the signature of introgressions from wild relatives after 1960.One Sentence SummaryA phylogeographical study reveals the complex history of wheat genetic diversity through time and space.

scholarly journals Genetic diversity assessment of sorghum (Sorghum bicolor (L.) Moench) accessions using single nucleotide polymorphism markers

2019 ◽  
Vol 17 (5) ◽  
pp. 412-420
Author(s):  
G. Afolayan ◽  
S. P. Deshpande ◽  
S. E. Aladele ◽  
A. O. Kolawole ◽  
I. Angarawai ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sorghum Bicolor ◽  
Agronomic Traits ◽  
Crop Improvement ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Diversity Assessment ◽  
Crop Research ◽  
International Crop Research Institute ◽  
Private Alleles

AbstractSorghum (Sorghum bicolor (L.) Moench) is an important resource to the national economy and it is essential to assess the genetic diversity in existing sorghum germplasm for better conservation, utilization and crop improvement. The aim of this study was to evaluate the level of genetic diversity within and among sorghum germplasms collected from diverse institutes in Nigeria and Mali using Single Nucleotide Polymorphic markers. Genetic diversity among the germplasm was low with an average polymorphism information content value of 0.24. Analysis of Molecular Variation revealed 6% variation among germplasm and 94% within germplasms. Dendrogram revealed three groups of clustering which indicate variations within the germplasms. Private alleles identified in the sorghum accessions from National Center for Genetic Resources and Biotechnology, Ibadan, Nigeria and International Crop Research Institute for the Semi-Arid Tropics, Kano, Nigeria shows their prospect for sorghum improvement and discovery of new agronomic traits. The presence of private alleles and genetic variation within the germplasms indicates that the accessions are valuable resources for future breeding programs.

scholarly journals Clonal propagation history shapes the intra-cultivar genetic diversity in ‘Malbec’ grapevines

2020 ◽  
Author(s):  
Luciano Calderón ◽  
Nuria Mauri ◽  
Claudio Muñoz ◽  
Pablo Carbonell-Bejerano ◽  
Laura Bree ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Clonal Propagation ◽  
Variant Calling ◽  
Red Wines ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Diversity Pattern ◽  
History Of ◽  
Potential Impact ◽  
Whole Genome Resequencing

AbstractGrapevine (Vitis vinifera L.) cultivars are clonally propagated to preserve their varietal attributes. However, novel genetic variation still accumulates due to somatic mutations. Aiming to study the potential impact of clonal propagation history on grapevines intra-cultivar genetic diversity, we have focused on ‘Malbec’. This cultivar is appreciated for red wines elaboration, it was originated in Southwestern France and introduced into Argentina during the 1850s. Here, we generated whole-genome resequencing data for four ‘Malbec’ clones with different historical backgrounds. A stringent variant calling procedure was established to identify reliable clonal polymorphisms, additionally corroborated by Sanger sequencing. This analysis retrieved 941 single nucleotide variants (SNVs), occurring among the analyzed clones. Based on a set of validated SNVs, a genotyping experiment was custom-designed to survey ‘Malbec’ genetic diversity. We successfully genotyped 214 samples and identified 14 different clonal genotypes, that clustered into two genetically divergent groups. Group-Ar was driven by clones with a long history of clonal propagation in Argentina, while Group-Fr was driven by clones that have longer remained in Europe. Findings show the ability of such approaches for clonal genotypes identification in grapevines. In particular, we provide evidence on how human actions may have shaped ‘Malbec’ extant genetic diversity pattern.

scholarly journals Utilization of Molecular Marker Based Genetic Diversity Patterns in Hybrid Parents to Develop Better Forage Quality Multi-Cut Hybrids in Pearl Millet

Agriculture ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 97 ◽  
Author(s):  
Govintharaj Ponnaiah ◽  
Shashi Kumar Gupta ◽  
Michael Blümmel ◽  
Maheswaran Marappa ◽  
Sumathi Pichaikannu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Pearl Millet ◽  
Morphological Traits ◽  
Forage Quality ◽  
Genotyping By Sequencing ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Clear Cut

Genetic diversity of 130 forage-type hybrid parents of pearl millet was investigated based on multiple season data of morphological traits and two type of markers: SSRs (Simple sequence repeats) and GBS identified SNPs (Genotyping by sequencing-Single nucleotide polymorphism). Most of the seed and pollinator parents clustered into two clear-cut separate groups based on marker based genetic distance. Significant variations were found for forage related morphological traits at different cutting intervals (first and second cut) in hybrid parents. Across two cuts, crude protein (CP) varied from 11% to 15%, while in vitro organic matter digestibility (IVOMD) varied from 51% to 56%. Eighty hybrids evaluated in multi-location trial along with their parents for forage traits showed that significant heterosis can be realized for forage traits. A low but positive significant correlation found between SSR based genetic distance (GD between parents of hybrid) and heterosis for most of the forage traits indicated that SSR-based GD can be used for predicting heterosis for GFY, DFY and CP in pearl millet. An attempt was made to associate marker-based clusters with forage quality traits, to enable breeders select parents for crossing purposes in forage breeding programs.

scholarly journals Marginal Grapevine Germplasm from Apulia (Southern Italy) Represents an Unexplored Source of Genetic Diversity

Agronomy ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 563 ◽  
Author(s):  
Monica Marilena Miazzi ◽  
Nunzio D’Agostino ◽  
Valentina di Rienzo ◽  
Pasquale Venerito ◽  
Vito Nicola Savino ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Resources ◽  
Genotyping By Sequencing ◽  
Snp Markers ◽  
Gene Pools ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Snp Data ◽  
Data Points ◽  
Genetic Clusters

The investigation on the genetic diversity of grapevine germplasm is crucial for a more efficient use of grapevine genetic resources in light of changing environmental conditions. Here, we used simple sequence repeats (SSRs) coupled with single nucleotide polymorphism (SNP) markers to disclose grapevine genetic diversity of a collection of Apulian minor/neglected genotypes. Their relationships with national or international cultivars were also examined. Genetic diversity was investigated using 10 SSR markers and 1,178 SNPs generated by genotyping by sequencing (GBS). Based on the SSR data, the 128 genotypes were classified into six main genetic clusters. Twenty-four putative cases of synonymy and 2 of misnamings were detected. Ten “unknown” autochthonous genotypes did not show high similarity to Apulian, national, or international varieties. We took advantage of available GBS-derived SNP data points for only forty genotypes to better investigate the genetic distance among them, identify private SNP alleles, and divergent loci putatively under selection. Based on SNP alleles, two interesting gene pools of minor/neglected Apulian samples were identified. Genetic divergence was investigated by FST and allowed the detection of loci capable of differentiating the gene pools. Overall, this work emphasizes the need for recovering the untapped genetic variability that characterizes minor/neglected grapevine Apulian genotypes and the requirement to preserve and use more efficiently grapevine genetic resources in breeding programs.

scholarly journals Genetic Diversity Assessed by Genotyping by Sequencing (GBS) in Watermelon Germplasm

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 822 ◽  
Author(s):  
Kyung Jun Lee ◽  
Jung-Ro Lee ◽  
Raveendar Sebastin ◽  
Myoung-Jae Shin ◽  
Seong-Hoon Kim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Discriminant Analysis ◽  
Single Nucleotide Polymorphisms ◽  
Genetic Differentiation ◽  
Principal Components ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Breeding Programs

Watermelon is an economically important vegetable fruit worldwide. The objective of this study was to conduct a genetic diversity of 68 watermelon accessions using single nucleotide polymorphisms (SNPs). Genotyping by sequencing (GBS) was used to discover SNPs and assess genetic diversity and population structure using STRUCTURE and discriminant analysis of principal components (DAPC) in watermelon accessions. Two groups of watermelons were used: 1) highly utilized 41 watermelon accessions at the National Agrobiodiversity Center (NAC) at the Rural Development Administration in South Korea; and 2) 27 Korean commercial watermelons. Results revealed the presence of four clusters within the populations differentiated principally based on seed companies. In addition, there was higher genetic differentiation among commercial watermelons of each company. It is hypothesized that the results obtained from this study would contribute towards the expansion of this crop as well as providing data about genetic diversity, which would be useful for the preservation of genetic resources or for future breeding programs.

scholarly journals Composite Bacterial Hopanoids and Their Microbial Producers across Oxygen Gradients in the Water Column of the California Current

2013 ◽  
Vol 79 (23) ◽  
pp. 7491-7501 ◽  
Author(s):  
Jenan J. Kharbush ◽  
Juan A. Ugalde ◽  
Shane L. Hogle ◽  
Eric E. Allen ◽  
Lihini I. Aluwihare
Keyword(s):  
Genetic Diversity ◽  
Water Column ◽  
Genetic Relationships ◽  
Structural Diversity ◽  
Low Oxygen ◽  
Structural Variations ◽  
Data Set ◽  
Pentacyclic Triterpenoid ◽  
History Of ◽  
Membrane Components

ABSTRACTHopanoids are pentacyclic triterpenoid lipids produced by many prokaryotes as cell membrane components. The structural variations of composite hopanoids, or bacteriohopanepolyols (BHPs), produced by various bacterial genera make them potentially useful molecular biomarkers of bacterial communities and metabolic processes in both modern and ancient environments. Building on previous work suggesting that organisms in low-oxygen environments are important contributors to BHP production in the marine water column and that there may be physiological roles for BHPs specific to these environments, this study investigated the relationship between trends in BHP structural diversity and abundance and the genetic diversity of BHP producers for the first time in a low-oxygen environment of the Eastern Tropical North Pacific. Amplification of the hopanoid biosynthesis gene for squalene hopene cyclase (sqhC) indicated far greater genetic diversity than would be predicted by examining BHP structural diversity alone and that greatersqhCgenetic diversity exists in the marine environment than is represented by cultured representatives and most marine metagenomes. In addition, the genetic relationships in this data set suggest microaerophilic environments as potential “hot spots” of BHP production. Finally, structural analysis of BHPs showed that an isomer of the commonly observed BHP bacteriohopanetetrol may be linked to a producer that is more abundant in low-oxygen environments. Results of this study increase the known diversity of BHP producers and provide a detailed phylogeny with implications for the role of hopanoids in modern bacteria, as well as the evolutionary history of hopanoid biosynthesis, both of which are important considerations for future interpretations of the marine sedimentary record.

scholarly journals Genetic Diversity of Local Accessions of Dimocarpus longan Revealed By ISSR Markers

2016 ◽  
Vol 17 (1) ◽  
pp. 25 ◽  
Author(s):  
Baiq Dina Mariana ◽  
A. Sugiyatno ◽  
A. Supriyanto
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Issr Markers ◽  
Breeding Programs ◽  
Dimocarpus Longan ◽  
History Of ◽  
Research Institute

<p>Keragaman Genetik Aksesi Lenggkeng Lokal Dimocarpus longan Berdasarkan Penanda ISSR. Lengkeng telah berkembang di Indonesia, namun studi tentang tanaman ini belum banyak dilakukan. Studi untuk mengetahui keragaman genetik lengkeng lokal telah dilakukan di Balai Penelitian Tanaman Jeruk dan Buah Subtropika (Balitjestro) pada bulan Maret- April 2008. Penanda ISSR digunakan untuk mengidentifikasi keragaman genetik antar delapan genotipe lengkeng lokal yang telah dikoleksi oleh Balitjestro. Dendogram yang dibuat berdasarkan UPGMA menggunakan metode SAHN menunjukkan nilai kemiripan sebesar 0,34-0,86. Nilai kemiripan tertinggi diperoleh dari KL I dan KL II (0,86) dan nilai kemiripan terendah diperoleh dari KL I dan KL V/KL VI (0,34). Penanda ISSR dapat digunakan untuk mengidentifikasi lengkeng dan dapat memberikan informasi yang berguna untuk program pemuliaan lengkeng di kemudian hari.</p><p> </p><p><strong>Abstrak</strong></p><p>There is no clear history of longan development in Indonesia even though it has developed well in Indonesia for many years. The study aimed at revealing genetic of diversity of local longan was done in Indonesian Citrus and Subtropical Research Institute (ICSFRI) from March to April 2008. ISSR markers were employed to identify the genetic variation among eight morphologically more or less alike accessions of longan ssp. Matrix data was counted and dendogram of samples was constructed using UPGMA and SAHN method. The cluster showed similarity value 0.34-0.86. The highest similarity value was observed between KL I and KL II (0.86) while the lowest one was obtained between KL I and KL V/KL VI (0.34). ISSR markers were able to identify the genetic diversity of longan and were helpful to provide information on genetic diversities especially for future breeding programs.</p>

scholarly journals PSIII-2 Assessment of runs of homozygosity and estimates of inbreeding in three purebred turkey (Meleagris gallopavo) lines

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 229-229
Author(s):  
Sarah M Adams ◽  
Martijn F Derks ◽  
Bayode Makanjuola ◽  
Benjamin Wood ◽  
Christine F Baes
Keyword(s):  
Single Nucleotide Polymorphism Array ◽  
Meleagris Gallopavo ◽  
Genomic Relationship Matrix ◽  
Relationship Matrix ◽  
Runs Of Homozygosity ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Inbreeding Coefficients ◽  
Fitness And Health ◽  
Dense Single Nucleotide Polymorphism

Abstract Runs of homozygosity (ROH) are continuous stretches of homozygous genotypes in an individual that have been passed down from a common ancestor and can be used to accurately characterize genomic data. These ROH are correlated with other measures of inbreeding and have been applied to quantify individual autozygosity. The aim of this study was to detect and describe ROH in the turkey genome and estimate and compare measures of pedigree-based inbreeding coefficients (FPED) and genomic-based inbreeding coefficients estimated from ROH (FROH) and the genomic relationship matrix (FGRM). Pedigree records (n = 2,616,890) and genotypic records (n = 6,371) were available from three purebred turkey (Meleagris gallopavo) lines. Genotypic records were collected between 2013 and 2019 and were obtained using a dense single nucleotide polymorphism array (56,452 SNP). The overall mean length of detected ROH per animal was 2.87±0.29 Mb and mean number of ROH per animal was 84.87±8.79. Short ROH with lengths of 1–2 Mb long were the most abundant throughout the genome, accounting for approximately 45% of the identified segments. Mean ROH coverage differed greatly between chromosomes and lines. Across all lines, genomic derived inbreeding coefficients (FROH=0.27; FGRM=0.32) were higher than coefficients estimated from pedigree records (FPED=0.14). Ranges of correlations between FROH and FPED (0.19–0.31), FROH and FGRM (0.68–0.73), and FPED and FGRM (0.17–0.30) were estimated. Results from the current research provide a fundamental description of inbreeding in the turkey genome which is critical considering the growing concerns of the detrimental effects of increased inbreeding on fitness and health in livestock production. The knowledge gained from this study may subsequently be used to evaluate and maintain genetic diversity that is necessary for genetic improvement and minimizing inbreeding in turkey breeding programs.

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