scholarly journals Insights into opium poppy (Papaver spp.) genetic diversity from genotyping-by-sequencing analysis

2022 ◽  
Vol 12 (1) ◽  
Author(s):  
Uyen Vu Thuy Hong ◽  
Muluneh Tamiru-Oli ◽  
Bhavna Hurgobin ◽  
Christopher R. Okey ◽  
Artur R. Abreu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Crop Improvement ◽  
Genotyping By Sequencing ◽  
Opium Poppy ◽  
Sequencing Analysis ◽  
Genetic Groups ◽  
Genebank Management ◽  
Core Sets ◽  
Definition Of ◽  
Number Of Branches

AbstractOpium poppy (Papaver somniferum) is one of the world’s oldest medicinal plants and a versatile model system to study secondary metabolism. However, our knowledge of its genetic diversity is limited, restricting utilization of the available germplasm for research and crop improvement. We used genotyping-by-sequencing to investigate the extent of genetic diversity and population structure in a collection of poppy germplasm consisting of 91 accessions originating in 30 countries of Europe, North Africa, America, and Asia. We identified five genetically distinct subpopulations using discriminate analysis of principal components and STRUCTURE analysis. Most accessions obtained from the same country were grouped together within subpopulations, likely a consequence of the restriction on movement of poppy germplasm. Alkaloid profiles of accessions were highly diverse, with morphine being dominant. Phylogenetic analysis identified genetic groups that were largely consistent with the subpopulations detected and that could be differentiated broadly based on traits such as number of branches and seed weight. These accessions and the associated genotypic data are valuable resources for further genetic diversity analysis, which could include definition of poppy core sets to facilitate genebank management and use of the diversity for genetic improvement of this valuable crop.

scholarly journals Insights into opium poppy (Papaver spp.) genetic diversity from genotyping-by-sequencing analysis

2021 ◽  
Author(s):  
Uyen Vu Thuy Hong ◽  
Muluneh Tamiru-Oli ◽  
Bhavna Hurgobin ◽  
Christopher R Okey ◽  
Artur R. Abreu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
North Africa ◽  
Crop Improvement ◽  
Strong Association ◽  
Geographic Origin ◽  
Genotyping By Sequencing ◽  
Papaver Somniferum ◽  
Opium Poppy ◽  
Germplasm Management ◽  
Sequencing Analysis

Opium poppy (Papaver somniferum) is one of the world's oldest medicinal plants and a versatile model system to study secondary metabolism. However, our knowledge of its genetic diversity is limited, restricting utilization of the available germplasm for research and crop improvement. We used genotyping-by-sequencing to investigate the level of genetic diversity and population structure in a collection of poppy germplasm consisting of 91 accessions originating in 30 countries of Europe, North Africa, America, and Asia. We identified five genetically distinct subpopulations. Although the accessions were from geographically diverse regions, no strong association was detected between geographic origin and subpopulation at regional and sub-regional levels. However, most accessions obtained from the same country were grouped together as genetically distinct, likely a consequence of the restriction on movement of poppy germplasm. Phylogenetic analysis identified clades that were largely consistent with the subpopulations detected. Clades could be differentiated broadly based on capsule dehiscence, plant stature and seed weight, traits believed to be associated with poppy domestication. Our study determined that the genetically diverse collection was likely composed of both wild and cultivated forms. This has direct implications for germplasm management and utilization of the available diversity for genetic improvement of poppy.

scholarly journals Global range expansion history of pepper (Capsicum spp.) revealed by over 10,000 genebank accessions

2021 ◽  
Vol 118 (34) ◽  
pp. e2104315118
Author(s):  
Pasquale Tripodi ◽  
Mark Timothy Rabanus-Wallace ◽  
Lorenzo Barchi ◽  
Sandip Kale ◽  
Salvatore Esposito ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genotyping By Sequencing ◽  
Focal Region ◽  
Nucleotide Polymorphisms ◽  
Trade Routes ◽  
Genebank Management ◽  
Capsicum Spp ◽  
History Of ◽  
Cultural Commodity

Genebanks collect and preserve vast collections of plants and detailed passport information, with the aim of preserving genetic diversity for conservation and breeding. Genetic characterization of such collections has the potential to elucidate the genetic histories of important crops, use marker–trait associations to identify loci controlling traits of interest, search for loci undergoing selection, and contribute to genebank management by identifying taxonomic misassignments and duplicates. We conducted a genomic scan with genotyping by sequencing (GBS) derived single nucleotide polymorphisms (SNPs) of 10,038 pepper (Capsicum spp.) accessions from worldwide genebanks and investigated the recent history of this iconic staple. Genomic data detected up to 1,618 duplicate accessions within and between genebanks and showed that taxonomic ambiguity and misclassification often involve interspecific hybrids that are difficult to classify morphologically. We deeply interrogated the genetic diversity of the commonly consumed Capsicum annuum to investigate its history, finding that the kinds of peppers collected in broad regions across the globe overlap considerably. The method ReMIXTURE—using genetic data to quantify the similarity between the complement of peppers from a focal region and those from other regions—was developed to supplement traditional population genetic analyses. The results reflect a vision of pepper as a highly desirable and tradable cultural commodity, spreading rapidly throughout the globe along major maritime and terrestrial trade routes. Marker associations and possible selective sweeps affecting traits such as pungency were observed, and these traits were shown to be distributed nonuniformly across the globe, suggesting that human preferences exerted a primary influence over domesticated pepper genetic structure.

scholarly journals European Vintage tomatoes galore: a result of farmers combinatorial assorting/swapping of a few diversity rich loci

2021 ◽  
Author(s):  
Jose Blanca ◽  
Clara Pons ◽  
Javier Montero-Pau ◽  
David Sanchez-Matarredona ◽  
Peio Ziarsolo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Morphological Traits ◽  
Balancing Selection ◽  
Genotyping By Sequencing ◽  
Polymorphic Loci ◽  
Comprehensive Collection ◽  
Low Genetic Diversity ◽  
Genetic Groups ◽  
History Of ◽  
Modern Varieties

A comprehensive collection of 1,254 tomato accessions corresponding to European heirlooms and landraces, together with modern varieties, early domesticates and wild relatives, were analyzed by genotyping by sequencing. A continuous genetic gradient between the vintage and modern varieties was observed. European vintage tomatoes displayed very low genetic diversity, with only 298 loci out of 64,943 variants being polymorphic at the 95% threshold. European vintage tomatoes could be classified in several genetic groups. Two main clusters consisting of Spanish and Italian accessions showed a higher genetic diversity than the rest varieties, suggesting that these regions might be independent secondary centers of diversity and with a different history. Other varieties seem to be the result of a more recent complex pattern of migrations and hybridizations among the European regions. Several polymorphic loci were associated in a GWAS with fruit morphological traits in the European vintage collection, and the corresponding alleles were found to contribute to the distinctive phenotypic characteristic of the genetic varietal groups. The few highly polymorphic loci associated with morphological traits in an otherwise diversity-poor genome suggests a history of balancing selection, in which tomato farmers maintained the morphological variation by applying a high selective pressure within different varietal types.

scholarly journals Interactions between genetics and environment shape Camelina seed oil composition

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Jordan R. Brock ◽  
Trey Scott ◽  
Amy Yoonjin Lee ◽  
Sergei L. Mosyakin ◽  
Kenneth M. Olsen
Keyword(s):  
Genetic Diversity ◽  
Fatty Acid Composition ◽  
Fatty Acid ◽  
Acid Composition ◽  
Seed Oil ◽  
Crop Improvement ◽  
Genotyping By Sequencing ◽  
Oilseed Crop ◽  
Environmental Niche ◽  
Oil Composition

Abstract Background Camelina sativa (gold-of-pleasure) is a traditional European oilseed crop and emerging biofuel source with high levels of desirable fatty acids. A twentieth century germplasm bottleneck depleted genetic diversity in the crop, leading to recent interest in using wild relatives for crop improvement. However, little is known about seed oil content and genetic diversity in wild Camelina species. Results We used gas chromatography, environmental niche assessment, and genotyping-by-sequencing to assess seed fatty acid composition, environmental distributions, and population structure in C. sativa and four congeners, with a primary focus on the crop’s wild progenitor, C. microcarpa. Fatty acid composition differed significantly between Camelina species, which occur in largely non-overlapping environments. The crop progenitor comprises three genetic subpopulations with discrete fatty acid compositions. Environment, subpopulation, and population-by-environment interactions were all important predictors for seed oil in these wild populations. A complementary growth chamber experiment using C. sativa confirmed that growing conditions can dramatically affect both oil quantity and fatty acid composition in Camelina. Conclusions Genetics, environmental conditions, and genotype-by-environment interactions all contribute to fatty acid variation in Camelina species. These insights suggest careful breeding may overcome the unfavorable FA compositions in oilseed crops that are predicted with warming climates.

scholarly journals Genetic diversity and GWAS of agronomic traits using an ICARDA lentil (Lens culinaris Medik.) Reference Plus collection

2021 ◽  
pp. 1-10
Author(s):  
Karthika Rajendran ◽  
Clarice J. Coyne ◽  
Ping Zheng ◽  
Gopesh Saha ◽  
Dorrie Main ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Lens Culinaris ◽  
Agronomic Traits ◽  
Plant Genetic Resources ◽  
Crop Improvement ◽  
Principal Component ◽  
Genotyping By Sequencing ◽  
Phenotypic Data ◽  
Reference Set ◽  
Genome Wide

Abstract Genotyping of lentil plant genetic resources holds the promise to increase the identification and utilization of useful genetic diversity for crop improvement. The International Center for Agriculture Research in the Dry Areas (ICARDA) lentil reference set plus collection of 176 accessions was genotyped using genotyping-by-sequencing (GBS) and 22,555 SNPs were identified. The population structure was investigated using Bayesian analysis (STRUCTURE, k = 3) and principal component analysis. The two methods are in concordance. Genome-wide association analysis (GWAS) using the filtered SNP set and ICARDA historical phenotypic data discovered putative markers for several agronomic traits including days to first flower, seeds per pod, seed weight and days to maturity. The genetic and genomic resources developed and utilized in this study are available to the research community interested in exploring the ICARDA reference set plus collection using GWAS.

Multivariate Analysis, Genetic Diversity and Phenotypic Correlation of Nineteen Exotic Groundnut Accessions

2016 ◽  
Vol 3 (1) ◽  
Author(s):  
YPJ AMARASINGHE ◽  
G . WIJESINGHE ◽  
R W PUSHPAKUMARA
Keyword(s):  
Genetic Diversity ◽  
Principal Component Analysis ◽  
Growth Parameters ◽  
Principal Component ◽  
Phenotypic Correlation ◽  
Clustering Method ◽  
Yield Parameters ◽  
Arachis Hypogaea L ◽  
Semi Arid ◽  
Number Of Branches

19 Groundnut ( Arachis hypogaea L. ) genotypes receiv ed from International Crops Research Institute for Semi Arid T ropics (ICRISA T) India w ere ev aluated in a non replicated trial and the characters w ere subjected to multiv ariate analysis to study the v ariability within the genotypes. The first 5 axes of the principal component analysis captured 78% of the total v ariability and identified yield parameters such as number of pods per plant, pod w eight per plant and growth parameters such as number of branches per plant, plant spread, and pod characteristics as the characters contributing most to total v ariation. Phenotypic correlation analysis rev ealed that the yield has positiv e correlation with the characters such as number of pods per plant and number of branches per plant. W ards clustering method has grouped the genotypes into 3 distinct clusters. The results can be applied in order to strengthen the breeding program

scholarly journals Genetic Diversity of Purple Passion Fruit, Passiflora edulis f. edulis, Based on Single-Nucleotide Polymorphism Markers Discovered through Genotyping by Sequencing

Diversity ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 144
Author(s):  
Nohra Castillo Rodríguez ◽  
Xingbo Wu ◽  
María Isabel Chacón ◽  
Luz Marina Melgarejo ◽  
Matthew Wohlgemuth Blair
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Genotyping By Sequencing ◽  
Passion Fruit ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Passiflora Edulis ◽  
Tropical Fruit ◽  
Commercial Cultivars ◽  
Purple Passion Fruit

Orphan crops, which include many of the tropical fruit species used in the juice industry, lack genomic resources and breeding efforts. Typical of this dilemma is the lack of commercial cultivars of purple passion fruit, Passiflora edulis f. edulis, and of information on the genetic resources of its substantial semiwild gene pool. In this study, we develop single-nucleotide polymorphism (SNP) markers for the species and show that the genetic diversity of this fruit crop has been reduced because of selection for cultivated genotypes compared to the semiwild landraces in its center of diversity. A specific objective of the present study was to determine the genetic diversity of cultivars, genebank accession, and landraces through genotyping by sequencing (GBS) and to conduct molecular evaluation of a broad collection for the species P. edulis from a source country, Colombia. We included control genotypes of yellow passion fruit, P. edulis f. flavicarpa. The goal was to evaluate differences between fruit types and compare landraces and genebank accessions from in situ accessions collected from farmers. In total, 3820 SNPs were identified as informative for this diversity study. However, the majority distinguished yellow and purple passion fruit, with 966 SNPs useful in purple passion fruits alone. In the population structure analysis, purple passion fruits were very distinct from the yellow ones. The results for purple passion fruits alone showed reduced diversity for the commercial cultivars while highlighting the higher diversity found among landraces from wild or semi-wild conditions. These landraces had higher heterozygosity, polymorphism, and overall genetic diversity. The implications for genetics and breeding as well as evolution and ecology of purple passion fruits based on the extant landrace diversity are discussed with consideration of manual or pollinator-assisted hybridization of this species.

scholarly journals Genetic Diversity of Landraces and Improved Varieties of Rice (Oryza sativa L.) in Taiwan

Rice ◽  
2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Ai-ling Hour ◽  
Wei-hsun Hsieh ◽  
Su-huang Chang ◽  
Yong-pei Wu ◽  
Han-shiuan Chin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Indigenous Peoples ◽  
Oryza Sativa L ◽  
Crop Improvement ◽  
Genetic Erosion ◽  
Germplasm Conservation ◽  
Gene Pools ◽  
Improved Varieties ◽  
Breeding Goals

Abstract Background Rice, the most important crop in Asia, has been cultivated in Taiwan for more than 5000 years. The landraces preserved by indigenous peoples and brought by immigrants from China hundreds of years ago exhibit large variation in morphology, implying that they comprise rich genetic resources. Breeding goals according to the preferences of farmers, consumers and government policies also alter gene pools and genetic diversity of improved varieties. To unveil how genetic diversity is affected by natural, farmers’, and breeders’ selections is crucial for germplasm conservation and crop improvement. Results A diversity panel of 148 rice accessions, including 47 cultivars and 59 landraces from Taiwan and 42 accessions from other countries, were genotyped by using 75 molecular markers that revealed an average of 12.7 alleles per locus with mean polymorphism information content of 0.72. These accessions could be grouped into five subpopulations corresponding to wild rice, japonica landraces, indica landraces, indica cultivars, and japonica cultivars. The genetic diversity within subpopulations was: wild rices > landraces > cultivars; and indica rice > japonica rice. Despite having less variation among cultivars, japonica landraces had greater genetic variation than indica landraces because the majority of Taiwanese japonica landraces preserved by indigenous peoples were classified as tropical japonica. Two major clusters of indica landraces were formed by phylogenetic analysis, in accordance with immigration from two origins. Genetic erosion had occurred in later japonica varieties due to a narrow selection of germplasm being incorporated into breeding programs for premium grain quality. Genetic differentiation between early and late cultivars was significant in japonica (FST = 0.3751) but not in indica (FST = 0.0045), indicating effects of different breeding goals on modern germplasm. Indigenous landraces with unique intermediate and admixed genetic backgrounds were untapped, representing valuable resources for rice breeding. Conclusions The genetic diversity of improved rice varieties has been substantially shaped by breeding goals, leading to differentiation between indica and japonica cultivars. Taiwanese landraces with different origins possess various and unique genetic backgrounds. Taiwanese rice germplasm provides diverse genetic variation for association mapping to unveil useful genes and is a precious genetic reservoir for rice improvement.

scholarly journals Genetic Diversity and Population Structure of Serbian Barley (Hordeum vulgare L.) Collection during a 40-Year Long Breeding Period

Agronomy ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 118
Author(s):  
Ljiljana Brbaklić ◽  
Dragana Trkulja ◽  
Sanja Mikić ◽  
Milan Mirosavljević ◽  
Vojislava Momčilović ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Hordeum Vulgare ◽  
Crop Improvement ◽  
Genetic Erosion ◽  
Breeding Period ◽  
Phenotypic Variance ◽  
Hordeum Vulgare L ◽  
Phenotypic Data ◽  
Breeding Material

Determination of genetic diversity and population structure of breeding material is an important prerequisite for discovering novel and valuable alleles aimed at crop improvement. This study’s main objective was to characterize genetic diversity and population structure of a collection representing a 40-year long historical period of barley (Hordeum vulgare L.) breeding, using microsatellites, pedigree, and phenotypic data. The set of 90 barley genotypes was phenotyped during three growing seasons and genotyped with 338 polymorphic alleles. The indicators of genetic diversity showed differentiation changes throughout the breeding periods. The population structure discriminated the breeding material into three distinctive groups. The principal coordinate analysis grouped the genotypes according to their growth habit and row type. An analysis of phenotypic variance (ANOVA) showed that almost all investigated traits varied significantly between row types, seasons, and breeding periods. A positive effect on yield progress during the 40-year long breeding period could be partly attributed to breeding for shorter plants, which reduced lodging and thus provided higher yield stability. The breeding material revealed a considerable diversity level based on microsatellite and phenotypic data without a tendency of genetic erosion throughout the breeding history and implied dynamic changes in genetic backgrounds, providing a great gene pool suitable for further barley improvement.

Sign in / Sign up

Export Citation Format

Share Document