scholarly journals Malus sieversii: A Diverse Central Asian Apple Species in the USDA-ARS National Plant Germplasm System

HortScience ◽  
2013 ◽  
Vol 48 (12) ◽  
pp. 1440-1444 ◽  
Author(s):  
Gayle M. Volk ◽  
Adam D. Henk ◽  
Christopher M. Richards ◽  
Philip L. Forsline ◽  
C. Thomas Chao
Keyword(s):  
Single Gene ◽  
Phenotypic Trait ◽  
Phenotypic Traits ◽  
Gene Pools ◽  
Phenotypic Differences ◽  
Plant Germplasm ◽  
Malus Sieversii ◽  
Central Asian ◽  
National Plant Germplasm System ◽  
Anthocyanin Production

There are several Central Asian Malus species and varieties in the USDA-ARS National Plant Germplasm System (NPGS) apple collection. Malus sieversii is the most comprehensively collected species native to Central Asia. Other taxa such as M. sieversii var. kirghisorum, M. sieversii var. turkmenorum, M. pumila, and M. pumila var. niedzwetzkyana have primarily been donated to the collection by other institutions and arboreta. We sought to determine if genetic and/or phenotypic differences among the individuals that make up the gene pools of these taxa in the NPGS exhibit unique characteristics. Genetic data, based on microsatellite analyses, suggested that the diversity within each taxa is significantly greater than that among taxa. Trait data also revealed very few differences among taxa, the primary characteristic being the dark red fruit coloration and tinted flesh color of the accessions assigned to M. pumila var. niedzwetzkyana resulting from a known single-gene mutation in anthocyanin production. We found that M. sieversii is a highly diverse species with a range in genetic and phenotypic trait variation that includes the characteristics of the other Central Asian taxa of interest. We conclude that the gene pools that comprise the accessions within the NPGS Central Asian Malus collection are highly overlapping with respect to both phenotypic traits and genotypic characters.

scholarly journals Novel Diversity Identified in a Wild Apple Population from the Kyrgyz Republic

HortScience ◽  
2009 ◽  
Vol 44 (2) ◽  
pp. 516-518 ◽  
Author(s):  
Gayle M. Volk ◽  
Christopher M. Richards ◽  
Adam D. Henk ◽  
Ann Reilley ◽  
Diane D. Miller ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Marker ◽  
Genetic Lineage ◽  
Mountain Range ◽  
Kyrgyz Republic ◽  
Plant Germplasm ◽  
Malus Sieversii ◽  
National Plant Germplasm System ◽  
Private Alleles

The genetic diversity of a wild Malus population collected in the Kyrgyz Republic was compared with seedlings of Malus sieversii collected in Kazakhstan. Based on microsatellite marker results, we conclude that the population of 49 individuals collected in the Kyrgyz Republic includes private alleles and this population is assigned to a common genetic lineage with M. sieversii individuals found in the Karatau Mountain range of Kazakhstan. We recommend that a subset of these individuals be included in the National Plant Germplasm System Malus collection so they may be made available to breeders, physiologists, and other scientists for further examination.

scholarly journals Comparative transcriptome analysis reveals genetic mechanisms of phenotypic differences between Landsberg erecta-0 and Columbia-0 ecotypes in Arabidopsis

2021 ◽  
Author(s):  
Zhenjiang Wu ◽  
Yaqiong Liu ◽  
Bingbing Li ◽  
Chaohui Xie ◽  
Tao Zhu ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Single Gene ◽  
Leaf Length ◽  
Phenotypic Trait ◽  
Comparative Transcriptome ◽  
Sequencing Data ◽  
Cold Response ◽  
Comparative Transcriptome Analysis ◽  
Phenotypic Differences ◽  
Differential Expressed Genes

Abstract As common ecotypes of Arabidopsis thaliana, obvious phenotypic differences have been observed between Landsberg erecta-0 (Ler-0) and Columbia-0 (Col-0). However, it is unlikely to explain a phenotypic trait from each single-gene mutant. In this study, a genotype to phenotype prediction using comparative transcriptome analysis was established to study multigene regulation in biological processes. Analyses of RNA sequencing data of Ler-0 and Col-0 revealed that the differences on gene expression in different organs were larger than those in different ecotypes. Among the 671 differential expressed genes between Ler-0 and Col-0, 273 genes were up-regulated and 398 genes were down-regulated in Ler-0. Gene Ontology (GO) analyses were performed by using these genes, and 43, 31 and 58 genes were enriched in response to cold, response to cold and response to hormone stimulus respectively. Due to these datas, we then tested the sensitivity of Col-0 and Ler-0 to cold and abscisic acid (ABA) stress, and Col-0 ecotype exhibited more tolerance to cold stress and ABA. We also quantified the cell and leaf length of Col-0 and Ler-0, and these different growth phenotypes may be partly caused by the genes which enriched in response to hormone stimulus. The differential expressed genes identified through the mRNA transcriptome provide a revealing insight into guiding phenotyping of organisms and providing genotype to phenotype relations for better understanding of plant growth, development and response to environments. This approach could also be applied to genetic mutants for discovery of novel phenotypes thus better understanding of the mutant gene functions.

Plant Materials Registered by Crop Science Incorporated into the National Plant Germplasm System

Crop Science ◽  
1988 ◽  
Vol 28 (4) ◽  
pp. 716-717 ◽  
Author(s):  
G. A. White ◽  
S. A. Eberhart ◽  
P. A. Miller ◽  
J. D. Mowder
Keyword(s):  
Plant Materials ◽  
Plant Germplasm ◽  
Crop Science ◽  
National Plant Germplasm System

scholarly journals Normal approximation for mixtures of normal distributions and the evolution of phenotypic traits

2021 ◽  
Vol 53 (1) ◽  
pp. 162-188
Author(s):  
Krzysztof Bartoszek ◽  
Torkel Erhardsson
Keyword(s):  
Normal Distribution ◽  
Phenotypic Trait ◽  
Phenotypic Traits ◽  
Normal Distributions ◽  
Average Value ◽  
Conditional Moments ◽  
Mixture Of Normal Distributions ◽  
Explicit Bounds ◽  
Mixtures Of Normal Distributions ◽  
Parameter Values

AbstractExplicit bounds are given for the Kolmogorov and Wasserstein distances between a mixture of normal distributions, by which we mean that the conditional distribution given some $\sigma$ -algebra is normal, and a normal distribution with properly chosen parameter values. The bounds depend only on the first two moments of the first two conditional moments given the $\sigma$ -algebra. The proof is based on Stein’s method. As an application, we consider the Yule–Ornstein–Uhlenbeck model, used in the field of phylogenetic comparative methods. We obtain bounds for both distances between the distribution of the average value of a phenotypic trait over n related species, and a normal distribution. The bounds imply and extend earlier limit theorems by Bartoszek and Sagitov.

scholarly journals Genomic diversity of Mycobacterium avium subsp. paratuberculosis: pangenomic approach for highlighting unique genomic features with newly constructed complete genomes

2021 ◽  
Vol 52 (1) ◽  
Author(s):  
Jaewon Lim ◽  
Hong-Tae Park ◽  
Seyoung Ko ◽  
Hyun-Eui Park ◽  
Gyumin Lee ◽  
...  
Keyword(s):  
Mycobacterium Avium ◽  
Phenotypic Diversity ◽  
Control Strategies ◽  
Genomic Diversity ◽  
Phenotypic Traits ◽  
Whole Genome ◽  
Genomic Features ◽  
Phenotypic Differences ◽  
Mycobacterium Avium Subsp Paratuberculosis ◽  
Type Strains

AbstractMycobacterium avium subsp. paratuberculosis (MAP) is a causative agent of Johne’s disease, which is a chronic granulomatous enteropathy in ruminants. Determining the genetic diversity of MAP is necessary to understand the epidemiology and biology of MAP, as well as establishing disease control strategies. In the present study, whole genome-based alignment and comparative analysis were performed using 40 publicly available MAP genomes, including newly sequenced Korean isolates. First, whole genome-based alignment was employed to identify new genomic structures in MAP genomes. Second, the genomic diversity of the MAP population was described by pangenome analysis. A phylogenetic tree based on the core genome and pangenome showed that the MAP was differentiated into two major types (C- and S-type), which was in keeping with the findings of previous studies. However, B-type strains were discriminated from C-type strains. Finally, functional analysis of the pangenome was performed using three virulence factor databases (i.e., PATRIC, VFDB, and Victors) to predict the phenotypic diversity of MAP in terms of pathogenicity. Based on the results of the pangenome analysis, we developed a real-time PCR technique to distinguish among S-, B- and C-type strains. In conclusion, the results of our study suggest that the phenotypic differences between MAP strains can be explained by their genetic polymorphisms. These results may help to elucidate the diversity of MAP, extending from genomic features to phenotypic traits.

scholarly journals Ancient genomic time transect from the Central Asian Steppe unravels the history of the Scythians

2021 ◽  
Vol 7 (13) ◽  
pp. eabe4414
Author(s):  
Guido Alberto Gnecchi-Ruscone ◽  
Elmira Khussainova ◽  
Nurzhibek Kahbatkyzy ◽  
Lyazzat Musralina ◽  
Maria A. Spyrou ◽  
...  
Keyword(s):  
Bronze Age ◽  
Iron Age ◽  
Gene Pools ◽  
Social Rules ◽  
Eurasian Steppe ◽  
Central Asian ◽  
Genome Wide ◽  
Genome Wide Data ◽  
History Of ◽  
First Millennium

The Scythians were a multitude of horse-warrior nomad cultures dwelling in the Eurasian steppe during the first millennium BCE. Because of the lack of first-hand written records, little is known about the origins and relations among the different cultures. To address these questions, we produced genome-wide data for 111 ancient individuals retrieved from 39 archaeological sites from the first millennia BCE and CE across the Central Asian Steppe. We uncovered major admixture events in the Late Bronze Age forming the genetic substratum for two main Iron Age gene-pools emerging around the Altai and the Urals respectively. Their demise was mirrored by new genetic turnovers, linked to the spread of the eastern nomad empires in the first centuries CE. Compared to the high genetic heterogeneity of the past, the homogenization of the present-day Kazakhs gene pool is notable, likely a result of 400 years of strict exogamous social rules.

Assessment of phenotypic diversity in the USDA, National Plant Germplasm System (NPGS) guayule germplasm collection

2022 ◽  
Vol 175 ◽  
pp. 114303
Author(s):  
V.M.V. Cruz ◽  
D.A. Dierig ◽  
A. Lynch ◽  
K. Hunnicutt ◽  
T.R. Sullivan ◽  
...  
Keyword(s):  
Phenotypic Diversity ◽  
Germplasm Collection ◽  
Plant Germplasm ◽  
National Plant Germplasm System

scholarly journals Genetic diversity of common bean (Phaseolus vulgaris L.) breeding collection in Serbia

Genetika ◽  
2019 ◽  
Vol 51 (1) ◽  
pp. 1-15 ◽  
Author(s):  
Aleksandra Savic ◽  
Milka Brdar-Jokanovic ◽  
Miodrag Dimitrijevic ◽  
Sofija Petrovic ◽  
Milan Zdravkovic ◽  
...  
Keyword(s):  
Common Bean ◽  
Gene Pool ◽  
Gene Diversity ◽  
Principal Component ◽  
Molecular Data ◽  
Phenotypic Traits ◽  
Gene Pools ◽  
Vegetable Crops ◽  
Novi Sad

The characterization of 41 common bean cultivars and landraces from breeding collection of Institute of Field and Vegetable Crops, Novi Sad, Serbia, was done based on phenotypic traits and microsatellite markers. Phenotypic traits were chosen from Bioversity International descriptor list. In addition, main yield components were investigated. Analysis of phaseolin type revealed affiliation of cultivars and landraces to Mesoamerican or Andean gene pool. Cultivars and landraces demonstrated significant diversity level with regard to studied phenotypic traits. Identified variation showed high potential for developing new cultivars with desirable combination of traits. Principal component analysis based on phenotypic traits separated bean cultivars and landraces in two groups, which corresponded to Mesoamerican and Andean determined according to phaseolin type. Putative hybrids, with combination of traits between gene pools were also identified. Analysis of microsatellite data, using twenty-two SSR primer pairs, showed medium gene diversity in studied material. Microsatellite-based cluster analysis separated genotypes in two discrete clusters and several subclusters. No clear separation according to gene pool was found between the clusters, however grouping according to gene pool and patterns of phenotypic variation, following these gene pools, were observed within subclusters. Knowledge on detailed relationships of cultivars and landraces based on phenotypic and molecular data would facilitate identification of candidates for future breeding.

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