Development of a large set of SNP markers for assessing phylogenetic relationships between the olive cultivars composing the Israeli olive germplasm collection

AbstractThis study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic information which would help in the selection of parental lines for a breeding program. The study found that the average polymorphism information content value of 0.288 which indicates a moderate genetic diversity for this L. acutangula germplasm. STRUCTURE analysis (ΔK at K = 6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. When plotted, the STRUCTURE bars to the area of collection, we observed an admixed genotype from surrounding accessions and a geneflow confirmed by the value of FST = 0.137. AMOVA based on STRUCTURE clustering showed a low 12.83% variation between subpopulations that correspond well with the negative inbreeding coefficient value (FIS = − 0.092) and low total fixation index (FIT = 0.057). There were distinguishing fruit shapes and length characteristics in specific accessions for each subpopulation. The genetic diversity and different fruit shapes in the L. acutangula germplasm could benefit the ridge gourd breeding programs to meet the demands and needs of consumers, farmers, and vegetable exporters such as increasing the yield of fruit by the fruit width but not by the fruit length to solve the problem of fruit breakage during exportation.

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Genome-wide association analysis of resistance to Pseudoperonospora cubensis in citron watermelon

Plant Disease ◽

10.1094/pdis-08-21-1611-re ◽

2021 ◽

Author(s):

Dennis Katuuramu ◽

Sandra Branham ◽

Amnon Levi ◽

Patrick Wechter

Keyword(s):

Candidate Genes ◽

Genome Wide Association Study ◽

Citrullus Lanatus ◽

Phenotypic Variability ◽

Germplasm Collection ◽

Snp Markers ◽

Genome Wide Association ◽

Pseudoperonospora Cubensis ◽

Genome Wide ◽

A Genome

Cultivated sweet watermelon (Citrullus lanatus) is an important vegetable crop for millions of people around the world. There are limited sources of resistance to economically important diseases within C. lanatus, whereas Citrullus amarus has a reservoir of traits that can be exploited to improve C. lanatus for resistance to biotic and abiotic stresses. Cucurbit downy mildew (CDM), caused by Pseudoperonospora cubensis, is an emerging threat to watermelon production. We screened 122 C. amarus accessions for resistance to CDM over two tests (environments). The accessions were genotyped by whole-genome resequencing to generate 2,126,759 single nucleotide polymorphic (SNP) markers. A genome-wide association study was deployed to uncover marker-trait associations and identify candidate genes underlying resistance to CDM. Our results indicate the presence of wide phenotypic variability (1.1 - 57.8%) for leaf area infection, representing a 50.7-fold variation for CDM resistance across the C. amarus germplasm collection. Broad-sense heritability estimate was 0.55, implying the presence of moderate genetic effects for resistance to CDM. The peak SNP markers associated with resistance to P. cubensis were located on chromosomes Ca03, Ca05, Ca07, and Ca11. The significant SNP markers accounted for up to 30% of the phenotypic variation and were associated with promising candidate genes encoding disease resistance proteins, leucine-rich repeat receptor-like protein kinase, and WRKY transcription factor. This information will be useful in understanding the genetic architecture of the P. cubensis-Citrullus spp. patho-system as well as development of resources for genomics-assisted breeding for resistance to CDM in watermelon.

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Molecular Characterization of a Cacao Germplasm Collection Maintained in Yunnan, China Using Single Nucleotide Polymorphism (SNP) Markers

Tropical Plant Biology ◽

10.1007/s12042-020-09267-y ◽

2020 ◽

Vol 13 (4) ◽

pp. 359-370

Author(s):

Boyi Wang ◽

Lambert A. Motilal ◽

Lyndel W. Meinhardt ◽

Jiantao Yin ◽

Dapeng Zhang

Keyword(s):

Single Nucleotide Polymorphism ◽

Molecular Characterization ◽

Germplasm Collection ◽

Snp Markers ◽

Nucleotide Polymorphism ◽

Single Nucleotide

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Genome-wide association mapping of agronomic traits and carbon isotope discrimination in a worldwide germplasm collection of spring wheat using SNP markers

Molecular Breeding ◽

10.1007/s11032-015-0264-y ◽

2015 ◽

Vol 35 (2) ◽

Cited By ~ 29

Author(s):

Freddy Mora ◽

Dalma Castillo ◽

Bettina Lado ◽

Ivan Matus ◽

Jesse Poland ◽

...

Keyword(s):

Association Mapping ◽

Carbon Isotope ◽

Spring Wheat ◽

Carbon Isotope Discrimination ◽

Agronomic Traits ◽

Germplasm Collection ◽

Snp Markers ◽

Genome Wide Association ◽

Isotope Discrimination ◽

Genome Wide

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Genotyping tools and resources to assess peanut germplasm: smut-resistant landraces as a case study

PeerJ ◽

10.7717/peerj.10581 ◽

2021 ◽

Vol 9 ◽

pp. e10581

Author(s):

Alicia N. Massa ◽

Marina Bressano ◽

Juan H. Soave ◽

Mario I. Buteler ◽

Guillermo Seijo ◽

...

Keyword(s):

Germplasm Collection ◽

Snp Markers ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Genotyping Platform ◽

Global Spread ◽

Rnase H2 ◽

Number Of Individuals ◽

The U.S

Peanut smut caused by Thecaphora frezii is a severe fungal disease currently endemic to Argentina and Brazil. The identification of smut resistant germplasm is crucial in view of the potential risk of a global spread. In a recent study, we reported new sources of smut resistance and demonstrated its introgression into elite peanut cultivars. Here, we revisited one of these sources (line I0322) to verify its presence in the U.S. peanut germplasm collection and to identify single nucleotide polymorphisms (SNPs) potentially associated with resistance. Five accessions of Arachis hypogaea subsp. fastigiata from the U.S. peanut collection, along with the resistant source and derived inbred lines were genotyped with a 48K SNP peanut array. A recently developed SNP genotyping platform called RNase H2 enzyme-based amplification (rhAmp) was further applied to validate selected SNPs in a larger number of individuals per accession. More than 14,000 SNPs and nine rhAmp assays confirmed the presence of a germplasm in the U.S. peanut collection that is 98.6% identical (P < 0.01, bootstrap t-test) to the resistant line I0322. We report this germplasm with accompanying genetic information, genotyping data, and diagnostic SNP markers.

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DNA Sequence Analysis of Microsatellite Markers Enhances Their Efficiency for Germplasm Management in an Italian Olive Collection

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.131.3.352 ◽

2006 ◽

Vol 131 (3) ◽

pp. 352-359 ◽

Cited By ~ 16

Author(s):

Innocenzo Muzzalupo ◽

Nicola Lombardo ◽

Aldo Musacchio ◽

Maria Elena Noce ◽

Giuseppe Pellegrino ◽

...

Keyword(s):

Sequence Analysis ◽

Microsatellite Markers ◽

Dna Sequence ◽

Genetic Relationships ◽

Germplasm Collection ◽

Electrophoretic Analysis ◽

Dna Sequence Analysis ◽

Germplasm Management ◽

Olive Cultivars ◽

High Level

Genetic diversity studies using microsatelite analysis were carried out in a set of 39 accessions of Olea europaea L., corresponding to the majority of the regional autochthon germplasm in Apulia. Samples of olive leaves were harvested from plants growing in the olive germplasm collection of the Consiglio per la Ricerca e Sperimentazione in Agricoltura (C.R.A.) - Istituto Sperimentale per l'Olivicoltura at Rende in Cosenza Italy. Herein, we evaluated the extent to which microsatellite analysis using electrophoresis was capable of identifying traditional olive cultivars. In addition, the DNA sequence of all amplicons was determined and the number of repeat units was established for each sample. Using five loci, electrophoretic analysis identified 24 genotype profiles, while DNA sequence analysis detected 28 different genotype profiles, identifying 54% of cultivars. The remaining 46% were composed of seven different accession groups containing genetically indistinguishable cultivars, which are presumably synonyms. This study demonstrates the utility of microsatellite markers for management of olive germplasm and points out the high level of polymorphisms in microsatellite repeats when coupled with DNA sequence analysis. The establishment of genetic relationships among cultivars in the Apulian germplasm collection allows for the construction of a molecular database that can be used to establish the genetic relationships between known and unknown cultivars.

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Harnessing Genetic Diversity in the USDA Pea Germplasm Collection Through Genomic Prediction

Frontiers in Genetics ◽

10.3389/fgene.2021.707754 ◽

2021 ◽

Vol 12 ◽

Author(s):

Md. Abdullah Al Bari ◽

Ping Zheng ◽

Indalecio Viera ◽

Hannah Worral ◽

Stephen Szwiec ◽

...

Keyword(s):

Genetic Diversity ◽

Seed Yield ◽

Genomic Prediction ◽

Complex Traits ◽

Prediction Models ◽

Germplasm Collection ◽

Predictive Ability ◽

Snp Markers ◽

Breeding Values ◽

Germplasm Collections

Phenotypic evaluation and efficient utilization of germplasm collections can be time-intensive, laborious, and expensive. However, with the plummeting costs of next-generation sequencing and the addition of genomic selection to the plant breeder’s toolbox, we now can more efficiently tap the genetic diversity within large germplasm collections. In this study, we applied and evaluated genomic prediction’s potential to a set of 482 pea (Pisum sativum L.) accessions—genotyped with 30,600 single nucleotide polymorphic (SNP) markers and phenotyped for seed yield and yield-related components—for enhancing selection of accessions from the USDA Pea Germplasm Collection. Genomic prediction models and several factors affecting predictive ability were evaluated in a series of cross-validation schemes across complex traits. Different genomic prediction models gave similar results, with predictive ability across traits ranging from 0.23 to 0.60, with no model working best across all traits. Increasing the training population size improved the predictive ability of most traits, including seed yield. Predictive abilities increased and reached a plateau with increasing number of markers presumably due to extensive linkage disequilibrium in the pea genome. Accounting for population structure effects did not significantly boost predictive ability, but we observed a slight improvement in seed yield. By applying the best genomic prediction model (e.g., RR-BLUP), we then examined the distribution of genotyped but nonphenotyped accessions and the reliability of genomic estimated breeding values (GEBV). The distribution of GEBV suggested that none of the nonphenotyped accessions were expected to perform outside the range of the phenotyped accessions. Desirable breeding values with higher reliability can be used to identify and screen favorable germplasm accessions. Expanding the training set and incorporating additional orthogonal information (e.g., transcriptomics, metabolomics, physiological traits, etc.) into the genomic prediction framework can enhance prediction accuracy.

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A species-discriminatory single-nucleotide polymorphism set reveals maintenance of species integrity in hybridizing European white oaks (Quercus spp.) despite high levels of admixture

Annals of Botany ◽

10.1093/aob/mcaa001 ◽

2020 ◽

Vol 125 (4) ◽

pp. 663-676 ◽

Cited By ~ 3

Author(s):

Oliver Reutimann ◽

Felix Gugerli ◽

Christian Rellstab

Keyword(s):

Single Nucleotide Polymorphism ◽

Diversity Index ◽

Snp Markers ◽

Genetic Admixture ◽

Large Set ◽

Nucleotide Polymorphism ◽

White Oak ◽

Mixed Stands ◽

Single Nucleotide ◽

Species Integrity

Abstract Background and Aims Hybridization and introgression play an important role in the evolution and diversification of plants. To assess the degree of past and current hybridization, the level of genetic admixture in populations needs to be investigated. Ongoing hybridization and blurred species separation have made it challenging to assign European white oak taxa based on leaf morphology and/or genetic markers and to assess the level of admixture. Therefore, there is a need for powerful markers that differentiate between taxa. Here, we established a condensed set of single-nucleotide polymorphism (SNP) markers to reliably differentiate between the three most common oak species in temperate European forests (Quercus robur, Q. petraea, Q. pubescens) and to assess the degree of admixture in a large set of selected Swiss populations. Methods A training set of 194 presumably pure reference samples from Switzerland and Europe was used to assign 633 test individuals with two different approaches (population genetic-based/Bayesian vs. assumption-free/discriminative classifier) using 58 selected SNPs from coding regions. Admixture was calculated at the individual and population level with the Shannon diversity index based on individual assignment probabilities. Key Results Depending on the approach, 97.5–100 % of training individuals were assigned correctly, and additional analyses showed that the established SNP set could be further reduced while maintaining its discriminatory power. The two assignment approaches showed high overlap (99 %) in assigning training individuals and slightly less overlap in test individuals (84 %). Levels of admixture varied widely among populations. Mixed stands of Q. petraea and Q. pubescens revealed much higher degrees of admixture than mixed stands of the other two taxon pairs, accentuating high levels of gene flow between these two taxa in Switzerland. Conclusions Our set of SNPs warrants reliable taxon discrimination with great potential for further applications. We show that the three European white oak taxa have largely retained their species integrity in Switzerland despite high levels of admixture.

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One century of Nordic barley breeding: nitrogen use efficiency, agronomic traits and genetic diversity

The Journal of Agricultural Science ◽

10.1017/s002185961600068x ◽

2016 ◽

Vol 155 (4) ◽

pp. 582-598 ◽

Cited By ~ 12

Author(s):

A. RAJALA ◽

P. PELTONEN-SAINIO ◽

M. JALLI ◽

L. JAUHIAINEN ◽

A. HANNUKKALA ◽

...

Keyword(s):

Genetic Diversity ◽

Nitrogen Use Efficiency ◽

Agronomic Traits ◽

N Uptake ◽

Germplasm Collection ◽

Snp Markers ◽

Nitrogen Use ◽

Single Nucleotide ◽

Snp Data ◽

Use Efficiency

SUMMARYThe current study aimed to evaluate breeding effect on nitrogen use efficiency (NUE), its components and some agronomic traits and disease resistance in barley by using extensive germplasm covering 72 landraces and 123 cultivars released since 1910. Trials were established in southern Finland with a modified strip-plot experimental design. Prior to sowing, blocks were placement fertilized with compound nitrogen : phosphorus : potassium (NPK) fertilizer (N-P-K: 20–3–8) at the rate of 35 and 70 kg N/ha and unfertilized plots were placed at the other end of the fertilization block. The germplasm collection was genotyped with 1536 single nucleotide polymorphism (SNP) markers and phenotyped during a 2-year field experiment in 2011/12. Independent of row type, a positive breeding effect was evident in NUE and for other plant N traits, except that grain N slightly decreased. Breeding has improved NUE by 0·08 kg/year (26% over the century). Nitrogen utilization and N uptake efficiencies were also improved by breeding as were straw length, lodging tolerance, grain yield and yield components, without any sign of levelling-off. Bred cultivars were more resistant to leaf-damaging diseases, especially to net blotch. The SNP data indicated no reduction in overall genetic diversity. However, genetic diversity differed along the barley chromosomes showing either reduced or increased diversity in certain regions when landraces were compared with modern varieties.

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