scholarly journals Management of a Walnut Germplasm Collection: Which of SSR or SNP Markers Are Most Suitable to Preserve Biodiversity?

2019 ◽  
Author(s):  
Anthony Bernard ◽  
Teresa Barreneche ◽  
Armel Donkpegan ◽  
Lheureux Fabrice ◽  
Elisabeth Dirlewanger
Keyword(s):  
Snp Array ◽  
Allelic Diversity ◽  
Germplasm Collection ◽  
Snp Markers ◽  
Germplasm Management ◽  
Core Collections ◽  
Construction Methods ◽  
Genetic Resources Management ◽  
Starting Point ◽  
Genomics Tools

AbstractThe preservation of the maximum of diversity within the smallest number of accessions is one of the challenges of germplasm management. To construct core-collections, the assessment of the population structure and the relationships between the accessions represents a key step and the choice of suitable molecular markers is the starting point. Since the expansion of available SNP-based genomics tools, a debate has emerged regarding the usefulness of the widely used microsatellites (SSRs) markers. In this study, we analysed a part of the INRAE walnut germplasm collection of 150 accessions, unique in Europe for walnut biodiversity conservation, by comparing the power of both types of marker. We found that the first level of structure is equally detected using 13 SSRs or the Axiom™ J. regia 700K SNP array, and is in relation with the geographical origin of the accessions. For K=2, there was no exchange of accession between the two groups when both markers were compared. We also highlighted empirically that approximately 100 SNPs are needed to obtain similar clustering to SSRs in Principal Coordinate Analysis (PCoA). The neighbor-joining trees constructed were also consistent between both types of marker. The main differences lied in the upper levels of structure from K=3 to K=6, more powerful using the SNPs, and in the percentage of the explained variation in PCoA for K=2, higher using SSRs. We then constructed core-collections of 50 accessions, a crucial step in genetic resources management to reduce the costs and preserve the allelic diversity. Using two different construction methods, both SSR and SNP markers were suitable and able to keep at least 88.57% of the alleles. 32/50 accessions were in common between the two markers, for both methods. We concluded that the use of either marker is dependent on the researcher’s goal.

scholarly journals Comparison of structure analyses and core collections for the management of walnut genetic resources

2020 ◽  
Vol 16 (5) ◽  
Author(s):  
Anthony Bernard ◽  
Teresa Barreneche ◽  
Armel Donkpegan ◽  
Fabrice Lheureux ◽  
Elisabeth Dirlewanger
Keyword(s):  
Genetic Resources ◽  
Plant Genetic Resources ◽  
Allelic Diversity ◽  
Germplasm Collection ◽  
Germplasm Management ◽  
Core Collections ◽  
Construction Methods ◽  
Genetic Resources Management ◽  
Starting Point ◽  
Key Steps

Abstract The preservation of maximum diversity within the smallest number of accessions is one of the challenges of germplasm management, and the assessment of the population structure, the relationships between the accessions, and the construction of core collections are the key steps. The choice of suitable molecular markers is often the starting point. In this study, we analyzed a part of the INRAE walnut germplasm collection, which is highly diverse and unique in Europe, consisting of 150 accessions from American, European, and Asian continents. Based on genotypic data already available, using 13 SSRs or 364,275 SNPs, we showed that the first level of structure is detected equally. We also highlighted empirically that approximately 100 SNPs are needed to obtain similar clustering to 13 SSRs in Principal Coordinate Analysis (PCoA). We constructed eight core collections following two strategies (percentage of total allelic diversity or number of accessions) and two construction methods based on different algorithms (“maximum length subtree” and “entry-to-nearest-entry” methods). We showed that core collections based on few SSR markers are able to capture at least 99.5% of the SNP allelic diversity, irrespective of the construction method used. Then, core collections based on each marker type are highly similar, using both construction methods. All these steps are crucial to identify the suitable tools and methods to improve plant genetic resources management.

scholarly journals Detecting strawberry cultivar misidentification in the Philippines using single nucleotide polymorphism markers from the anthocyanin reductase gene

2020 ◽  
Author(s):  
Nadine Adellia Ledesma ◽  
John Mark Matulac ◽  
Jesus Emmanuel Sevilleja ◽  
Maria Luisa Enriquez
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Germplasm Collection ◽  
Optimal Growth ◽  
Molecular Classification ◽  
The Philippines ◽  
Snp Markers ◽  
Germplasm Management ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Small Holder Farmers

ABSTRACTBACKGROUNDCommercial strawberry production in the Philippines is done by small-holder farmers in La Trinidad, Benguet, where the climate is conducive for optimal growth of this temperate crop. However, these farmers are not cognizant of the importance of proper cultivar identification, particularly during runner propagation, distribution, and transplanting. Thus, there is a high likelihood that misidentification of commonly grown cultivars has taken place.OBJECTIVEThe study aimed to develop single nucleotide polymorphism markers and use them to detect possible misidentification among strawberry cultivars.METHODSLeaf samples from several cultivars were obtained from farmers and the germplasm collection of a local university in La Trinidad, Benguet, Philippines. Expressed sequence tags from the ANR gene were screened for putative SNPs. Eleven SNP markers were developed and used to discriminate among the collected samples.RESULTSThe SNP markers grouped the cultivars into five genotypic clusters with seven distinct genotypic identities. Clustering analysis revealed inconsistencies between the farmers’ identification and the molecular classification. ‘Sweet Charlie’ samples were assigned to four genotypic clusters and ‘Strawberry Festival’ samples were grouped into three separate clusters.CONCLUSIONThere is a high probability that cultivar misidentification has indeed occurred. The molecular markers developed in this study could assist in future cultivar verification efforts, germplasm management, and breeding programs.

scholarly journals Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Grimar Abdiel Perez ◽  
Pumipat Tongyoo ◽  
Julapark Chunwongse ◽  
Hans de Jong ◽  
Anucha Wongpraneekul ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Germplasm Collection ◽  
Snp Markers ◽  
Fixation Index ◽  
Breeding Programs ◽  
Total Fixation ◽  
Unrooted Phylogenetic Tree ◽  
Luffa Acutangula ◽  
Selection Of

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.

scholarly journals Genome-wide association for heifer reproduction and calf performance traits in beef cattle

Genome ◽  
2015 ◽  
Vol 58 (12) ◽  
pp. 549-557 ◽  
Author(s):  
Everestus C. Akanno ◽  
Graham Plastow ◽  
Carolyn Fitzsimmons ◽  
Stephen P. Miller ◽  
Vern Baron ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Genome Wide Association Study ◽  
Average Daily Gain ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Research Centre ◽  
Genome Wide ◽  
A Genome ◽  
Starting Point ◽  
And Performance

The aim of this study was to identify SNP markers that associate with variation in beef heifer reproduction and performance of their calves. A genome-wide association study was performed by means of the generalized quasi-likelihood score (GQLS) method using heifer genotypes from the BovineSNP50 BeadChip and estimated breeding values for pre-breeding body weight (PBW), pregnancy rate (PR), calving difficulty (CD), age at first calving (AFC), calf birth weight (BWT), calf weaning weight (WWT), and calf pre-weaning average daily gain (ADG). Data consisted of 785 replacement heifers from three Canadian research herds, namely Brandon Research Centre, Brandon, Manitoba, University of Alberta Roy Berg Kinsella Ranch, Kinsella, Alberta, and Lacombe Research Centre, Lacombe, Alberta. After applying a false discovery rate correction at a 5% significance level, a total of 4, 3, 3, 9, 6, 2, and 1 SNPs were significantly associated with PBW, PR, CD, AFC, BWT, WWT, and ADG, respectively. These SNPs were located on chromosomes 1, 5–7, 9, 13–16, 19–21, 24, 25, and 27–29. Chromosomes 1, 5, and 24 had SNPs with pleiotropic effects. New significant SNPs that impact functional traits were detected, many of which have not been previously reported. The results of this study support quantitative genetic studies related to the inheritance of these traits, and provides new knowledge regarding beef cattle quantitative trait loci effects. The identification of these SNPs provides a starting point to identify genes affecting heifer reproduction traits and performance of their calves (BWT, WWT, and ADG). They also contribute to a better understanding of the biology underlying these traits and will be potentially useful in marker- and genome-assisted selection and management.

scholarly journals Advanced genebank management of genetic resources of European wild apple, Malus sylvestris, using genome-wide SNP array data

2021 ◽  
Vol 17 (4) ◽  
Author(s):  
Joukje Buiteveld ◽  
Herma JJ Koehorst-van Putten ◽  
Linda Kodde ◽  
Ivo Laros ◽  
Giorgio Tumino ◽  
...  
Keyword(s):  
Genetic Resources ◽  
Genetic Relationship ◽  
Snp Array ◽  
Seed Orchard ◽  
Effective Population ◽  
Malus Sylvestris ◽  
Genebank Management ◽  
Genetic Resources Management ◽  
Genebank Collection ◽  
Close Genetic Relationship

AbstractThe Netherlands’ field genebank collection of European wild apple (Malus sylvestris), consisting of 115 accessions, was studied in order to determine whether duplicates and mistakes had been introduced, and to develop a strategy to optimize the planting design of the collection as a seed orchard. We used the apple 20K Infinium single nucleotide polymorphism (SNP) array, developed in M. domestica, for the first time for genotyping in M. sylvestris. We could readily detect the clonal copies and unexpected duplicates. Thirty-two M. sylvestris accessions (29%) showed a close genetic relationship (parent-child, full-sib, or half-sib) to another accession, which reflects the small effective population size of the in situ populations. Traces of introgression from M. domestica were only found in 7 individuals. This indicates that pollination preferentially took place among the M. sylvestris trees. We conclude that the collection can be considered as mainly pure M. sylvestris accessions. The results imply that it should be managed as one unit when used for seed production. A bias in allele frequencies in the seeds may be prevented by not harvesting all accessions with a close genetic relationship to the others in the seed orchard. We discuss the value of using the SNP array to elaborate the M. sylvestris genetic resources more in depth, including for phasing the markers in a subset of the accessions, as a first step towards genetic resources management at the level of haplotypes.

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

Plant Disease ◽  
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.

scholarly journals Genomic patterns of introgression in interspecific populations created by crossing wheat with its wild relative

2019 ◽  
Author(s):  
Moses Nyine ◽  
Elina Adhikari ◽  
Marshall Clinesmith ◽  
Katherine W. Jordan ◽  
Allan K. Fritz ◽  
...  
Keyword(s):  
Aegilops Tauschii ◽  
Allelic Diversity ◽  
Sequence Divergence ◽  
Snp Markers ◽  
D Genome ◽  
Entire Genome ◽  
Wild Allele ◽  
Negative Epistasis ◽  
The Hill ◽  
Genomic Patterns

AbstractIntrogression from wild relatives is a valuable source of novel allelic diversity for breeding. We investigated the genomic patterns of introgression from Aegilops tauschii, the diploid ancestor of the wheat D genome, into winter wheat (Triticum aestivum) cultivars. The population of 351 BC1F3:5 lines was selected based on phenology from crosses between six hexaploid wheat lines and 21 wheat-Ae. tauschii octoploids. SNP markers developed for this population and a diverse panel of 116 Ae. tauschii accessions by complexity-reduced genome sequencing were used to detect introgression based on the identity-by-descent analysis. Overall, introgression frequency positively correlated with recombination rate, with a high incidence of introgression at the ends of chromosomes and low in the pericentromeric regions, and was negatively related to sequence divergence between the parental genomes. Reduced introgression in the pericentromeric low-recombining regions spans nearly 2/3 of each chromosome arm, suggestive of the polygenic nature of introgression barriers that could be associated with multilocus negative epistasis between the alleles of wild and cultivated wheat. On the contrary, negative selection against the wild allele of Tg, controlling free-threshing trait and located in the high-recombining chromosomal region, led to reduced introgression only within ∼10 Mbp region around Tg. These results are consistent with the effect of selection on linked variation described by the Hill-Robertson effect, and offer insights into the introgression population development for crop imrpovement to ensure retention of introgressed diversity across entire genome.

scholarly journals Genotypic Characterization of the U.S. Peanut Core Collection

2020 ◽  
Vol 10 (11) ◽  
pp. 4013-4026
Author(s):  
Paul I. Otyama ◽  
Roshan Kulkarni ◽  
Kelly Chamberlin ◽  
Peggy Ozias-Akins ◽  
Ye Chu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Core Collection ◽  
Regional Distribution ◽  
Country Of Origin ◽  
Snp Array ◽  
Germplasm Collection ◽  
Genotypic Diversity ◽  
Cultivated Peanut ◽  
Food And Feed ◽  
Genetic Clustering

Cultivated peanut (Arachis hypogaea) is an important oil, food, and feed crop worldwide. The USDA peanut germplasm collection currently contains 8,982 accessions. In the 1990s, 812 accessions were selected as a core collection on the basis of phenotype and country of origin. The present study reports genotyping results for the entire available core collection. Each accession was genotyped with the Arachis_Axiom2 SNP array, yielding 14,430 high-quality, informative SNPs across the collection. Additionally, a subset of 253 accessions was replicated, using between two and five seeds per accession, to assess heterogeneity within these accessions. The genotypic diversity of the core is mostly captured in five genotypic clusters, which have some correspondence with botanical variety and market type. There is little genetic clustering by country of origin, reflecting peanut’s rapid global dispersion in the 18th and 19th centuries. A genetic cluster associated with the hypogaea/aequatoriana/peruviana varieties, with accessions coming primarily from Bolivia, Peru, and Ecuador, is consistent with these having been the earliest landraces. The genetics, phenotypic characteristics, and biogeography are all consistent with previous reports of tetraploid peanut originating in Southeast Bolivia. Analysis of the genotype data indicates an early genetic radiation, followed by regional distribution of major genetic classes through South America, and then a global dissemination that retains much of the early genetic diversity in peanut. Comparison of the genotypic data relative to alleles from the diploid progenitors also indicates that subgenome exchanges, both large and small, have been major contributors to the genetic diversity in peanut.

scholarly journals High-Resolution Mapping of the Novel Early Leaf Senescence Gene Els2 in Common Wheat

Plants ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 698
Author(s):  
Na Wang ◽  
Yanzhou Xie ◽  
Yingzhuang Li ◽  
Shengnan Wu ◽  
Shuxian Li ◽  
...  
Keyword(s):  
High Resolution ◽  
Leaf Senescence ◽  
Chinese Spring ◽  
Snp Array ◽  
Triticum Aestivum L ◽  
Snp Markers ◽  
F2 Population ◽  
High Resolution Map ◽  
Kasp Markers ◽  
Early Leaf Senescence

Early leaf senescence negatively impacts the grain yield in wheat (Triticum aestivum L.). Induced mutants provide an important resource for mapping and cloning of genes for early leaf senescence. In our previous study, Els2, a single incomplete dominance gene, that caused early leaf senescence phenotype in the wheat mutant LF2099, had been mapped on the long arm of chromosome 2B. The objective of this study was to develop molecular markers tightly linked to the Els2 gene and construct a high-resolution map surrounding the Els2 gene. Three tightly linked single-nucleotide polymorphism (SNP) markers were obtained from the Illumina Wheat 90K iSelect SNP genotyping array and converted to Kompetitive allele-specific polymerase chain reaction (KASP) markers. To saturate the Els2 region, the Axiom® Wheat 660K SNP array was used to screen bulked extreme phenotype DNA pools, and 9 KASP markers were developed. For fine mapping of the Els2 gene, these KASP markers and previously identified polymorphic markers were analyzed in a large F2 population of the LF2099 × Chinese Spring cross. The Els2 gene was located in a 0.24-cM genetic region flanked by the KASP markers AX-111643885 and AX-111128667, which corresponded to a physical interval of 1.61 Mb in the Chinese Spring chromosome 2BL containing 27 predicted genes with high confidence. The study laid a foundation for a map-based clone of the Els2 gene controlling the mutation phenotype and revealing the molecular regulatory mechanism of wheat leaf senescence.

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