Exploitation of SSR, SRAP and CAPS-SNP markers for genetic diversity of Citrus 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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Assessing genetic diversity and population structure in a citrus germplasm collection utilizing simple sequence repeat markers (SSRs)

Theoretical and Applied Genetics ◽

10.1007/s00122-006-0255-9 ◽

2006 ◽

Vol 112 (8) ◽

pp. 1519-1531 ◽

Cited By ~ 218

Author(s):

Noelle A. Barkley ◽

Mikeal L. Roose ◽

Robert R. Krueger ◽

Claire T. Federici

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Simple Sequence Repeat ◽

Germplasm Collection ◽

Sequence Repeat ◽

Simple Sequence Repeat Markers ◽

Citrus Germplasm ◽

Simple Sequence

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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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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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A Genome-Wide Genetic Diversity Scan Reveals Multiple Signatures of Selection in a European Soybean Collection Compared to Chinese Collections of Wild and Cultivated Soybean Accessions

Frontiers in Plant Science ◽

10.3389/fpls.2021.631767 ◽

2021 ◽

Vol 12 ◽

Author(s):

Aamir Saleem ◽

Hilde Muylle ◽

Jonas Aper ◽

Tom Ruttink ◽

Jiao Wang ◽

...

Keyword(s):

Genetic Diversity ◽

Oil Content ◽

Selective Sweep ◽

Germplasm Collection ◽

Snp Markers ◽

Selective Sweeps ◽

Genome Wide ◽

Population Structure Analysis ◽

A Genome ◽

Signatures Of Selection

Targeted and untargeted selections including domestication and breeding efforts can reduce genetic diversity in breeding germplasm and create selective sweeps in crop genomes. The genomic regions at which selective sweeps are detected can reveal important information about signatures of selection. We have analyzed the genetic diversity within a soybean germplasm collection relevant for breeding in Europe (the EUCLEG collection), and have identified selective sweeps through a genome-wide scan comparing that collection to Chinese soybean collections. This work involved genotyping of 480 EUCLEG soybean accessions, including 210 improved varieties, 216 breeding lines and 54 landraces using the 355K SoySNP microarray. SNP calling of 477 EUCLEG accessions together with 328 Chinese soybean accessions identified 224,993 high-quality SNP markers. Population structure analysis revealed a clear differentiation between the EUCLEG collection and the Chinese materials. Further, the EUCLEG collection was sub-structured into five subgroups that were differentiated by geographical origin. No clear association between subgroups and maturity group was detected. The genetic diversity was lower in the EUCLEG collection compared to the Chinese collections. Selective sweep analysis revealed 23 selective sweep regions distributed over 12 chromosomes. Co-localization of these selective sweep regions with previously reported QTLs and genes revealed that various signatures of selection in the EUCLEG collection may be related to domestication and improvement traits including seed protein and oil content, phenology, nitrogen fixation, yield components, diseases resistance and quality. No signatures of selection related to stem determinacy were detected. In addition, absence of signatures of selection for a substantial number of QTLs related to yield, protein content, oil content and phenological traits suggests the presence of substantial genetic diversity in the EUCLEG collection. Taken together, the results obtained demonstrate that the available genetic diversity in the EUCLEG collection can be further exploited for research and breeding purposes. However, incorporation of exotic material can be considered to broaden its genetic base.

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Comparative analysis of genetic diversity in Citrus germplasm collection using AFLP, SSAP, SAMPL and SSR markers

Scientia Horticulturae ◽

10.1016/j.scienta.2011.06.015 ◽

2011 ◽

Vol 129 (4) ◽

pp. 798-803 ◽

Cited By ~ 32

Author(s):

Manosh Kumar Biswas ◽

Lijun Chai ◽

Mohamed Hamdy Amar ◽

Xianlong Zhang ◽

Xiu-xin Deng

Keyword(s):

Genetic Diversity ◽

Comparative Analysis ◽

Ssr Markers ◽

Germplasm Collection ◽

Citrus Germplasm

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Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape

BMC Plant Biology ◽

10.1186/1471-2229-13-39 ◽

2013 ◽

Vol 13 (1) ◽

pp. 39 ◽

Cited By ~ 159

Author(s):

Francesco Emanuelli ◽

Silvia Lorenzi ◽

Lukasz Grzeskowiak ◽

Valentina Catalano ◽

Marco Stefanini ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Germplasm Collection ◽

Snp Markers ◽

Ssr And Snp Markers

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Estimation of genetic diversity and relatedness in a mango germplasm collection using SNP markers and a simplified visual analysis method

Scientia Horticulturae ◽

10.1016/j.scienta.2019.03.037 ◽

2019 ◽

Vol 252 ◽

pp. 156-168 ◽

Cited By ~ 4

Author(s):

David N. Kuhn ◽

Natalie Dillon ◽

Ian Bally ◽

Amy Groh ◽

Jordon Rahaman ◽

...

Keyword(s):

Genetic Diversity ◽

Visual Analysis ◽

Germplasm Collection ◽

Snp Markers ◽

Analysis Method

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RAPD primer screening as a preliminary study to analyze the genetic diversity of Citrus spp. in South Sulawesi, Indonesia

IOP Conference Series Earth and Environmental Science ◽

10.1088/1755-1315/886/1/012017 ◽

2021 ◽

Vol 886 (1) ◽

pp. 012017

Author(s):

M Tuwo ◽

T Kuswinanti ◽

A Nasruddin ◽

E Tambaru

Keyword(s):

Genetic Diversity ◽

Random Amplified Polymorphic Dna ◽

Germplasm Collection ◽

Breeding Programs ◽

Citrus Breeding ◽

South Sulawesi ◽

Citrus Germplasm ◽

Rapd Primer ◽

Preliminary Study ◽

Polymorphic Bands

Abstract The typical citrus germplasm collection in South Sulawesi has not been thoroughly characterized, especially in several citrus development centers, which have begun to be promoted again after the decline in productivity due to CVPD infection. The study of citrus diversity is very important to support future citrus breeding programs. Random amplified polymorphic DNA (RAPD) has been widely used for the analysis of genetic diversity among species in populations. In this study, 23 RAPD primers were used on Citrus cultivated in Selayar and Pangkep Regencies, which are citrus development areas in South Sulawesi. A total of 19 primers (OPA-05, OPA-09, OPA-17, OPC-09, OPC-17, OPE-04, OPH-04, OPH-15, OPN-14, 0PN-16, OPR-08, OPR-20, OPW-06, OPW-09, OPX-07, OPX-11, OPX-17, UBC-18, and UBC-51) can form polymorphic bands in randomly selected DNA samples. Monomorphic bands were formed by OPA-12 and OPD-07 primer in 12 samples. The primers OPX-13 and OPX-16 produced unclear bands. These 19 primers can be used to amplify DNA and determine the genetic diversity of Citrus in further analysis.

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