Molecular marker diversity of SCN-resistant sources in soybean

Genome ◽  
2006 ◽  
Vol 49 (8) ◽  
pp. 938-949 ◽  
Author(s):  
Yiwu Chen ◽  
Dechun Wang ◽  
Prakash Arelli ◽  
Mohsen Ebrahimi ◽  
Randall L Nelson
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Soybean Cyst Nematode ◽  
Polymorphic Information Content ◽  
Genetic Relationships ◽  
Germplasm Collection ◽  
Nematode Resistance ◽  
The United States ◽  
Cyst Nematode ◽  
Clustering Methods

Soybean cyst nematode (SCN) (Heterodera glycines Ichinohe; HG) is one of the most destructive pests of soybean (Glycine max (L.) Merr.) in the United States. Over 100 SCN-resistant accessions within the USDA Soybean Germplasm Collection have been identified, but little is known about the genetic diversity of this SCN-resistant germplasm. The objective of this research was to evaluate the genetic variation and determine the genetic relationships among SCN-resistant accessions. One hundred twenty-two genotypes were evaluated by 85 simple sequence repeat (SSR) markers from 20 linkage groups. Non-hierarchical (VARCLUS) and hierarchical (Ward's) clustering were combined with multidimensional scaling (MDS) to determine relationships among tested lines. The 85 SSR markers produced 566 allelic fragments with a mean polymorphic information content (PIC) value of 0.35. The 122 lines were grouped into 7 clusters by 2 different clustering methods and the MDS results consistently corresponded to the assigned clusters. Assigned clusters were dominated by genotypes that possess one or more unique SCN resistance genes and were associated with geographical origins. The results of analysis of molecular variance (AMOVA) showed that the variation differences among clusters and individual lines were significant, but the differences among individuals within clusters were not significant.Key words: soybean cyst nematode resistance, genetic diversity, SSR markers, cluster analysis, soybean.

Classification methods and identification of reniform nematode resistance in known soybean cyst nematode resistant soybean genotypes

Plant Disease ◽  
2021 ◽  
Author(s):  
Mariola Usovsky ◽  
Robert Robbins ◽  
Juliet Fultz Wilkes ◽  
Devany Crippen ◽  
Vijay Shankar ◽  
...  
Keyword(s):  
Soybean Cyst Nematode ◽  
Germplasm Collection ◽  
Nematode Species ◽  
The United States ◽  
Cyst Nematode ◽  
Classification Methods ◽  
Reniform Nematode ◽  
Plant Introductions ◽  
Scn Resistance ◽  
Moderately Resistant

Plant parasitic nematodes are a major yield-limiting factor of soybean in the United States and Canada. It has been indicated that soybean cyst nematode (SCN, Heterodera glycines Ichinohe) and reniform nematode (RN, Rotylenchulus reniformis Linford and Oliveira) resistance could be genetically related. For many years fragmentary data has shown this relationship. This report evaluates RN reproduction on 418 plant introductions (PIs) selected from the USDA Soybean Germplasm Collection with reported SCN resistance. The germplasm was divided into two tests of 214 PIs reported as resistant, and 204 PIs moderately resistant to SCN. The defining and reporting of RN resistance changed several times in the last 30 years, causing inconsistencies in RN resistance classification among multiple experiments. Comparison of four RN resistance classification methods was performed: (1) ≤10% as compared to the susceptible check, (2) using normalized reproduction index (RI) values, and transformed data (3) log10 (x) and (4) log10 (x+1), in an optimal univariate k-means clustering analysis. The method of transformed data log10 (x) was selected as the most accurate for classification of RN resistance. Among 418 PIs with reported SCN resistance, the log10 (x) method grouped 59 PIs (15%) as resistant, and 130 PIs (31%) as moderately resistant to RN. Genotyping of a subset of the most resistant PIs to both nematode species revealed their strong correlation with rhg1-a allele. This research identified genotypes with resistance to two nematode species and potential new sources of RN resistance that could be valuable to breeders in developing resistant cultivars.

Genetic diversity of loquat germplasm (Eriobotrya japonica (Thunb) Lindl) assessed by SSR markers

Genome ◽  
2005 ◽  
Vol 48 (1) ◽  
pp. 108-114 ◽  
Author(s):  
José Miguel Soriano ◽  
Carlos Romero ◽  
Santiago Vilanova ◽  
Gerardo Llácer ◽  
María Luisa Badenes
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Malus Domestica ◽  
Genetic Relationships ◽  
Germplasm Collection ◽  
Mean Value ◽  
Eriobotrya Japonica ◽  
Fixation Index ◽  
Group Method ◽  
Malus Domestica Borkh

Genetic relationships among 40 loquat (Eriobotrya japonica (Thunb) Lindl) accessions that originated from different countries and that are part of the germplasm collection of the Instituto Valenciano de Investigaciones Agrarias (IVIA) (Valencia, Spain) were evaluated using microsatellites. Thirty primer pairs flanking microsatellites previously identified in Malus × domestica (Borkh.) were assayed. Thirteen of them amplified polymorphic products and unambiguously distinguished 34 genotypes from the 40 accessions analyzed. Six accessions showing identical marker patterns were Spanish local varieties thought to have been derived from 'Algerie' by a mutational process very common in loquat species. A total of 39 alleles were detected in the population studied, with a mean value of 2.4 alleles per locus. The expected and observed heterozygosities were 0.46 and 51% on average, respectively, leading to a negative value of the Wright's fixation index (–0.20). The values of these parameters indicate a smaller degree of genetic diversity in the set of loquat accessions analyzed than in other members of the Rosaceae family. Unweighted pair-group method (UPGMA) cluster analysis, based on Nei's genetic distance, generally grouped genotypes according to their geographic origins and pedigrees. The high number of alleles and the high expected heterozygosity detected with SSR markers developed in Malus × domestica (Borkh.) make them a suitable tool for loquat cultivar identification, confirming microsatellite marker transportability among genera in the Rosaceae family.Key words: Eriobotrya japonica, SSR markers, microsatellites, genetic diversity.

scholarly journals Application of wheat SSR markers for detection of genetic diversity in triticale (x Triticosecale witt. )

Genetika ◽  
2015 ◽  
Vol 47 (3) ◽  
pp. 983-992
Author(s):  
Zelmíra Balázová ◽  
Andrej Trebichalský ◽  
Zdenka Gálová ◽  
Radomíra Hornyák-Gregáňová
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Ssr Marker ◽  
Diversity Index ◽  
Polymorphic Information Content ◽  
Genetic Relationships ◽  
Average Frequency ◽  
Polymorphic Markers ◽  
Average Value ◽  
Ssrs Markers

Present study aims to testify usefulness of particular wheat SSR markers for the detection of genetic diversity degree in the set of 59 triticale cultivars and new lines coming from different European countries and USA. For this purpose, a set of fifteen SSR markers were used. One SSR marker (Xwmc429) gave a uniform spectrum. The set of fourteen polymorphic markers provided 94 alleles with an average frequency of 6.71 alleles per locus. The number of alleles ranged between 2 (Xbarc 195) and 10 (Xbarc 137). Resulting from the number and frequency of alleles, diversity index (DI), polymorphic information content (PIC) and probabilities of identity (PI) were calculated. An average value of PIC for 14 markers was 0.640, the highest value was calculated for wheat SSR marker Xgwm 46 (0.809). Based on UPGMA algorithm, a dendrogram was constructed. It was able to separate 57 of 59 cultivars (96,6 %) from each other. American new-line NE-422T significantly separated from all cultivars and new lines. Only two french cultivars Bienvenu and Wilfried had not been separated from each other. A tested set of SSR markers allowed to better understand genetic relationships among European cultivars and American new lines. In general, a dendrogram along with results of calculated genetic indicators such as PIC, PI and DI point out at SSRs markers as high informative and usefull tool in genetic diversity research between close-related species.

scholarly journals Characterization of Ugandan Sweetpotato Germplasm Using Fluorescent Labeled Simple Sequence Repeat Markers

HortScience ◽  
2010 ◽  
Vol 45 (2) ◽  
pp. 225-230 ◽  
Author(s):  
Benard Yada ◽  
Phinehas Tukamuhabwa ◽  
Bramwell Wanjala ◽  
Dong-Jin Kim ◽  
Robert A. Skilton ◽  
...  
Keyword(s):  
Cluster Analysis ◽  
Genetic Distance ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Ipomoea Batatas ◽  
Polymorphic Information Content ◽  
Genetic Relationships ◽  
Germplasm Collection ◽  
Sequence Repeat ◽  
Simple Sequence

The genetic relationships among 192 superior, high–yielding, and disease-resistant sweetpotato [Ipomoea batatas (L.) Lam] accessions from the Ugandan germplasm collection were analyzed using 10 fluorescent labeled simple sequence repeat (SSR) markers. Relatedness among the genotypes was estimated using the Nei and Li genetic distance coefficient, cluster analysis and principle component analysis methods of NTSYS-pc software. The polymorphic information content of the SSR markers used in this study ranged from 0.23 to 0.76 for loci IB-S07 and IB-R12, respectively, with a mean value of 0.62. The number of polymorphic alleles detected per locus ranged from two to six with a mean of four, a confirmation of the effectiveness of microsatellite detection on an automated ABI 3730 sequencer. The mean pairwise genetic distance among the 192 genotypes was 0.57, an indication of moderately high genetic diversity. Cluster analysis divided the accessions into four major groups with no relationship to the district of origin. Two sets of duplicates were identified through SSR genotyping in this study. Up to 190 distinct accessions for use as potential parental genotypes in hybridization schemes for cultivar development in the region were identified.

Screening of Early Maturing Soybean Accessions for Resistance against HG Type 2.5.7 of Soybean Cyst Nematode, Heterodera glycines

2021 ◽  
Author(s):  
Krishna Acharya ◽  
Guiping Yan
Keyword(s):  
Soybean Cyst Nematode ◽  
Heterodera Glycines ◽  
Nematode Resistance ◽  
The United States ◽  
Cyst Nematode ◽  
Primary Methods ◽  
Resistance Response ◽  
Early Maturity ◽  
Resistant Cultivars ◽  
Moderately Resistant

Soybean cyst nematode (SCN; Heterodera glycines) is one of the devastating soybean pests worldwide, including the United States. Resistant cultivars combined with crop rotation are the primary methods for managing this nematode. SCN is known to have genetically diverse populations and can develop new virulent forms over time due to the continuous planting of cultivars derived from same source of resistance. Thus, identifying novel SCN resistant sources is of paramount importance for soybean breeding for nematode resistance. In this study, we screened 149 early maturity soybean [Glycine max (L.)] accessions for resistance to SCN HG type 2.5.7, which is one of the prevalent virulent SCN populations in North Dakota. SCN white females were extracted from individual plants of each accession after 35 days of growth in greenhouse conditions. The females were counted to determine a female index [FI = (average number of females on a tested accession/average number of females in Barnes, a susceptible soybean check) x 100]. The resistance response of each soybean accession was categorized as resistant, moderately resistant, moderately susceptible, and susceptible. Out of the soybean 149 accessions tested, only 13 were resistant in both runs of the experiments. The majority of screened soybean accessions were susceptible or moderately susceptible to the SCN HG type 2.5.7. The resistant soybean accessions identified in this study have the potential to be used in breeding SCN-resistant cultivars after further elucidation of the resistance genes or loci.

scholarly journals Genetic relationships of soybean cyst nematode resistance originated in Gedenshirazu and PI84751 on Rhg1 and Rhg4 loci

2012 ◽  
Vol 61 (5) ◽  
pp. 602-607 ◽  
Author(s):  
Chika Suzuki ◽  
Yoshinori Tanaka ◽  
Toru Takeuchi ◽  
Setsuzo Yumoto ◽  
Shigehisa Shirai
Keyword(s):  
Soybean Cyst Nematode ◽  
Genetic Relationships ◽  
Nematode Resistance ◽  
Cyst Nematode ◽  
Soybean Cyst Nematode Resistance

scholarly journals Copy Number Quantification for the Soybean Cyst Nematode Resistance Locus rhg1 in the Soybean Varieties of Taiwan

Agronomy ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1346
Author(s):  
Cheng-Chun Huang ◽  
Jiue-in Yang ◽  
Kuo-Lung Chou ◽  
Chen-Hsiang Lin ◽  
Hao-Xun Chang
Keyword(s):  
Copy Number ◽  
Soybean Cyst Nematode ◽  
Crop Protection ◽  
Nematode Resistance ◽  
The United States ◽  
Cyst Nematode ◽  
Agricultural Product ◽  
Resistance Locus ◽  
Nucleotide Polymorphisms ◽  
Market Needs

Disease resistance is one of the most successful strategies in crop protection. For example, the implementation of PI 88788 type resistance, which contains high copy numbers of Resistance to Heterodera glycines 1 (rhg1) loci, into the commercial soybean varieties of the United States has significantly reduced the yield losses caused by soybean cyst nematode (SCN, H. glycines). Vegetable soybean, or edamame, has become a major exporting agricultural product in Taiwan with an annual revenue over $80 million USD since 2017. Several local varieties have been developed to fulfill the market needs such as the traits of flavor and sweetness. However, it remains unclear if the historical breeding programs ever incorporated rhg1 resistance into the varieties of Taiwan. This study applied the TaqMan qPCR method to measure the fluorescent signals specific to the rhg1 locus on the chromosome 18 of soybean, and the ratio of VIC and FAM signals were analyzed to predict the rhg1 copy number in the 21 soybean varieties of Taiwan. The results indicated the copy number and the single nucleotide polymorphisms of the 21 soybean varieties were identical to the susceptible soybean variety ‘Williams 82’. As importation of soybean will be continuously needed to fulfill the market and because SCN is absent in the soybean fields of Taiwan, lacking rhg1 resistance in the local soybean varieties may put the edamame industry at risk and early implementation of SCN resistance in the breeding program, alongside the application of quarantine regulations, will be the key to maintain the SCN-free status and to sustain the edamame industry in Taiwan.

scholarly journals Genetic Diversity of Torch Ginger (Etlingera elatior) Germplasm Revealed by ISSR and SSR Markers

2019 ◽  
Vol 2019 ◽  
pp. 1-14 ◽  
Author(s):  
Nor Asiah Ismail ◽  
M. Y. Rafii ◽  
T. M. M. Mahmud ◽  
M. M. Hanafi ◽  
Gous Miah
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Ssr Markers ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Allelic Diversity ◽  
Germplasm Collection ◽  
Peninsular Malaysia ◽  
Molecular Characteristics ◽  
Etlingera Elatior

Fifty-seven accessions of torch ginger (Etlingera elatior) collected from seven states in Peninsular Malaysia were evaluated for their molecular characteristics using ISSR and SSR markers to assess the pattern of genetic diversity and association among the characteristics. Diversity study through molecular characterization showed that high variability existed among the 57 torch ginger accessions. ISSR and SSR molecular markers revealed the presence of high genetic variability among the torch ginger accessions. The combination of different molecular markers offered reliable and convincing information about the genetic diversity of torch ginger germplasm. This study found that SSR marker was more informative compared to ISSR marker in determination of gene diversity, polymorphic information content (PIC), and heterozygosity in this population. SSR also revealed high ability in evaluating diversity levels, genetic structure, and relationships of torch ginger due to their codominance and rich allelic diversity. High level of genetic diversity discovered by SSR markers showed the effectiveness of this marker to detect the polymorphism in this germplasm collection.

scholarly journals Analysis of Genetic Diversity and Population Structure of Pigeonpea [Cajanus cajan (L.) Millsp] Accessions Using SSR Markers

Plants ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1643
Author(s):  
Didas Kimaro ◽  
Rob Melis ◽  
Julia Sibiya ◽  
Hussein Shimelis ◽  
Admire Shayanowako
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Genetic Improvement ◽  
Polymorphic Information Content ◽  
Geographic Origin ◽  
Germplasm Collection ◽  
Fixation Index ◽  
Population Structure Analysis ◽  
The Mean

Understanding the genetic diversity present amongst crop genotypes is an efficient utilization of germplasm for genetic improvement. The present study was aimed at evaluating genetic diversity and population structure of 48 pigeonpea genotypes from four populations collected from diverse sources. The 48 pigeonpea entries were genotyped using 33 simple sequence repeat (SSR) markers that are polymorphic to assess molecular genetic diversity and genetic relatedness. The informative marker combinations revealed a total of 155 alleles at 33 loci, with an average of 4.78 alleles detected per marker with the mean polymorphic information content (PIC) value of 0.46. Population structure analysis using model based revealed that the germplasm was grouped into two subpopulations. The analysis of molecular variance (AMOVA) revealed that 53.3% of genetic variation existed within individuals. Relatively low population differentiation was recorded amongst the test populations indicated by the mean fixation index (Fst) value of 0.032. The Tanzanian pigeonpea germplasm collection was grouped into three major clusters. The clustering pattern revealed a lack of relationship between geographic origin and genetic diversity. This study provides a foundation for the selection of parental material for genetic improvement.

Identification of novel haplotype of a cyst nematode resistance gene, GmSNAP18 in soybean [Glycine max (L.) Merr.]

2020 ◽  
Vol 80 (03) ◽  
Author(s):  
Ik-Young Choi ◽  
Prakash Basnet ◽  
Hana Yoo ◽  
Neha Samir Roy ◽  
Rahul Vasudeo Ramekar ◽  
...  
Keyword(s):  
Soybean Cyst Nematode ◽  
Gene Families ◽  
Nematode Resistance ◽  
Cyst Nematode ◽  
Soybean Breeding ◽  
Resistant Varieties ◽  
Soybean Genotypes ◽  
Glycine Max L ◽  
Scn Resistance

Soybean cyst nematode (SCN) is one of the most damaging pest of soybean. Discovery and characterization of the genes involved in SCN resistance are important in soybean breeding. Soluble NSF attachment protein (SNAP) genes are related to SCN resistance in soybean. SNAP genes include five gene families, and 2 haplotypes of exons 6 and 9 of SNAP18 are considered resistant to the SCN. In present study the haplotypes of GmSNAP18 were surveyed and chacterized in a total of 60 diverse soybean genotypes including Korean cultivars, landraces, and wild-types. The target region of exons 6 and 9 in GmSNAP18 region was amplified and sequenced to examine nucleotide variation. Characterization of 5 haplotypes identified in present study for the GmSNAP18 gene revealed two haplotypes as resistant, 1 as susceptible and two as novel. A total of twelve genotypes showed resistant haplotypes, and 45 cultivars were found susceptible. Interestingly, the two novel haplotypes were present in 3 soybean lines. The information provided here about the haplotypic variation of GmSNAP18 gene can be further explored for soybean breeding to develop resistant varieties.

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