Genetic assessment of safflower (<i><scp>C</scp>arthamus tinctorius </i><scp>L</scp>.) collection with microsatellite markers acquired via pyrosequencing method

Lee, Gi-An; Sung, Joseph J.Y.; Lee, Sok-Young; Chung, Jong‐Wook; Yi, Jung-Yoon; Kim, Yeon-Gyu; Lee, Myung Chul

doi:10.1111/1755-0998.12146

Cited by 40 publications

(55 citation statements)

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“…) and safflower (Lee et al . ). High‐throughput molecular genotyping is now also starting to be used in major crops: a recent study used genotyping‐by‐sequencing to characterize lines in the USA national maize inbred seed bank (Romay et al .…”

Section: Discussionmentioning

confidence: 97%

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High‐throughput genotyping for species identification and diversity assessment in germplasm collections

Mason

Zhang

Tollenaere

et al. 2015

Molecular Ecology Resources

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Germplasm collections provide an extremely valuable resource for breeders and researchers. However, misclassification of accessions by species often hinders the effective use of these collections. We propose that use of high-throughput genotyping tools can provide a fast, efficient and cost-effective way of confirming species in germplasm collections, as well as providing valuable genetic diversity data. We genotyped 180 Brassicaceae samples sourced from the Australian Grains Genebank across the recently released Illumina Infinium Brassica 60K SNP array. Of these, 76 were provided on the basis of suspected misclassification and another 104 were sourced independently from the germplasm collection. Presence of the A- and C-genomes combined with principle components analysis clearly separated Brassica rapa, B. oleracea, B. napus, B. carinata and B. juncea samples into distinct species groups. Several lines were further validated using chromosome counts. Overall, 18% of samples (32/180) were misclassified on the basis of species. Within these 180 samples, 23/76 (30%) supplied on the basis of suspected misclassification were misclassified, and 9/105 (9%) of the samples randomly sourced from the Australian Grains Genebank were misclassified. Surprisingly, several individuals were also found to be the product of interspecific hybridization events. The SNP (single nucleotide polymorphism) array proved effective at confirming species, and provided useful information related to genetic diversity. As similar genomic resources become available for different crops, high-throughput molecular genotyping will offer an efficient and cost-effective method to screen germplasm collections worldwide, facilitating more effective use of these valuable resources by breeders and researchers.

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Section: Discussionmentioning

confidence: 97%

“…; Lee et al . ). However, generation of inexpensive high‐throughput molecular marker data is now becoming routine for many genera.…”

Section: Introductionmentioning

confidence: 97%

High‐throughput genotyping for species identification and diversity assessment in germplasm collections

Mason

Zhang

Tollenaere

et al. 2015

Molecular Ecology Resources

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“…The reproducibility of PCR product size was evaluated by performing three replications using two different samples for each SSR primer. The M13F-tail PCR method of Schuelke (2000) was used to measure the size of PCR products, as described previously (Lee et al, 2014). The PCR master mix was prepared as follows: Each 20 μl reaction mixture contained 20 ng template gDNA, 1X PCR buffer, 2 uM specific primer, 200 uM dNTPs, 4 uM M13 universal primer, 6 uM normal reverse primer, and 0.5 U Taq-polymerase (SolGent, Korea).…”

Section: Genotyping With Microsatellite Markersmentioning

confidence: 99%

Genetic Diversity and Population Structure of Korean Soybean Collection Using 75 Microsatellite Markers

Lee¹,

Choi²,

Yi³

et al. 2014

Korean J. Crop Sci.

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Soybean (Glycine max L.) is crucial legume crop as source of high quality vegetable protein and oil, and Korea is regarded as a part of center of soybean origin. To expand the information of conserved genetic diversity, we analyzed the genetic variability of soybean collection mainly introduced Korean accessions using 75 microsatellite markers. A total of 1,503 alleles with an average value of 20.0 alleles were detected among 644 accessions. Korean collection revealed average allele number of 13.4 while Chinese, Japanese and Southeast Asian accessions showed 9.0, 5.4 and 6.5 mean alleles, respectively. Especially, Korean accessions showed more number of private allele per locus as 3.4 contrary to other geographical groups. The mean expected heterozygosity and polymorphic information content was 0.654 and 0.616, respectively, and expected heterozygosity values were not significantly distinguished according to the geographical groups. The phylogenetic dendrogram and deduced population structure based on DNA profiles of 75 SSR loci showed Korean accessions formed distinct gene pool against Chinese accessions, and could be divided into five subpopulations. Korean soybean accessions have specific genetic diversity and might be serve the valuable alleles for bio-industry as a part of the center of soybean origin.

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“…Application of morphological descriptors and geographical origin to assess the variability of around 2000 lines of safflower revealed a wide range of phenotypic variation for several traits, based on which safflower accessions were classified into 10 "regional gene pools" (Ashri 1975). Several recent studies used molecular markers, viz., random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR), amplified fragment length polymorphism (AFLP), sequence-related amplified polymorphism (SRAP), and simple sequence repeat (SSR), for variation analysis either exclusively or in conjunction with morphological data for the crop (Sehgal and Raina 2005;Johnson et al 2007;Yang et al 2007;Amini et al 2008;Peng et al 2008;Chapman et al 2009Chapman et al , 2010Khan et al 2009;Mahasi et al 2009;Hamdan et al 2011; Barati and Arzani 2012;Mokhtari et al 2013;Lee et al 2014). However, low sample size from selected regional gene pools and lack of a global representation of available germplasm were limitations in most of these studies, which may therefore not provide an accurate representation of the available genetic diversity and population structure in safflower.…”

Section: Introductionmentioning

confidence: 99%

“…Chapman et al (2010) used 24 EST-SSR markers to survey a representative germplasm collection of 76 accessions belonging to ten centers proposed by Ashri (1975) and redesignated them to five distinct clusters. Recently, Lee et al (2014) proposed three clusters along with few admixture groupings by analyzing 100 safflower accessions from Far East (mainly Korea), India-Pakistan, and Middle East regional gene pools using 30 microsatellite markers. These admixtures indicated that gene flow occurred between gene pools as a consequence of natural selection and human intervention.…”

Section: Introductionmentioning

confidence: 99%

Assessment of Genetic Diversity and Population Structure in a Global Reference Collection of 531 Accessions of Carthamus tinctorius L. (Safflower) Using AFLP Markers

et al. 2014

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Carthamus tinctorius L. (safflower) is an important oilseed crop that is cultivated in several countries. The present study investigates the genetic diversity and population structure of 531 safflower accessions from 43 countries representing all safflower growing regions of the world. Diversity analysis was performed using ten informative EcoRI/ MseI amplified fragment length polymorphism primer pairs that were identified by screening 150 primer combinations. The selected primer pairs generated 381 fragments of which 157 were polymorphic among the analyzed accessions. The genetic diversity indices obtained for the entire collection (I= 0.4536, H=0.2955) indicated high levels of molecular variability. The distance-based, neighbor-joining method classified the accessions into six clusters with internal subgroupings that were in consonance with 19 clusters obtained using Bayesian model-based BAPS analysis. Clusters obtained through STRUCTURE analysis (at K=4) could not be correlated with their geographically diverse origins, while BAPS analysis (at K=19) revealed geographical delineation with low admixture levels among most of the studied accessions. Accessions from Far East and Egypt clustered in distinct groups, indicating conserved nature of their gene pools. The Near East and Iran-Afghanistan regions were collectively found to harbor maximum diversity in accordance with earlier reports. Accessions from the Indian subcontinent showed substantial diversity that was previously undetected. The American accessions showed low molecular variability in contrast to earlier studies. Genetic sub-structuring within gene pools and interrelationships between accessions belonging to different regional pools was also observed. To the best of our knowledge, this is the first comprehensive study of existing genetic variability in a large collection of safflower germplasm with a global distribution, which provides a more accurate representation of genetic structuring in the crop. This information will facilitate selection of elite genotypes for broadening the genetic base of various breeding programs in safflower.

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Genetic assessment of safflower (Carthamus tinctorius L.) collection with microsatellite markers acquired via pyrosequencing method

Cited by 40 publications

References 40 publications

High‐throughput genotyping for species identification and diversity assessment in germplasm collections

High‐throughput genotyping for species identification and diversity assessment in germplasm collections

Genetic Diversity and Population Structure of Korean Soybean Collection Using 75 Microsatellite Markers

Assessment of Genetic Diversity and Population Structure in a Global Reference Collection of 531 Accessions of Carthamus tinctorius L. (Safflower) Using AFLP Markers

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