Identification and validation of a core set of informative genic SSR and SNP markers for assaying functional diversity in barley

Varshney, Rajeev K.; Thiel, Thomas; Sretenović-Rajičić, T.; Baum, Michaël; Valkoun, J.; Guo, Pan; Grando, S.; Ceccarelli, Salvatore; Graner, Andreas

doi:10.1007/s11032-007-9151-5

Cited by 69 publications

(48 citation statements)

References 44 publications

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“…Among them, SSR marker BMAC0113 linked to QTLs for days to heading in barley (Pillen et al, 2003(Pillen et al, , 2004 was validated again through GLM analysis as it showed association with TEE. Moreover, EST-SSR marker GBM1464 that showed association with plant height in the present study was previously reported that had a functional association (Varshney et al, 2008). "Character-specific molecular markers" are positively considered by UPOV's BMT to be used in DUS testing, provided that they can reliably estimate traditional characteristics (UPOV, 2013).…”

Section: Discussionsupporting

confidence: 56%

Association mapping for morphological traits relevant to registration of barley varieties

Jamali

Mohammadi

Sadeghzadeh

2018

Span. j. agric. res.

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Elucidating marker-trait associations would have fruitful implications in distinctness, uniformity, and stability (DUS) tests of new varieties required for both variety registration and granting plant breeders' rights. As the number of new varieties with narrow genetic bases increases, the necessity for deployment of molecular markers to complement morphological DUS traits gets particular attention. We used simple sequence repeats (SSRs) and sequence related amplification polymorphisms (SRAPs) markers in association mapping of morphological traits in a collection of 143 barley landraces and advanced breeding lines. This panel represented a diverse and uniform sample in terms of both quantitative and categorical traits whilst it was structurally partitioned by number of ear rows (six-and two-rowed) and seasonal growth habit (winter and spring types) characteristics. SSRs were more powerful compared with SRAPs in separating six-and two-rowed genotypes based on both model-based Bayesian and neighbor joining clustering methods. A number of associated SSR and SRAP markers were found for 15 out of 36 DUS traits after considering Bonferroni correction through linear models (GLM and MLM) and chi-square-based tests (SA and AAT). This is also the first report of association of awn roughness and grain color with molecular markers in barley. Moreover, SSR marker BMAC0113 appeared associated with time of ear emergence (TEE), confirming previous findings. These markers could be beneficial to complement and speed up DUS testing of new varieties, as well as for improving management of barley reference collections.Additional keywords: LD mapping; Hordeum vulgare L.; DUS traits; SSRs & SRAPs markers. Abbreviations used: AAT (allelic association test); AFLP (amplified fragment length polymorphism); AR (awn roughness); DUS (distinctness, uniformity, stability); ED (ear density); GLM (general linear model); GSLN (spiculation of inner lateral nerves of lemma); KCAL (color of grain aleurone layer); MLM (mixed linear model); NER (number of ear rows); SA (stratified analysis); SGH (seasonal growth habit); SRAP (sequence-related amplified polymorphism); SSR (simple sequence repeats); TEE (time of ear emergence).

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Section: Discussionsupporting

confidence: 56%

Association mapping for morphological traits relevant to registration of barley varieties

Jamali

Mohammadi

Sadeghzadeh

2018

Span. j. agric. res.

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“…PIC was averaged over the fragments for each primer combination. The marker index was calculated as given in Varshney et al [25]:…”

Section: Discussionmentioning

confidence: 99%

Genetic Diversity Analysis of Jatropha Species from Costa Rica Using AFLP Markers

CeNAT-CONARE¹,

José²,

Rica³

2015

AJPS

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The genetic diversity from species of the genus Jatropha collected from Costa Rica was analyzed by AFLP (amplified fragments length polymorphism). The study consisted of 114 accessions from 15 populations of 4 different species: J. curcas, J. costaricensis, J. gossypifolia and J. stevensii. These were collected from different locations in Costa Rica. Three different primers were used, resulting in 428 loci, and they were classified in three categories: unique and double bands (UBD), rare bands (RB) and shared bands (SB). The UBD were excluded for a total of 339 polymorphic loci used for the UPGMA dendrogram and principal component analysis (PCA). The species that obtained the highest average of polymorphic loci was J. curcas, which obtained the highest percentage of polymorphic loci (80.24%), followed by J. gossypifolia (79.35%), J. costaricensis (78.76%), and finally J. stevensii (40.71%). The average for the polymorphic loci was of 69.76%. Thus, the phylogeny of the Jatropha species in Costa Rica was elucidated, showing J. curcas more related to J. stevensii and this one with J. costaricensis, and J. gossypifolia as the most distant member of the genus. For the best of our knowledge this is the first report of a genetic analysis of J. costaricensis and J. stevensii. The obtained molecular evidence showed high levels of polymorphisms in the present study compared with reports from Africa, India, and China. The molecular diversity estimated in our analysis, together with agronomical or morphological data, can be very useful for plant breeding programs, given the importance of Jatropha species in oil production. Interestingly, Central American Jatropha material can be used to increase the genetic base of J. curcas populations localized in Asia and Africa, where reduced genetic diversity has been reported.

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“…PIC, which according to Varshney et al (2007) take into account the total number of fragments detected for each locus of a given primer and the frequency of these alleles in the set of genotypes investigated, in this study ranged from 0.70 (UBC 835) to 0.1468 (UBC 827), with mean of 0.4294.…”

Section: Molecular Characterizationmentioning

confidence: 94%

Morphological descriptors and ISSR molecular markers in the evaluation of genetic variability of Tectona grandis genotypes

et al. 2017

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ABSTRACT. This study aimed to evaluate the genetic variability of the teak germplasm bank, using morphological traits and inter-simple sequence repeat molecular markers. Thirty clones were evaluated in a randomized complete block design with three replicates, and each plot was composed of three plants. A joint analysis of quantitative and qualitative variables was performed using the Gower algorithm. Quantitative, qualitative, and molecular variables were analyzed simultaneously using the Ward-MLM procedure. There is genetic variability among the 30 teak genotypes studied, considering the quantitative, qualitative, and molecular variables by the Ward-MLM statistical procedure. Morphological traits used proved to be efficient for the study of genetic variability; however, it was not possible to compose a descriptor table for clonal teak genotypes based on the traits evaluated. The Gower method was efficient in discriminating the groups, demonstrating that the simultaneous analysis of qualitative and quantitative data is feasible and can allow greater efficiency in the knowledge of the variability among teak genotypes. The genotype 22 showed to be the most divergent compared to the other genotypes, except for the cluster of genotypes by the UPGMA method based on the Gower distance obtained by the Ward-MLM procedure, which formed a group with genotypes 9 and 30, in the morphological and molecular analyses and was grouped alone.

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Identification and validation of a core set of informative genic SSR and SNP markers for assaying functional diversity in barley

Cited by 69 publications

References 44 publications

Association mapping for morphological traits relevant to registration of barley varieties

Association mapping for morphological traits relevant to registration of barley varieties

Genetic Diversity Analysis of Jatropha Species from Costa Rica Using AFLP Markers

Morphological descriptors and ISSR molecular markers in the evaluation of genetic variability of Tectona grandis genotypes

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