Genome-wide mining, characterization, and development of microsatellite markers in Tartary buckwheat (Fagopyrum tataricum Garetn.)

Fang, Xiaomei; Huang, Kehui; Nie, J.; Zhang, Yuanli; Zhang, Yuke; Li, Yingshuang; Wang, Wenwen; Xu, Xin; Ruan, Renwu; Yuan, Xiaohui; Zhang, Zhengsheng; Yi, Zelin

doi:10.1007/s10681-019-2502-6

Cited by 9 publications

(6 citation statements)

References 44 publications

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“…In addition, the analysed collections for both species were originally from different regions of the world, whereas the collections used in the above studies were from restricted regions, which may explain the higher level of genetic diversity in our study. In agreement with our agro-morphological data and with previous studies using molecular markers such as RAPD [ 50 , 67 ] and SSR [ 23 , 47 ], our SSR data also showed clear genetic differentiation between common and Tartary buckwheat, confirming cross incompatibility between the two species. However, within species, the level of genetic diversity was not significantly different between regions and accessions were not geographically structured, indicating weak genetic differentiation between regions.…”

Section: Discussionsupporting

confidence: 92%

“…A set of 24 genus-specific SSR markers was used to investigate the genetic diversity of the studied accessions. The markers were selected based on their transferability, high polymorphism, and representative distribution among genomes and are, therefore, originating from different denomination groups: Fem [ 63 ] (five markers); SXAU [ 38 ] (five markers); Ft [ 67 ] (eight markers); GB-FE [ 65 ] (four markers); and TBP [ 68 ] (two markers) ( Table S3 ). Depending on each primer pair, PCR reactions were performed under touch-down conditions as described in Pipan and Meglič [ 78 ].…”

Section: Methodsmentioning

confidence: 99%

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Agro-Morphological and Molecular Characterization Reveal Deep Insights in Promising Genetic Diversity and Marker-Trait Associations in Fagopyrum esculentum and Fagopyrum tataricum

Pipan,

Sinkovič,

Neji

et al. 2023

Plants

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Characterisation of genetic diversity is critical to adequately exploit the potential of germplasm collections and identify important traits for breeding programs and sustainable crop improvement. Here, we characterised the phenotypic and genetic diversity of a global collection of the two cultivated buckwheat species Fagopyrum esculentum and Fagopyrum tataricum (190 and 51 accessions, respectively) using 37 agro-morphological traits and 24 SSR markers. A wide range of variation was observed in both species for most of the traits analysed. The two species differed significantly in most traits, with traits related to seeds and flowering contributing most to differentiation. The accessions of each species were divided into three major phenoclusters with no clear geographic clustering. At the molecular level, the polymorphic SSR markers were highly informative, with an average polymorphic information content (PIC) of over 0.65 in both species. Genetic diversity, as determined by Nei’s expected heterozygosity (He), was high (He = 0.77 and He = 0.66, respectively) and differed significantly between species (p = 0.03) but was homogeneously distributed between regions, confirming the lack of genetic structure as determined by clustering approaches. The weak genetic structure revealed by the phenotypic and SSR data and the low fixation indices in both species suggested frequent seed exchange and extensive cultivation and selection. In addition, 93 and 140 significant (p < 0.05) marker-trait associations (MTAs) were identified in both species using a general linear model and a mixed linear model, most of which explained >20% of the phenotypic variation in associated traits. Core collections of 23 and 13 phenotypically and genetically diverse accessions, respectively, were developed for F. esculentum and F. tataricum. Overall, the data analysed provided deep insights into the agro-morphological and genetic diversity and genetic relationships among F. esculentum and F. tataricum accessions and pointed to future directions for genomics-based breeding programs and germplasm management.

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Section: Discussionsupporting

confidence: 92%

Section: Methodsmentioning

confidence: 99%

Agro-Morphological and Molecular Characterization Reveal Deep Insights in Promising Genetic Diversity and Marker-Trait Associations in Fagopyrum esculentum and Fagopyrum tataricum

Pipan,

Sinkovič,

Neji

et al. 2023

Plants

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“…We also found that single-nucleotide and dinucleotide repeats were the main repeat types with the most significant number of mononucleotides repeat units (56.52%), followed by dinucleotide distribution units (27.31%). The highest proportion of mononucleotide repeat units was also identified in G. uralensis (60.73%) [34], S. splendens Ker-Gawler (41.6%) [35], Punica granatum L. (51.95%) [36], and Eucommia ulmoides (54.34%) [37], whereas dinucleotide repeat units were the dominant motifs in Fagopyrum tataricum (L.) Gaertn (69.72%) [38], Rhododendron simsii Planch (94.58%) [39], and Gastrodia elata Bl (78.88%) [40]. In this study, there were 228 types of abundant SSR repeats in P. sibiricum.…”

Section: Discussionmentioning

confidence: 99%

SSR Loci Analysis in Transcriptome and Molecular Marker Development in Polygonatum sibiricum

Yang

Jiang

Wang³

et al. 2022

BioMed Research International

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To study the SSR loci information and develop molecular markers, a total of 435,858 unigenes in transcriptome of Polygonatum sibiricum were used to explore SSR. The distribution frequency of SSR and the basic characteristics of repeat motifs were analyzed using MISA software, and SSR primers were designed by Primer 3.0 software and then validated by PCR. Moreover, the gene function analysis of SSR Unigene was obtained by Blast. The results showed that 112,728 SSR loci were found in the transcriptome of Polygonatum sibiricum, which distributed in 435,858 unigenes with a distribution frequency of 25.86%. Mo-nucleotide and Di-nucleotide repeat were the main types, accounted for 83.83% of all SSRs. The repeat motifs of A/T and AC/GT were the predominant repeat types of Mo-nucleotide and Di-nucleotide, respectively. A total of 113,305 pairs of SSR primers with the potential to produce polymorphism were designed for maker development. One hundred and fifty-four of the 500 randomly selected primers not only produced fragments with expected molecular size but also had high polymorphism, which could accurately separate the tested varieties. The gene function of unigenes containing SSR was mostly related to the molecular function of Polygonatum sibiricum. The SSR markers in transcriptome of Polygonatum sibiricum show rich type, strong specificity, and high potential of polymorphism, which will benefit the candidate gene mining and marker-assisted breeding. The developed markers can also provide technical methods for molecular identification of intraspecific species of Polygonatum Mill. and maker-assisted breeding of superior varieties of Polygonatum Mill.

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“…Some seeds have unique traits with thorns and wings. Few studies on the genetic diversity of Tartary buckwheat, combining morphological diversity of seed characteristics with molecular marker techniques, have been conducted [23].…”

Section: Introductionmentioning

confidence: 99%

Diversity of Tartary Buckwheat (Fagopyrum tataricum) Landraces from Liangshan, Southwest China: Evidence from Morphology and SSR Markers

et al. 2022

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Tartary buckwheat (Fagopyrum tataricum) has been cultivated for over one thousand years in the Liangshan Prefecture of Sichuan, China. Growing population pressures, economic modernization pressures, and the erosion of traditional culture have led to the rapid loss of area covered by Tartary buckwheat landraces. Morphological and molecular characterization of 112 Tartary buckwheat accessions from 29 populations were assessed based on 10 morphological traits of seeds and 10 SSR markers, respectively. The coefficient of variation and Shannon index showed diversity within the morphological characteristics of the seeds. All accessions were divided into three categories according to phylogenetic dendrogram analysis, which was consistent with folk nomenclature and taxonomy. Genetic analysis using SSR markers identified 45 alleles with a mean value of 4.5 alleles per locus. The high average PIC value (0.459) indicated polymorphism of the SSR markers. The genetic similarity coefficient of the 112 Tartary buckwheat accessions showed a high level of genetic diversity ranging from 0.130 to 0.978. The genetic structure analysis revealed high genetic differentiation (Nei = 0.255). The folk nomenclature, folk taxonomy, and sociocultural norms may also contribute to a significant influence on the diversity of folk nomenclature and taxonomy. The assessment of the genetic diversity of Tartary buckwheat landraces and detection of SSR loci associated with traits could be used as scientific guidance for selecting Tartary buckwheat seed for improved production relative to local farmers and consumer preferences. Local traditional knowledge (seed exchange network) and culture also contribute to breeding and the maintenance of the genetic diversity of Tartary buckwheat.

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Genome-wide mining, characterization, and development of microsatellite markers in Tartary buckwheat (Fagopyrum tataricum Garetn.)

Cited by 9 publications

References 44 publications

Agro-Morphological and Molecular Characterization Reveal Deep Insights in Promising Genetic Diversity and Marker-Trait Associations in Fagopyrum esculentum and Fagopyrum tataricum

Agro-Morphological and Molecular Characterization Reveal Deep Insights in Promising Genetic Diversity and Marker-Trait Associations in Fagopyrum esculentum and Fagopyrum tataricum

SSR Loci Analysis in Transcriptome and Molecular Marker Development in Polygonatum sibiricum

Diversity of Tartary Buckwheat (Fagopyrum tataricum) Landraces from Liangshan, Southwest China: Evidence from Morphology and SSR Markers

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