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Cited by 32Genetic Mapping and Diversity in Plants and AnimalsCocoa and Sweet Potato AgronomyPlant Disease Resistance and Genetics

Development and identification of SSR markers associated with starch properties and β-carotene content in the storage root of sweet potato (Ipomoea batatas L.)

Open access
Zhang, Kai, Wu, Zhengdan, Tang, Daobin, Lv, Changwen, Luo, Kai, Zhao, Yong, Liu, Xun, Huang, Yuanxin +1 more·2016·Frontiers in Plant Science
DOI 10.3389/fpls.2016.00223PMC PMC4773602
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Abstract

Sweet potato (Ipomoea batatas L.) is a nutritious food crop and, based on the high starch content of its storage root, a potential bioethanol feedstock. Enhancing the nutritional value and starch quantity of storage roots are important goals of sweet potato breeding programs aimed at developing improved varieties for direct consumption, processing, and industrial uses. However, developing improved lines of sweet potato is challenging due to the genetic complexity of this plant and the lack of genome information. Short sequence repeat (SSR) markers are powerful molecular tools for tracking important loci in crops and for molecular-based breeding strategies; however, few SSR markers and marker-trait associations have hitherto been identified in sweet potato. In this study, we identified 1824 SSRs by using a de novo assembly of publicly available ESTs and mRNAs in sweet potato, and designed 1476 primer pairs based on SSR-containing sequences. We mapped 214 pairs of primers in a natural population comprised of 239 germplasms, and identified 1278 alleles with an average of 5.972 alleles per locus and a major allele frequency of 0.7702. Population structure analysis revealed two subpopulations in this panel of germplasms, and phenotypic characterization demonstrated that this panel is suitable for association mapping of starch-related traits. We identified 32, 16, and 17 SSR markers associated with starch content, β-carotene content, and starch composition in the storage root, respectively, using association analysis and further evaluation of a subset of sweet potato genotypes with various characteristics. The SSR markers identified here can be used to select varieties with desired traits and to investigate the genetic mechanism underlying starch and carotenoid formation in the starchy roots of sweet potato.

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Written from the paper’s full text.

TL;DR

This study developed and mapped SSR markers in sweet potato and tested them for association with storage-root starch properties and β-carotene content in a 239-genotype panel. It reports 32, 16, and 17 SSR markers associated with starch content, β-carotene content, and starch composition, respectively, after association analysis and subset validation.

Key findings

  • From de novo assembly of public ESTs/mRNAs and high-throughput reads, the authors identified 1,824 SSRs and designed 1,476 primer pairs; 214 polymorphic primer pairs were mapped in 239 germplasms, yielding 1,278 alleles with an average of 5.972 alleles per locus, major allele frequency 0.7702, mean PIC 0.2571, and mean genetic diversity 0.3122.
  • Population structure analysis indicated two subpopulations: 176 genotypes assigned to Pop 1, 17 to Pop 2, and 46 retained as admixed.
  • Association analysis found 63 SSR markers associated with dry matter/starch content, 44 with β-carotene content, and 54 with starch composition-related traits (P < 0.01); after further validation, 32, 16, and 17 markers, respectively, distinguished genotypes with different starch, β-carotene, or amylose properties.
  • Phenotypic ranges across 239 genotypes included dry matter 12.446–43.987%, starch 4.476–31.899%, amylose 7.280–35.512%, amylose/amylopectin 0.166–0.430, and maximum β-carotene 8.538 mg/100 g flesh weight (Tainong 69 in 2012).

Methods

  • A natural population of 239 sweet potato genotypes (cultivars, wild varieties, farmer varieties, landraces, and breeding clones) was grown in Beibei, Chongqing, China, in 2011–2013; dry matter, starch, amylose, amylopectin, and β-carotene were measured, with trait assessments performed in triplicate each year.
  • SSR markers were developed by assembling public EST/mRNA and sequencing reads with Trinity and CLC Genomics Workbench, mining SSRs with MISA, and designing primers with Primer Premier 7.0; 306 primer pairs were initially screened on eight accessions, and 214 polymorphic pairs were used on the 239 genotypes.
  • Marker-trait association used GLM and MLM in TASSEL 5.0 with Q and/or K matrices, 1,000 permutations, and a significance threshold of P < 0.01; selected markers were validated in six diverse genotypes and, for five markers, in a 303-accession hybrid population.

Limitations

  • The paper states that β-carotene content, amylose content, and amylose/amylopectin varied markedly across the 3 years and are easily affected by environmental factors, so accurate mapping should use multiple locations and years; most β-carotene and starch-composition markers were associated with trait values from only 1 year.
  • The paper states that the highest β-carotene content observed (about 8 mg/100 g flesh weight) was below the reported 13.83 mg/100 g fresh weight, and that the small number of high-β-carotene genotypes may affect association results; it also notes no commercial standard or mature method for sweet potato amylose measurement.
  • The paper states that validation used only a small subset of genotypes and that it remains to be established whether all identified SSR markers can identify these traits across all sweet potato cultivars; the significance threshold was also described as relatively high because sweet potato is a genetically challenging hexaploid.

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Integrity signals

Registry

Crossref · 10.3389/fpls.2016.00223

Cites

70 of 70 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 55 cited sources checked · 0 supported · 0 flagged

  • Findingown data

    Population structure analysis revealed two subpopulations in this panel of germplasms.

    “Population structure analysis revealed two subpopulations in this panel of germplasms”
    Quote in the paperNot a substantial claim
  • Findingown data

    A significant positive correlation between amylose content and A/P ratio (P < 0.01; in 2011 and 2012) was detected.

    “A significant positive correlation between amylose content and A/P ratio (two-sided test; P < 0.01; in 2011 and 2012) was detected”
    Quote in the paperNot a substantial claim
  • Findingown data

    One-way ANOVA showed no significant difference in dry matter and starch contents of storage root among the 3 years.

    “One-way ANOVA analysis showed that there was no significant difference in the dry matter and starch contents of the storage root”
    Quote in the paperNot a substantial claim
  • Findingown data

    A total of 1631 sequences containing SSRs were identified.

    “We identified 1631 sequences containing SSRs, and found that 167 of these sequences contained more than one SSR (Table 3).”
    Quote in the paperNot a substantial claim
  • Findingown data

    Starch content measured in 2013 was not significantly (P = 0.594) positively correlated with amylose content.

    “However, the starch content measured in 2013 was not significantly (P = 0.594) positively correlated with the amylose content”
    Quote in the paperNot a substantial claim
  • May combine two claims. 24
  • Classified as probably not a substantial claim. 37
  • The quote only partly states this claim. 2

  • May combine two claims.

    Findingown data

    1278 alleles were identified with an average of 5.972 alleles per locus and a major allele frequency of 0.7702.

    “and identified 1278 alleles with an average of 5.972 alleles per locus and a major allele frequency of 0.7702.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    The remaining 72 types of motifs accounted for 58.772% of all SSR motifs.

    “The remaining 72 types of motifs accounted for 58.772% of all SSR motifs (Figure 3).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Among the identified SSRs, tri- and di-nucleotide repeat motifs were the most abundant, with tri-nucleotide at 1015 (55.647%) and di-nucleotide at 604 (33.114%), followed by tetra- (154, 8.443%), penta- (27, 1.480%), and hexa-nucleotide (24, 1.316%) repeat motifs.

    “Among the identified SSRs, the tri-, and di-nucleotide repeat motifs were the most abundant (1015, 55.647; 604, 33.114%, respectively), followed by tetra- (154, 8.443%), penta- (27, 1.480%), and hexa-nucleotide (24, 1.316%) repeat motifs (Table 3).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    Of the 1631 SSR-containing sequences, 167 contained more than one SSR.

    “We identified 1631 sequences containing SSRs, and found that 167 of these sequences contained more than one SSR (Table 3).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingown data

    The AG/CT dinucleotide repeat was the most abundant motif type among the detected SSRs, at 428 (23.465% of all SSR motifs), followed by the trinucleotide repeat motif AAG/CTT at 324 (17.763%).

    “The AG/CT dinucleotide repeat was the most abundant type of motif amongst the detected SSRs (428, 23.465% of all SSR motifs), followed by the trinucleotide repeat motif AAG/CTT (324, 17.763%).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    SSR units of different type and length were not evenly distributed.

    “SSR units of different type and length were not evenly distributed.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Findingown data

    A total of 887 polymorphic amplicons generated from 214 primer pairs were subjected to marker-trait association analysis after excluding amplicons that were not of the expected length.

    “Excluding amplicons that were not of the expected length, a total of 887 polymorphic amplicons generated from 214 primer pairs were subjected to marker-trait association analysis.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    A total of 1278 clean and distinct bands were revealed with a major allele frequency of 0.7702.

    “A total of 1278 clean and distinct bands were revealed with a major allele frequency of 0.7702.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The number of polymorphic bands obtained with each primer varied from 1 to 16, with a mean of 5.972, and most SSR markers produced 2-5 bands each.

    “The number of polymorphic bands obtained with each primer varied from 1 to 16, with a mean of 5.972, and most of the SSR markers produced 2–5 bands each.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The mean polymorphism information content (PIC) was 0.2571, and the mean genetic diversity was 0.3122.

    “The mean polymorphism information content (PIC) was 0.2571, and the mean genetic diversity was 0.3122.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    A maximum SSR length of 253 bp was observed.

    “A maximum SSR length of 253 bp was observed.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The tested P-values ranged from 3.70 × 10−10 (SIP029) to 0.00997 (SIP205), and the marker R2 ranged from 0.01592 (SIP285) to 0.28505 (SIP029).

    “The tested P-values ranged from 3.70 × 10−10 (SIP029) to 0.00997 (SIP205), and the marker R2 ranged from 0.01592 (SIP285) to 0.28505 (SIP029).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The log likelihood revealed by STRUCTURE increased gradually from K = 1 to 20 and showed no obvious optimum.

    “The log likelihood revealed by STRUCTURE increased gradually from K = 1 to 20 and showed no obvious optimum (Supplementary Material 4).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The other 34 SSR markers that were significantly associated with the starch content trait also generated differential bands in the selected genotypes, but did not completely distinguish between genotypes with different range of starch content.

    “However, the other 34 SSR markers that were shown to be significantly associated with the starch content trait (Supplementary Material 7) also generated differential bands in the selected genotypes, but did not completely distinguish between genotypes with different range of starch content (Supplementary Material 8).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    Of the designed primers, 447, 808, 134, 22, 22, and 43 were for di-, tri-, tetra-, penta-, hexa-nucleotide, and compound formation repeats, respectively.

    “Of these designed primers, 447, 808, 134, 22, 22, and 43 were for di-, tri-, tetra-, penta-, hexa-nucleotide, and compound formation repeats, respectively (Supplementary Material 2).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    Most primer pairs also amplified fragments that were larger or smaller than expected, in addition to generating PCR products of the expected sizes.

    “Except for generating PCR products of the expected sizes, most primer pairs also amplified fragments that were larger or smaller than expected.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingown data

    The most abundant SSR length was 18 bp (922 SSRs), accounting for 50.548% of total SSRs, followed by 20 and 21 bp (239 and 193 SSRs, 13.103% and 10.581% of total SSRs, respectively).

    “In addition, the most abundant SSR length was 18 bp (922 SSRs), accounting for 50.548% of the total SSRs, followed by 20 and 21 bp (239 and 193 SSRs, 13.103% and 10.581% of total SSRs, respectively).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    With membership probabilities of ≥ 0.70, 176 genotypes were assigned into Pop 1 and 17 genotypes into Pop 2.

    “With membership probabilities of ≥ 0.70, 176 genotypes were assigned into Pop 1 and 17 genotypes into Pop 2.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Twenty-five of these SSR markers could be identified when analyzed using all four models, with tested P-values ranging from 1.53 × 10−25 (marker SIP215, associated with A/P) to 0.00999 (marker SIP004, associated with amylose content).

    “Twenty-five of these SSR markers could be identified when analyzed using all the four models, and the tested P-value ranged from 1.53 × 10−25 (marker SIP215, associated with A/P) to 0.00999 (marker SIP004, associated with amylose content).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The other 37 SSR markers that were significantly associated with starch composition-related traits also generated differential bands in the selected cultivars, but did not distinguish between cultivars with high and low amylose content.

    “However, the other 37 SSR markers that were shown to be significantly associated with starch composition-related traits of storage root also generated differential bands in the selected cultivars, but did not distinguish between cultivars with high and low amylose content (Supplementary Materials 11, 12).”
    Quote in the paperNot a substantial claim

  • May combine two claims. The quote only partly states this claim.

    Findingown data

    The six cultivars used for starch composition marker validation had average storage root starch contents over the 3-year period of 30.383 ± 3.713, 19.585 ± 0.231, 10.857 ± 0.109, 20.210 ± 2.434, 18.336 ± 1.773, and 11.100 ± 0.824%, respectively.

    “and high, medium, and low average storage root starch contents over the 3-year period (30.383 ± 3.713, 19.585 ± 0.231, and 10.857 ± 0.109%, respectively).”
    • Also stated in: § Marker-trait association analysis and further verification of associated SSR markers · plain
      “and high, medium, and low average storage root starch contents over the 3-year period (20.210 ± 2.434, 18.336 ± 1.773, and 11.100 ± 0.824%, respectively).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Fourteen markers were only identified using the naive model, with tested P-values ranging from 4.61 × 10−4 (marker SIP106, associated with amylose content) to 0.00989 (marker SIP110, associated with amylose content).

    “However, 14 markers were only identified using the naive model, and the tested P-value ranged from 4.61 × 10−4 (marker SIP106, associated with amylose content) to 0.00989 (marker SIP110, associated with amylose content).”
    Quote in the paperNot a substantial claim

  • The quote only partly states this claim.

    Findingown data

    The six cultivars used for starch composition marker validation had average storage root amylose contents over the 3-year period of 28.465 ± 0.798, 26.081 ± 3.688, 28.114 ± 1.776, 15.266 ± 1.656, 13.599 ± 1.206, and 12.076 ± 1.279%, respectively.

    “Lanes 2–4 (from left to right) are Mianfen No. 1, Nancy Hall, and 0929-106, which had high average storage root amylose contents over the 3-year period (28.465 ± 0.798, 26.081 ± 3.688, and 28.114 ± 1.776%, respectively)”
    • Also stated in: § Marker-trait association analysis and further verification of associated SSR markers · plain
      “Lanes 5–7 are Sanheshu, Jishu 52, and Wugonghong, respectively, with low average storage root amylose contents over the 3-year period (15.266 ± 1.656, 13.599 ± 1.206, and 12.076 ± 1.279%, respectively)”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Twelve markers were only identified when MLM (Q+K and K model) were used, with tested P-values ranging from 2.52 × 10−4 (marker SIP279, associated with A/P) to 0.00928 (marker SIP126, associated with amylose content).

    “Twelve markers were only identified when MLM (Q+K and K model) were used, which tested P-value ranged from 2.52 × 10−4 (marker SIP279, associated with A/P) to 0.00928 (marker SIP126, associated with amylose content).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The six sweet potato accessions used for β-carotene marker validation had average β-carotene contents over the 3-year period of 9.064 ± 1.133, 6.249 ± 1.502, 4.510 ± 0.442, 2.707 ± 0.263, and 0.132 ± 0.026 mg/100 g flesh weight, and Zhe 147 had β-carotene levels below the detection limit.

    “(A), Ning 4-6 (average β-carotene content over the 3-year period of 9.064 ± 1.133 mg/100 g flesh weight); (B), Fengshouhong (6.249 ± 1.502 mg/100 g flesh weight); (C), Erlangshao (4.510 ± 0.442 mg/100 g flesh weight); (D), S1-5 (2.707 ± 0.263 mg/100 g flesh weight); (E), Xichengshu 007 (0.132 ± 0.026 mg/100 g flesh weight); and (F) Zhe 147 (white-fleshed sweet potato with β-carotene levels that f”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The other 28 SSR markers also showed differential bands in the selected genotypes, but showed less distinguishing effect on genotypes with specific β-carotene properties.

    “Compared to these markers, the other 28 SSR markers also showed differential bands in the selected genotypes, but showed less distinguishing effect on genotypes with specific β-carotene properties (Supplementary Materials 9, 10).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingown data

    Sweet potato contains about 63,000 unigenes, and its genome encodes around 63,000 genes.

    “We found that sweet potato contains about 63,000 unigenes. This result was also obtained in our recent transcriptome analysis of 17 sweet potato samples (unpublished data), indicating that the sweet potato genome encodes around 63,000 genes.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Sweet potato storage root has high starch content, making it a cheap and strong candidate source for biofuel production.

    “Its high starch content renders sweet potato a cheap and strong candidate source for biofuel production (Ziska et al., 2009; Nedunchezhiyan et al., 2012).”
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    • cites Ziska et al., 2009 source

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    • cites Nedunchezhiyan et al., 2012

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    Interpretationreasoning

    Genetic markers linked to target traits need to be identified.

    “Genetic markers linked to target traits therefore need to be identified.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim. May combine two claims.

    Premisecitation

    Marker combinations associated with target traits can be identified using a natural population and further validated by testing whether expected phenotypic effects are reproducible in different populations.

    “Marker combinations associated with target traits can be identified using a natural population and further validated by testing whether the expected phenotypic effects are reproducible in populations that differ from the one in which the marker-trait association was originally identified (Li et al., 2013).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Li et al., 2013

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    Premisecitation

    Association mapping is a powerful approach for identifying genotype-phenotype correlations within a diverse collection of germplasms or breeding materials.

    “Association mapping (also known as linkage disequilibrium mapping) is a powerful approach for identifying genotype (marker)-phenotype (trait) correlations within a diverse collection of germplasms or breeding materials (Myles et al., 2009; Wang M. L. et al., 2011).”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites Myles et al., 2009 source

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    • cites Wang M. L. et al., 2011

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    Premisecitation

    High level of β-carotene in orange-fleshed sweet potato may help mitigate vitamin A deficiency-related blindness and maternal mortality in many developing countries.

    “The high level of β-carotene (a precursor of vitamin A) (Low et al., 2007; Teow et al., 2007) in orange-fleshed sweet potato (OFSP, Low et al., 2007; Burri, 2011) may help to mitigate vitamin A deficiency-related blindness and maternal mortality in many developing countries (Schafleitner et al., 2010; Vimala et al., 2011; Wang Z. et al., 2011; Agili et al., 2012; Mitra, 2012).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Schafleitner et al., 2010 source

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    • cites Vimala et al., 2011 source

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    Premisecitation

    The storage root of sweet potato is an excellent source of health-promoting compounds such as β-carotene and antioxidative anthocyanins.

    “Furthermore, the storage root of sweet potato is considered an excellent source of health-promoting compounds, such as β-carotene and antioxidative anthocyanins (Bovell-Benjamin, 2007).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Bovell-Benjamin, 2007 source

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    Premisecitation

    Starch composition in the storage root, particularly the ratio of amylose to amylopectin, influences the physicochemical properties of starch.

    “the composition of starch in the storage root, particularly the ratio of amylose to amylopectin, also influences the physicochemical properties of starch (Hamada et al., 2006; Zhou et al., 2015)”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites Hamada et al., 2006 source

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    Premisecitation

    Dry matter content of the storage root is essential for post harvest processing.

    “The dry matter content of the storage root is essential for post harvest processing (Nedunchezhiyan et al., 2010)”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Nedunchezhiyan et al., 2010

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    Study design and conductnone given

    All PCR amplifications and electrophoresis analyses for each SSR marker were repeated more than three times.

    “All PCR amplifications and electrophoresis analyses for each SSR marker were repeated more than three times.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Study design and conductcitation

    The number of permutations was set at 1000 to obtain the permutation-based test of marker significance and the experiment-wise P-value for marker significance.

    “The number of permutations was set at 1000 to obtain the permutation-based test (Anderson and Ter Braak, 2003) of marker significance and the experiment-wise P-value for marker significance.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Anderson and Ter Braak, 2003

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    Study design and conductnone given

    The assessment of dry matter content, starch content, β-carotene content, and starch composition were carried out in triplicate in each experimental year.

    “The assessment of dry matter content, starch content, β-carotene content, and starch composition were carried out in triplicate in each experimental year.”
    Quote in the paperNot a substantial claim

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    Study design and conductnone given

    Only markers with an allele frequency of 5% or greater were included in the association analysis.

    “Only markers with an allele frequency of 5% or greater were included in the association analysis.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Study design and conductcitation

    Association analyses were performed using various mixed models with subpopulation membership percentages as fixed covariates or kinship as a random effect, including naive, Q, Q+K, and K models.

    “We performed association analyses using various mixed models (Yu et al., 2006; Myles et al., 2009), which with subpopulation membership percentages as fixed covariates or kinship as a random effect, including (1) naive model, without controlling for Q and K, (2) Q model, controlling for Q, (3) Q+K model, controlling for both Q and K, and (4) K model, controlling for K (Supplementary Material 6).”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites Yu et al., 2006

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    • cites Myles et al., 2009 source

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    Study design and conductnone given

    All samples were genotyped at least in triplicate.

    “All samples were genotyped at least in triplicate.”
    Quote in the paperNot a substantial claim

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    Premisecitation

    Other pairs of primers were designed based on SSR-containing EST sequences.

    “Of the above-mentioned SSR markers, 142 were derived from the genomic library of sweet potato (Buteler et al., 1999; Hu et al., 2004) and other pairs of primers were designed based on SSR-containing EST sequences.”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Buteler et al., 1999 source

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    • cites Hu et al., 2004

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    Premisecitation

    At least 2099 PCR primers have been designed on the basis of SSRs in sweet potato since 1999.

    “SSRs have previously been identified in sweet potato (Buteler et al., 1999; Hu et al., 2004; Schafleitner et al., 2010; Wang et al., 2010; Wang Z. et al., 2011; Tao et al., 2012; Xie et al., 2012), and at least 2099 PCR primers have been designed on the basis of these SSRs since 1999.”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Buteler et al., 1999 source

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    • cites Hu et al., 2004

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    • cites Schafleitner et al., 2010 source

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    Premisecitation

    SSRs have previously been identified in sweet potato.

    “SSRs have previously been identified in sweet potato (Buteler et al., 1999; Hu et al., 2004; Schafleitner et al., 2010; Wang et al., 2010; Wang Z. et al., 2011; Tao et al., 2012; Xie et al., 2012), and at least 2099 PCR primers have been designed on the basis of these SSRs since 1999.”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Buteler et al., 1999 source

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    • cites Hu et al., 2004

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    • cites Schafleitner et al., 2010 source

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    Premisecitation

    Of the above-mentioned SSR markers, 142 were derived from the genomic library of sweet potato.

    “Of the above-mentioned SSR markers, 142 were derived from the genomic library of sweet potato (Buteler et al., 1999; Hu et al., 2004) and other pairs of primers were designed based on SSR-containing EST sequences.”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Buteler et al., 1999 source

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    • cites Hu et al., 2004

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    Premisenone given

    Few studies have examined the usage of these SSR markers in MAS or QTL localization.

    “Few studies have examined the usage of these SSR markers in MAS or QTL localization.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    AAT/ATT was reported as an abundant EST SSR motif in sweet potato.

    “AAT/ATT was also reported as an abundant EST SSR motif in sweet potato (Wang et al., 2010; Wang Z. et al., 2011).”
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    • cites Wang et al., 2010 source

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    • cites Wang Z. et al., 2011

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Among these SSR markers, 1214 pairs of PCR primers were found to be polymorphic, or yielded reproducible and strong amplification products when used to analyze different sweet potato accessions.

    “Among these SSR markers, 1214 pairs of PCR primers were found to be polymorphic, or yielded reproducible and strong amplification products when used to analyze different sweet potato accessions (Buteler et al., 1999; Hu et al., 2004; Schafleitner et al., 2010; Wang et al., 2010; Wang Z. et al., 2011).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Buteler et al., 1999 source

      Not checked in the free run.

    • cites Hu et al., 2004

      Not checked in the free run.

    • cites Schafleitner et al., 2010 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    AG/CT, AAG/CTT, and AT/TA motifs occur at the highest frequency in sweet potato EST or cDNA SSRs.

    “These motifs were previously shown to occur at the highest frequency in sweet potato EST or cDNA SSRs, especially the AG/CT, AAG/CTT, and AT/TA motifs (Wang et al., 2010; Wang Z. et al., 2011; Tao et al., 2012).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Wang et al., 2010 source

      Not checked in the free run.

    • cites Wang Z. et al., 2011

      Not checked in the free run.

    • cites Tao et al., 2012 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Marker-trait associations vary with the model used for associations with minor effects.

    “Li et al. (2008) reported that marker-trait associations vary with the model used for associations with minor effects.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Li et al., 2008

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    STRUCTURE determines the number and composition of subpopulations based on Hardy-Weinberg equilibrium and linkage equilibrium.

    “This method attempts to determine the number and composition of subpopulations based on Hardy-Weinberg equilibrium and linkage equilibrium (Hubisz et al., 2009; Zhang et al., 2014).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Hubisz et al., 2009 source

      Not checked in the free run.

    • cites Zhang et al., 2014 source

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Premisecitation

    Undesired population structures can mimic the signal of associations and lead to false positives or missed real effects.

    “To avoid the influence of undesired population structures that can mimic the signal of associations and lead to false positives or missed real effects (Marchini et al., 2004), we estimated the population structure of 239 sweet potato genotypes using the model-based approach as implemented in STRUCTURE.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Marchini et al., 2004 source

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    Dry matter and starch content might be mainly controlled by genetic factors and could be regarded as a stable trait in genetic or association analyses.

    “Thus, the dry matter and starch content might be mainly controlled by genetic factors and could be regarded as a stable trait in genetic or association analyses.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Starch content and composition of storage roots are complex traits controlled by multiple genetic and environmental factors.

    “Starch content and composition of storage roots are complex traits controlled by multiple genetic and environmental factors (Li et al., 2008; Rukundo et al., 2013; Schreiber et al., 2014).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Li et al., 2008

      Not checked in the free run.

    • cites Rukundo et al., 2013

      Not checked in the free run.

    • cites Schreiber et al., 2014 source

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    Combinations of these markers could be used to select plants with desirable traits or to predict trait values early in the selection process.

    “Verifying the ability of these markers to distinguish between cultivars confirmed that the markers had good discriminability and that combinations of these markers could be used to select plants with desirable traits or to predict trait values early in the selection process.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationreasoning

    These findings enhance understanding of the mechanisms underlying the inheritance and formation of complex traits in sweet potato and provide a valuable resource for discovering genes involved in starch and carotenoid biosynthesis in the storage roots of sweet potato.

    “Together, these findings enhance our understanding of the mechanisms underlying the inheritance and formation of complex traits in sweet potato, and provide a valuable resource for discovering genes involved in starch and carotenoid biosynthesis in the storage roots of sweet potato.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Study design and conductreasoning

    The threshold of significance (P-value) used in this study was relatively high.

    “Furthermore, compared with other main crops or model organisms, sweet potato is a genetically challenging hexaploid that can hardly be considered as a model species, and therefore the threshold of significance (P-value) used in this study was relatively high.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Sweet potato is a genetically challenging hexaploid that can hardly be considered a model species.
57 of 57

  • The paper relies on this without support.

    Association analysis between SSR markers and traits across diverse genetic backgrounds has not been performed.

    “Association analysis between these SSR markers and traits across diverse genetic backgrounds has not been performed.”

  • The paper relies on this without support.

    Cultivated sweet potato is a hexaploid (2n = 6x = 90) outcrossing crop with a large genome size (2205 Mb) and a high degree of heterozygosity, making genetic analysis and QTL identification challenging.

    “Given that cultivated sweet potato is a hexaploid (2n = 6x = 90) outcrossing crop with a large genome size (2205 Mb) and a high degree of heterozygosity, genetic analysis, and QTL identification are challenging.”

  • The paper relies on this without support.

    This is the first report of an SSR marker-trait association analysis of multiple agronomic quality traits in sweet potato.

    “This is the first report of an SSR marker-trait association analysis of multiple agronomic quality traits in sweet potato.”

  • The paper relies on this without support.

    The 239 sweet potato genotypes used in the association analysis are representative of sweet potato germplasm.

    “for further analysis in 239 sweet potato genotypes”

  • The paper relies on this without support.

    The phenotypic trait values measured over the 3 years accurately reflect the genotypes' dry matter, starch, β-carotene, amylose, and A/P traits.

    “Due to differences in values recorded in the 3 years of the experiment (Table 1), most of these markers were found to be associated with β-carotene content value measured in 1 year only.”

  • The paper relies on this without support.

    Sweet potato is a genetically challenging hexaploid that can hardly be considered a model species.

    “Furthermore, compared with other main crops or model organisms, sweet potato is a genetically challenging hexaploid that can hardly be considered as a model species, and therefore the threshold of significance (P-value) used in this study was relatively high.”

  • The paper relies on this without support.

    Sweet potato is a highly heterozygous crop.

    “As sweet potato is a highly heterozygous crop, molecular breeding of this crop is a technically challenging goal.”

  • The paper relies on this without support.

    There was no commercial standard sample and mature method for sweet potato amylose measurement.

    “Furthermore, considering that there was no commercial standard sample and mature method for sweet potato amylose measurement, our starch composition-related trait data might be confirmed using novel accurate assessment methods.”

  • The paper relies on this without support.

    Slow progress in efforts to breed OFSP lines with high β-carotene content hinders the collection of varieties with a wide range of β-carotene content.

    “However, slow progress in efforts to breed OFSP lines with high β-carotene content hinders the collection of varieties with a wide range of β-carotene content.”
9 of 9

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • In previous studies, SR dry matter and starch content varied greatly among genotypes, but for each genotype, these traits were relatively stable among different planting years or environments, and genotype had a larger effect than environment on these traits.

    “In our previous studies, we found that the SR dry matter and starch content varied greatly among genotypes, but that for each genotype, these traits were relatively stable among different planting years or environments, and the genotype had a larger effect than did the environment on these traits (Lu et al., 2015; Zhang et al., 2016).”

    From Comparative Transcriptome Analysis Reveals Critical Function of Sucrose Metabolism Related-Enzymes in Starch Accumulation in the Storage Root of Sweet Potato (2017) · cites this paper as Zhang et al., 2016

    Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

    Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • Overall amylose maximum is below the 2013 maximum

    Minor

    The stated overall maximum of 35.512% cannot encompass the table's 2013 maximum of 37.191%.

  • Average transcript length conflicts with total bases and transcript count

    Minor

    Dividing the reported 53,867,441 bases by 62,968 transcripts gives approximately 855 bp per transcript, not 833 bp.

    Reported 833 · recomputed 855.473272

  • Claim of significant year-to-year change in A/P conflicts with Table 1

    Minor

    The text says the year-to-year variation in starch composition was significant at P < 0.001, but Table 1 reports P = 0.194 for the amylose-to-amylopectin ratio, a starch-composition measure.

3 of 3

Cites

Flagged first, then by citations

Research works printed but not linked: 5

  1. Gichuru, 2006, A preliminary analysis of diversity among East African sweetpotato landraces using morphological and simple sequence repeats (SSR) markers, 159
  2. Huang, 2010, Determination of amylose content in sweet potato by single wavelength colorimetry, J. Chin. Cereals. Oils. Associ., 25, 100
  3. Nedunchezhiyan, 2010, Effects of organic production of orange fleshed sweet potato (Ipomoea batatas L.) on root yield, quality and soil biological health, Int. Res. J. Plant. Sci., 1, 136
  4. Nedunchezhiyan, 2012, Sweet potato agronomy, Fruit. Veg. Cereal. Sci. Biotech., 6, 1
  5. Wang, 1989, Conversion table of the starch content in sweet potato, Acta. Agron. Sin., 15, 94

Cited by

Sorted by citations

Related

Authors
Zhang, K., Wu, Z., Tang, D., Lv, C., Luo, K., Zhao, Y., Liu, X., Huang, Y., & Wang, J.
Affiliations
Southwest University (CN)
Corresponding author
  • Zhang, Kai
  • Wang, Jichun
ORCID
Venue
Frontiers in Plant Science
Publisher
Frontiers Media SA
Published
2016-03-02
Volume
7
Pages
223-223
ISSN
1664-462X (ISSN-L)
DOI
10.3389/fpls.2016.00223
PMC
PMC4773602
OpenAlex
W2321150462
Semantic Scholar
ae94aee270fd0a1d4cafd1704174c234e1e7b927
Cited by
32
References
70
Citations by year
2026: 1 · 2025: 3 · 2024: 4 · 2023: 2 · 2022: 3 · 2021: 3 · 2020: 8 · 2019: 3 · 2018: 1 · 2017: 4
FWCI
2.15
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Frontiers in Plant Science (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders
  • National Natural Science Foundation of China (31101192)
  • Ministry of Education of the People's Republic of China
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
  • Life Sciences › Agricultural and Biological Sciences › Horticulture › Cocoa and Sweet Potato Agronomy
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Disease Resistance and Genetics
Keywords
Ipomoea batatas, microsatellite markers, starch content, beta-carotene content, tuberous roots, starch composition, marker-trait association, de novo assembly, population structure, germplasm panel, carotenoid biosynthesis, bioethanol feedstock

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-10.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-10.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

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