Single Marker Analysis Research Articles

Potential SNPs related to microspore culture inRaphanus sativusbased on a single-marker analysis

Radish (Raphanus sativus) is an economically important crop grown for its edible roots and leaves. It is a self-incompatible, outcrossing species, making the production of homozygous lines and the development of breeding populations difficult. However, this can be overcome with haploids production techniques using isolated microspores, providing the rapid production of homozygous lines for breeding. Thus, it would be useful to identify radishes with a high regeneration rate from microspore culture. In the current study, 96 radish cultivars or germplasms were evaluated for high regeneration rates. Also, a single-marker analysis (SMA) was applied to detect single nucleotide polymorphisms (SNPs) potentially associated with this trait using genotype-by-sequencing (GBS) technology. The regeneration rate from microspore culture of 96 lines showed a wide range, from 0% to 269.5%. From the SMA, 52 markers were detected at a p value of 0.001 and a total of 11 physically nearby genes with high levels of similarity in various species were identified as candidates for high regeneration rates. This result could be used for clarifying the genetic basis underlying these traits and developing molecular markers associated with regeneration rates and would be beneficial for generating homozygous inbred lines.

Development of heat tolerant introgression lines and preliminary quantitative trait loci (QTL) analysis at flowering stage in Oryza sativa L.

The efficacy of modern rice varieties has been challenged by global warming because of their incapability to tolerate heat stress. Breeding for heat tolerance (HT) is therefore essential. Molecular breeding studies on HT in hybrid rice is sparse although HT quantitative trait loci (QTL) have been discovered. China is the leading country for hybrid rice production, however, introgression of HT alleles to hybrids is not practiced in breeding programmes. Therefore, the objectives of this study were to introgress HT alleles from indica donors Bg 90-2 and Mengguandamagu to SH 527, a popular parent in hybrid variety development, and to identify the associated DNA markers with HT to facilitate hybrid rice molecular breeding in China. The BC2F2:4 introgression lines were produced by crossing donor and recurrent parents and their performances were evaluated at two provinces of China in 2011 and 2012 under normal and heat stress conditions. The data were subjected to ANOVA and HT was compared against the standard heat-check variety N22. Out of 600 SSR markers, 61 and 59 markers were polymorphic for the two crosses SH 527/ Bg 90 ‒ 2 and SH 527/ Mengguandamagu, respectively and introgression lines were subsequently genotyped. The single-marker analysis was performed to detect marker trait associations. A total of 46 HT introgression lines were obtained with 88.3 % of homozygosity for HT alleles and seven high yielding HT lines were specifically selected for the provinces. Under heat stress, 42 significant marker trait associations were detected. Two of these were previously reported in HT QTLs implying their applicability in rice breeding programmes.

Methods and results from the genome-wide association group at GAW20

BackgroundThis paper summarizes the contributions from the Genome-wide Association Study group (GWAS group) of the GAW20. The GWAS group contributions focused on topics such as association tests, phenotype imputation, and application of empirical kinships. The goals of the GWAS group contributions were varied. A real or a simulated data set based on the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) study was employed by different methods. Different outcomes and covariates were considered, and quality control procedures varied throughout the contributions.ResultsThe consideration of heritability and family structure played a major role in some contributions. The inclusion of family information and adaptive weights based on data were found to improve power in genome-wide association studies. It was proven that gene-level approaches are more powerful than single-marker analysis. Other contributions focused on the comparison between pedigree-based kinship and empirical kinship matrices, and investigated similar results in heritability estimation, association mapping, and genomic prediction. A new approach for linkage mapping of triglyceride levels was able to identify a novel linkage signal.ConclusionsThis summary paper reports on promising statistical approaches and findings of the members of the GWAS group applied on real and simulated data which encompass the current topics of epigenetic and pharmacogenomics.

A positional candidate gene association analysis of susceptibility to paratuberculosis on bovine chromosome 7

Mycobacterium avium subspecies paratuberculosis (MAP) is the causative pathogen for paratuberculosis, which is a chronic inflammation of the small intestine in ruminants and some wild animals. It affects negatively on the economics of dairy operations worldwide and has a zoonotic concern for its potential relationship to Crohn's disease in humans. In this study, we used different approaches to investigate genetic markers associated with MAP infection on bovine chromosome 7. The interleukin-2-inducible T-cell kinase (ITK) gene is a non-receptor tyrosine kinase expressed in T cells, which also is involved in regulation and development of immune cells and some inflammatory diseases. The gene was suggested in a previous GWAS analysis as a positional candidate gene located on BTA7 for MAP infection. In this study, bovine ITK was sequenced and seventeen identified SNPs were genotyped in 1419 Holstein and Jersey cows. Association analysis revealed no significantly associated SNP in the bovine ITK gene using either single marker or haplotype analyses. In a complementary analysis, Holstein genotypes were imputed from 50 K SNPs to the full genome sequence of BTA7. Single SNP association tests identified two SNPs at 15 Mb (p = 5 × 10−7) significantly associated with MAP infection. Our results suggest an additional region of BTA7 contributes to susceptibility to MAP infection in cattle, relative to our previous report, and further investigations are required.

Validation of QTLs for grain iron and zinc concentration in wheat (Triticum aestivum L.)

Markers linked to QTLs are useful in practical plant breeding, only if they get validated in genotypes of independent populations and diverse genetic backgrounds. 41 SSR markers reported linked to QTLs for grain iron (Fe) and zinc (Zn) concentration in wheat were analysed. Only 16 of them showed polymorphism and the remaining 25 turned out to be monomorphic in 48 wheat genotypes used in the present study. Single marker analysis (SMA) for the 16 polymorphic markers was carried out to assess the linkage between marker and the trait, based on which two markers (Xbarc186 and Xbarc74) for grain Fe concentration and three markers (Xgwm3, Xwms149 and Xgwm538) for grain Zn concentration were validated in the present study. The phenotypic variations explained by Xbarc186, Xbarc74, Xgwm3, Xwms149 and Xgwm538 were 40.2% and 19.8%, 10.7%, 21.7%, and 39.6%, respectively. The validation of these SSRs may be useful in breeding wheat with high grain Fe and Zn concentration.

Validation of molecular marker associated with powdery mildew resistance in mungbean

Powdery mildew caused by Erysiphe polygoni, is one of the major diseases of mungbean (Vigna radiata L. Wilczek), causes yield loss up to 20-40%. The present investigation was undertaken to study the SSR markers associated with powdery mildew resistance in mungbean. The resistant line, TARM1 was crossed with highly susceptible, but popular variety DGGV2 and the F1s were selfed to obtain F2. F2 population was evaluated for response to PM under field conditions. Of the 64 SSR markers studied, only four were found to be polymorphic between two parents (TARM1 and DGGV2). Single marker analysis indicated that one SSR marker (MB-SSR238) showed association with powdery mildew resistance in mungbean, explaining the phenotypic variance of 11.64%.

Genetic analysis and marker assisted backcrossing for transfer of mosaic virus resistance in cowpea [Vigna unguiculata (L.) Walp.

Cowpea mosaic virus (CpMV) is known to cause yield loss of as much as 80-100 per cent. Among different approaches available in the management of this disease development and release of resistant varieties is the most viable option for farmers. Hence an investigation was carried out to study the inheritance of resistance to cowpea mosaic virus (CpMV) and to identify DNA markers linked to genomic regions conferring resistance to CpMV. The resistance was found to be governed by single recessive gene in the 191 F2:3 progenies derived from the cross C-152 (susceptible) × V-57817 (resistant). Single marker analysis with 191 F2 individuals and 106 polymorphic SSR markers indicated that two markers, MA15 and MA80 were linked to CpMV resistance as evidenced by significant mean sum of squares due to between marker classes and putative linkage of these markers for resistance to CpMV was confirmed by bulked segregant analysis. Through linkage map constructed utilizing 91 polymorphic SSR markers it was possible for us to show that the two markers MA15 and MA80 were included in the linkage group 6 and the marker gene was likely to be present between these markers. Marker assisted backcrossing was practiced to transfer resistance gene in to an agronomically superior variety C-152.

Assessing European Wheat Sensitivities to Parastagonospora nodorum Necrotrophic Effectors and Fine-Mapping the Snn3-B1 Locus Conferring Sensitivity to the Effector SnTox3.

Parastagonospora nodorum is a necrotrophic fungal pathogen of wheat (Triticum aestivum L.), one of the world’s most important crops. P. nodorum mediates host cell death using proteinaceous necrotrophic effectors, presumably liberating nutrients that allow the infection process to continue. The identification of pathogen effectors has allowed host genetic resistance mechanisms to be separated into their constituent parts. In P. nodorum, three proteinaceous effectors have been cloned: SnToxA, SnTox1, and SnTox3. Here, we survey sensitivity to all three effectors in a panel of 480 European wheat varieties, and fine-map the wheat SnTox3 sensitivity locus Snn3-B1 using genome-wide association scans (GWAS) and an eight-founder wheat multi-parent advanced generation inter-cross (MAGIC) population. Using a Bonferroni corrected P ≤ 0.05 significance threshold, GWAS identified 10 significant markers defining a single locus, Snn3-B1, located on the short arm of chromosome 5B explaining 32% of the phenotypic variation [peak single nucleotide polymorphisms (SNPs), Excalibur_c47452_183 and GENE-3324_338, -log10P = 20.44]. Single marker analysis of SnTox3 sensitivity in the MAGIC population located Snn3-B1 via five significant SNPs, defining a 6.2-kb region that included the two peak SNPs identified in the association mapping panel. Accordingly, SNP Excalibur_c47452_183 was converted to the KASP genotyping system, and validated by screening a subset of 95 wheat varieties, providing a valuable resource for marker assisted breeding and for further genetic investigation. In addition, composite interval mapping in the MAGIC population identified six minor SnTox3 sensitivity quantitative trait loci, on chromosomes 2A (QTox3.niab-2A.1, P-value = 9.17-7), 2B (QTox3.niab-2B.1, P = 0.018), 3B (QTox3.niab-3B.1, P = 48.51-4), 4D (QTox3.niab-4D.1, P = 0.028), 6A (QTox3.niab-6A.1, P = 8.51-4), and 7B (QTox3.niab-7B.1, P = 0.020), each accounting for between 3.1 and 6.0 % of the phenotypic variance. Collectively, the outcomes of this study provides breeders with knowledge and resources regarding the sensitivity of European wheat germplasm to P. nodorum effectors, as well as simple diagnostic markers for determining allelic state at Snn3-B1.

Genome-wide association study identifies loci for body shape in the large yellow croaker (Larimichthys crocea)

The large yellow croaker (Larimichthys crocea) is an important maricultured fish species in southeast China. Body shape is an important economic trait for this species, because consumers prefer to purchase fish that have a slender shape. Furthermore, investigating the genetic basis of this trait may be useful for understanding the evolution of fish body shape in general. This study randomly selected 500 large yellow croakers to perform genome-wide association study of this trait. We used Genotyping-By-Sequencing technology combined with a genome-wide prediction model (BayesC) to identify and test QTLs. We also compared the association results using BayesC and single-marker analysis, and found that BayesC outperformed single-marker analysis in detecting significant SNPs explaining a proportion of the total genetic variance in this experiment. Using 124,419 SNP markers, 10 candidate genes, correspond to 4 QTL regions located around 3.5, 1.8, 23.9 and 10.8 Mb on chromosomes 2, 4, 8 and 22 respectively, were suggested to be relevant to the trait. All of these genes may directly or indirectly participate in bone development. These genes may provide a valuable reference for marker-assisted selective breeding and investigating the genetic basis of the evolution of fish body shape.

Identification of quantitative trait loci for fat percentage in buffaloes

The milk fat percentage records of 2174 daughters belonging to 12 half sib families were analyzed for the identification of QTLs on 8 chromosomes in buffaloes using chromosome scans. The single marker analysis revealed 49 markers to be associated with milk fat percentage in 10 sire families. The interval mapping using R/qtl identified 43 QTLs on 8 chromosomes of buffalo. The meta-QTL analysis was carried out to define consensus QTLs in buffaloes and total 28 meta-QTL regions could be identified for milk fat percentage. Most of the QTLs identified in the experiments have been reported for cattle; however, few new chromosomal locations were also identified to be associated with fat percentage in buffaloes. The additional QTLs identified in buffalo may be due to high level of heterozygosity in buffalo compared to Holstein Friesian and other exotic milk breeds for which QTLs have beenreported. Assuming buffalo-cattle synteny, a total of 1118 genes were identified underlying the QTL regions, out of these 45 genes were identified to be associated with lipid metabolism. The interaction among the genes and gene ontology analysis confirmed their association with lipid metabolism. These 45 genes have potential to be candidate genes for milk fat percentage in buffaloes and underlie the QTL regions identified in buffaloes in the present study.

English

Breeding for resistance to flower bud thrips (Megalurothrips sjostedti) in cowpea has been hindered by the quantitative nature of resistance. To identify simple sequence repeat (SSR) markers associated with resistance to flower bud thrips that could be used for marker-assisted breeding, a F2 population was generated from a cross between genotypes TVU-123 (resistant) and WC36 (susceptible). The population was evaluated for thrips damage scores, thrips counts, and pods number per plant under artificial infestation. Sixty-six microsatellites markers were screened between the two parental lines and seven polymorphic markers were used to genotype 100 F2 plants. Single marker analysis was used to evaluate an association between the markers and traits. Transgressive segregation among the F2 plants for resistance to flower thrips was observed. A significant negative relationship was observed between thrips damage scores and pods number per plant. Markers CP37/38 and CP215/216 were significantly associated with thrips damage scores and thrips counts, respectively. The two markers explained 7 and 11.2% of the total variation in thrips damage scores and thrips counts with positive and negative effects, respectively. Mainly additive gene effects were observed. A more detailed study using more markers on these loci should provide better understanding of this complex trait.  Key words: Cowpea, single marker analysis, polymorphism, simple sequence repeat (SSR) markers.

The influence of DCDC2 risk genetic variants on reading: Testing main and haplotypic effects

Developmental dyslexia (DD) is a complex neurodevelopmental heritable disorder. Among DD candidate genes, DCDC2 is one of the most replicated, with rs793862, READ1 and rs793842 likely contribute to phenotypic variability in reading (dis)ability. In this study, we tested the effects of these genetic variants on DD as a categorical trait and on quantitative reading-related measures in a sample of 555 Italian nuclear families with 930 offspring, of which 687 were diagnosed with DD. We conducted both single-marker and haplotype analyses, finding that the READ1-deletion was significantly associated with reading, whereas no significant haplotype associations were found. Our findings add further evidence to support the hypothesis of a DCDC2 contribution to inter-individual variation in distinct indicators of reading (dis)ability in transparent languages (i.e., reading accuracy and speed), suggesting a potential pleiotropic effect.

Identification of quantitative trait loci for milk yield in Murrah buffaloes

A reference family consisting of 12 half sib sire families were created for the identification of QTLs for milk yield in buffaloes. Daughters were recorded for monthly test day milk yield. The number of daughters per sire varied from 50 to 335 daughters per sire. Seventy nine polymorphic microsatellite markers located on 8 chromosomes were genotyped for 2281 daughters of the 12 sires. Whole chromosome scanning was done using single marker analysis and interval mapping using three different algorithms. The analysis was carried out sire family wise. QTLs (63) were identified in single marker analysis and 32 QTLs were identified using interval mapping. The significance of LOD score was tested using permutation tests. The metaQTL analysis was carried out to find out the consensus chromosomal regions associated with milk yield in buffaloes. Five models were utilised and the best was selected on the basis of Akaike Information content. Total 23 chromosomal regions were identified for milk yield in buffaloes. 2 metaQTL chromosomal regions were identified on buffalo chromosome BBU2q; 3 metaQTLs each on buffalo chromosomes BBU8, BBU10 and BBU15 and 4 metaQTL regions each on BBU1q, BBU6, BBU9.

Association Between DLX4 Polymorphisms and Nonsyndromic Orofacial Clefts in a Chinese Han Population.

Distal-less 4 ( DLX4) was recently identified as the causative gene for a syndromic form of cleft lip with or without cleft palate, and further biological analyses have established the importance of Dlx4 gene in craniofacial development, which suggested DLX4 as a promising candidate to further investigate any possible association between DLX4 polymorphisms and risk to nonsyndromic orofacial clefts (NSOFCs). Single-nucleotide polymorphisms (SNPs) with minor allele frequency >5% in the Han Chinese population which locate in the 5' flanking region, 5'/3'-untranslated region, or coding region with nonsynonymous changes in DLX4 were selected. Four SNPs (rs58769681, rs1058562, rs1058564, and rs8066341) were thus included in the following genotyping using the TaqMan 5'-exonuclease allelic discrimination assay in a case-control cohort with 1522 individuals. None of SNPs were associated with NSOFCat the allele and genotype levels in general and stratified single-marker analysis, including genotypic distributions under different modes of inheritance. In linkage disequilibrium (LD) analysis, we found strong LD ( r2 > 0.8) between any 2 of the SNPs, respectively. Further haplotyping identified haplotypes C-C (formed by rs1058564 and rs1058562) and C-C-A (formed by rs1058564, rs1058562, and rs58769681) which reached the significance threshold ( P < .05); nevertheless, none of them survived the multiple comparison correction. Our findings indicated the hypothesis that DLX4 variants contributing to NSOFC risk should be interpreted with caution. Further replications in diverse ethnic origins and larger cohorts are still warranted.

Gene-based analysis of genes related to neurotrophic pathway suggests association of BDNF and VEGFA with antidepressant treatment-response in depressed patients

It is well established that brain-derived neurotrophic factor (BDNF) signaling pathway plays a key role in the pathophysiology of major depressive disorder (MDD) and in therapeutic mechanisms of antidepressants. We aim to identify genetic vairiants related to MDD susceptibility and antidepressant therapeutic response by using gene-based association analysis with genes related to the neurotrophic pathway. The present study investigated the role of genetic variants in the 10 neurotrophic-related genes (BDNF, NGFR, NTRK2, MTOR, VEGFA, S100A10, SERPINE1, ARHGAP33, GSK3B, CREB1) in MDD susceptibility through a case-control (455 MDD patients and 2,998 healthy controls) study and in antidepressant efficacy (n = 455). Measures of antidepressant therapeutic efficacy were evaluated using the 21-item Hamilton Rating Scale for Depression. Our single-marker and gene-based analyses with ten genes related to the neurotrophic pathway identified 6 polymorphisms that reached a significant level (p-value < 5.0 × 10−3) in both meta- and mega-analyses in antidepressant therapeutic response. One polymorphism was mapped to BDNF and 5 other polymorphisms were mapped to VEGFA. For case-control association study, we found that all of these reported polymorphisms and genes did not reach a suggestive level. The present study supported a role of BDNF and VEGFA variants in MDD therapeutic response.

Single-marker and multi-marker approaches to appraise the relationships between biomarkers and microalbuminuria in Chinese middle-aged and elderly from communities: a cross-sectional analysis

BackgroundAnalyzing the relationships between biomarkers representing distinct pathophysiologic pathways and microalbuminuria (MA) can strengthen the identifying ability for renal damage and illuminate previously unrecognized pathways for the pathogenesis of renal damage. The current analysis was to clarify the associations between biomarkers, including N-terminal prohormone of brain natriuretic peptide (NT-proBNP), high-sensitivity C-reactive protein (hsCRP), homocysteine and uric acid (UA), and MA in Chinese middle-aged and elderly from communities.MethodsAll 839 residents had complete set of these biomarkers and full assessment of MA.ResultsPrevalence of participants with MA was 13.5% (113 participants). Levels of age, systolic blood pressure (SBP), fasting blood glucose (FBG), homocysteine and NT-proBNP and proportion of cigarette smoking in participants with MA significantly exceeded those in participants without MA (p < 0.05 for all). In single-marker and multi-marker models of linear and logistic regression analyses, homocysteine and NT-proBNP levels (p < 0.05 for all) rather than hsCRP and UA levels (p > 0.05 for all) were statistically significant in relation to MA. Additionally, no matter which biomarker was directed at, levels of age, SBP and FBG and proportion of cigarette smoking had significant associations with MA. Homocysteine and NT-proBNP levels (p < 0.05 for all) rather than hsCRP and UA levels (p > 0.05 for all) had significant abilities to identify MA.ConclusionBoth single-marker and multi-marker analyses confirmed that homocysteine and NT-proBNP were associated with MA in Chinese middle-aged and elderly from communities after adjustment for multiple confounders.

The Impact of FSHR Gene Polymorphisms Ala307Thr and Asn680Ser in the Endometriosis Development

Endometriosis is an estrogen-dependent inflammatory disease that affects a large number of women in reproductive age. Follicle-stimulating hormone (FSH) plays a role in steroidogenesis and acts through a transmembrane glycoprotein, FSH receptor (FSHR). Polymorphisms in FSHR gene were previously associated with variability in FSH serum level and reproductive outcomes, but its relation with endometriosis has not been clarified and demonstrated conflicting results, ranging from strong links to no association to endometriosis. Inspired by these findings, we aimed to investigate the influence of FSHR Ala307Thr and Asn680Ser polymorphisms in the risk of endometriosis development and/or progression and the status of fertility in 352 women with endometriosis and 510 fertile controls. Single-marker analysis revealed no significant difference for both Ala307Thr and Asn680Ser polymorphisms between overall endometriosis and control group. However, when the endometriosis group was subdivided according to fertility status and disease stage, a positive association was found between 680Ser/Ser or GG genotype of the Asn680Ser polymorphism and fertile women with endometriosis (p = 0.004). Combined alleles of FSHR polymorphisms revealed that "GG/307Ala680Ser" was more frequently found in fertile women with endometriosis (haplotype frequency of 45.4% in fertile women with endometriosis and 38.3% in controls, p = 0.041). The combined alleles of FSHR polymorphisms disclosed that "GG/307Ala680Ser" was more frequently found in fertile women with endometriosis (haplotype frequency of 45.4% in fertile women with endometriosis and 38.3% in controls, p = 0.049), while "GA/307Ala680Asn" haplotype was less frequently found in endometriosis group (haplotype frequency of 6.5% in cases and 11.9% in controls, p = < 0.001), regardless of fertility status and stage of the disease. The findings suggest that 680Ser-Ser/GG genotype and "GG/307Ala680Ser" haplotype increase the risk of endometriosis in fertile women, while "GA/307Ala680Asn" haplotype decreases the risk of endometriosis development and progression.

Soybean Resistance to White Mold: Evaluation of Soybean Germplasm Under Different Conditions and Validation of QTL.

Soybean (Glycine max L. Merr.) white mold (SWM), caused by Sclerotinia sclerotiorum (Lib) de Barry), is a devastating fungal disease in the Upper Midwest of the United States and southern Canada. Various methods exist to evaluate for SWM resistance and many quantitative trait loci (QTL) with minor effect governing SWM resistance have been identified in prior studies. This study aimed to predict field resistance to SWM using low-cost and efficient greenhouse inoculation methods and to confirm the QTL reported in previous studies. Three related but independent studies were conducted in the field, greenhouse, and laboratory to evaluate for SWM resistance. The first study evaluated 66 soybean plant introductions (PIs) with known field resistance to SWM using the greenhouse drop-mycelium inoculation method. These 66 PIs were significantly (P < 0.043) different for resistance to SWM. However, year was highly significant (P < 0.00001), while PI x year interaction was not significant (P < 0.623). The second study compared plant mortality (PM) of 35 soybean breeding lines or varieties in greenhouse inoculation methods with disease severity index (DSI) in field evaluations. Moderate correlation (r) between PM under drop-mycelium method and DSI in field trials (r = 0.65, p < 0.0001) was obtained. The PM under spray-mycelium was also correlated significantly with DSI from field trials (r = 0.51, p < 0.0018). Likewise, significant correlation (r = 0.62, p < 0.0001) was obtained between PM across greenhouse inoculation methods and DSI across field trials. These findings suggest that greenhouse inoculation methods could predict the field resistance to SWM. The third study attempted to validate 33 QTL reported in prior studies using seven populations that comprised a total of 392 F4 : 6 lines derived from crosses involving a partially resistant cultivar “Skylla,” five partially resistant PIs, and a known susceptible cultivar “E00290.” The estimates of broad-sense heritability (h2) ranged from 0.39 to 0.66 in the populations. Of the seven populations, four had h2 estimates that were significantly different from zero (p < 0.05). Single marker analysis across populations and inoculation methods identified 11 significant SSRs (p < 0.05) corresponding to 10 QTL identified by prior studies. Thus, these five new PIs could be used as new sources of resistant alleles to develop SWM resistant commercial cultivars.

Quantitative Analysis of Multi-components by Single Marker and Fingerprint Analysis of Achyranthes bidentata Blume.

A simple and effective method of high performance liquid chromatography (HPLC) with diode array detection was established to identify the origin of Achyranthes bidentata Blume and evaluate its quality, based on chromatographic fingerprint combined with the similarity analysis, hierarchical cluster analysis and the quantitative analysis of multi-components by single marker (QAMS). In the chromatographic fingerprint, 16 peaks were selected as the common model to evaluate the similarities among 18 batches (S1-S18) of A. bidentata Blume samples collected from different origins in China. The similarities values for 18 batches of samples were more than 0.75, which compared with control fingerprint. Furthermore, 18 batches of A. bidentata Blume samples were categorized into two groups for quantitative analysis, the quantification of three bioactive constituents (β-ecdysterone, cyasterone and 5-hydroxymethyl furfural) between QAMS and external standard method proved the consistency of the two methods, the three constituents showed good regression (R > 0.9995) within linear ranges, and their recoveries were within the range of 97.6-101.5%. This study demonstrated that the quality of A. bidentata Blume can be successfully evaluated by means of a combination of HPLC chromatographic fingerprint and QAMS approach.

Detection and validation of EST-SSR markers associated with sugar-related traits in sugarcane using linkage and association mapping

Sugar-related traits are of great importance in sugarcane breeding. In the present study, quantitative trait loci (QTL) mapping validated with association mapping was used to identify expressed sequence tag-simple sequence repeats (EST-SSRs) associated with sugar-related traits. For linkage mapping, 524 EST-SSRs, 241 Amplified Fragment Length Polymorphisms, and 10 genomic SSR markers were mapped using 283 F1 progenies derived from an interspecific cross. Six regions were identified using Multiple QTL Mapping, and 14 unlinked markers using single marker analysis. Association analysis was performed on a set of 200 accessions, based on the mixed linear model. Validation of the EST-SSR markers using association mapping within the target QTL genomic regions identified two EST-SSR markers showing a putative relationship with uridine diphosphate (UDP) glycosyltransferase, and beta-amylase, which are associated with pol and sugar yield. These functional markers can be used for marker-assisted selection of sugarcane.