Polymorphic tandem DNA repeats activate the human telomerase reverse transcriptase gene.

Multiple independent sequence variants of the hTERT locus have been associated with telomere length and cancer risks in genome-wide association studies. Here, we identified an intronic variable number tandem repeat, VNTR2-1, as an enhancer-like element, which activated hTERT transcription in a cell in a chromatin-dependent manner. VNTR2-1, consisting of 42-bp repeats with an array of enhancer boxes, cooperated with the proximal promoter in the regulation of hTERT transcription by basic helix-loop-helix transcription factors and maintained hTERT expression during embryonic stem-cell differentiation. Genomic deletion of VNTR2-1 in MelJuSo melanoma cells markedly reduced hTERT transcription, leading to telomere shortening, cellular senescence, and impairment of xenograft tumor growth. Interestingly, VNTR2-1 lengths varied widely in human populations; hTERT alleles with shorter VNTR2-1 were underrepresented in African American centenarians, indicating its role in human aging. Therefore, this polymorphic element is likely a missing link in the telomerase regulatory network and a molecular basis for genetic diversities of telomere homeostasis and age-related disease susceptibilities.

Favorable alleles mining for gelatinization temperature, gel consistency and amylose content in Oryza sativa by association mapping.

BACKGROUND: Improving the gelatinization temperature (GT), gel consistency (GC) and amylose content (AC) for parental grain eating and cooking qualities (ECQs) are key factors for enhancing average grain ECQs for hybrid japonica rice. RESULTS: In this study, a genome-wide association mapping (GWAS) for ECQs was performed on a selected sample of 462 rice accessions in 5 environments using 262 simple sequence repeat markers. We identified 10 loci and 27 favorable alleles for GT, GC and AC, and some of these loci were overlapped with starch synthesis-related genes. Four SSR loci for the GT trait were distributed on chromosomes 3, 5, 8, and 9, of which two SSR loci were novel. Two SSR loci associated with the GC trait were distributed on chromosomes 3 and 6, although only one SSR locus was novel. Four SSR loci associated with the AC trait were distributed on chromosomes 3, 6, 10, and 11, of which three SSR loci were novel. The novel loci RM6712 and RM6327 were simultaneously identified in more than 2 environments and were potentially reliable QTLs for ECQs, with 15 parental combinations being predicted. These QTLs and parental combinations should be used in molecular breeding to improve japonica rice average ECQs. CONCLUSIONS: Among the 10 SSR loci associated with GT, GC and AC for grain ECQs detected in 27 favorable alleles, the favorable allele RM3600-90bp on chromosome 9 could significantly reduce GT, RM5753-115bp on chromosome 6 could significantly increase GC, and RM6327-230bp on chromosome 11 could significantly reduce AC in hybrid japonica rice mixed rice samples.

Mining of favorable alleles for lodging resistance traits in rice (oryza sativa) through association mapping.

MAIN CONCLUSION: Fourteen new quantitative trait loci (QTLs) and ten favorable alleles were identified for lodging resistance traits in a natural population of rice. Parental combinations were designed to improve lodging resistance. Lodging is one of the most critical constraints to rice yield, and therefore, mining favorable alleles for lodging resistance traits is imperative for the advancement of cultivated rice and selection for market demand. This investigation was performed on a selected sample of 521 rice cultivars using 262 SSR markers in 2016 and 2017. Lodging resistance traits were evaluated by plant height (PH), stem length (SL), stem diameter (SD), anti-thrust per stem (AT/S), and stem index (SI), with AT/S, used as the lodging resistance index. A genome-wide association map was generated by combining phenotypic and genotypic data. Eight subpopulations were found by structure software, and the linkage disequilibrium (LD) ranged from 30 to 80 cM. Identification of 68 marker-trait associations (MTAs) linking in 64 SSR markers for five traits was done. QTL were detected, including 15 for PH, 14 for SL, 14 for SD, 7 for AT/S, and 18 for SI. A number of favorable alleles were also discovered, including 22, 24, 19, 12, and 28 alleles for PH, SL, SD, AT/S, and SI, respectively. These favorable alleles might be used to design parental combinations, and the predictable results found by relieving the favorable alleles per QTL. The accessions containing favorable alleles for lodging resistant traits mined in this study could be useful for breeding superior rice cultivars.

Genetic structure analysis of cultivated Scrophularia ningpoensis in Zhejiang Province / 中草药

Objective To observe the genetic structure of cultivated Scrophularia ningpoensis in Zhejiang Province.Methods The genetic structures of six typical S.ningpoensis populations were analyzed by fluorescence AFLP marker.Results Bands(12 552) were generated by seven pairs of AFLP primer combinations,of which 8 808 were polymorphic,and the polymorphic rate was 70.17%.The variety ranges of PPB among different populations were 41.67%—55.56%,and 47.30% in average.I was between 0.190 8—0.238 3,and 0.221 8 in average.Ne was between 1.201 4—1.280 6,and 1.236 9 in average.Gst was 0.127 1,Nm was 3.432 4.UPGMA Cluster analysis showed that the six populations can be divided into two clusters,as that of Tiantai,Jinyun,and Jingning were one sub-cluster,and Dongyang,Pan′an,and Xianju were another one sub-cluster.Conclusion There is a relative high genetic diversity level in cultured S.ningpoensis of Zhejiang Province.Genetic differentiation exists among populations,but it exists in population mostly.There is a relative high genetic intercommunion among populations.The genetic distance is not related to the geographic environment.