Bulked-segregant analysis by deep sequencing(BSA-seq) is a widely used method for mapping QTL(quantitative trait loci) due to its simplicity, speed, cost-effectiveness, and efficiency. However, the ability of BSA-seq ...Bulked-segregant analysis by deep sequencing(BSA-seq) is a widely used method for mapping QTL(quantitative trait loci) due to its simplicity, speed, cost-effectiveness, and efficiency. However, the ability of BSA-seq to detect QTL is often limited by inappropriate experimental designs, as evidenced by numerous practical studies. Most BSA-seq studies have utilized small to medium-sized populations, with F2populations being the most common choice. Nevertheless, theoretical studies have shown that using a large population with an appropriate pool size can significantly enhance the power and resolution of QTL detection in BSA-seq, with F_(3)populations offering notable advantages over F2populations. To provide an experimental demonstration, we tested the power of BSA-seq to identify QTL controlling days from sowing to heading(DTH) in a 7200-plant rice F_(3)population in two environments, with a pool size of approximately 500. Each experiment identified 34 QTL, an order of magnitude greater than reported in most BSA-seq experiments, of which 23 were detected in both experiments, with 17 of these located near41 previously reported QTL and eight cloned genes known to control DTH in rice. These results indicate that QTL mapping by BSA-seq in large F_(3)populations and multi-environment experiments can achieve high power, resolution, and reliability.展开更多
Hepatocellular carcinoma(HCC)is a leading cause of death worldwide.Current therapies are effective for HCC patients with early disease,but many patients suffer recurrence after surgery and have a poor response to chem...Hepatocellular carcinoma(HCC)is a leading cause of death worldwide.Current therapies are effective for HCC patients with early disease,but many patients suffer recurrence after surgery and have a poor response to chemotherapy.Therefore,new therapeutic targets are needed.We analyzed gene expression profiles between HCC tissues and normal adjacent tissues from public databases and found that the expression of genes involved in lipid metabolism was significantly different.The analysis showed that AKR1C3 was upregulated in tumors,and high AKR1C3 expression was associated with a poorer prognosis in HCC patients.In vitro,assays demonstrated that the knockdown of AKR1C3 or the addition of the AKR1C3 inhibitor indomethacin suppressed the growth and colony formation of HCC cell lines.Knockdown of AKR1C3 in Huh7 cells reduced tumor growth in vivo.To explore the mechanism,we performed pathway enrichment analysis,and the results linked the expression of AKR1C3 with prostaglandin F2 alpha(PGF2a)downstream target genes.Suppression of AKR1C3 activity reduced the production of PGF2a,and supplementation with PGF2a restored the growth of indomethacin-treated Huh7 cells.Knockdown of the PGF receptor(PTGFR)and treatment with a PTGFR inhibitor significantly reduced HCC growth.We showed that indomethacin potentiated the sensitivity of Huh7 cells to sorafenib.In summary,our results indicate that AKR1C3 upregulation may promote HCC growth by promoting the production of PGF2α,and suppression of PTGFR limited HCC growth.Therefore,targeting the AKR1C3-PGF2a-PTGFR axis may be a new strategy for the treatment of HCC.展开更多
Normal corn germplasm can be used to improve popcorn （Zea mays L.） through 1-2 backcrosses with popcorn as recurrent parents. Popping characteristics of derived lines from popcorn × dent or flint corn crosses p...Normal corn germplasm can be used to improve popcorn （Zea mays L.） through 1-2 backcrosses with popcorn as recurrent parents. Popping characteristics of derived lines from popcorn × dent or flint corn crosses play a determinant role in popcorn breeding. Advanced backcross QTL methods can effectively combine QTL identification and plant breeding. 220 selected BC2F2 families developed from a cross between Dan 232, a dent corn inbred line, and N04, an elite popcorn inbred line, were evaluated for three popping characteristics, popping volume, flake size, and popping rate, under two environmental conditions. Using composite interval mapping, a total of 10 significant QTLs were detected, and of these, 2 to 4 QTLs were identified for each trait. Six QTLs had favorable alleles contributed by Dan 232. Comparison with the 15 QTLs detected in the F2：3 families showed that 3 QTLs were the same in both populations. The QTLs should be redetected in generations developed through severe selection. Improved N04 and near isogenic lines could be developed from this BC2F2 population through selfing or another 1 to 2 backcrosses with N04.展开更多
Recent studies showed that pseudogenes can regulate the expression of their coding gene partners by competing for miRNAs. The E2F family plays a crucial role in the control of cell cycle checkpoint. E2F3P1 is a pseudo...Recent studies showed that pseudogenes can regulate the expression of their coding gene partners by competing for miRNAs. The E2F family plays a crucial role in the control of cell cycle checkpoint. E2F3P1 is a pseudogene of E2F3. Few studies focused on genetic variations on pseudogenes. In this study, we performed a case-control study to assess the association between single nucleotide polymorphisms （SNPs） in E2F3P1 and hepatocellular carcinoma （HCC） risk in 1050 hepatitis B virus （HBV）-positive HCC cases and 1050 chronic HBV carders. Logistic regres- sion analysis was applied to estimate odds ratios （ORs） and 95% confidence intervals （CIs） for the associations between genotypes and HCC risk. We found that the variant CT/TT genotypes of rs1838149 were associated with a significantly decreased risk of HCC （adjusted OR = 0,66, 95% CIs = 0.51-0.86, P = 0.002） compared to those with wildtype CC homozygote. Furthermore, the AA genotype of rs9909601 had an increased HCC risk with an adjusted OR of 1.41 （95% CIs = 1.07-1.86）, and the A allele of rs9909601 was significantly associated with HCC risk com- pared to those with the G allele （adjusted OR = 1.17, 95% CIs = 1.03-1.33, P = 0.017）. These results indicate that genetic variations in the pseudogene E2F3P1 may confer HCC risk.展开更多
基金supported by Natural Science Foundation of Fujian Province (CN) (2020I0009, 2022J01596)Cooperation Project on University Industry-Education-Research of Fujian Provincial Science and Technology Plan (CN) (2022N5011)+1 种基金Lancang-Mekong Cooperation Special Fund (2017-2020)International Sci-Tech Cooperation and Communication Program of Fujian Agriculture and Forestry University (KXGH17014)。
文摘Bulked-segregant analysis by deep sequencing(BSA-seq) is a widely used method for mapping QTL(quantitative trait loci) due to its simplicity, speed, cost-effectiveness, and efficiency. However, the ability of BSA-seq to detect QTL is often limited by inappropriate experimental designs, as evidenced by numerous practical studies. Most BSA-seq studies have utilized small to medium-sized populations, with F2populations being the most common choice. Nevertheless, theoretical studies have shown that using a large population with an appropriate pool size can significantly enhance the power and resolution of QTL detection in BSA-seq, with F_(3)populations offering notable advantages over F2populations. To provide an experimental demonstration, we tested the power of BSA-seq to identify QTL controlling days from sowing to heading(DTH) in a 7200-plant rice F_(3)population in two environments, with a pool size of approximately 500. Each experiment identified 34 QTL, an order of magnitude greater than reported in most BSA-seq experiments, of which 23 were detected in both experiments, with 17 of these located near41 previously reported QTL and eight cloned genes known to control DTH in rice. These results indicate that QTL mapping by BSA-seq in large F_(3)populations and multi-environment experiments can achieve high power, resolution, and reliability.
基金National Yang Ming Chiao Tung University Far Eastern Memorial Hospital Joint Research Programs(NYCU-FEMH 109DN03,110DN06,111DN04,112DN05).
文摘Hepatocellular carcinoma(HCC)is a leading cause of death worldwide.Current therapies are effective for HCC patients with early disease,but many patients suffer recurrence after surgery and have a poor response to chemotherapy.Therefore,new therapeutic targets are needed.We analyzed gene expression profiles between HCC tissues and normal adjacent tissues from public databases and found that the expression of genes involved in lipid metabolism was significantly different.The analysis showed that AKR1C3 was upregulated in tumors,and high AKR1C3 expression was associated with a poorer prognosis in HCC patients.In vitro,assays demonstrated that the knockdown of AKR1C3 or the addition of the AKR1C3 inhibitor indomethacin suppressed the growth and colony formation of HCC cell lines.Knockdown of AKR1C3 in Huh7 cells reduced tumor growth in vivo.To explore the mechanism,we performed pathway enrichment analysis,and the results linked the expression of AKR1C3 with prostaglandin F2 alpha(PGF2a)downstream target genes.Suppression of AKR1C3 activity reduced the production of PGF2a,and supplementation with PGF2a restored the growth of indomethacin-treated Huh7 cells.Knockdown of the PGF receptor(PTGFR)and treatment with a PTGFR inhibitor significantly reduced HCC growth.We showed that indomethacin potentiated the sensitivity of Huh7 cells to sorafenib.In summary,our results indicate that AKR1C3 upregulation may promote HCC growth by promoting the production of PGF2α,and suppression of PTGFR limited HCC growth.Therefore,targeting the AKR1C3-PGF2a-PTGFR axis may be a new strategy for the treatment of HCC.
基金funded by the Natural Science Founda-tion of Henan Province of China (0511032900).
文摘Normal corn germplasm can be used to improve popcorn （Zea mays L.） through 1-2 backcrosses with popcorn as recurrent parents. Popping characteristics of derived lines from popcorn × dent or flint corn crosses play a determinant role in popcorn breeding. Advanced backcross QTL methods can effectively combine QTL identification and plant breeding. 220 selected BC2F2 families developed from a cross between Dan 232, a dent corn inbred line, and N04, an elite popcorn inbred line, were evaluated for three popping characteristics, popping volume, flake size, and popping rate, under two environmental conditions. Using composite interval mapping, a total of 10 significant QTLs were detected, and of these, 2 to 4 QTLs were identified for each trait. Six QTLs had favorable alleles contributed by Dan 232. Comparison with the 15 QTLs detected in the F2：3 families showed that 3 QTLs were the same in both populations. The QTLs should be redetected in generations developed through severe selection. Improved N04 and near isogenic lines could be developed from this BC2F2 population through selfing or another 1 to 2 backcrosses with N04.
基金funded by the National Key Basic Research Program (2013CB911400)the Foundation for the Program for New Century Excellent Talents in University (NCET-10-0178)+5 种基金the Author of National Excellent Doctoral Dissertation (201081)the National Natural Science Foundation of China (30800946 and 81072344)the State Key Infectious Disease Project of China (2012ZX10002010, 2012ZX10002016)the National Major S&T Projects 2011ZX10004902)the National Science Fund for Creative Research Groups (30921006)the Priority Academic Program for the Development of Jiangsu Higher Education Institutions (Public Health and Preventive Medicine)
文摘Recent studies showed that pseudogenes can regulate the expression of their coding gene partners by competing for miRNAs. The E2F family plays a crucial role in the control of cell cycle checkpoint. E2F3P1 is a pseudogene of E2F3. Few studies focused on genetic variations on pseudogenes. In this study, we performed a case-control study to assess the association between single nucleotide polymorphisms （SNPs） in E2F3P1 and hepatocellular carcinoma （HCC） risk in 1050 hepatitis B virus （HBV）-positive HCC cases and 1050 chronic HBV carders. Logistic regres- sion analysis was applied to estimate odds ratios （ORs） and 95% confidence intervals （CIs） for the associations between genotypes and HCC risk. We found that the variant CT/TT genotypes of rs1838149 were associated with a significantly decreased risk of HCC （adjusted OR = 0,66, 95% CIs = 0.51-0.86, P = 0.002） compared to those with wildtype CC homozygote. Furthermore, the AA genotype of rs9909601 had an increased HCC risk with an adjusted OR of 1.41 （95% CIs = 1.07-1.86）, and the A allele of rs9909601 was significantly associated with HCC risk com- pared to those with the G allele （adjusted OR = 1.17, 95% CIs = 1.03-1.33, P = 0.017）. These results indicate that genetic variations in the pseudogene E2F3P1 may confer HCC risk.
