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
Bivalve aquaculture plays a crucial role in the aquaculture industry due to the economic value of many bivalve species.Understanding the underlying genetic basis of bivalve growth regulation is essential for enhancing...Bivalve aquaculture plays a crucial role in the aquaculture industry due to the economic value of many bivalve species.Understanding the underlying genetic basis of bivalve growth regulation is essential for enhancing germplasm innovation and ensuring sustainable development of the industry.Though numerous candidate genes have been identified,their functional validation remains challenging.Fortunately,the dwarf surf clam(Mulinia lateralis)serves as a promising model organism for investigating genetic mechanisms underlying growth regulation in bivalves.The GWAS study in the Yesso scallop(Patinopecten yessoensis)has pinpointed the E2F3 gene as a key regulator of growth-related traits.However,the specific role of E2F3 in bivalve growth remains unclear.This study aimed to further confirm the regulatory function of the E2F3 gene in the dwarf surf clam through RNA interference experiments.Our results revealed several genes are associated with individual growth and development,including CTS7,HSP70B2,and PGLYRP3,as well as genes involved in lipid metabolism such as FABP2 and FASN.Functional enrichment analysis indicated that E2F3 primarily modulates critical processes like amino acid and lipid metabolism.These findings suggest that E2F3 likely regulates growth in the dwarf surf clam by influencing amino acid and lipid metabolism.Overall,this study advances our understanding on the function of E2F3 gene in growth regulation in bivalves,providing valuable insights for future research in this field.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
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 National Natural Science Foundation of China (No. U2106231)the Key Research and Development Project of Shandong Province (No. 2021 ZLGX03)the National Key Research and Development Program of China (No. 2022YFD2400303)
文摘Bivalve aquaculture plays a crucial role in the aquaculture industry due to the economic value of many bivalve species.Understanding the underlying genetic basis of bivalve growth regulation is essential for enhancing germplasm innovation and ensuring sustainable development of the industry.Though numerous candidate genes have been identified,their functional validation remains challenging.Fortunately,the dwarf surf clam(Mulinia lateralis)serves as a promising model organism for investigating genetic mechanisms underlying growth regulation in bivalves.The GWAS study in the Yesso scallop(Patinopecten yessoensis)has pinpointed the E2F3 gene as a key regulator of growth-related traits.However,the specific role of E2F3 in bivalve growth remains unclear.This study aimed to further confirm the regulatory function of the E2F3 gene in the dwarf surf clam through RNA interference experiments.Our results revealed several genes are associated with individual growth and development,including CTS7,HSP70B2,and PGLYRP3,as well as genes involved in lipid metabolism such as FABP2 and FASN.Functional enrichment analysis indicated that E2F3 primarily modulates critical processes like amino acid and lipid metabolism.These findings suggest that E2F3 likely regulates growth in the dwarf surf clam by influencing amino acid and lipid metabolism.Overall,this study advances our understanding on the function of E2F3 gene in growth regulation in bivalves,providing valuable insights for future research in this field.
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.
