Understanding the relationship between genotype and phenotype is a major biological question and being able to predict phenotypes based on molecular genotypes is integral to molecular breeding. Whole- genome duplicati...Understanding the relationship between genotype and phenotype is a major biological question and being able to predict phenotypes based on molecular genotypes is integral to molecular breeding. Whole- genome duplications have shaped the history of all flowering plants and present challenges to elucidating the relationship between genotype and phenotype, especially in neopolyploid species. Although single nucleotide polymorphisms （SNPs） have become popular tools for genetic mapping, discovery and appli- cation of SNPs in polyploids has been difficult. Here, we summarize common experimental approaches to SNP calling, highlighting recent polyploid successes. To examine the impact of software choice on these analyses, we called SNPs among five peanut genotypes using different alignment programs （BWA-mem and Bowtie 2） and variant callers （SAMtools, GATK, and Freebayes）. Alignments produced by Bowtie 2 and BWA-mem and analyzed in SAMtools shared 24.5% concordant SNPs, and SAMtools, GATK, and Freebayes shared 1.4% concordant SNPs. A subsequent analysis of simulated Brassica napus chromosome 1A and 1C genotypes demonstrated that, of the three software programs, SAMtools performed with the highest sensitivity and specificity on Bowtie 2 alignments. These results, however, are likely to vary among species, and we therefore propose a series of best practices for SNP calling in polyploids.展开更多
AIM: To investigate mitochondrial ATP 6 and 8 poly-morphisms in the colon and ileum of patients with ir-ritable bowel syndrome with diarrhea (IBS-D). METHODS: Twenty-eight patients fulfilling the Rome Ⅲ criteria for ...AIM: To investigate mitochondrial ATP 6 and 8 poly-morphisms in the colon and ileum of patients with ir-ritable bowel syndrome with diarrhea (IBS-D). METHODS: Twenty-eight patients fulfilling the Rome Ⅲ criteria for IBS-D and 28 healthy subjects were in-vestigated. All study participants underwent screening colonoscopy and mucosal biopsies were obtained from the colon and/or terminal ileum. Genomic DNA was ex-tracted from specimens based on standard protocols. Mitochondrial ATP (MT-ATP) 6 and 8 genes in speci-mens were polymerase chain reaction amplified and sequenced. Sequencing data were analyzed via Variant Reporter Software and compared with the reference sequence from Genbank (accession No. NC_012920) to indicate possible polymorphisms. The protocol was registered at www.clinicaltrials.gov as NCT01028898. RESULTS: Twenty-five polymorphic sites of MT-ATP 6 and 8 genes were detected and 12 of them were missense mutations. A median of two polymorphic sites in MT-ATP genes was found in colon specimens of controls while a median of three polymorphic sites was noted in patients with IBS-D (Mann-Whitney test, P=0.012). The variants of the colon and ileum speci-mens from the same subjects were identical in all but one case. Symptom duration in IBS was not found to be a significant factor associated with the mtDNA polymorphism (Spearman correlation, P=0.592). The mitochondrial DNA change at 8860 was present in all cases of both groups. The frequency of the 8701 poly-morphism was found to be the second most frequent; however, no statistical difference was noted between the groups (χ2 test, P=0.584). CONCLUSION: Patients with IBS-D have a higher inci-dence of MT-ATP 6 and 8 polymorphisms than healthy subjects, implying that the mtDNA polymorphism may play a role in IBS-D.展开更多
Objectives Peroxisome proliferator-activated receptor-γ2（PPARγ2） variant Pro12Ala was demonstrated with risk of coronary heart disease （CHD） and type 2 diabetes mellitus （T2DM）. Another variant C-689T in the p...Objectives Peroxisome proliferator-activated receptor-γ2（PPARγ2） variant Pro12Ala was demonstrated with risk of coronary heart disease （CHD） and type 2 diabetes mellitus （T2DM）. Another variant C-689T in the promoter was reported with lower receptor activity but lack of reports on association between C-689T and CHD or T2DM. Methods A total of 351 subjects without CHD and T2DM （controls） and 125 patients with CHD and T2DM （cases） were enrolled in our case-control study. Polymerase chain reaction-restricted fragments length polymorphism （PCR-RFLP） was used to detect Pro12Ala and C-689T polymorphisms. And effects on CHD merged with T2DM of the two polymorphisms were analyzed in individual and haplotype analyses. Results In the study, Pro12Pro, Pro12Ala and Ala12Ala genotype frequencies were 92.9%, 6.8% and 0.3% in controls; 92.8%, 7.2% and 0.0% in cases respectively whilst CC, CT and TT genotype frequencies were 93.4%, 6.3% and 0.3% in controls; 92.8%, 7.2% and 0.0% in cases respectively. Pro12Ala and C-689T polymorphisms were in strong linkage disequilibrium （D＇=0.81, P=0.000） and the observed haplotype frequency of Pro-C, Pro-T, Ala-C and Ala-T was 0.957, 0.006, 0.008 and 0.028 respectively. No significant associations were detected between the two polymorphisms and CHD merged with T2DM in either individual or haplotype analyses. In subjects with obesity [body mass index （BMI）≥25 kg/m^2], we found that both Pro12Ala and C-689T polymorphisms were associated with BMI. In haplotype analyses, we found that Pro12Ala and C-689T haplotypes had associations with systolic blood pressure in total population, with BMI, waist circle and total cholesterol（TC） in obesity subgroup and with fasting blood glucose and TC in males. Conclusions PPARγ2 Pro12Ala and C-689T polymorphisms and haplotypes affect the profiles of CHD merged with T2DM in Chinese Han people.展开更多
This paper aims to determine the possible role of estrogen receptor-β （ERβ） gene Rsal polymorphism on sperm fertility and early embryonic development in humans. Three groups of Chinese men were recruited： in vitr...This paper aims to determine the possible role of estrogen receptor-β （ERβ） gene Rsal polymorphism on sperm fertility and early embryonic development in humans. Three groups of Chinese men were recruited： in vitro fertilization （IVF） group, including 374 couples who underwent conventional IVF; intracytoplasmic sperm injection （ICSI） group, including 294 couples who underwent an ICSI procedure using ejaculated sperm; and azoospermic group, consisting of 197 couples who underwent ICSI using either testis or epididymis sperm. Rsal polymorphism in the ERβ gene was detected by polymerase chain reaction （PCR）-restriction fragment length polymorphism technique; fertilization and high-quality embryo rates were evaluated for each group. In each group, no significant differences were found in the overall rates of fertilization and high-quality embryos among GG, AG and AA genotypes. However, the proportion of cycles possessing a satisfactory high-quality embryo rate with the AA genotype was significantly lower than that in the wild-type GG genotype from each group. These results demonstrated that sperm possessing the ERβ RsalA genotype may have reduced fertilization ability and decreased early embryonic developmental potential, which could directly or indirectly contribute to the low fertilization rate and early embryonic developmental arrest in some cases.展开更多
Microbial ferric iron reduction, with organic carbon or hydrogen as the electron donor, is one of the most important biogeochemical processes in anoxic paddy soils; however, the diversity and community structure of hy...Microbial ferric iron reduction, with organic carbon or hydrogen as the electron donor, is one of the most important biogeochemical processes in anoxic paddy soils; however, the diversity and community structure of hydrogen-dependent dissimilatory iron-reducers remain unknown. Potential H2-dependent Fe（III）-reducing bacteria in paddy soils were explored using enrichment cultures with ferrihydrite or goethite as the electron acceptor and hydrogen as the electron donor. Terminal restriction fragment length polymorphism （T-RFLP） analysis and cloning/sequencing were conducted to reveal bacterial community structure. Results showed that Geobacter and Clost^dium were the dominant bacteria in the enrichment cultures. Fe（III） oxide mineral phases showed a strong effect on the community structure; Geobaeter and Clostridium were dominant in the ferrihydrite treatment, while Glostridium spp. were dominant in the goethite treatment. These suggested that H2-dependent Fe（lII）-redueing bacteria might be widely distributed in paddy soils and that besides Geobacter, Clostmdium spp. might also be an important group of H2-dependent Fe（III）-reducing microorganisms.展开更多
文摘Understanding the relationship between genotype and phenotype is a major biological question and being able to predict phenotypes based on molecular genotypes is integral to molecular breeding. Whole- genome duplications have shaped the history of all flowering plants and present challenges to elucidating the relationship between genotype and phenotype, especially in neopolyploid species. Although single nucleotide polymorphisms （SNPs） have become popular tools for genetic mapping, discovery and appli- cation of SNPs in polyploids has been difficult. Here, we summarize common experimental approaches to SNP calling, highlighting recent polyploid successes. To examine the impact of software choice on these analyses, we called SNPs among five peanut genotypes using different alignment programs （BWA-mem and Bowtie 2） and variant callers （SAMtools, GATK, and Freebayes）. Alignments produced by Bowtie 2 and BWA-mem and analyzed in SAMtools shared 24.5% concordant SNPs, and SAMtools, GATK, and Freebayes shared 1.4% concordant SNPs. A subsequent analysis of simulated Brassica napus chromosome 1A and 1C genotypes demonstrated that, of the three software programs, SAMtools performed with the highest sensitivity and specificity on Bowtie 2 alignments. These results, however, are likely to vary among species, and we therefore propose a series of best practices for SNP calling in polyploids.
文摘AIM: To investigate mitochondrial ATP 6 and 8 poly-morphisms in the colon and ileum of patients with ir-ritable bowel syndrome with diarrhea (IBS-D). METHODS: Twenty-eight patients fulfilling the Rome Ⅲ criteria for IBS-D and 28 healthy subjects were in-vestigated. All study participants underwent screening colonoscopy and mucosal biopsies were obtained from the colon and/or terminal ileum. Genomic DNA was ex-tracted from specimens based on standard protocols. Mitochondrial ATP (MT-ATP) 6 and 8 genes in speci-mens were polymerase chain reaction amplified and sequenced. Sequencing data were analyzed via Variant Reporter Software and compared with the reference sequence from Genbank (accession No. NC_012920) to indicate possible polymorphisms. The protocol was registered at www.clinicaltrials.gov as NCT01028898. RESULTS: Twenty-five polymorphic sites of MT-ATP 6 and 8 genes were detected and 12 of them were missense mutations. A median of two polymorphic sites in MT-ATP genes was found in colon specimens of controls while a median of three polymorphic sites was noted in patients with IBS-D (Mann-Whitney test, P=0.012). The variants of the colon and ileum speci-mens from the same subjects were identical in all but one case. Symptom duration in IBS was not found to be a significant factor associated with the mtDNA polymorphism (Spearman correlation, P=0.592). The mitochondrial DNA change at 8860 was present in all cases of both groups. The frequency of the 8701 poly-morphism was found to be the second most frequent; however, no statistical difference was noted between the groups (χ2 test, P=0.584). CONCLUSION: Patients with IBS-D have a higher inci-dence of MT-ATP 6 and 8 polymorphisms than healthy subjects, implying that the mtDNA polymorphism may play a role in IBS-D.
文摘Objectives Peroxisome proliferator-activated receptor-γ2（PPARγ2） variant Pro12Ala was demonstrated with risk of coronary heart disease （CHD） and type 2 diabetes mellitus （T2DM）. Another variant C-689T in the promoter was reported with lower receptor activity but lack of reports on association between C-689T and CHD or T2DM. Methods A total of 351 subjects without CHD and T2DM （controls） and 125 patients with CHD and T2DM （cases） were enrolled in our case-control study. Polymerase chain reaction-restricted fragments length polymorphism （PCR-RFLP） was used to detect Pro12Ala and C-689T polymorphisms. And effects on CHD merged with T2DM of the two polymorphisms were analyzed in individual and haplotype analyses. Results In the study, Pro12Pro, Pro12Ala and Ala12Ala genotype frequencies were 92.9%, 6.8% and 0.3% in controls; 92.8%, 7.2% and 0.0% in cases respectively whilst CC, CT and TT genotype frequencies were 93.4%, 6.3% and 0.3% in controls; 92.8%, 7.2% and 0.0% in cases respectively. Pro12Ala and C-689T polymorphisms were in strong linkage disequilibrium （D＇=0.81, P=0.000） and the observed haplotype frequency of Pro-C, Pro-T, Ala-C and Ala-T was 0.957, 0.006, 0.008 and 0.028 respectively. No significant associations were detected between the two polymorphisms and CHD merged with T2DM in either individual or haplotype analyses. In subjects with obesity [body mass index （BMI）≥25 kg/m^2], we found that both Pro12Ala and C-689T polymorphisms were associated with BMI. In haplotype analyses, we found that Pro12Ala and C-689T haplotypes had associations with systolic blood pressure in total population, with BMI, waist circle and total cholesterol（TC） in obesity subgroup and with fasting blood glucose and TC in males. Conclusions PPARγ2 Pro12Ala and C-689T polymorphisms and haplotypes affect the profiles of CHD merged with T2DM in Chinese Han people.
文摘This paper aims to determine the possible role of estrogen receptor-β （ERβ） gene Rsal polymorphism on sperm fertility and early embryonic development in humans. Three groups of Chinese men were recruited： in vitro fertilization （IVF） group, including 374 couples who underwent conventional IVF; intracytoplasmic sperm injection （ICSI） group, including 294 couples who underwent an ICSI procedure using ejaculated sperm; and azoospermic group, consisting of 197 couples who underwent ICSI using either testis or epididymis sperm. Rsal polymorphism in the ERβ gene was detected by polymerase chain reaction （PCR）-restriction fragment length polymorphism technique; fertilization and high-quality embryo rates were evaluated for each group. In each group, no significant differences were found in the overall rates of fertilization and high-quality embryos among GG, AG and AA genotypes. However, the proportion of cycles possessing a satisfactory high-quality embryo rate with the AA genotype was significantly lower than that in the wild-type GG genotype from each group. These results demonstrated that sperm possessing the ERβ RsalA genotype may have reduced fertilization ability and decreased early embryonic developmental potential, which could directly or indirectly contribute to the low fertilization rate and early embryonic developmental arrest in some cases.
基金Supported by the National Natural Science Foundation of China (No.41090282)
文摘Microbial ferric iron reduction, with organic carbon or hydrogen as the electron donor, is one of the most important biogeochemical processes in anoxic paddy soils; however, the diversity and community structure of hydrogen-dependent dissimilatory iron-reducers remain unknown. Potential H2-dependent Fe（III）-reducing bacteria in paddy soils were explored using enrichment cultures with ferrihydrite or goethite as the electron acceptor and hydrogen as the electron donor. Terminal restriction fragment length polymorphism （T-RFLP） analysis and cloning/sequencing were conducted to reveal bacterial community structure. Results showed that Geobacter and Clost^dium were the dominant bacteria in the enrichment cultures. Fe（III） oxide mineral phases showed a strong effect on the community structure; Geobaeter and Clostridium were dominant in the ferrihydrite treatment, while Glostridium spp. were dominant in the goethite treatment. These suggested that H2-dependent Fe（lII）-redueing bacteria might be widely distributed in paddy soils and that besides Geobacter, Clostmdium spp. might also be an important group of H2-dependent Fe（III）-reducing microorganisms.
