QTL-seq and transcriptomic integrative analyses reveal two positively regulated genes that control the low-temperature germination ability of MTP-maize introgression lines.

KEY MESSAGE: Two candidate genes (ZmbZIP113 and ZmTSAH1) controlling low-temperature germination ability were identified by QTL-seq and integrative transcriptomic analyses. The functional verification results showed that two candidate genes positively regulated the low-temperature germination ability of IB030. Low-temperature conditions cause slow maize (Zea mays L.) seed metabolism, resulting in slow seedling emergence and irregular seedling emergence, which can cause serious yield loss. Thus, improving a maize cultivar's low-temperature germination ability (LTGA) is vital for increasing yield production. Wild relatives of maize, such as Z. perennis and Tripsacum dactyloides, are strongly tolerant of cold stress and can thus be used to improve the LTGA of maize. In a previous study, the genetic bridge MTP was constructed (from maize, T. dactyloides, and Z. perennis) and used to obtain a highly LTGA maize introgression line (IB030) by backcross breeding. In this study, IB030 (Strong-LTGA) and Mo17 (Weak-LTGA) were selected as parents to construct an F2 offspring. Additionally, two major QTLs (qCS1-1 and qCS10-1) were mapped. Then, RNA-seq was performed using seeds of IB030 and the recurrent parent B73 treated at 10 °C for 27 days and 25 °C for 7 days, respectively, and two candidate genes (ZmbZIP113 and ZmTSAH1) controlling LTGA were located using QTL-seq and integrative transcriptomic analyses. The functional verification results showed that the two candidate genes positively regulated LTGA of IB030. Notably, homologous cloning showed that the source of variation in both candidate genes was the stable inheritance of introgressed alleles from Z. perennis. This study was thus able to analyze the LTGA mechanism of IB030 and identify resistance genes for genetic improvement in maize, and it proved that using MTP genetic bridge confers desirable traits or phenotypes of Z. perennis and tripsacum essential to maize breeding systems.

QTL Mapping and a Transcriptome Integrative Analysis Uncover the Candidate Genes That Control the Cold Tolerance of Maize Introgression Lines at the Seedling Stage.

Chilling injury owing to low temperatures severely affects the growth and development of maize (Zea mays.L) seedlings during the early and late spring seasons. The existing maize germplasm is deficient in the resources required to improve maize's ability to tolerate cold injury. Therefore, it is crucial to introduce and identify excellent gene/QTLs that confer cold tolerance to maize for sustainable crop production. Wild relatives of maize, such as Z. perennis and Tripsacum dactyloides, are strongly tolerant to cold and can be used to improve the cold tolerance of maize. In a previous study, a genetic bridge among maize that utilized Z. perennis and T. dactyloides was created and used to obtain a highly cold-tolerant maize introgression line (MIL)-IB030 by backcross breeding. In this study, two candidate genes that control relative electrical conductivity were located on MIL-IB030 by forward genetics combined with a weighted gene co-expression network analysis. The results of the phenotypic, genotypic, gene expression, and functional verification suggest that two candidate genes positively regulate cold tolerance in MIL-IB030 and could be used to improve the cold tolerance of cultivated maize. This study provides a workable route to introduce and mine excellent genes/QTLs to improve the cold tolerance of maize and also lays a theoretical and practical foundation to improve cultivated maize against low-temperature stress.

Pretreatment HIV drug resistance in adults initiating antiretroviral therapy in China, 2017.

BACKGROUND: After the scale-up of antiretroviral therapy (ART) for HIV infected people, increasing numbers of patients have pretreatment drug resistance (PDR). In this study, the prevalence of PDR was evaluated in adults initiating antiretroviral therapy in China. METHODS: Blood samples were obtained from 1943 patients who initiated antiretroviral therapy (ART) in 2017 from 13 provinces or cities in China. Pol sequences were used to analyze drug resistance and construct transmission networks. Logistic regression model was used to estimate the potential factors associated with PDR. RESULTS: In total, 1711 eligible patients (76.0% male; 87.8% aged ≥ 25 years) were included, of which 117 (6.8%) had PDR. The highest rates of PDR were 12.2% in Liangshan Prefecture of Sichuan and 9.3 and 8.9% in Dehong and Lincang Prefecture of Yunnan. A multivariate logistic regression analysis revealed that PDR was significantly higher among intravenous drug users (adjusted Odds Ratio (aOR) = 2.64, 95% CI: 1.57-4.44) and individuals from Liangshan, Dehong, and Lincang (aOR = 2.04, 95% CI: 1.26-3.30). In total, 754 sequences were used to generate 164 transmission networks. Five transmission networks had two or three sequences containing the same mutations, two networks contained subjects from Liangshan, and one network contained subjects from Dehong. CONCLUSIONS: Overall, the PDR prevalence was moderate, with a particularly high prevalence in areas with severe HIV epidemics. These results indicate the importance of continuous PDR monitoring in patients initiating antiretroviral therapy.

[An investigation of vaccination in children with human immunodeficiency virus infection].

OBJECTIVE: To investigate the status of vaccination in children with human immunodeficiency virus (HIV) infection. METHODS: A questionnaire survey was performed in 148 children in Hunan province, China who were registered in China's Acquired Immune Deficiency Syndrome Comprehensive Response Information Management System up to December 31, 2016 and were aged <15 years at the time of confirmed diagnosis of HIV infection. The information on vaccination, diagnosis of HIV infection, and diagnosis and treatment of related diseases was collected. RESULTS: Of the 148 children with HIV infection, there were 70 boys (47.3%) and 78 girls (52.7%); 140 children had an age of 3.8 (0.2-14.8) years at the time of confirmed diagnosis, and 8 children refused to answer this question. Mother-to-child transmission was found in 133 children (91.7%), blood transmission in 1 child (0.7%), and unknown in 14 children (9.5%). Of the 148 children, 129 (87.2%) received antiviral therapy and 19 (12.8%) did not receive such treatment. The vaccination rates of hepatitis B vaccine, bacille Calmette-Guérin vaccine, poliomyelitis live attenuated vaccine and diphtheria-pertussis-tetanus vaccine ranged from 70.9% to 77.7%, which was significantly lower than the national level (≥97%); the vaccination rates of the other vaccines in the National Immunization Program gradually decreased with age. No severe adverse effects were reported after vaccination. CONCLUSIONS: Mother-to-child transmission is the main route of HIV infection in Chinese children. The diagnosis of children with HIV infection is significantly delayed, with low vaccination rates. Efforts should be made to strengthen early diagnosis, early treatment and vaccination in children with HIV infection, in order to improve their quality of life.

Prevalence of hepatitis B virus and hepatitis C virus in patients with human immunodeficiency virus infection in Central China.

Co-infection of hepatitis B virus (HBV) and/or hepatitis C virus (HCV) with human immunodeficiency virus (HIV) has an adverse effect on liver disease progression. This study investigated the prevalence of HBV and/or HCV co-infection in HIV-infected patients in Central China. A total of 978 HIV-infected patients from Hunan Province were enrolled. HBV serum markers, anti-hepatitis-C-virus antibody (anti-HCV), HBV DNA, and HBV genotypes were analyzed. The prevalence of hepatitis B surface antigen (HBsAg) and anti-HCV in HIV-infected patients was 19.4 % and 62.4 %, respectively. The prevalence of anti-HCV in HIV-positive intravenous drug users was 93.6 %. Among HBsAg-positive patients, 88.1 % were found to have at least one HBV serum marker. The rates of HIV mono-infection, HBV/HIV dual infection, HCV/HIV dual infection, and HBV/HCV/HIV triple infection were 30.4 %, 7.2 %, 50.2 %, and 12.2 %, respectively. Antibody to HBsAg (Anti-HBs) was more common in anti-HCV-positive than anti-HCV-negative patients (53.3 % vs 40.2 %, P = 0.000), but isolated hepatitis B core antibody (anti-HBc) was more common in anti-HCV-negative than anti-HCV-positive patients (24.2 % vs 12.3 %, P = 0.000). Hepatitis B e antigen (HBeAg) and sexual transmission were independent risk factors for active HBV replication. Intravenous drug use and male sex were independent risk factors, but old age and presence of HBeAg were independent protective factors for anti-HCV. Co-infection of HBV and/or HCV with HIV infection is common in central China. HCV status is associated with anti-HBs and isolated anti-HBc in co-infected patients.

[Genetic characteristics of HIV-1 CRF01_AE strains in four provinces, southern China].

OBJECTIVE: To analyze the genetic characteristics of HIV-1 CRF01_AE strains prevailing in the four provinces of southern China. METHODS: Plasma samples were collected from the newly diagnosed HIV-1 individuals reported in 2006 in Guangdong, Guangxi, Jiangxi and Hunan province. The gag and env gene fragments were amplified from RNA template extracted from plasma using RT and nested PCR methods. CRF01_AE sequences were analyzed by phylogenetic methods and characterized by calculating the genetic distance and Entropy analysis. RESULTS: Two main epidemic clusters were found to exist in the CRF01_AE strains from 210 HIV-1 CRF01_ AE infected individuals collected in the 4 provinces, southern China. It was found that no international reference strain was closely correlated with cluster I, which including 123 samples. The strains in cluster II, consisting 57 cases of samples, were closely related with the strains identified in Vietnam. Genetic distance analysis of gag and env genes showed that the diversity of cluster I was obviously less than that of cluster II. Data on nucleotide polymorphism showed that nucleotides compositions of 42 sites in gag and 40 sites in env were significantly different between the two clusters. When compared with cluster II, the polymorphism decreased at 61 nucleotide sites but increased at 21 sites in cluster I. CONCLUSION: This was the first report describing that two main epidemic clusters were existed in CRF01_AE strains prevailing in the 4 provinces, Southern China. The virus in cluster I was the dominant strain in this region, with shorter period of circulation and higher proportion seen in the HIV-infected population, which might belong to CRF01_AE strain with certain features facilitating the spread of the virus. The virus in cluster II was highly homology with the CRF01_AE strains from Vietnam, and seemed to have had several events of epidemics in populations in border regions of China and Vietnam.

[Study on the threshold of HIV-1 drug resistance in Hunan province].

OBJECTIVE: To survey the prevalence of HIV-1 drug resistance in patients newly diagnosed as HIV positive and who were younger than 25 years of age but had not received treatment with antiretroviral treatment (ART) in Hunan province. METHODS: Serum specimens of HIV infected individuals were collected and HIV-1 pol genetic mutations associated with drug resistance were identified with PCR and interpreted with Stanford HIV Drug Resistance Database. RESULTS: A total number of 69 patients whose HIV sequences were amplified successfully with 2 (2.9%) specimens appeared mutations associated with HIV-1 drug resistance in the reverse transcriptase region, including one as V75M and the other one as K103N and V181C. Data showed that the prevalence of drug resistance in Hunan was 2.9%. CONCLUSION: The first line regiments of national ART seemed still effective. Most of the AIDS patients did not need to be tested on drug resistance status before starting ART. However, it is important to start HIV drug resistance surveillance in no time.