Maize is a globally important crop that was a classic model plant for genetic studies. Here, we report a 2.2 Gb draft genome sequence of an elite maize line, HuangZaoSi (HZS). Hybrids bred from HZS-improved lines (HILs) are planted in more than 60% of maize fields in China. Proteome clustering of six completed sequenced maize genomes show that 638 proteins fall into 264 HZS-specific gene families with the majority of contributions from tandem duplication events. Resequencing and comparative analysis of 40 HZSrelated lines reveals the breeding history of HILs. More than 60% of identified selective sweeps were clustered in identity-by-descent conserved regions, and yield-related genes/QTLs were enriched in HZS characteristic selected regions. Furthermore, we demonstrated that HZS-specific family genes were not uniformly distributed in the genome but enriched in improvement/function-related genomic regions. This study provides an important and novel resource for maize genome research and expands our knowledge on the breadth of genomic variation and improvement history of maize.

BackgroundMolecular epidemiological studies have shown that gene polymorphisms of vitamin D receptor (VDR) are associated with prostate cancer risks. However, previous results from many molecular studies remain inconsistent.MethodsBlood samples were collected from 122 prostate cancer patients and 130 age-matched control subjects in the Han population of Southern China. The differences of VDR gene polymorphism between cancer cases and controls were determined by PCR-RFLP, examiming FokI (exon 2), BsmI, Tru9I, ApaI (intron 9), and TaqI (exon 9). Associations between the VDR gene polymorphism and prostate cancer risk were calculated in an unconditional logistic regression model. Linkage disequilibrium and haplotypes were analyzed with the SHEsis software.ResultsOf five polymorphisms, BsmI was shown to associate with prostate cancer, while FokI, Tru9I, ApaI, and TaqI did not show any significant association. After adjustment for age, the BsmI 'B' allele was associated with an almost 1/3-fold risk (OR = 0.35, 95%CI: 0.15-0.80) of the occurrence of prostate cancer, a 1/5-fold risk (OR = 0.20, 95%CI: 0.06-0.68) of poorly differentiated prostate cancer, and a 1/10-fold risk (OR = 0.10, 95%CI: 0.01-0.78) of aggressive prostate cancer compared with the 'b' allele, especially among older men (>71 years). In addition, haplotype analysis revealed that the 'F-b-U-A-T' was more frequent found in cases than in controls (3.4% vs 0.0%, P = 0.0035), while the frequency of haplotype 'F-B-U-a-T' was 0.8% in cases, significantly lower than in controls (3.9%, P = 0.019).ConclusionOur experiments provide evidences that genetic polymorphisms in the VDR gene may be potential risk factors for prostate cancer in the Han population of southern China and the susceptibility to prostate cancer is associated with ethnicity and geographic location.

Despite the availability of numerous molecular markers in maize, effective evaluation of all types of germplasm resources, accurate identification of varieties and analysis of a large number of materials in a timely, low-cost manner is challenging. Here, we present Maize6H-60K, a genome-wide single nucleotide polymorphism (SNP) array to facilitate maize genotyping. We first identified 160 million variants by sequencing data of 388 representative inbreds and then tiled 200 000 high-quality variants on a screening array. These variants were further narrowed down to 61 282 using stringent filtering criteria. Among the 60 000 markers, 21 460 SNPs (35%) were within genic regions and 12 835 (21%) were located in coding regions. To assess their effectiveness, 329 inbreds, 221 hybrids, 34 parent-offspring sets and six breeding samples were genotyped. Overall, 48 972 SNPs (80%) were categorized into the highest quality class, that of 'poly high resolution'. A total of 54 658 (89.29%) and 53 091 (86.73%) SNPs had minor allele frequency values ≥ 0.20 in inbreds and hybrids respectively. A linkage disequilibrium (LD) analysis revealed that LD decline was in equilibrium when r 2 was between 0.10 and 0.15, which corresponds to a physical distance of 400-600 kb. UPGMA clustering analysis divided the 329 inbred lines into nine groups that were consistent with known pedigrees. A background analysis of breeding materials indicated that the 60 000 markers were suitable for evaluation of breeding populations constructed by materials between or within heterotic groups. The developed Maize6H-60K array should be an important tool in maize genetic studies, variety identification and molecular breeding.

Southern corn rust (SCR) caused by Puccinia polysora Underw. is a major disease causing severe yield losses during maize production. Here, we identified and mapped the SCR resistance gene RppM from the near-isogenic line Kangxiujing2416 (Jing2416K), which harbors RppM in the genetic background of the susceptible inbred line Jing2416. In this study, the inheritance of SCR resistance was investigated in F 2 and F 3 populations derived from a cross between Jing2416K and Jing2416. The observed 3:1 segregation ratio of resistant to susceptible plants indicated that the SCR resistance is controlled by a single dominant gene. Using an F 2 population, we performed bulked segregant analysis (BSA) sequencing and mapped RppM to a 3.69-Mb region on chromosome arm 10S. To further narrow down the region harboring RppM, we developed 13 insertion/deletion (InDel) markers based on the sequencing data. Finally, RppM was mapped to a region spanning 110-kb using susceptible individuals from a large F 2 population. Two genes (Zm00001d023265 and Zm00001d023267) encoding putative CC-NBS-LRR (coiledcoiled, nucleotide-binding site, and leucine-rich repeat) proteins, a common characteristic of R genes, were located in this region (B73 RefGen_v4 reference genome). Sequencing and comparison of the two genes cloned from Jing2416K and Jing2416 revealed sequence variations in their coding regions. The relative expression levels of these two genes in Jing2416K were found to be significantly higher than those in Jing2416. Zm00001d023265 and Zm00001d023267 are thus potential RppM candidates.

The detection of genetically modified (GM) maize events is an inevitable necessity under the strict regulatory systems of many countries. To screen for GM maize events, we developed a multiplex PCR system to specifically detect 29 GM maize events as well as the cauliflower mosaic virus 35S promoter, the Agrobacterium tumefaciens nos terminator, the Streptomyces viridochromogenes pat gene, and the endogenous zSSIIb maize reference gene. These targets were divided into five panels for screening and event-specific detection by multiplex (10-plex, 7-plex, 7-plex, 4-plex, and 5-plex) PCR. All amplification products were separated and visualized by fluorescence capillary electrophoresis (CE). By taking advantage of the high resolution, multiple fluorescence detection, and high sensitivity of CE, our system was able to identify all targets simultaneously with a limit of detection of 0.1%. The accurate identification of specific amplification peaks from different GM maize materials by CE confirmed the specificity of the system. To verify the practical applicability of this system, we analyzed 20 blind samples. We successfully identified five MON810, four TC1507, and three MIR162 samples. The detection of concomitant elements also verified the accuracy of this approach. Our system can, therefore, be used for the screening and detection of GM maize events. The system, which is easy to use, facilitates high-throughput detection with the help of a high-throughput platform and automated identification software. Multiplex PCR coupled with CE is, thus, very suitable for the detection of genetically modified organisms (GMOs) with a large number of detection targets. Additional multiplexed electrophoretic targets can be easily incorporated as well, thereby increasing the usefulness of this system as the number of GMO events continues to increase.

Impairment of theory of mind (ToM) is a common phenomenon following traumatic brain injury (TBI) that has clear effects on patients' social functioning. A growing body of research has focused on this area, and several methods have been developed to assess ToM deficiency. Although an informant assessment scale would be useful for examining individuals with TBI, very few studies have adopted this approach. The purpose of the present study was to develop an informant assessment scale of ToM for adults with traumatic brain injury (IASToM-aTBI) and to test its reliability and validity with 196 adults with TBI and 80 normal adults. A 44-item scale was developed following a literature review, interviews with patient informants, consultations with experts, item analysis, and exploratory factor analysis (EFA). The following three common factors were extracted: social interaction, understanding of beliefs, and understanding of emotions. The psychometric analyses indicate that the scale has good internal consistency reliability, split-half reliability, test-retest reliability, inter-rater reliability, structural validity, discriminate validity and criterion validity. These results provide preliminary evidence that supports the reliability and validity of the IASToM-aTBI as a ToM assessment tool for adults with TBI.

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To strengthen the management of maize varieties and the protection of intellectual property rights to new varieties, we constructed a comprehensive single nucleotide polymorphism (SNP)-DNA standard fingerprint database of 20,075 materials covering nationally and provincially approved maize hybrid lines, hybridized combinations, and inbred lines. The database was based on 200 core SNPs selected from 60 K SNPs distributed in intragenic regions, including 106 (53.0%) located in exons. Average minor allele frequencies (MAF) of the 200 SNPs in 6755 maize hybrids, 7837 hybridized combinations, and 3478 inbred lines were 0.385, 0.350, and 0.378, respectively, with corresponding average polymorphism information content (PIC) values of 0.354, 0.335, and 0.351. Heterozygous genotype frequencies of maize hybrids, hybridized combinations, and inbred lines averaged 0.48, 0.47, and 0.012, respectively. The number of different loci in the three different maize groups ranged from one up to 164, 160, and 140, respectively. The percentage of different SNPs within 5% (the number of difference SNPs is less than 10) accounted for 0.013%, 0.011%, and 0.030% among pairwise comparisons of samples within hybrid lines, hybridized combinations and inbred lines, respectively. Genetic distances between varieties based on the 200 core SNPs were highly correlated with those obtained using 60 K SNPs, with a correlation coefficient of 0.82 and 0.87 in in inbred and hybrid lines, respectively. The maize SNP-DNA fingerprint database established in this study can play an important role in variety authentication, purity determination and the protection of variety rights, thereby providing reliable, comprehensive data support for use in the seed industry.