Identification and Validation of Candidate Genes Conferring Resistance to Downy Mildew in Maize (Zea mays L.).

Downy mildew (DM) is a major disease of maize that causes significant yield loss in subtropical and tropical regions around the world. A variety of DM strains have been reported, and the resistance to them is polygenically controlled. In this study, we analyzed the quantitative trait loci (QTLs) involved in resistance to Peronosclerospora sorghi (sorghum DM), P. maydis (Java DM), and Sclerophthora macrospora (crazy top DM) using a recombinant inbred line (RIL) from a cross between B73 (susceptible) and Ki11 (resistant), and the candidate genes for P. sorghi, P. maydis, and S. macrospora resistance were discovered. The linkage map was constructed with 234 simple sequence repeat (SSR) and restriction fragment length polymorphism (RFLP) markers, which was identified seven QTLs (chromosomes 2, 3, 6, and 9) for three DM strains. The major QTL, located on chromosome 2, consists of 12.95% of phenotypic variation explained (PVE) and a logarithm of odds (LOD) score of 14.12. Sixty-two candidate genes for P. sorghi, P. maydis, and S. macrospora resistance were obtained between the flanked markers in the QTL regions. The relative expression level of candidate genes was evaluated by quantitative real-time polymerase chain reaction (qRT-PCR) using resistant (CML228, Ki3, and Ki11) and susceptible (B73 and CML270) genotypes. For the 62 candidate genes, 15 genes were upregulated in resistant genotypes. Among these, three (GRMZM2G028643, GRMZM2G128315, and GRMZM2G330907) and AC210003.2_FG004 were annotated as leucine-rich repeat (LRR) and peroxidase (POX) genes, respectively. These candidate genes in the QTL regions provide valuable information for further studies related to P. sorghi, P. maydis, and S. macrospora resistance.

Transcriptome Analysis of Flowering Time Genes under Drought Stress in Maize Leaves.

Flowering time is an important factor determining yield and seed quality in maize. A change in flowering time is a strategy used to survive abiotic stresses. Among abiotic stresses, drought can increase anthesis-silking intervals (ASI), resulting in negative effects on maize yield. We have analyzed the correlation between flowering time and drought stress using RNA-seq and bioinformatics tools. Our results identified a total of 619 genes and 126 transcripts whose expression was altered by drought stress in the maize B73 leaves under short-day condition. Among drought responsive genes, we also identified 20 genes involved in flowering times. Gene Ontology (GO) enrichment analysis was used to predict the functions of the drought-responsive genes and transcripts. GO categories related to flowering time included reproduction, flower development, pollen-pistil interaction, and post-embryonic development. Transcript levels of several genes that have previously been shown to affect flowering time, such as PRR37, transcription factor HY5, and CONSTANS, were significantly altered by drought conditions. Furthermore, we also identified several drought-responsive transcripts containing C2H2 zinc finger, CCCH, and NAC domains, which are frequently involved in transcriptional regulation and may thus have potential to alter gene expression programs to change maize flowering time. Overall, our results provide a genome-wide analysis of differentially expressed genes (DEGs), novel transcripts, and isoform variants expressed during the reproductive stage of maize plants subjected to drought stress and short-day condition. Further characterization of the drought-responsive transcripts identified in this study has the potential to advance our understanding of the mechanisms that regulate flowering time under drought stress.

Identification of downy mildew resistance gene candidates by positional cloning in maize (Zea mays subsp. mays; Poaceae).

PREMISE OF THE STUDY: Positional cloning in combination with phenotyping is a general approach to identify disease-resistance gene candidates in plants; however, it requires several time-consuming steps including population or fine mapping. Therefore, in the present study, we suggest a new combined strategy to improve the identification of disease-resistance gene candidates. METHODS AND RESULTS: Downy mildew (DM)-resistant maize was selected from five cultivars using a spreader row technique. Positional cloning and bioinformatics tools were used to identify the DM-resistance quantitative trait locus marker (bnlg1702) and 47 protein-coding gene annotations. Eventually, five DM-resistance gene candidates, including bZIP34, Bak1, and Ppr, were identified by quantitative reverse-transcription PCR (RT-PCR) without fine mapping of the bnlg1702 locus. CONCLUSIONS: The combined protocol with the spreader row technique, quantitative trait locus positional cloning, and quantitative RT-PCR was effective for identifying DM-resistance candidate genes. This cloning approach may be applied to other whole-genome-sequenced crops or resistance to other diseases.

Effects of spatial resolution and tube current on computer-aided detection of polyps on CT colonographic images: phantom study.

PURPOSE: To prospectively evaluate the effects of z-axis spatial resolution and tube current on the sensitivity of a commercially available computed tomographic (CT) colonography computer-aided diagnosis (CAD) system for polyp detection by using pig colon phantoms. MATERIALS AND METHODS: Ninety-six polyps were created and analyzed in 14 pig colon phantoms. CT colonography was performed by using a 16-detector CT scanner at 0.75-mm collimation; 10, 50, 100, and 160 mAs; and a pitch of 1.5. At each milliampere-second setting, the CT images were reconstructed with a section thickness (ST) of 1.5 mm and a reconstruction increment (RI) of 1.3 mm. To evaluate the effect of z-axis spatial resolution, CT images were also reconstructed at 100 mAs with various SI and RI combinations (respectively: 1.0 and 0.7 mm, 3.0 and 2.0 mm, 3.0 and 3.0 mm, 5.0 and 5.0 mm). The phantom data were then analyzed by using a CAD program. CAD performance with different CT parameters was calculated and compared in terms of per-polyp sensitivity and number of false-positive (FP) findings per data set. RESULTS: At a constant tube current of 100 mAs, the polyp detection rate was significantly higher in data sets obtained with SI and RI combinations of 1.0 and 0.7 mm, respectively (81% [78/96]), and 1.5 and 1.3 mm, respectively (75% [72/96]), than in those obtained with the three thicker ST-RI settings (27% [26/96] to 64% [61/96]) (P < .01). A similar trend was observed, regardless of polyp size or morphology. However, the number of FP findings at the 1.0 mm and 0.7 mm setting (8.9 per phantom) was also significantly greater than that at the thicker ST-RI settings (4.0-6.1 per phantom) (P < .05). At a constant z-axis spatial resolution (1.5-mm ST, 1.3-mm RI), CAD polyp detection rate and number of FP findings per phantom remained nearly constant-close to 78% (75/96) and 6.1, respectively-at various tube current settings. CONCLUSION: CAD performance in polyp detection at CT colonography is highly dependent on z-axis spatial resolution. However, tube current is not an influencing factor in CAD performance at a given z-axis spatial resolution. SUPPLEMENTAL MATERIAL: http://radiology.rsnajnls.org/cgi/content/full/2482071025/DC1.