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In this study, we utilized published carrot sequences as well as heterologous PCR approaches with primers derived from sequence information of other plant species to isolate 24 putative genes coding for carotenoid bio-synthesis enzymes in carrot. Twenty-two of these genes were placed on the carrot genetic linkage map developed from a cross between orange-rooted and white- rooted carrot. The carotenoid genes were distributed in eight of the nine linkage groups in the carrot genome recommending their use for merging maps. Two genes co-localized with a genomic region spanning one of the most significant quantitative trait loci (QTL) for carotenoid accumulation.

The American cranberry (Vaccinium macrocarpon Ait.) is a major commercial fruit crop in North America, but limited genetic resources have been developed for the species. Furthermore, the paucity of codominant DNA markers has hampered the advance of genetic research in cranberry and the Ericaceae family in general. Therefore, we used Roche 454 sequencing technology to perform low-coverage whole genome shotgun sequencing of the cranberry cultivar ‘HyRed’. After de novo assembly, the obtained sequence covered 266.3 Mb of the estimated 540–590 Mb in cranberry genome. A total of 107,244 SSR loci were detected with an overall density across the genome of 403 SSR/Mb. The AG repeat was the most frequent motif in cranberry accounting for 35% of all SSRs and together with AAG and AAAT accounted for 46% of all loci discovered. To validate the SSR loci, we designed 96 primer-pairs using contig sequence data containing perfect SSR repeats, and studied the genetic diversity of 25 cranberry genotypes. We identified 48 polymorphic SSR loci with 2–15 alleles per locus for a total of 323 alleles in the 25 cranberry genotypes. Genetic clustering by principal coordinates and genetic structure analyzes confirmed the heterogeneous nature of cranberries. The parentage composition of several hybrid cultivars was evident from the structure analyzes. Whole genome shotgun 454 sequencing was a cost-effective and efficient way to identify numerous SSR repeats in the cranberry sequence for marker development.

Background Transmission of Plasmodium greatly depends on the foraging behaviour of its mosquito vector ( Anopheles spp.). The accessibility of blood hosts and availability of plant sugar (i.e., nectar) sources, together with mosquito energy state, have been shown to modulate blood feeding (and thus biting rates) of anopheline mosquitoes. In this study, the influence of mosquito starvation status and availability of nectar on the decision of female Anopheles gambiae mosquitoes to leave a bed net-protected blood host was examined. Methods Two small-scale mesocosm experiments were conducted using female mosquitoes starved for 0, 24 or 48 h, that were released inside a specially constructed hut with mesh-sealed exits and containing a bed net-protected human volunteer. Floral cues were positioned on one side of the hut or the other. Several biologically plausible exponential decay models were developed that characterized the emigration rates of mosquitoes from the huts. These varied from simple random loss to leaving rates dependent upon energy state and time. These model fits were evaluated by examining their fitted parameter estimates and comparing Akaike information criterion. Results Starved mosquitoes left domiciles at a higher rate than recently fed individuals however, there was no difference between 1- and 2-day-starved mosquitoes. There was also no effect of floral cue placement. The best fitting emigration model was one based on both mosquito energy state and time whereas the worst fitting model was one based on the assumption of constant leaving rates, independent of time and energy state. Conclusions The results confirm that mosquito-leaving behaviour is energy-state dependent, and provide some of the first evidence of state-dependent domicile emigration in An. gambiae , which may play a role in malarial transmission dynamics. Employment of simple, first-principle, mechanistic models can be very useful to our understanding of why and how mosquitoes leave domiciles.

The nutritional value and yield potential of US Western Shipping melon (USWS; Cucumis melo L.) could be improved through the introgression of genes for early fruit maturity (FM) and the enhancement of the quantity of β-carotene (QβC) in fruit mesocarp (i.e., flesh color). Therefore, a set of 116 F₃ families derived from the monoecious, early FM Chinese line 'Q 3-2-2' (no β-carotene, white mesocarp) and the andromonoecious, late FM USWS line 'Top Mark' (possessing β-carotene, orange mesocarp) were examined during 2 years in Wisconsin, USA to identify quantitative trait loci (QTL) associated with FM and QβC. A 171-point F₂₋₃ based map was constructed and used for QTL analysis. Three QTL associated with QβC were detected, which explained a significant portion of the observed phenotypic variation (flesh color; R ² = 4.0-50.0%). The map position of one QTL (β-carM.E.9.1) was uniformly aligned with one carotenoid-related gene (Orange gene), suggesting its likely role in QβC in this melon population and putative relationship with the melon white flesh (wf) gene. Two major (FM.6.1 and FM.11.1; R ² >= 20%) and one minor QTL (FM.2.1; R ² = 8%) were found to be associated with FM. This map was then merged with a previous recombinant inbred line (RIL)-based map used to identify seven QTL associated with QβC in melon fruit. This consensus map [300 molecular markers (187 co-dominant melon and 14 interspecific; 10 LG)] provides a framework for the further dissection and cloning of published QTL, which will consequently lead to more effective trait introgression in melon.

Purpose Artificial intelligence (AI) based commercial software can be used to automatically delineate organs at risk (OAR), with potential for efficiency savings in the radiotherapy treatment planning pathway, and reduction of inter‐ and intra‐observer variability. There has been little research investigating gross failure rates and failure modes of such systems. Method 50 head and neck (H&N) patient data sets with “gold standard” contours were compared to AI‐generated contours to produce expected mean and standard deviation values for the Dice Similarity Coefficient (DSC), for four common H&N OARs (brainstem, mandible, left and right parotid). An AI‐based commercial system was applied to 500 H&N patients. AI‐generated contours were compared to manual contours, outlined by an expert human, and a gross failure was set at three standard deviations below the expected mean DSC. Failures were inspected to assess reason for failure of the AI‐based system with failures relating to suboptimal manual contouring censored. True failures were classified into 4 sub‐types (setup position, anatomy, image artefacts and unknown). Results There were 24 true failures of the AI‐based commercial software, a gross failure rate of 1.2%. Fifteen failures were due to patient anatomy, four were due to dental image artefacts, three were due to patient position and two were unknown. True failure rates by OAR were 0.4% (brainstem), 2.2% (mandible), 1.4% (left parotid) and 0.8% (right parotid). Conclusion True failures of the AI‐based system were predominantly associated with a non‐standard element within the CT scan. It is likely that these non‐standard elements were the reason for the gross failure, and suggests that patient datasets used to train the AI model did not contain sufficient heterogeneity of data. Regardless of the reasons for failure, the true failure rate for the AI‐based system in the H&N region for the OARs investigated was low (∼1%).

The metabolic precursor of vitamin A, β-carotene, is essential for human health. The gene(s) controlling β-carotene quantity (QβC) has been introgressed from Xishuangbanna gourd (XIS, possessing β-carotene; Cucumis sativus L. var. xishuangbannanesis Qi et Yuan; 2n = 2x = 14) into cultivated cucumber (no β-carotene; Cucumis sativus L.). To determine the inheritance of QβC in cucumber fruit endocarp, F1 progeny and a set of 124 F7 recombinant inbred lines (RILs) derived from the cultivated cucumber line CC3 and XIS line SWCC8 were evaluated for QβC during 2009 and 2010 in Nanjing, China. Segregation analysis revealed that endocarp QβC of greenhouse-grown fruit was controlled by a single recessive gene. Further, marker analysis indicated the gene controlling QβC was linked to seven SSR markers on linkage group 3, where their order was SSR20710–SSR19511–SSR15419–SSR07706–ore–SSR23231–SSR11633–SSR20270. These markers and the putative candidate gene were mapped to cucumber chromosome 3DS. An evaluation of 30 genetically diverse cucumber lines indicated that marker SSR07706 has utility in further genetic analyses of the QβC orange endocarp gene, designated ore. Moreover, the markers defined herein may have utility for marker-assisted selection directed towards the development of cucumber germplasm with high fruit β-carotene content.

Understanding how mosquito host-seeking behavior changes according to different energy levels in Anopheles gambiae (Diptera: Culicidae) when confronted with a known chemical barrier (N,N-Diethyl-3-methylbenzamide; DEET) is of interest for vector control strategies. We used two identical straight-tube olfactometers to mimic domiciles containing a simulated blood host (human foot odor from a recently-used sock) wrapped in a DEET impregnated net (1 or 0.1 %) and a sugar source (honey) placed some distance away. The energy level of the mosquitoes was manipulated by depriving females of sugar for 6, 24 and 48 h, and we monitored their responses in the olfactometer. Energy level did not have a significant impact on behavior. However, significant differences in residence time at the sock and overall activity level of the mosquito were recorded wherein mosquitoes exposed to DEET responded less readily to the blood-host scent, almost never probing its source. We propose that DEET is perceived by the mosquito as such a strong risk that energy levels do not affect its behavioral outcome. This study, along with previous work showing DEET efficacy, suggests that DEET is an important asset in mosquito control campaigns.

Garlic (Allium sativum L.) is a long-cultivated, clonally propagated diploid plant (2n=2x=16). With routine seed production now underway, we used populations (MP1 and MP2) generated by self-pollination of unrelated plants to generate two low-density genetic maps of garlic, consisting of amplified fragment length polymorphism (AFLP) and gene-specific markers. We did not observe any two plants with identical marker patterns in either population, indicating that they were the result of amphimixis rather than apomixis. This is an important finding, since several Alliums are facultative apomicts. A total of 360 markers segregated in MP1 (12.8 AFLP markers per primer combination) and 321 markers segregated in MP2 (13.9 per primer combination) to indicate a fairly high level of genetic heterozygosity in the garlic nuclear genome. Of these markers, 15.3% in MP1 and 24.3% in MP2 had segregation ratios distorted from the expected 3:1. Interestingly, 94.7% of those distorted segregations fit a 15:1 segregation ratio for duplicated loci, suggesting extensive levels of duplication in the garlic genome and supporting similar observations for onion. The genetic map for the MP1 family with 216 markers spanned 1,166 cM of the garlic genome (5.4 cM average), while 143 markers of MP2 spanned 862 cM (6.0 cM average). Gene-specific markers for alliinase, chitinase, sucrose 1-fructosyltransferase (SST-1), and chalcone synthase (CHS) were mapped, demonstrating the immediate utility of the garlic genetic map. These two garlic families had relatively few segregating AFLP markers in common, which supports their relatively distant relationship based on diversity analysis. Of those markers that were conserved, linkages were also conserved.

Objective: The purpose of this study was to determine if lycopene and β-carotene are bioavailable from lycopene red carrots and if lycopene absorption is affected by carrot fiber. Design: Two crossover studies in humans attempted to compare the relative bioavailability of lycopene and β-carotene from tomato paste to a genetically selected lycopene red carrot during chronic feeding. Each study contained three treatment groups. The vehicle of administration was muffins. Intervention and methods: Study 1 (n=9) used white carrots (0 mg lycopene/day), red carrots (5 mg/day), and tomato paste (20 mg/day). Study 2 (n=10) used red carrots (2.6 mg/day), tomato paste (5 mg/day), and tomato paste plus white carrots (5 mg/day). Each intervention lasted 11 days with a 10-day washout period between treatments. Serum lycopene and β-carotene were measured by HPLC. Results: Statistical analysis indicated a significant effect of muffin type in study 1 (P<0.001), and a significant treatment by sequence interaction in study 2 (P=0.04). The response to increasing amounts of lycopene is linear at the levels fed in these studies (r=0.94). The data suggest that maintenance of serum lycopene concentrations at 0.3 mol/l occurs at about 2 mg/day of lycopene from mixed dietary sources and a serum plateau occurs at 20 mg/day. Conclusions: These results show that lycopene and β-carotene are bioavailable from red carrots and lycopene absorption seems to be affected by carrot fiber. Making inferences from both studies, the lycopene in the red carrot is about 44% as bioavailable as that from tomato paste. Red carrots provide an alternative to tomato paste as a good dietary source of lycopene and also provide bioavailable β-carotene.

Melon (Cucumis melo L.) is highly nutritious vegetable species and an important source of β-carotene (Vitamin A), which is an important nutrient in the human diet. A previously developed set of 81 recombinant inbred lines (RIL) derived from Group Cantalupensis US Western Shipper market type germplasm was examined in two locations [Wisconsin (WI) and California (CA), USA] over 2 years to identify quantitative trait loci (QTL) associated with quantity of beta-carotene (QβC) in mature fruit. A moderately saturated 256-point RIL-based map [104 SSR, 7 CAPS, 4 SNP in putative carotenoid candidate genes, 140 dominant markers and one morphological trait (a) spanning 12 linkage groups (LG)] was used for QβC-QTL analysis. Eight QTL were detected in this evaluation that were distributed across four LG that explained a significant portion of the associated phenotypic variation for QβC (R ² = 8 to 31.0%). Broad sense heritabilities for QβC obtained from RIL grown in WI. and CA were 0.56 and 0.68, respectively, and 0.62 over combined locations. The consistence of QβC in high/low RIL within location across years was confirmed in experiments conducted over 2 years. QTL map positions were not uniformly associated with putative carotenoid genes, although one QTL (β-car6.1) interval was located 10 cM from a β-carotene hydroxylase gene. These results suggest that accumulation of β-carotene in melon is under complex genetic control. This study provides the initial step for defining the genetic control of QβC in melon leading to the development of varieties with enhanced β-carotene content.