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Identification of genetically diverse cacao with disease resistance, high productivity, and desirable organoleptic traits is vitally important to the agricultural crop’s long-term sustainability. Environmental changes, pests, and diseases as well as nation’s sovereign property rights have led to a decrease in accessibility and exchange of germplasm of interest. Having been introduced during colonial times, naturalized cacao in Puerto Rico could serve as an unexplored source of genetic diversity in improvement programs. An island-wide survey was carried out to identify naturalized trees and to determine their genetic associations to reference cacao accessions. Samples were genotyped with Expressed Sequence Tag-derived single nucleotide polymorphism (SNP) markers. Principal coordinate, cluster, and population structure analysis using the genotype data for both local and reference samples assigned individuals into five distinct genetic backgrounds: Criollo, Trinitario, Amelonado, Upper Amazon Forastero (UAF), and Nacional. Puerto Rican cacao fit into four (Criollo, Trinitario, Amelonado and UAF) of the five genetic backgrounds, being mainly composed of individuals of Criollo ancestry. Based on historical evidence, cacao of Criollo background was probably brought to Puerto Rico from Venezuela and/or Central America during colonial times. Trinitario, Amelonado, and UAF genetic backgrounds are most likely products of more modern introductions. Genotyping cacao in Puerto Rico provides information on the history and possible origin of the naturalized trees on the island. In addition, the assessment has allowed the targeting of material for incorporation and long-term conservation filling gaps in the existing collection and providing new germplasm to be evaluated for agronomic performance.

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.

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.

The nutritional value of cucumber (Cucumis sativus L.) can be improved by the introgression of β-carotene (i.e., provitamin A and/or orange flesh) genes from “Xishuangbanna gourd” (XIS; Cucumis sativus var. xishuangbannanesis Qi et Yuan) into US pickling cucumber. However, the genetics of β-carotene content has not been clearly defined in this US market type. Thus, three previous populations derived from a US pickling cucumber (‘Addis') × XIS mating were evaluated for β-carotene content, from which the high β-carotene inbred line (S₄), ‘EOM 402-10', was developed. A cross was then made between the US pickling cucumber inbred line ‘Gy7' [gynoecious, no β-carotene, white flesh; P₁] and ‘EOM 402-10' [monoecious, possessing β-carotene, orange flesh; P₂] to determine the inheritance of β-carotene in fruit mesocarp and endocarp tissue. Parents and derived cross-progenies (F₁, F₂, BC₁P₁, and BC₁P₂) were evaluated for β-carotene content in a greenhouse in Madison, Wisconsin. While F₁ and BC₁P₁ progeny produced mature fruits possessing white, light-green, and green (0.01-0.02 μg g⁻¹ β-carotene) mesocarp, the F₂ and BC₁P₂ progeny mesocarp segregated in various hues of white, green, yellow (0.01-0.34 μg g⁻¹ β-carotene), and orange (1.90-2.72 μg g⁻¹ β-carotene). Mesocarp and endocarp F₂ segregation adequately fit a 15:1 [low-β-carotene (0.01-0.34 μg g⁻¹): high-β-carotene (1.90-2.72 μg g⁻¹)] and 3:1 (low-β-carotene: high-β-carotene) ratio, respectively. Likewise, segregation of carotene concentration in mesocarp and endocarp tissues in BC₁P₂ progeny adequately fit a 3:1 (low-β-carotene: high-β-carotene) and 1:1 (low-β-carotene: high-β-carotene) ratio, respectively. Progeny segregations indicate that two recessive genes control the β-carotene content in the mesocarp, while one recessive gene controls β-carotene content in the endocarp. Single marker analysis of F₂ progeny using the carotenoid biosynthesis gene Phytoene synthase determined that there was no association between this gene and the observed β-carotene variation in either fruit mesocarp or endocarp.

Melon (Cucumis melo L.) fruit production in U.S. can be improved through the introgression of early fruit maturity (FM) and the enhancement of fruit color [i.e., quantity of β-carotene (QβC); orange mesocarp]. However, the genetics of FM and QβC have not been clearly defined in U.S. Western Shipping market class melons (USWS). Thus, a cross was made between the monoecious, early FM Chinese line ‘Q 3-2-2' (non-carotene accumulating, white mesocarp) and the andromonecious, comparatively late FM USWS line ‘Top Mark' (carotene accumulating; orange mesocarp) to determine the inheritance of FM and QβC in melon. Parents and derived cross-progenies (F₁, F₂, F₃, BC₁P₁, and BC₁P₂) were evaluated for FM and QβC at Hancock, Wisconsin over 2 years. Estimates of narrow-sense heritability (h N ² ) for QβC and FM as defined by F₁, F₂, and BC (by individuals) were 0.55 and 0.62, respectively, while estimates based on F₃ families were 0.68 and 0.57, respectively for these traits. Mesocarp color segregation (F₂ and BC₁P₂) fit a two gene recessive epistatic model, which in turn, interacts with other minor genes. Although the inheritance of QβC and FM is complex, introgression (e.g., by backcrossing) of early FM genes resident in Chinese germplasm into USWS market types is possible. Such introgression may lead to increased yield potential in USWS market types while retaining relatively high β-carotene fruit content (i.e., orange mesocarp), if stringent, multiple location and early generation family selection (F₃₋₄) is practiced for FM with concomitant selection for QβC.

Of central importance in adapting plants of tropical origin to temperate cultivation has been selection of daylength-neutral genotypes that flower early in the temperate summer and take full advantage of its long days. A cross between tropical and temperate sorghums [Sorghum propinquum (Kunth) Hitchc.×S. bicolor (L.) Moench], revealed a quantitative trait locus (QTL), FlrAvgD1, accounting for 85.7% of variation in flowering time under long days. Fine-scale genetic mapping placed FlrAvgD1 on chromosome 6 within the physically largest centiMorgan in the genome. Forward genetic data from “converted” sorghums validated the QTL. Association genetic evidence from a diversity panel delineated the QTL to a 10-kb interval containing only one annotated gene, Sb06g012260, that was shown by reverse genetics to complement a recessive allele. Sb06g012260 (SbFT12) contains a phosphatidylethanolamine-binding (PEBP) protein domain characteristic of members of the “FT” family of flowering genes acting as a floral suppressor. Sb06g012260 appears to have evolved ∼40 Ma in a panicoid ancestor after divergence from oryzoid and pooid lineages. A species-specific Sb06g012260 mutation may have contributed to spread to temperate regions by S. halepense (“Johnsongrass”), one of the world’s most widespread invasives. Alternative alleles for another family member, Sb02g029725 (SbFT6), mapping near another flowering QTL, also showed highly significant association with photoperiod response index (P = 1.53×10 − 6). The evolution of Sb06g012260 adds to evidence that single gene duplicates play large roles in important environmental adaptations. Increased knowledge of Sb06g012260 opens new doors to improvement of sorghum and other grain and cellulosic biomass crops.

In January 2013, North China Plain experienced several serious haze events. Cimel sunphotometer measurements at seven sites over rural, suburban and urban regions of North China Plain from 1 to 30 January 2013 were used to further our understanding of spatial-temporal variation of aerosol optical parameters and aerosol radiative forcing (ARF). It was found that Aerosol Optical Depth at 500 nm (AOD500 nm) during non-pollution periods at all stations was lower than 0.30 and increased significantly to greater than 1.00 as pollution events developed. The Angstrom exponent (Alpha) was larger than 0.80 for all stations most of the time. AOD500 nm averages increased from north to south during both polluted and non-polluted periods on the three urban sites in Beijing. The fine mode AOD during pollution periods is about a factor of 2.5 times larger than that during the non-pollution period at urban sites but a factor of 5.0 at suburban and rural sites. The fine mode fraction of AOD675 nm was higher than 80% for all sites during January 2013. The absorption AOD675 nm at rural sites was only about 0.01 during pollution periods, while ~0.03–0.07 and 0.01–0.03 during pollution and non-pollution periods at other sites, respectively. Single scattering albedo varied between 0.87 and 0.95 during January 2013 over North China Plain. The size distribution showed an obvious tri-peak pattern during the most serious period. The fine mode effective radius in the pollution period was about 0.01–0.08 μm larger than during non-pollution periods, while the coarse mode radius in pollution periods was about 0.06–0.38 μm less than that during non-pollution periods. The total, fine and coarse mode particle volumes varied by about 0.06–0.34 μm3, 0.03–0.23 μm3, and 0.03–0.10 μm3, respectively, throughout January 2013. During the most intense period (1–16 January), ARF at the surface exceeded −50 W m−2, −180 W m−2, and −200 W m−2 at rural, suburban, and urban sites, respectively. The ARF readings at the top of the atmosphere were approximately −30 W m−2 in rural and −40–60 W m−2 in urban areas. Positive ARF at the top of the atmosphere at the Huimin suburban site was found to be different from others as a result of the high surface albedo due to snow cover.

Aerosol optical depth (AOD) has become a crucial metric for assessing global climate change. Although global and regional AOD trends have been studied extensively, it remains unclear what factors are driving the inter-decadal variations in regional AOD and how to quantify the relative contribution of each dominant factor. This study used a long-term (1980–2016) aerosol dataset from the Modern-Era Retrospective Analysis for Research and Applications, version 2 (MERRA-2) reanalysis, along with two satellite-based AOD datasets (MODIS/Terra and MISR) from 2001 to 2016, to investigate the long-term trends in global and regional aerosol loading. Statistical models based on emission factors and meteorological parameters were developed to identify the main factors driving the inter-decadal changes of regional AOD and to quantify their contribution. Evaluation of the MERRA-2 AOD with the ground-based measurements of AERONET indicated significant spatial agreement on the global scale (r= 0.85, root-mean-square error = 0.12, mean fractional error = 38.7 %, fractional gross error = 9.86 % and index of agreement = 0.94). However, when AOD observations from the China Aerosol Remote Sensing Network (CARSNET) were employed for independent verification, the results showed that MERRA-2 AODs generally underestimated CARSNET AODs in China (relative mean bias = 0.72 and fractional gross error =−34.3 %). In general, MERRA-2 was able to quantitatively reproduce the annual and seasonal AOD trends on both regional and global scales, as observed by MODIS/Terra, although some differences were found when compared to MISR. Over the 37-year period in this study, significant decreasing trends were observed over Europe and the eastern United States. In contrast, eastern China and southern Asia showed AOD increases, but the increasing trend of the former reversed sharply in the most recent decade. The statistical analyses suggested that the meteorological parameters explained a larger proportion of the AOD variability (20.4 %–72.8 %) over almost all regions of interest (ROIs) during 1980–2014 when compared with emission factors (0 %–56 %). Further analysis also showed that SO2 was the dominant emission factor, explaining 12.7 %–32.6 % of the variation in AOD over anthropogenic-aerosol-dominant regions, while black carbon or organic carbon was the leading factor over the biomass-burning-dominant (BBD) regions, contributing 24.0 %–27.7 % of the variation. Additionally, wind speed was found to be the leading meteorological parameter, explaining 11.8 %–30.3 % of the variance over the mineral-dust-dominant regions, while ambient humidity (including soil moisture and relative humidity) was the top meteorological parameter over the BBD regions, accounting for 11.7 %–35.5 % of the variation. The results of this study indicate that the variation in meteorological parameters is a key factor in determining the inter-decadal change in regional AOD.

The emergence of Zika virus (ZIKV) as a global health threat has highlighted the unmet need for ZIKV-specific vaccines and antiviral treatments. ZIKV infects dendritic cells (DC), which have pivotal functions in activating innate and adaptive antiviral responses; however, the mechanisms by which DC function is subverted to establish ZIKV infection are unclear. Here we develop a genomics profiling method that enables discrete analysis of ZIKV-infected versus neighboring, uninfected primary human DCs to increase the sensitivity and specificity with which ZIKV-modulated pathways can be identified. The results show that ZIKV infection specifically increases the expression of genes enriched for lipid metabolism-related functions. ZIKV infection also increases the recruitment of sterol regulatory element-binding protein (SREBP) transcription factors to lipid gene promoters, while pharmacologic inhibition or genetic silencing of SREBP2 suppresses ZIKV infection of DCs. Our data thus identify SREBP2-activated transcription as a mechanism for promoting ZIKV infection amenable to therapeutic targeting. Zika virus (ZIKV) infection suppresses the induction of dendritic cell (DC)-derived immunity, but the underlying mechanistical insights are still lacking. Here the authors show, using in vitro systems profiling of DC transcriptome and epigenome, that ZIKV specifically alters SREBP2-related expression of inflammation- and metabolism-related genes to modulate DC functions.