Genome-Wide Association Study to Identify Possible Candidate Genes of Snap Bean Leaf and Pod Color.

Color can be an indicator of plant health, quality, and productivity, and is useful to researchers to understand plant nutritional content in their studies. Color may be related to chlorophyll content and photosynthetic activity and provides information for those studying diseases and mineral nutrition because every nutrient deficiency and many diseases produce symptoms that affect color. In order to identify significant loci related to both leaf and pod color in a snap bean (Phaseolus vulgaris L.) diversity panel, a genome-wide association study (GWAS) was carried out. Leaf color in one and pod traits in multiple environments were characterized using a colorimeter. L*a*b* color data were recorded and used to calculate chroma (C*) and hue angle (H°). Leaves were evaluated at three positions (lower, middle, and upper) in the canopy and both pod exterior and interior colors were obtained. GWAS was conducted using two reference genomes that represent the Andean (G19833) and Middle American (5-593) domestication centers. Narrow sense heritabilities were calculated using the mixed linear model (MLM) method in genome association and prediction integrated tool (GAPIT), and significant single nucleotide polymorphisms (SNPs) for each color parameter were obtained using the Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK) GWAS model with two principal components (PCAs). In comparison to pod color traits, narrow sense heritabilities of leaf traits were low and similar for both reference genomes. Generally, narrow sense heritability for all traits was highest in the lower, followed by middle, and then upper leaf positions. Heritability for both pod interior and exterior color traits was higher using the G19833 reference genome compared to 5-593 when evaluated by year and means across years. Forty-five significant SNPs associated with leaf traits and 872 associated with pods, totaling 917 significant SNPs were identified. Only one SNP was found in common for both leaf and pod traits on Pv03 in the 5-593 reference genome. One-hundred thirteen significant SNPs, 30 in leaves and 83 in pods had phenotypic variation explained (PVE) of 10% or greater. Fourteen SNPs (four from G19833 and ten from 5-593) with ≥10 PVE%, large SNP effect, and largest p-value for L* and H° pod exterior was identified on Pv01, Pv02, Pv03, and Pv08. More SNPs were associated with pod traits than with leaf traits. The pod interior did not exhibit colors produced by anthocyanins or flavonols which allowed the differentiation of potential candidate genes associated with chloroplast and photosynthetic activity compared to the pod exterior where candidate genes related to both flavonoids and photosynthesis affected color. Several SNPs were associated with known qualitative genes including the wax pod locus (y), persistent color (pc), purple pods (V), and two genes expressed in seeds but not previously reported to affect other plant tissues (B and J). An evaluation of significant SNPs within annotated genes found a number, within a 200 kb window, involved in both flavonoid and photosynthetic biosynthetic pathways.

A robust SNP-haplotype assay for Bct gene region conferring resistance to beet curly top virus in common bean (Phaseolus vulgaris L.).

Beet curly top virus (BCTV), which is synonymous with curly top virus (CTV), causes significant yield loss in common bean (snap and dry beans) cultivars and several other important crops. Common bean cultivars have been found to be resistant to CTV, but screening for resistance is challenging due to the cyclical nature of epidemics and spotty feeding by the leafhopper that vectors the virus. We used an SNP dataset for the Snap Bean Association Panel (SnAP) agro-inoculated with CTV-Logan (CA/Logan) strain to locate the Bct gene region to a 1.7-Mb interval on chromosome Pv07 using genome-wide association study (GWAS) analysis. Recombinant lines from the SnAP were used to further narrow the Bct region to a 58.0-kb interval. A missense SNP (S07_2970381) in candidate gene Phvul.007G036300 Exonuclease V (EXO5) was identified as the most likely causal mutation, and it was the most significant SNP detected by GWAS in a dry bean population (DBP) naturally infected by the CTV-Worland (Wor) strain. Tm-shift assay markers developed for SNP S07_2970381 and two linked SNPs, S07_2970276 and S07_2966197, were useful for tracking different origins of the Bct EXO5 candidate gene resistance to CTV in common bean. The three SNPs identified four haplotypes, with haplotype 3-1 (Haplo3-1) of Middle American origin associated with the highest levels of CTV resistance. This SNP-haplotype assay will enable breeders to track resistance sources and to develop cultivars with better CTV resistance.

Genetic variation in a tepary bean (Phaseolus acutifolius A. Gray) diversity panel reveals loci associated with biotic stress resistance.

Tepary bean (Phaseolus acutifolius A. Gray), indigenous to the arid climates of northern Mexico and the Southwest United States, diverged from common bean (Phaseolus vulgaris L.), approximately 2 million years ago and exhibits a wide range of resistance to biotic stressors. The tepary genome is highly syntenic to the common bean genome providing a foundation for discovery and breeding of agronomic traits between these two crop species. Although a limited number of adaptive traits from tepary bean have been introgressed into common bean, hybridization barriers between these two species required the development of bridging lines to alleviate this barrier. Thus, to fully utilize the extant tepary bean germplasm as both a crop and as a donor of adaptive traits, we developed a diversity panel of 422 cultivated, weedy, and wild tepary bean accessions which were then genotyped and phenotyped to enable population genetic analyses and genome-wide association studies for their response to a range of biotic stressors. Population structure analyses of the panel revealed eight subpopulations and the differentiation of botanical varieties within P. acutifolius. Genome-wide association studies revealed loci and candidate genes underlying biotic stress resistance including quantitative trait loci for resistance to weevils, common bacterial blight, Fusarium wilt, and bean common mosaic necrosis virus that can be harnessed not only for tepary bean but also common bean improvement.

Mapping of the bs5 and bs6 non-race-specific recessive resistances against bacterial spot of pepper.

Bacterial spot caused by Xanthomonas euvesicatoria is a major disease of pepper (Capsicum annuum L.) in warm and humid production environments. Use of genetically resistant cultivars is an effective approach to manage bacterial spot. Two recessive resistance genes, bs5 and bs6, confer non-race-specific resistance against bacterial spot. The objective of our study was to map these two loci in the pepper genome. We used a genotyping-by-sequencing approach to initially map the position of the two resistances. Segregating populations for bs5 and bs6 were developed by crossing susceptible Early CalWonder (ECW) with near-isogenic lines ECW50R (bs5 introgression) or ECW60R (bs6 introgression). Following fine-mapping, bs5 was delimited to a ~535 Kbp interval on chromosome 3, and bs6 to a ~666 Kbp interval in chromosome 6. We identified 14 and 8 candidate resistance genes for bs5 and bs6, respectively, based on predicted protein coding polymorphisms between ECW and the corresponding resistant parent. This research enhances marker-assisted selection of bs5 and bs6 in breeding programs and is a crucial step towards elucidating the molecular mechanisms underlying the resistances.

Human and dog Bayesian dietary mixing models using bone collagen stable isotope ratios from ancestral Iroquoian sites in southern Ontario.

Under the archaeological canine surrogacy approach (CSA) it is assumed that because dogs were reliant on humans for food, they had similar diets to the people with whom they lived. As a result, the stable isotope ratios of their tissues (bone collagen and apatite, tooth enamel and dentine collagen) will be close to those of the humans with whom they cohabited. Therefore, in the absence of human tissue, dog tissue isotopes can be used to help reconstruct past human diets. Here δ13C and δ15N ratios on previously published dog and human bone collagen from fourteenth-seventeenth century AD ancestral Iroquoian village archaeological sites and ossuaries in southern Ontario are used with MixSIAR, a Bayesian dietary mixing model, to determine if the dog stable isotope ratios are good proxies for human isotope ratios in dietary modeling for this context. The modeling results indicate that human dietary protein came primarily from maize and high trophic level fish and dogs from maize, terrestrial animals, low trophic level fish, and human feces. While isotopes from dog tissues can be used as general analogs for human tissue isotopes under CSA, greater insights into dog diets can be achieved with Bayesian dietary mixing models.

Genome-Wide Association Study (GWAS) of White Mold Resistance in Snap Bean.

White mold can result in snap bean yield losses of 90 to 100% when field conditions favor the pathogen. A genome-wide association study (GWAS) was conducted to detect loci significantly associated with white mold resistance in a panel of snap bean (Phaseolus vulgaris L.) cultivars. Two populations of snap bean were used in this study. The first population was the BeanCAP (Coordinated Agriculture Project) Snap Bean Diversity Panel (SBDP) (n = 136), and the second population was the Snap Bean Association Panel (SnAP) (n = 378). SBDP was evaluated for white mold reaction in the field in 2012 and 2013, and SnAP was screened in a greenhouse only using the seedling straw test in 2016. Two reference genomes representing the Andean and Middle American centers of domestication were utilized to align the genotyping-by-sequencing (GBS) data. A GWAS was performed using FarmCPU with one principal component after comparing five models. Thirty-four single-nucleotide polymorphisms (SNPs) significantly associated with white mold resistance were detected. Eleven significant SNPs were identified by the seedling straw test, and 23 significant SNPs were identified by field data. Fifteen SNPs were identified within a 100 kb window containing pentatricopeptide repeat (PPR)-encoding genes, and eleven were close to leucine-rich repeat (LRR)-encoding genes, suggesting that these two classes are of outsized importance for snap bean resistance to white mold.

The Monongahela tradition in "real time": Bayesian analysis of radiocarbon dates.

Despite advances in techniques, methods, and theory, northeastern North American archaeologists continue to use early to mid-twentieth century culture historical taxa as units of analysis and narrative. There is a distinct need to move away from this archaeological practice to enable fuller understandings of past human lives. One tool that enables such a move is Bayesian analysis of radiocarbon dates, which provides a means of constructing continuous chronologies. A large dataset of radiocarbon dates for late prehistoric (ca AD 900/1000-1650) sites in the lower upper Ohio River basin in southwestern Pennsylvania and adjacent portions of Maryland, Ohio, and West Virginia is used here as an example. The results allow a preliminary assessment of how the settlement plans of contemporaneous villages varied considerably, reflecting decisions of the village occupants how to structure built environments to meet their needs.

Resolving Indigenous village occupations and social history across the long century of European permanent settlement in Northeastern North America: The Mohawk River Valley ~1450-1635 CE.

The timeframe of Indigenous settlements in Northeast North America in the 15th-17th centuries CE has until very recently been largely described in terms of European material culture and history. An independent chronology was usually absent. Radiocarbon dating has recently begun to change this conventional model radically. The challenge, if an alternative, independent timeframe and history is to be created, is to articulate a high-resolution chronology appropriate and comparable with the lived histories of the Indigenous village settlements of the period. Improving substantially on previous initial work, we report here high-resolution defined chronologies for the three most extensively excavated and iconic ancestral Kanien'kehá꞉ka (Mohawk) village sites in New York (Smith-Pagerie, Klock and Garoga), and a fourth early historic Indigenous site, Brigg's Run, and re-assess the wider chronology of the Mohawk River Valley in the mid-15th to earlier 17th centuries. This new chronology confirms initial suggestions from radiocarbon that a wholesale reappraisal of past assumptions is necessary, since our dates conflict completely with past dates and the previously presumed temporal order of these three iconic sites. In turn, a wider reassessment of northeastern North American early history and re-interpretation of Atlantic connectivities in the later 15th through early 17th centuries is required. Our new closely defined date ranges are achieved employing detailed archival analysis of excavation records to establish the contextual history for radiocarbon-dated samples from each site, tree-ring defined short time series from wood charcoal samples fitted against the radiocarbon calibration curve ('wiggle-matching'), and Bayesian chronological modelling for each of the individual sites integrating all available prior knowledge and radiocarbon dating probabilities. We define (our preferred model) most likely (68.3% highest posterior density) village occupation ranges for Smith-Pagerie of ~1478-1498, Klock of ~1499-1521, Garoga of ~1550-1582, and Brigg's Run of ~1619-1632.

The tepary bean genome provides insight into evolution and domestication under heat stress.

Tepary bean (Phaseolus acutifolis A. Gray), native to the Sonoran Desert, is highly adapted to heat and drought. It is a sister species of common bean (Phaseolus vulgaris L.), the most important legume protein source for direct human consumption, and whose production is threatened by climate change. Here, we report on the tepary genome including exploration of possible mechanisms for resilience to moderate heat stress and a reduced disease resistance gene repertoire, consistent with adaptation to arid and hot environments. Extensive collinearity and shared gene content among these Phaseolus species will facilitate engineering climate adaptation in common bean, a key food security crop, and accelerate tepary bean improvement.

Using Maize δ15N values to assess soil fertility in fifteenth- and sixteenth-century ad Iroquoian agricultural fields.

Native Americans developed agronomic practices throughout the Western Hemisphere adapted to regional climate, edaphic conditions, and the extent of dependence on agriculture for subsistence. These included the mounding or "corn hill" system in northeastern North America. Iroquoian language speakers of present-day New York, USA, and Ontario and Québec, Canada were among those who used this system. While well-known, there has been little archaeological documentation of the system. As a result, there is scant archaeological evidence on how Iroquoian farmers maintained soil fertility in their often-extensive agricultural fields. Using δ15N values obtained on fifteenth- and sixteenth-century AD maize kernels from archaeological sites in New York and Ontario, adjusted to take into account changes that result from charring as determined through experiments, we demonstrate that Iroquoian farmers were successful at maintaining nitrogen in their agricultural fields. These results add to our archaeological knowledge of Iroquoian agronomic practices. Our results also indicate the potential value of obtaining δ15N values on archaeological maize in the investigation of Native American agronomic practices.

Radiocarbon, Bayesian chronological modeling and early European metal circulation in the sixteenth-century AD Mohawk River Valley, USA.

European metal artifacts in assemblages from sites predating the physical presence of Europeans in Northern Iroquoia in present-day New York, USA and southern Ontario, Canada have been used as chronological markers for the mid-sixteenth century AD. In the Mohawk River Valley of New York, European metal artifacts at sites pre-dating the physical presence of Europeans have been used by archaeologists as a terminus post quem (TPQ) of 1525 to 1550 in regional chronologies. This has been done under the assumption that these metals did not begin to circulate until after sustained European presence on the northern Atlantic coast beginning in 1517. Here we use Bayesian chronological modeling of a large set of radiocarbon dates to refine our understanding of early European metal circulation in the Mohawk River Valley. Our results indicate that European iron and cuprous metals arrived earlier than previously thought, by the beginning of the sixteenth century, and cannot be used as TPQs. Together with recent Bayesian chronological analyses of radiocarbon dates from several sites in southern Ontario, these results add to our evolving understanding of intra-regional variation in Northern Iroquoia of sixteenth-century AD circulation and adoption of European goods.

Fish and maize: Bayesian mixing models of fourteenth- through seventeenth-century AD ancestral Wendat diets, Ontario, Canada.

Freshwater and marine fish have been important components of human diets for millennia. The Great Lakes of North America, their tributaries and smaller regional freshwater bodies are important Native American fisheries. The ethnohistorical record, zooarchaeological remains, and isotopic values on human bone and tooth collagen indicate the importance of fish in fourteenth- through seventeenth-century ancestral Wendat diets in southern Ontario, which is bordered by three of the Great Lakes. Maize (Zea mays ssp. mays) was the primary grain of Native American agricultural systems in the centuries prior to and following sustained European presence. Here we report new Bayesian dietary mixing models using previously published δ13C and δ15N values on ancestral Wendat bone and tooth collagen and tooth enamel. The results confirm previous estimates from δ13C values that ancestral Wendat diets included high proportions of maize but indicate much higher proportions of fish than has previously been recognized. The results also suggest that terrestrial animals contributed less to ancestral Wendat diets than is typically interpreted based on zooarchaeological records.

An Electrocatalytic Screen-Printed Amperometric Sensor for the Selective Measurement of Thiamine (Vitamin B1) in Food Supplements.

An electrocatalytic screen-printed sensor has been investigated for the measurement of the biologically important biomolecule vitamin B1 (thiamine) for the first time in food supplements. Under basic conditions, the vitamin was converted to its electrochemically active thiolate anion species. It was shown that an electrocatalytic oxidation reaction occurred with the screen-printed carbon electrode containing the mediator cobalt phthalocyanine (CoPC-SPCE). This had the advantage of producing an analytical response current at an operating potential of 0 V vs. Ag/AgCl compared to +0.34 V obtained with plain SPCEs. This resulted in improved selectivity and limit of detection. Detailed studies on the underlying mechanism occurring with the sensor are reported in this paper. A linear response was obtained between 0.1 and 20 µg mL-1, which was suitable for the quantification of the vitamin in two commercial products containing vitamin B1. The mean recovery for a multivitamin tablet with a declared content of 5 mg was 101% (coefficient of variation (CV) of 9.6%). A multivitamin drink, which had a much lower concentration of vitamin B1 (0.22 mg/100 mL), gave a mean recovery of 93.3% (CV 7.2%). These results indicate that our sensor holds promise for quality control of food supplements and other food types.

Freshwater reservoir offsets on radiocarbon-dated dog bone from the headwaters of the St. Lawrence River, USA.

Isotopic analysis of dog (Canis lupus familiaris) bone recovered from archaeological sites as proxies for human bone is becoming common in North America. Chronological placement of the dogs is often determined through radiocarbon dating of dog bone. The Great Lakes, their tributaries, and nearby lakes and streams were important fisheries for Native Americans prior to and after sustained European presence in the region. Carbon entering the food web in freshwater systems is often not in full isotopic equilibrium with the atmosphere, giving rise to spuriously old radiocarbon ages in fish, other aquatic organisms, and their consumers. These freshwater reservoir offsets (FROs) have been noted on human and dog bone in several areas of the world. Here we report the results of multi-tracer Bayesian dietary modeling using δ15N and δ13C values on dog bone collagen from mid-fifteenth to mid-sixteenth-century Iroquoian village sites at the headwaters of the St. Lawrence River, New York, USA. Results indicate that fish was an important component of dog diets. A comparison of radiocarbon dates on dog bone with dates on deer bone or maize from the same sites indicate FROs ranging from 97 ± 24 to 220 ± 39 14Cyr with a weighted mean of 132 ± 8 14Cyr. These results suggest that dog bone should not be used for radiocarbon dating in the absence of modeling to determine fish consumption and that previously reported radiocarbon dates on human bone from the larger region are likely to have FROs given the known importance of fish in regional human diets.

An analysis of network brokerage and geographic location in fifteenth-century AD Northern Iroquoia.

Iroquoian villagers living in present-day Jefferson County, New York, at the headwaters of the St. Lawrence River and the east shore of Lake Ontario, played important roles in regional interactions during the fifteenth century AD, as brokers linking populations on the north shore of Lake Ontario with populations in eastern New York. This study employs a social network analysis and least cost path analysis to assess the degree to which geographical location may have facilitated the brokerage positions of site clusters within pan-Iroquoian social networks. The results indicate that location was a significant factor in determining brokerage. In the sixteenth century AD, when Jefferson County was abandoned, measurable increases in social distance between other Iroquoian populations obtained. These results add to our understandings of the dynamic social landscape of fifteenth and sixteenth century AD northern Iroquoia, complementing recent analyses elsewhere of the roles played in regional interaction networks by populations located along geopolitical frontiers.

Correction: Freshwater reservoir offsets and food crusts: Isotope, AMS, and lipid analyses of experimental cooking residues.

[This corrects the article DOI: 10.1371/journal.pone.0196407.].

Freshwater reservoir offsets and food crusts: Isotope, AMS, and lipid analyses of experimental cooking residues.

Freshwater reservoir offsets (FROs) occur when AMS dates on charred, encrusted food residues on pottery predate a pot's chronological context because of the presence of ancient carbon from aquatic resources such as fish. Research over the past two decades has demonstrated that FROs vary widely within and between water bodies and between fish in those water bodies. Lipid analyses have identified aquatic biomarkers that can be extracted from cooking residues as potential evidence for FROs. However, lacking has been efforts to determine empirically how much fish with FROs needs to be cooked in a pot with other resources to result in significant FRO on encrusted cooking residue and what percentage of fish C in a residue is needed to result in the recovery of aquatic biomarkers. Here we provide preliminary assessments of both issues. Our results indicate that in historically-contingent, high alkalinity environments <20% C from fish may result in a statistically significant FRO, but that biomarkers for aquatic resources may be present in the absence of a significant FRO.

Development of a simple, low cost chronoamperometric assay for fructose based on a commercial graphite-nanoparticle modified screen-printed carbon electrode.

This paper describes the development of a simple, low cost chronoamperometric assay, for the measurement of fructose, using a graphite-nanoparticle modified screen-printed electrode (SPCE-G-COOH). Cyclic voltammetry showed that the response of the SPCE-G-COOH enhanced the sensitivity and precision, towards the enzymatically generated ferrocyanide species, over a plain SPCE; therefore the former was employed in subsequent studies. Calibration studies were carried out using chronoamperometry with a 40µl mixture containing fructose, mediator and FDH, deposited onto the SPCE-G-COOH. The response was linear from 0.1mM to 1.0mM. A commercial fruit juice sample was analysed using the developed assay and the fructose concentration was calculated to be 477mM with a precision of 3.03% (n=5). Following fortification (477mM fructose) the mean recovery was found to be 97.12% with a coefficient of variation of 6.42% (n=5); consequently, the method holds promise for the analysis of commercial fruit juices.

Alpha-synuclein ferrireductase activity is detectible in vivo, is altered in Parkinson's disease and increases the neurotoxicity of DOPAL.

The normal cellular role of α-synuclein is of potential importance in understanding diseases in which an aggregated form of the protein has been implicated. A potential loss or change in the normal function of α-synuclein could play a role in the aetiology of diseases such as Parkinson's disease. Recently, it has been suggested that α-synuclein could cause the enzymatic reduction of iron and a cellular increase in Fe(II) levels. Experiments were carried out to determine if such activity could be measured in vivo. Experiments with rats overexpressing human α-synuclein in nigral dopaminergic neurons demonstrated a correlation between α-synuclein expression and ferrireductase activity. Furthermore, studies on tissue from Parkinson's disease patient brains showed a significant decrease in ferrireductase activity, possibly due to deposition of large amounts of inactive protein. Cellular studies suggest that increase ferrireductase activity results in increased levels of dopamine metabolites and increased sensitivity to the toxicity of DOPAL. These findings demonstrate that α-synuclein ferrireductase activity is present in vivo and its alteration may play a role in neuron loss in disease.

Effects of population dispersal on regional signaling networks: An example from northern Iroquoia.

The dispersal of Iroquoian groups from St. Lawrence River valley during the 15th and 16th centuries A.D. has been a source of archaeological inquiry for decades. Social network analysis presented here indicates that sites from Jefferson County, New York at the head of the St. Lawrence River controlled interactions within regional social signaling networks during the 15th century A.D. Measures indicate that Jefferson County sites were in brokerage liaison positions between sites in New York and Ontario. In the network for the subsequent century, to which no Jefferson County sites are assigned, no single group took the place of Jefferson County in controlling network flow. The dispersal of Jefferson County populations effectively ended this brokerage function concomitant with the emergence of the nascent Huron-Wendat and Iroquois confederacies and may have contributed to the escalation of conflict between these entities. These results add to a growing literature on the use of network analyses with archaeological data and contribute new insights into processes of population relocation and geopolitical realignment, as well as the role of borderlands and frontiers in nonstate societies.