This collection of papers by leading international experts on the subject of ancient Egyptian coffins, builds on a project based at the Fitzwilliam Museum, Cambridge, to study and record in detail ...its collection. Papers address a series of topics including: the development of coffins in antiquity, including iconographic and text-based studies, providing new insights into ancient Egyptian belief systems at different periods and regional differences in coffin presentation; the post-antiquity history of coffins, including their acquisition and subsequent treatment in museums around the world; developments in technical examination and methods of studying coffins, especially the use of multispectral imaging to provide non-invasive analysis of materials, and what this tells us about construction and decorative techniques at different periods and in response to the availability of different materials and increasing evidence of the re-use of materials and complete re-working of coffins for new owners, leading us to question fundamental attitudes to the purpose of coffins as containers of human remains and the practices of craftsmen in the funerary industry. The papers stem from a conference held at the Museum to accompany a major new exhibition.
There is an increased demand for food-grade grains grown sustainably. Hard red winter wheat has comparative advantages for organic farm rotations due to fall soil cover, weed competition, and grain ...yields. However, limitations of currently available cultivars such as poor disease resistance, winter hardiness, and baking quality, challenges its adoption and use. Our goal was to develop a participatory hard red winter wheat breeding program for the US Upper Midwest involving farmers, millers, and bakers. Specifically, our goals include (1) an evaluation of genotype-by-environment interaction (GEI) and genotypic stability for both agronomic and quality traits, and (2) the development of on-farm trials as well as baking and sensory evaluations of genotypes to include farmers, millers, and bakers’ perspectives in the breeding process. Selection in early generations for diseases and protein content was followed by multi-environment evaluations for agronomic, disease, and quality traits in three locations during five years, on-farm evaluations, baking trials, and sensory evaluations. GEI was substantial for most traits, but no repeatable environmental conditions were significant contributors to GEI making selection for stability a critical trait. Breeding lines had similar performance in on-station and on-farm trials compared to commercial checks, but some breeding lines were more stable than the checks for agronomic, quality traits, and baking performance. These results suggest that stable lines can be developed using a participatory breeding approach under organic management. Crop improvement explicitly targeting sustainable agriculture practices for selection with farm to table participatory perspectives are critical to achieve long-term sustainable crop production.
Key message
We describe a hard red winter wheat breeding program focused on developing genotypes adapted to organic systems in the US Upper Midwest for high-end artisan baking quality using participatory approaches.
Biennial vegetable crops are challenging to breed due to long breeding cycle times. At the same time, it is important to preserve a strong biennial growth habit, avoiding premature flowering that ...renders the crop unmarketable. Gene banks carry important genetic variation which may be essential to improve crop resilience, but these collections are underutilized due to lack of characterization for key traits like bolting tendency for biennial vegetable crops. Due to concerns about introducing undesirable traits such as premature flowering into elite germplasm, many accessions may not be considered for other key traits that benefit growers, leaving crops more vulnerable to pests, diseases, and abiotic stresses. In this study, we develop a method for characterizing flowering to identify accessions that are predominantly biennial, which could be incorporated into biennial breeding programs without substantially increasing the risk of annual growth habits. This should increase the use of these accessions if they are also sources of other important traits such as disease resistance. We developed the CarrotOmics flowering habit trait ontology and evaluated flowering habit in the largest (N=695), and most diverse collection of cultivated carrots studied to date. Over 80% of accessions were collected from the Eurasian supercontinent, which includes the primary and secondary centers of carrot diversity. We successfully identified untapped genetic diversity in biennial carrot germplasm (n=197 with 0% plants flowering) and predominantly-biennial germplasm (n=357 with <15% plants flowering). High broad-sense heritability for flowering habit (0.81 < H
< 0.93) indicates a strong genetic component of this trait, suggesting that these carrot accessions should be consistently biennial. Breeders can select biennial plants and eliminate annual plants from a predominantly biennial population. The establishment of the predominantly biennial subcategory nearly doubles the availability of germplasm with commercial potential and accounts for 54% of the germplasm collection we evaluated. This subcollection is a useful source of genetic diversity for breeders. This method could also be applied to other biennial vegetable genetic resources and to introduce higher levels of genetic diversity into commercial cultivars, to reduce crop genetic vulnerability. We encourage breeders and researchers of biennial crops to optimize this strategy for their particular crop.
Increased use of intellectual property rights over plant germplasm has led to a complicated landscape for exchange among plant breeders. Our goal was to examine phenotypic and genotypic diversity ...present in commercially available carrot (Daucus carota L. var. sativus) germplasm in relation to the freedom to operate-the ability for plant breeders to access and use crop genetic diversity. A collection of 140 commercially available carrot cultivars were grown in replicated field trials in the Madison, WI area in 2013 and 2014. Phenotypic measurements were recorded for leaf and root characteristics. Illumina sequencing was used to conduct genotyping by sequencing analysis on all cultivars to understand the range of genetic diversity present. Additionally, the intellectual property rights associated with each cultivar was noted to determine the freedom to operate. We found that although one-third of the commercially available US carrot cultivars in our study are restricted through some form of intellectual property rights, the genetic and phenotypic variability of the protected cultivars does not represent a completely separate group from the available material. Phenotypic analyses including ANOVA and principal components analysis, suggest that many of the traits differed significantly based on market class, but not by whether the cultivar had freedom to operate. The principal components and Fst analyses on the genotyping by sequencing data revealed that carrot market classes (Fst = 0.065) and freedom to operate classes (Fst = 0.023) were not genetically distinct, and that principle components 1 and 2 account for only 10.1% of the total genotypic variation, implying that cultivated carrot germplasm in the US forms an unstructured population. Our findings suggest that the genetic diversity present in carrot cultivars that have freedom to operate is potentially large enough to support carrot breeding efforts in most market classes given present levels of intellectual property protection.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Carrot (
L.) is a high value, nutritious, and colorful crop, but delivering carrots from seed to table can be a struggle for carrot growers. Weed competitive ability is a critical trait for crop ...success that carrot and its apiaceous relatives often lack owing to their characteristic slow shoot growth and erratic seedling emergence, even among genetically uniform lines. This study is the first field-based, multi-year experiment to evaluate shoot-growth trait variation over a 100-day growing season in a carrot diversity panel (N=695) that includes genetically diverse carrot accessions from the United States Department of Agriculture National Plant Germplasm System. We report phenotypic variability for shoot-growth characteristics, the first broad-sense heritability estimates for seedling emergence (0.68 < H
< 0.80) and early-season canopy coverage ( 0.61 < H
< 0.65), and consistent broad-sense heritability for late-season canopy height (0.76 < H
< 0.82), indicating quantitative inheritance and potential for improvement through plant breeding. Strong correlation between emergence and canopy coverage (0.62 < r < 0.72) suggests that improvement of seedling emergence has great potential to increase yield and weed competitive ability. Accessions with high emergence and vigorous canopy growth are of immediate use to breeders targeting stand establishment, weed-tolerance, or weed-suppressant carrots, which is of particular advantage to the organic carrot production sector, reducing the costs and labor associated with herbicide application and weeding. We developed a standardized vocabulary and protocol to describe shoot-growth and facilitate collaboration and communication across carrot research groups. Our study facilitates identification and utilization of carrot genetic resources, conservation of agrobiodiversity, and development of breeding stocks for weed-competitive ability, with the long-term goal of delivering improved carrot cultivars to breeders, growers, and consumers. Accession selection can be further optimized for efficient breeding by combining shoot growth data with phenological data in this study's companion paper to identify ideotypes based on global market needs.
Carrots are among the richest sources of provitamin A carotenes in the human diet, but genetic variation in the carotenoid pathway does not fully explain the high levels of carotenoids in carrot ...roots. Using a diverse collection of modern and historic domesticated varieties, and wild carrot accessions, an association analysis for orange pigmentation revealed a significant genomic region that contains the
gene, advancing it as a candidate for carotenoid presence in carrot. Analysis of sequence variation at the
locus revealed a nonsynonymous mutation cosegregating with carotenoid content. This mutation was absent in all wild carrot samples and nearly fixed in all orange domesticated samples.
has been found to control carotenoid presence in other crops but has not previously been described in carrot. Our analysis also allowed us to more completely characterize the genetic structure of carrot, showing that the Western domesticated carrot largely forms one genetic group, despite dramatic phenotypic differences among market classes. Eastern domesticated and wild accessions form a second group, which reflects the recent cultivation history of carrots in Central Asia. Other wild accessions form distinct geographic groups, particularly on the Iberian peninsula and in Northern Africa. Using genome-wide
, nucleotide diversity, and the cross-population composite likelihood ratio, we analyzed the genome for regions putatively under selection during domestication and identified 12 regions that were significant for all three methods of detection, one of which includes the
gene. The
domestication allele appears to have been selected after the initial domestication of yellow carrots in the East, near the proposed center of domestication in Central Asia. The rapid fixation of the
domestication allele in almost all orange and nonorange carrots in the West may explain why it has not been found with less genetically diverse mapping populations.
Low-input and organic farming systems have notable differences in nitrogen (N) sources, cycling and management strategies compared to conventional systems with high inputs of synthetic N fertilizer. ...In low-input and organic systems, there is greater reliance on complex rotations including annual and perennial crops, organic N sources, and internal N cycling that more closely mimic natural systems. These differences in farming system practices fundamentally affect N availability and N use efficiency (NUE) and could impact crop traits and breeding strategies required to optimize NUE. We assess genetic and environmental factors that could assist breeders in improving crop performance in low-input and organic farming systems by examining NUE in natural and agricultural ecosystems. Crop plants have often been bred for high N productivity, while plants adapted to low N ecosystems often have lower productivity and higher levels of internal N conservation. Breeders can potentially combine N productivity and N conservation through the use of elite and wild germplasm. Beneficial genetic traits include the ability to maintain photosynthesis and N uptake under N stress and the ability to extract soil N at low concentrations, perhaps through beneficial associations with soil microorganisms. In addition, breeding for specific adaptation to climactic and management practices so that crop uptake patterns match N availability patterns, while minimizing pathways of N loss, will be critical to improving NUE.
Summary
The native, perennial shrub American hazelnut (Corylus americana) is cultivated in the Midwestern United States for its significant ecological benefits, as well as its high‐value nut crop. ...Implementation of modern breeding methods and quantitative genetic analyses of C. americana requires high‐quality reference genomes, a resource that is currently lacking. We therefore developed the first chromosome‐scale assemblies for this species using the accessions ‘Rush’ and ‘Winkler’. Genomes were assembled using HiFi PacBio reads and Arima Hi‐C data, and Oxford Nanopore reads and a high‐density genetic map were used to perform error correction. N50 scores are 31.9 Mb and 35.3 Mb, with 90.2% and 97.1% of the total genome assembled into the 11 pseudomolecules, for ‘Rush’ and ‘Winkler’, respectively. Gene prediction was performed using custom RNAseq libraries and protein homology data. ‘Rush’ has a BUSCO score of 99.0 for its assembly and 99.0 for its annotation, while ‘Winkler’ had corresponding scores of 96.9 and 96.5, indicating high‐quality assemblies. These two independent assemblies enable unbiased assessment of structural variation within C. americana, as well as patterns of syntenic relationships across the Corylus genus. Furthermore, we identified high‐density SNP marker sets from genotyping‐by‐sequencing data using 1343 C. americana, C. avellana and C. americana × C. avellana hybrids, in order to assess population structure in natural and breeding populations. Finally, the transcriptomes of these assemblies, as well as several other recently published Corylus genomes, were utilized to perform phylogenetic analysis of sporophytic self‐incompatibility (SSI) in hazelnut, providing evidence of unique molecular pathways governing self‐incompatibility in Corylus.
Participatory plant breeding and rapid sensory evaluation are effective techniques for organic cultivar development. Table beet is an important crop for organic growers, and geosmin, a volatile ...compound which confers earthy aroma, has been suggested as the attribute around which hedonic liking of beet is organized. Open pollinated table beet populations with diverse pigmentation and low (LGC) or high (HGC) geosmin concentration served as starting materials for the first PPB effort in table beet. This project sought to develop consumer-accepted specialty beet cultivars for organic systems and to gauge consumer perception of and preference for geosmin concentration in non-laboratory conditions. LGC and HGC initial populations were significantly different in mean geosmin concentration but not mean TDS. LGC populations diverged significantly in geosmin concentration over two cycles of selection for hedonic liking, due to drift rather than selection. PPB yielded cultivars ‘Evansville Ember’, ‘Snowglobe’, ‘Blushing Not Bashful’, ‘Evansville Orbit’, and ‘Moving Target’. Cultivar novelty and market development were strengthened by chef input and association with a publicly funded seed system development group. Geosmin concentration was not the central determinant of hedonic liking or perceived earthy flavor in table beet. Earthiness was inconsistently associated with geosmin concentration and hedonic liking. Sweetness and bitterness were positively and negatively correlated with liking, respectively, although sweetness was not associated with variation in TDS. Cultivars with a broad range of geosmin concentration were well accepted by consumers, and manipulating expectation—via appearance—may be as powerful as manipulating flavor compounds in influencing liking of table beet.
Abstract
Geosmin, a degraded sesquiterpene molecule with earthy and musty odor, imbues table beet with its characteristic aroma. Geosmin is heritable and endogenously produced in table beet; its ...earthy aroma is sought by some consumers but deters others. Geosmin biosynthesis is catalyzed by a bifunctional geosmin synthase enzyme in diverse bacteria and fungi, but a mechanism for geosmin biosynthesis in plants has not been reported. This work employed association analysis and selective genotyping of a segregating F2:3 mapping population to seek QTL associated with geosmin concentration in table beet. GBS reads were aligned to sugar beet reference genome EL10.2, and association analysis revealed two QTL for geosmin concentration on Beta vulgaris ssp. vulgaris chromosome 8. QTL at EL10.2 positions 28,017,624 and 38,488,687 each show effect size 8.7 μg·kg-1 geosmin and explain 8.5% and 6.4% of total variation in geosmin concentration, respectively. Resolution was low due to large recombination bin size and imperfect alignment between the reference genome and mapping population, but population size and selection proportion were sufficient to detect moderate to large effect QTL. This study, the first molecular genetic mapping experiment in table beet, succeeded in finding QTL for geosmin concentration in table beet, and it provides the basis for fine mapping or candidate gene investigation of functional loci for this distinctive sensory trait.
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