► Identifying genetic markers for yield requires rapid quantification of crop traits. ► Proximal sensing offers promise for field-based phenotyping (FBP). ► Efficient data integration and ...modeling-assisted analysis are key for FBP. ► FBP scaled to thousands of field plots is a feasible, attainable goal. ► FBP systems require new, integrative collaborations that cross disciplines.
A major challenge for crop research in the 21st century is how to predict crop performance as a function of genetic architecture. Advances in “next generation” DNA sequencing have greatly improved genotyping efficiency and reduced genotyping costs. Methods for characterizing plant traits (phenotypes), however, have much progressed more slowly over the past 30 years, and constraints in phenotyping capability limit our ability to dissect the genetics of quantitative traits, especially those related to harvestable yield and stress tolerance. As a case in point, mapping populations for major crops may consist of 20 or more families, each represented by as many as 200 lines, necessitating field trials with over 20,000 plots at a single location. Investing in the resources and labor needed to quantify even a few agronomic traits for linkage with genetic markers in such massive populations is currently impractical for most breeding programs. Herein, we define key criteria, experimental approaches, equipment and data analysis tools required for robust, high-throughput field-based phenotyping (FBP). The focus is on simultaneous proximal sensing for spectral reflectance, canopy temperature, and plant architecture where a vehicle carrying replicated sets of sensors records data on multiple plots, with the potential to record data throughout the crop life cycle. The potential to assess traits, such as adaptations to water deficits or acute heat stress, several times during a single diurnal cycle is especially valuable for quantifying stress recovery. Simulation modeling and related tools can help estimate physiological traits such as canopy conductance and rooting capacity. Many of the underlying techniques and requisite instruments are available and in use for precision crop management. Further innovations are required to better integrate the functions of multiple instruments and to ensure efficient, robust analysis of the large volumes of data that are anticipated. A complement to the core proximal sensing is high-throughput phenotyping of specific traits such as nutrient status, seed composition, and other biochemical characteristics, as well as underground root architecture. The ability to “ground truth” results with conventional measurements is also necessary. The development of new sensors and imaging systems undoubtedly will continue to improve our ability to phenotype very large experiments or breeding nurseries, with the core FBP abilities achievable through strong interdisciplinary efforts that assemble and adapt existing technologies in novel ways.
Dissecting the molecular control of rubber biosynthesis: expression analysis of genes controlling pathway enzymes and rubber particle-associated proteins. Display omitted
► The first transcriptome of ...cold-acclimated guayule is described. ► All enzymes from both the MEV and MEP pathways were present. ► Isoprenoid pathway gene expression did not correlate with rubber synthesis rate. ► Gene expression levels for AOS and CPT were higher during the colder months.
Natural rubber biosynthesis in guayule (Parthenium argentatum Gray) is associated with moderately cold night temperatures. To begin to dissect the molecular events triggered by cold temperatures that govern rubber synthesis induction in guayule, the transcriptome of bark tissue, where rubber is produced, was investigated. A total of 11,748 quality expressed sequence tags (ESTs) were obtained. The vast majority of ESTs encoded proteins that are similar to stress-related proteins, whereas those encoding rubber biosynthesis-related proteins comprised just over one percent of the ESTs. Sequence information derived from the ESTs was used to design primers for quantitative analysis of the expression of genes that encode selected enzymes and proteins with potential impact on rubber biosynthesis in field-grown guayule plants, including 3-hydroxy-3-methylglutaryl-CoA synthase, 3-hydroxy-3-methylglutaryl-CoA reductase, farnesyl pyrophosphate synthase, squalene synthase, small rubber particle protein, allene oxide synthase, and cis-prenyl transferase. Gene expression was studied for field-grown plants during the normal course of seasonal variation in temperature (monthly average maximum 41.7°C to minimum 0°C, from November 2005 through March 2007) and rubber transferase enzymatic activity was also evaluated. Levels of gene expression did not correlate with air temperatures nor with rubber transferase activity. Interestingly, a sudden increase in night temperature 10days before harvest took place in advance of the highest CPT gene expression level.
•Vernonia, lesquerella and camelina are feedstock for biofuel and other products.•The lygus bug is a potential pest on these desert-adapted plants.•A feeding study was conducted to determine lygus ...preference for these crops.•Lygus were observed most often on vernonia and least often on camelina.•Lygus is a potential threat to the production of these three crops.
The desert-adapted crops vernonia (Centrapalus pauciflorus), lesquerella (Physaria fendleri), and camelina (Camelina sativa) are being grown in the arid southwestern USA as potential feedstock for biofuel and/or other environmentally friendly products. A plant feeding choice test was conducted to determine the relative attractiveness of these three “new” crops to a possible insect pest, Lygus hesperus Knight. Adult L. hesperus were readily observed feeding or resting on the flowering structures of each plant type, but they were seen most often on vernonia and least often on camelina. Lygus hesperus readily deposited their eggs on each plant species, but again, the greatest amount of egg deposition was found on vernonia and the least on camelina. These studies indicate that L. hesperus might pose a threat to the production of these new crops. Moreover, the commercial expansion of these crops could significantly alter the population dynamics of the existing arthropod community. New challenges for managing this pest during regional crop production changes are discussed.
Guayule, a shrub native to the Chihuahuan desert, is a natural source of high quality, hypoallergenic rubber. Unlike rubber trees that produce rubber in laticifers, the rubber in guayule is produced ...in parenchyma cells of the bark tissue of stems and roots. Consequently, guayule tissue must be mechanically broken before the rubber can be extracted and analyzed. Since rubber extraction and analysis is time-consuming, progress towards increasing the rubber content of guayule through breeding or better cultivation practices has been limited by the slow rate of sample processing. To address the need for faster and more efficient sample throughput, conditions were optimized for automated extraction of dried guayule tissue using accelerated solvent extraction (ASE) and rapid methods were developed to replace gravimetric determination of resin and rubber content. For resin analysis, ultraviolet absorbance was used to determine resin concentration after ASE of the tissue with acetone or acetonitrile. For rubber analysis, evaporative light scattering (ELS) was used to determine the amount of rubber recovered after ASE of the tissue with cyclohexane. Extraction of guayule tissue with high latex rubber content verified that the amounts of resin and rubber determined by these methods were similar to the amounts determined gravimetrically. Since these methods automate extraction and increase the speed of resin and rubber quantification, they could be used in combination with ASE to increase the throughput and efficiency of guayule evaluation in germplasm enhancement and agronomic improvement programs.
•Scored tens of thousands of SNP markers across guayule, mariola, and wild quinine.•Identified at least two distinct genetic sources of guayule germplasm.•Interspecific Parthenium hybrids had ...multiple ploidy levels and high aneuploidy.•Discovered cryptic interspecific hybrids within wild and cultivated accessions.•Wild quinine has a ∼1.5-fold larger nuclear genome size than guayule or mariola.
Guayule (Parthenium argentatum A. Gray) is a perennial woody shrub native to the North American Chihuahuan Desert that holds promise as a sustainable source of natural rubber and hypoallergenic latex. The improvement of guayule for commercial-scale production could be accelerated through genomics-assisted breeding, but such a strategy is severely limited by the paucity of available genomic tools and well-characterized genetic resources. To that end, we used genotyping-by-sequencing (GBS) to simultaneously identify and genotype tens of thousands of single-nucleotide polymorphism (SNP) markers across 62 plant samples from seven wild and cultivated guayule, three Parthenium interspecific hybrid, four mariola (Parthenium incanum Kunth), and one wild quinine (Parthenium integrifolium L.) accession(s) that have been characterized for ploidy level and nuclear genome size in this and a prior study. Phylogenetic analysis using the SNP data identified at least two distinct sources of guayule breeding material in the cultivated accessions, previously unknown multi-species hybrids within two Parthenium hybrid cultivars, and guayule/mariola hybrids within one guayule and one mariola wild collected accession. Similar to previously reported results for guayule and mariola, we observed aneuploidy and multiple ploidy levels among individual plants (mixed ploidy) within three Parthenium interspecific hybrid accessions newly characterized in this study. Nuclear genome size characterization of wild quinine, a first for this species, found an estimated haploid nuclear genome size (5757Mb) for the tetraploid (2n=4x=72) accession that was more than 1.5-fold larger than that of tetraploid (2n=4x=72) guayule or mariola. Together, these results further underscore the need for a comprehensive characterization of available guayule germplasm and sister taxa with both SNP markers and flow cytometry, illustrate the novel utility of GBS for the genus Parthenium, and lay the foundation for genomics-assisted breeding in guayule.
About 15
Parthenium species grow in the North American continent with
Parthenium argentatum (guayule) as the only species containing harvestable amounts of the rubber latex. The predicted ...commercialization of the guayule plant for its hypoallergenic latex will result in a significant amount of waste fiber or bagasse biomass that can also be put to use for making wood, paper, and other chemical products, as well as in energy production. Thus, the guayule wood and bark fibers can be considered a new source of plant biomass that may be used as a direct substitute for forest-based wood fiber. However, little information is available on the chemical composition of the wood and bark tissues of guayule (
P. argentatum)
. The objectives of this study were to determine the chemical and fiber composition of guayule and to compare it with other wood fiber sources.
Three germplasm lines of mature guayule (Cal-6, AZ-101, and G7-15) and another species of
Parthenium (
P. tomentosum, PT), juvenile soft maple (
Acer rubrum), a deciduous tree, and milkweed (
Asclepias syriaca L.) that has long fibers were the plant sources. Separate wood and bark tissues were analyzed for hot water, 1% sodium hydroxide, and alcohol–toluene extracts. In addition, the lignin, holocellulose, alpha-cellulose, and pentosan contents were determined.
All the chemical components in the wood fibers for the
Partheniums were equal to or greater than the juvenile maple tree. Milkweed had higher alpha-cellulose and lower alcohol–toluene extract contents than both the guayule and soft maple. The guayule bark fibers had more chemical extracts than the wood fibers. The specific gravity of guayule wood was greater than the deciduous wood species. However, the fiber lengths of soft maple wood, guayule wood, and milkweed are similar. Based on the chemical composition,
P. argentatum and
P. tomentosum could serve as raw materials for the paper and chemical industries as well as for energy production.
•Nearly 50,000 SNP markers used to genotype 69 guayule accessions.•Big Bend area of Texas contains novel guayule genotypes.•High yielding guayule cultivars have introgressions from other Parthenium ...species.
The fragility of a single-source, geographically concentrated supply of natural rubber, a critical material of the modern economy, has brought guayule (Parthenium argentatum A. Gray) to the forefront as an alternative source of natural rubber. The improvement of guayule for commercial-scale production has been limited by the lack of genomic tools and well-characterized genetic resources required for genomics-assisted breeding. To address this issue, we developed nearly 50,000 single-nucleotide polymorphism (SNP) genetic markers and genotyped 69 accessions of guayule and its sister taxa mariola (Parthenium incanum Kunth), representing the entire publically available US national germplasm collection. We identified multiple interspecific hybrid accessions previously considered guayule, including five guayule-mariola hybrids and non-mariola interspecific hybrid accessions AZ-2 and AZ-3, two commonly used high-yielding cultivars. We dissected patterns of genetic diversity within the collection to identify a highly diverse subset of guayule accessions, and showed that wild guayule stands in Big Bend National Park, Texas, USA have the potential to provide hitherto untapped guayule genetic diversity. Together, these results provide the most thorough genetic characterization of guayule germplasm to date and lay the foundation for rapid genetic improvement of commercial guayule germplasm.
Guayule (Parthenium argentatum A. Gray) is a potential source of natural rubber, but attempts to domesticate and cultivate this perennial crop for large-scale production in the southwestern United ...States have been intermittent over the past century. Genetic improvement through modern plant breeding is needed to increase its yield potential and suitability for commercialization. Natural variation for ploidy level is extensive among individuals in wild guayule populations, but less is known about the extent of ploidy level variation in guayule breeding germplasm. Because ploidy variation is among the factors that slow the rate of genetic gain in guayule breeding programs, determining the ploidy level of publicly available guayule accessions would help to accelerate the development of stable, high yielding cultivars. To that end, we adapted flow cytometry to examine the ploidy of 34 guayule accessions available from the National Plant Germplasm System. The data revealed a natural polyploid series ranging from diploid (2n = 2x = 36) to pentaploid (2n = 5x = 90), with 4x being the predominant ploidy. Interestingly, not all plants sampled from an accession had the same ploidy level (mixed ploidy). Notably, the integration of ploidy and pedigree data uncovered complex ploidy variation in guayule breeding programs. The frequency and range of ploidy variation observed in this germplasm will help to direct future breeding efforts as well as linkage analysis and genome-wide association studies.
Breeding guayule for commercial production Ray, Dennis T.; Coffelt, Terry A.; Dierig, David A.
Industrial crops and products,
07/2005, Letnik:
22, Številka:
1
Journal Article
Recenzirano
Breeding a new domestic crop, such as guayule, is not appreciably different from enhancement and breeding of conventional crops. In both instances, plant breeders take the available germplasm and ...search for genetic variability in the desired traits. The major differences are that in new crops plant breeders are often working with an unfamiliar species that is not yet fully domesticated and the available germplasm is often limited.
The main objective of the guayule breeding program is to facilitate successful commercialization by developing higher yielding cultivars. Improvement has been accomplished, with newer lines yielding up to 250% more rubber than lines developed in the 1940s and 1950s. This is surprising because the genetic base from which improvements have been made appears to be very narrow, and because guayule reproduces predominately by apomixis (asexual reproduction by seed). Improvements through breeding are dependent upon genetic diversity within the available germplasm, and being able to identify different genotypes. The available germplasm exhibits extreme variability both within and between lines for morphological traits such as height, width, and biomass; chemical constituents such as rubber, resin, and latex contents; and genetic and chromosomal markers. The measured variation is due partly to the facultative (asexual reproduction and sexuality coexisting) nature of apomixis in guayule, which periodically releases genetic variation among progeny. A great amount of this measured variation is due to environment, and selections, to take advantage of genetic differences, must be made within the first 2 years of growth. There have been relatively few individuals involved in guayule breeding. Thus, with limited resources and time, most of the improvements have been made through single-plant selections from within populations. Although this method has the potential for only modest long-term gains, improvements occur relatively quickly. Indirect measures have been developed to increase breeding efficiency. For instance, most selections are made for plant height, width and biomass because they are highly correlated with rubber yield. As guayule approaches commercialization, breeding will become a priority and other breeding schemes will be tested and utilized such as: mass selection; recurrent selection among sexually reproducing diploids, followed by chromosome doubling; family selection; crossing high yielding apomictic plants; and crossing high yielding apomictic plants to sexual diploid plants to release new genetic combinations.
•Guayule (2x–6x) had a more extensive natural ploidy series than mariola (3x–5x).•Guayule and mariola accessions had mixed ploidy and aneuploidy.•Nuclear genome size (haploid) estimates of guayule ...ranged from 1624 to 4812Mb.•Nuclear genome size (haploid) estimates of mariola ranged from 2616 to 4181Mb.•Lettuce and sunflower have ∼2-fold larger nuclear genome size than diploid guayule.
Guayule (Parthenium argentatum A. Gray) has tremendous potential as a domestic source of natural rubber production in the southwestern United States. However, genetic improvement of guayule has been slowed by its complex mode of reproduction, natural ploidy series, and lack of genetic and genomic resources. The interspecific hybridization of guayule with its closest sister taxon mariola (P. incanum Kunth) offers an opportunity to access novel genetic variation for guayule breeding programs, but mariola accessions available from the U.S. National Plant Germplasm System (NPGS) have never been evaluated for natural variation in ploidy level. In addition, the nuclear genome sizes for guayule and mariola at any ploidy level are unknown. To that end, we examined the ploidy of 10 mariola accessions, which revealed a natural polyploid series ranging from triploid (2n=3x=54) to pentaploid (2n=5x=90). In contrast, a ploidy analysis of five guayule accessions uncovered a natural polyploid series that ranged from diploid (2n=2x=36) to hexaploid (2n=6x=108). More than one ploidy level among individual plants (mixed ploidy) and instances of aneuploid plants were observed for accessions of both guayule and mariola. The nuclear genome sizes of guayule and mariola were similar at identical ploidy levels, and the genome size of diploid guayule (1624Mb) was almost twofold smaller than the genomes of sunflower (H. annuus L. 2n=2x=34) and lettuce (L. sativa L.; 2n=2x=18), two other Compositae (Asteraceae) species that are being genome-sequenced. The results from this study will serve as a foundation for interspecific breeding and genome sequencing of guayule and mariola.
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