Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Plant Breeding”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 127 records · Page 7Linked to original sources
PubMed2025

Genomic prediction-aided incorporation of genetic resources into elite breeding: lessons from a collaborative multiparental design in flint maize.

A public private cooperative mating design between elite maize inbred lines and diversity donors shows that genomic prediction holds great promise to improve the use of genetic resources. Genetic diversity is essential for plant breeding, enabling long-term gains and adaptation to climate change and new agronomical practices. Breeders can access diverse genetic resources to enhance elite germplasm and introduce new favorable variations. The limited performance of genetic resources may hamper their use. To overcome this, a bridging population can be implemented to evaluate and select progenies from crosses between diversity donors and elite lines before their introduction in breeding programs. The choice of such crosses can be dealt with the usefulness criterion (UC), which determines its ability to produce transgressive individuals. This paper investigates the use of genome-wide marker effects to predict (i) the performance of individuals derived from crosses between donors and elite lines and (ii) the UC of crosses not observed yet. It also compares donor introduction strategies based on the UC or the H criterion, which considers the genome-wide donor-elite complementarity. We used a flint maize collaborative multi-parental BC1-S2 population, consisting in materials from six breeding companies and one public institute crossed to different donors. The 20 crosses had contrasted means and genetic variances, and most of them presented transgressive individuals above the elite parent. Results emphasize the importance of half-siblings derived from the elite line parent of the predicted cross to efficiently predict progeny performances or the UC. They also showed that using the H criterion appears promising to select iteratively donors that best complement initial elite materials. The paper concludes with guidelines for implementing a bridging population using genome-wide marker-based predictions.

Zea mays↗
PubMed2001

An efficient method for the physical mapping of transgenes in barley using in situ hybridization.

The genetic transformation of crops by particle bombardment and Agrobacterium tumefaciens systems have the potential to complement conventional plant breeding programmes. However, before deployment, transgenic plants need to be characterized in detail, and physical mapping is an integral part of this process. Therefore, it is important to have a highly efficient method for transgene detection by fluorescence in situ hybridization (FISH). This study describes a new approach, which provides efficient control of probe length and labelling, both of which play an important role in in situ hybridization of transgenes. The approach is based on reducing the size of the plasmid prior to labelling by nick translation, rather than using the whole or linearized plasmid, or varying the amounts of DNaseI in the nick translation mixture. This provided much more efficient labelling of the probe, which yielded optimal hybridization. minimal fluorescent background, and accurate physical location of the transgene.

DNA Probes↗
PubMed2005

Genetic diversity and population structure of teosinte.

The teosintes, the closest wild relatives of maize, are important resources for the study of maize genetics and evolution and for plant breeding. We genotyped 237 individual teosinte plants for 93 microsatellites. Phylogenetic relationships among species and subspecific taxa were largely consistent with prior analyses for other types of molecular markers. Plants of all species formed monophyletic clades, although relationships among species were not fully resolved. Phylogenetic analysis indicated that the Mexican annual teosintes divide into two clusters that largely correspond to the previously defined subspecies, Z. mays ssp. parviglumis and ssp. mexicana, although there are a few samples that represent either evolutionary intermediates or hybrids between these two subspecies. The Mexican annual teosintes show genetic substructuring along geographic lines. Hybridization or introgression between some teosintes and maize occurs at a low level and appears most common with Z. mays ssp. mexicana. Phylogeographic and phylogenetic analyses of the Mexican annual teosintes indicated that ssp. parviglumis diversified in the eastern part of its distribution and spread from east to west and that ssp. mexicana diversified in the Central Plateau of Mexico and spread along multiple paths to the north and east. We defined core sets of collections of Z. mays ssp. mexicana and ssp. parviglumis that attempt to capture the maximum number of microsatellite alleles for given sample sizes.

Alleles↗
PubMed2005

Molecular chemistry imaging to reveal structural features of various plant feed tissues.

Synchrotron Fourier transform infrared (FTIR) microspectroscopy as a rapid, direct, and non-destructive analytical technique can explore molecular chemical features of the micro-structure of biological samples. However, the application of this synchrotron technology to feed science and feed chemistry is extremely rare. This article reviews that with synchrotron FTIR microspectroscopy, the molecular chemistry of various feed tissues could be imaged. These images revealed spatial intensity and distribution of chemical functional groups in various feeds tissues within cellular dimensions. Such information can be used for plant breeding program for selecting superior variety of plant for targeted feed purposes and for prediction of feed quality and nutritive value. The final purpose of this article shows that Synchrotron FTIR microspectroscopy can be used for biological structure study.

Plants, Edible↗
PubMed2006

Arbuscular mycorrhizal fungi contribute to phosphorus uptake by wheat grown in a phosphorus-fixing soil even in the absence of positive growth responses.

We used 32P to quantify the contribution of an arbuscular mycorrhizal (AM) fungus (Glomus intraradices) to phosphorus (P) uptake by wheat (Triticum aestivum), grown in compartmented pots. The soil was from a major cereal-growing area, the Eyre Peninsula, South Australia; it was highly calcareous and P-fixing. Fertilizer P was added to soil at 20 mg kg(-1), as solid or liquid. Two extraction methods were used to estimate plant-available P. Fungal colonization was well established at harvest (36 d). Application of P decreased both colonization and hyphal length density in soil, with small differences between different P fertilizers. Plants showed large positive responses in terms of growth or total P uptake to all P additions, and showed no positive (or even negative) responses to AM colonization, regardless of P application. 32P was detected only in AM plants, and we calculated that over 50% of P uptake by plants was absorbed via AM fungi, even when P was added. The results add to the growing body of knowledge that 'nonresponsive' AM plants have a functional AM pathway for P transfer to the plant; it should not be ignored in breeding plants for root traits designed to improve P uptake.

Mycorrhizae↗
PubMed2000

Disturbance Frequency and Community Stability in Native Tallgrass Prairie.

Ecological communities are spatially and temporally variable in response to a variety of biotic and abiotic forces. It is not always clear, however, if spatial and temporal variability leads to instability in communities. Instability may result from strong biotic interactions or from stochastic processes acting on small populations. I used 10-15 yr of annual data from the Konza Prairie Long-Term Ecological Research site to examine whether plant, breeding bird, grasshopper, and small mammal communities in tallgrass prairie exhibit stability or directional change in response to different experimentally induced fire frequencies. Based on ordination and ANOVA, plant and grasshopper communities on annually burned sites differed significantly from plant and grasshopper communities on less frequently burned sites. Breeding birds and small mammals differed among sites as well, but these differences were not clearly related to disturbance frequency. A modified time series analysis indicated that plant communities were undergoing directional change (unstable) on all watersheds, regardless of fire frequency. Contrary to expectations, directional change was greatest on the annually burned sites and lowest on the infrequently burned sites. Unlike the plant communities, breeding bird, grasshopper, and small mammal communities were temporally stable, despite high-compositional variability from 1 yr to the next. Stability among the consumer communities within these dynamic plant communities occurs because three-dimensional vegetation structure does not change over time, despite changes in plant species composition. Evidence suggests that instability in the plant community results from strong biotic interactions among temporally persistent core species and stochastic dynamics among infrequent satellite species. Overall, community stability cannot be assessed if the pattern of temporal dynamics is unknown. Long-term empirical studies of different taxa under different disturbance regimes are needed to determine over what time frames and spatial scales communities may be stable. Such studies are essential for the development of generalities regarding the relationship between disturbance frequency and community stability in terrestrial and aquatic systems.

community dynamics↗
PubMed2026

Development of a low-coverage whole genome sequencing screen for apomixis using a diverse set of Malus germplasm.

In the past decade, plant biologists have made several major discoveries pertaining to the genetic basis of apomixis (clonal propagation by seed) that have shown promise in preserving high-value hybrid rice and sorghum genotypes. This progress was made possible by foundational gene discovery efforts in model species and natural apomicts, but pleiotropic obstacles still limit its broad agricultural adoption, especially in eudicots. Thus, it follows that investigations of novel apomicts should lead to the development of new molecular tools for plant breeding. The two most common ways to identify clonal seed production are flow-cytometry seed screens and genome sequencing to compare the DNA sequences of the maternal parent and progeny, traditionally using low-throughput markers. While flow-cytometry has been the dominant method for more than two decades, it provides indirect information on the genetics of a resulting embryo and can be ineffective in certain species. Here we developed a method using short-read whole-genome sequencing at moderately low coverage (averaging 3X and 6X) to screen diverse Malus genotypes maintained in a USDA germplasm collection for clonal seed production. In total, we sequenced 55 genotypes, 1,216 of their embryos, and identified 17 previously undescribed apomictic genotypes. Several more were detected with the flow cytometry seed screen, which helped resolve certain types of reproduction and sources of noise in low-coverage datasets. This low-pass screening-by-sequencing method is a relatively low-cost, rapid method for detecting apomictic genotypes in diverse plant germplasm and when used thoughtfully in conjunction with flow cytometry, provides a new way to visualize the genetic outcomes of sexual and asexual reproduction in plants.

Apomixis↗
PubMed2026

Finlay-Wilkinson random regression for yield and yield stability prediction in cereals.

Year-to-year climate variability poses a challenge for agriculture by increasing crop yield variability; therefore, there is a need to identify genotypes that can withstand these fluctuations. With the right selection criteria, genotypes with yield stability across variable environmental conditions can be selected. Methods such as Finlay-Wilkinson random regression (FWRR) may allow us to use sparse datasets-common in plant breeding pipelines-and incorporate genomic data to leverage phenotypic information from related genotypes to predict yield stability. Our objective was to examine how the number of environments and the variance among those environments affect stability predictions. We also integrate FWRR as a genomic prediction tool for characterizing yield stability, comparing it to the traditional genomic prediction models as a reference. We used three datasets: one highly unbalanced dataset for oats (Avena sativa L.) and two completely balanced datasets with different numbers of environments for barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.). We fit standard Finlay-Wilkinson (FW) and FWRR models to estimate grain yield and stability under various scenarios. We found that the estimated stability values obtained were similar using balanced datasets for FW or FWRR. FWRR also achieved moderate predictive ability for stability using unbalanced datasets under 10-fold cross-validation (CV1) with new genotypes. In terms of environmental representation, selecting the right set of environments for inclusion in the model was more important than adding more environments. Our results suggest the possibility of using FWRR to select stable genotypes earlier in line development, as well as to design resource-efficient stability-testing schemes.

Hordeum↗
PubMed2002

Improving iron, zinc and vitamin A nutrition through plant biotechnology.

Recent understanding of plant metabolism has made it possible to increase the iron, zinc and beta-carotene (provitamin A) content in staple foods by both conventional plant breeding and genetic engineering. Improving the micronutrient composition of plant foods may become a sustainable strategy to combat deficiencies in human populations, replacing or complementing other strategies such as food fortification or nutrient supplementation.

Anemia, Iron-Deficiency↗
PubMed2006

Genetic analysis of resistance to yellow rust in hexaploid wheat using a mixture model for multiple crosses.

DNA-based molecular markers have been used in numerous studies for tagging specific genes in wheat for subsequent use in marker-assisted selection. Usually in plant breeding, procedures for mapping genes are based on analysis of a single segregating population. However, breeding programmes routinely evaluate large numbers of progeny derived from multiple-related crosses with some parental lines shared. In most such related crosses, the number of progeny is quite small. Thus, statistical techniques for detecting quantitative trait loci (QTLs) using data from conventional multi-cross breeding programmes are interesting. The objective of this study is to present a mixture model for QTL mapping in crosses of multiple inbred varieties with non-normal phenotype distributions and to use this model to map QTLs for yellow rust resistance in elite wheat breeding material. Three doubled haploid populations consisting of 41, 42 and 55 lines, respectively, originating from four parental varieties were studied. Multi-cross QTL analysis with three specific pathogen isolates of Puccinia striiformis f. sp. tritici and a mixture of the isolates revealed QTLs for resistance at four different genomic locations. These QTLs were found on chromosome 2AL, 2AS, 2BL and 6BL and explained between 21 and 41% of the phenotypic variation. Two of these QTLs, one on the long arm of chromosome 2A and one on the short arm of chromosome 2A were identical to the known yellow rust resistance genes Yr32 and Yr17, respectively, whereas the QTLs located on the long arms of chromosomes 2B and 6B may reflect types of resistance to yellow rust, which have not previously been mapped.

Basidiomycota↗
PubMed2002

Genetic modification of lignin concentration affects fitness of perennial herbaceous plants.

Populations of four perennial herbaceous species that were genetically modified for altered lignin content (or associated forage digestibility) by conventional plant breeding were evaluated for two agricultural fitness traits, plant survival and plant biomass, in three Northcentral USA environments for more than 4 years. Reduced lignin concentration or increased digestibility resulted in increased winter mortality in two of four species and reduced biomass in one species. Results from other experiment indicate that these apparent genetic correlations may be ephemeral, suggesting that selection for fitness can be successful within high-digestibility or low-lignin germplasm. Results indicate that perennial plants genetically engineered with altered lignin concentration or composition for use in livestock, pulp and paper, or bioenergy production should be evaluated for fitness in field environments prior to use in agriculture.

Journal Article↗
PubMed1999

Gene discovery and product development for grain quality traits.

The composition of oils, proteins, and carbohydrates in seeds of corn, soybean, and other crops has been modified to produce grains with enhanced value. Both plant breeding and molecular technologies have been used to produce plants carrying the desired traits. Genomics-based strategies for gene discovery, coupled with high-throughput transformation processes and miniaturized, automated analytical and functionality assays, have accelerated the identification of product candidates. Molecular marker-based breeding strategies have been used to accelerate the process of moving trait genes into high-yielding germplasm for commercialization. These products are being tested for applications in food, feed, and industrial markets.

Biotechnology↗
PubMed2001

A survey of beef muscle color and pH.

The objectives of this study were to define a beef carcass population in terms of muscle color, ultimate pH, and electrical impedance; to determine the relationships among color, pH, and impedance and with other carcasses characteristics; and to determine the effect of packing plant, breed type, and sex class on these variables. One thousand beef carcasses were selected at three packing plants to match the breed type, sex class, marbling score, dark-cutting discount, overall maturity, carcass weight, and yield grade distributions reported for the U.S. beef carcass population by the 1995 National Beef Quality Audit. Data collected on these carcasses included USDA quality and yield grade data and measurements of muscle color (L*, a*, b*), muscle pH, and electrical impedance of the longissimus muscle. About one-half (53.1%) of the carcasses fell within a muscle pH range of 5.40 to 5.49, and 81.3% of the carcasses fell within a longissimus muscle pH range of 5.40 to 5.59. A longissimus muscle pH of 5.87 was the approximate cut-off between normal and dark-cutting carcasses. Frequency distributions indicated that L* values were normally distributed, whereas a* and b* values were abnormally distributed (skewed because of a longer tail for lower values, a tail corresponding with dark-cutting carcasses). Electrical impedance was highly variable among carcasses but was not highly related to any other variable measured. Color measurements (L*, a*, b*) were correlated (P < 0.05) with lean maturity score (-.58, -.31, and -.43, respectively) and with muscle pH (-.40, -.58, and -.56, respectively). In addition, fat thickness was correlated with muscle pH and color (P < 0.05). There was a threshold at approximately .76 cm fat thickness, below which carcasses had higher muscle pH values and lower colorimeter readings. Steer carcasses (L* = 39.62, a* = 25.20, and b* = 11.03) had slightly higher colorimeter readings (P < 0.05) than heifer carcasses (L* = 39.20, a* = 24.78, and b* = 10.80) even though muscle pH was not different between steer and heifer carcasses. Dairy-type carcasses (pH = 5.59, L* = 37.56, a* = 23.40, and b* = 9.68) had higher muscle pH values and lower colorimeter readings than either native-type (pH = 5.50, L* = 39.55, a* = 25.13, and b* = 11.00) or Brahman-type (pH = 5.46, L* = 39.75, a* = 25.17, and b* = 11.05) carcasses (P < 0.05).

Algorithms↗
PubMedDate not supplied

Current methods for assessing safety of genetically modified crops as exemplified by data on Roundup Ready soybeans.

Several laboratories have used recombinant DNA technology in plant breeding to improve compositional, processing, and agronomic characteristics of plants. These transformed plants have been extensively tested in field trials, have gained full regulatory approvals and are currently being marketed in a number of countries around the world. This paper briefly summarizes the approach used to assure the safety of foods and feeds derived from these genetically modified crops, as exemplified by data on Roundup Ready soybeans that has been developed by Monsanto Company using biotechnology in order to confer tolerance to glyphosate, the active ingredient in Roundup herbicide, by the production of the CP4 enolpyruvylshikimate-3-phosphate synthase protein. The results of the studies demonstrate that Roundup Ready soybeans are as safe as traditional soybeans with respect to food and feed safety.

Agriculture↗
PubMed1994

Microbial attachment and feed digestion in the rumen.

Direct microscopic examination of the rumen and its contents shows microbial populations largely attached to feed particles in the digesta. Most feeds contain a surface layer that is resistant to attachment and therefore to digestion. Infiltration of these recalcitrant epidermal layers through damage sites or through focused enzymatic attack is essential for initiation of the digestive process. Proliferation of primary colonizing cells produces glycocalyx-enclosed microcolonies. Secondary colonizers from the ruminal fluid associate with microcolonies, resulting in the formation of multispecies microbial biofilms. These metabolically related organisms associate with their preferred substrates and produce the myriad of enzymes necessary for the digestion of chemically and structurally complex plant tissues. Upon accessing the internal, enzyme-susceptible tissues, microbial "digestive consortia" attach to a variety of nutrients, including protein, cellulose, and starch and digest insoluble feed materials from the inside out. Substances that prevent microbial attachment or promote detachment (e.g., condensed tannins, methylcellulose) can completely inhibit cellulose digestion. As the microbial consortium matures and adapts to a particular type of feed, it becomes inherently stable and its participant microorganisms are notoriously difficult to manipulate due to the impenetrable nature of biofilms. Properties of feed that place constraints on microbial attachment and biofilm formation can have a profound effect on both the rate and extent of feed digestion in the rumen. Developments in feed processing (i.e., chemical and physical), plant breeding, and genetic engineering (both of ruminal microorganisms and plants) that overcome these constraints through the promotion of microbial attachment and biofilm formation could substantially benefit ruminant production.

Animal Feed↗
PubMed2003

From plant genomics to breeding practice.

New alleles are constantly accumulated during intentional crop selection. The molecular understanding of these alleles has stimulated new genomic approaches to mapping quantitative trait loci (QTL) and haplotype multiplicity of the genes concerned. A limited number of quantitative trait nucleotides responsible for QTL variation have been described, but an acceleration in their rate of discovery is expected with the adoption of linkage disequilibrium and candidate gene strategies for QTL fine mapping and cloning. Additional layers of regulatory variation have been studied that could also contribute to the molecular basis of quantitative genetics of crop traits. Despite this progress, the role of marker-assisted selection in plant breeding will ultimately depend on the genetic model underlying quantitative variation.

Breeding↗
PubMed2003

Molecular diversity in French bread wheat accessions related to temporal trends and breeding programmes.

A set of 41 wheat microsatellite markers (WMS), giving 42 polymorphic loci (two loci on each chromosome), was used to describe genetic diversity in a sample of 559 French bread wheat accessions (landraces and registered varieties) cultivated between 1800 and 2000. A total of 609 alleles were detected. Allele number per locus ranged from 3 to 28, with a mean allele number of 14.5. On the average, about 72% of the total number of alleles were observed with a frequency of less than 5% and were considered to be rare alleles. WMS markers used showed different levels of gene diversity: the highest PIC value occurred in the B genome (0.686) compared to 0.641 and 0.659 for the A and D genomes, respectively. When comparing landraces with registered varieties gathered in seven temporal groups, a cluster analysis based on an F(st) matrix provided a clear separation of landraces from the seven variety groups, while a shift was observed between varieties registered before and after 1970. There was a decrease of about 25% in allelic richness between landraces and varieties. In contrast, when considering only registered varieties, changes in diversity related to temporal trends appeared more qualitative than quantitative, except at the end of the 1960s, when a bottleneck might have occurred. New varieties appear to be increasingly similar to each other in relation to allelic composition, while differences between landraces are more and more pronounced over time. Finally, considering a sub-sample of 193 varieties representative of breeding material selected during the twentieth century by the six most important plant breeding companies, few differences in diversity were observed between the different breeding programmes. The observed structure of diversity in French bread wheat collections is discussed in terms of consequences, both for plant breeders and for managers of crop genetic resources.

Alleles↗
PubMed1999

A fertile amphiploid between diploid wheat (Triticum tauschii) and crested wheat grass (Agropyron cristatum).

Alloploidy, one of the most efficient evolutionary mechanisms in nature, has not been extensively exploited in plant breeding programmes. Many genomic combinations remain to be created by plant breeders, to be used directly as new crops or indirectly to widen the genetic basis of crops. The Triticeae tribe, to which wheat belongs, is among the botanical groups in which this strategy has been successfully explored. However, there remain valuable genomic combinations that have not been obtained at the diploid level. The Agropyron complex (wheat-grasses) has recently been the focus of attention for interspecific hybridization, but intergeneric hybrids or amphiploids with wheat have not been reported at the diploid level. Here we report synthesis of a tetraploid amphiploid between Triticum tauschii and Agropyron cristatum by crossing two tetraploid accessions. Using total genome in situ hybridization (GISH) staining on metaphase I pollen mother cells, data on allosyndetic and autosyndetic chromosome pairing have been obtained. These data support the view that the A. cristatum tetraploid parent used in the synthesis of the amphiploid has a segmental alloploidy nature.

Chromosome Mapping↗