Family-based association mapping in crop species

Identification of allelic variants associated with complex traits provides molecular genetic information associated with variability upon which both artificial and natural selections are based. Family-based association mapping (FBAM) takes advantage of linkage disequilibrium among segregating progeny within crosses and among parents to provide greater power than association mapping and greater resolution than linkage mapping. Herein, we discuss the potential adaption of human family-based association tests and quantitative transmission disequilibrium tests for use in crop species. The rapid technological advancement of next generation sequencing will enable sequencing of all parents in a planned crossing design, with subsequent imputation of genotypes for all segregating progeny. These technical advancements are easily adapted to mating designs routinely used by plant breeders. Thus, FBAM has the potential to be widely adopted for discovering alleles, common and rare, underlying complex traits in crop species.     

Epistatic association mapping in homozygous crop cultivars

The genetic dissection of complex traits plays a crucial role in crop breeding. However, genetic analysis and crop breeding have heretofore been performed separately. In this study, we designed a new approach that integrates epistatic association analysis in crop cultivars with breeding by design. First, we proposed an epistatic association mapping (EAM) approach in homozygous crop cultivars. The phenotypic values of complex traits, along with molecular marker information, were used to perform EAM. In our EAM, all the main-effect quantitative trait loci (QTLs), environmental effects, QTL-by-environment interactions and QTL-by-QTL interactions were included in a full model and estimated by empirical Bayes approach. A series of Monte Carlo simulations was performed to confirm the reliability of the new method. Next, the information from all detected QTLs was used to mine novel alleles for each locus and to design elite cross combination. Finally, the new approach was adopted to dissect the genetic basis of seed length in 215 soybean cultivars obtained, by stratified random sampling, from 6 geographic ecotypes in China. As a result, 19 main-effect QTLs and 3 epistatic QTLs were identified, more than 10 novel alleles were mined and 3 elite parental combinations, such as Daqingdou and Zhengzhou790034, were predicted.     

Whole-genome association mapping in elite inbred crop varieties

We have previously shown that linkage disequilibrium (LD) in the elite cultivated barley (Hordeum vulgare) gene pool extends, on average, for <1-5 cM. Based on this information, we have developed a platform for whole genome association studies that comprises a collection of elite lines that we have characterized at 3060 genome-wide single nucleotide polymorphism (SNP) marker loci. Interrogating this data set shows that significant population substructure is present within the elite gene pool and that diversity and LD vary considerably across each of the seven barley chromosomes. However, we also show that a subpopulation comprised of only the two-rowed spring germplasm is less structured and well suited to whole genome association studies without the need for extensive statistical intervention to account for structure. At the current marker density, the two-rowed spring population is suited for fine mapping simple traits that are located outside of the genetic centromeres with a resolution that is sufficient for candidate gene identification by exploiting conservation of synteny with fully sequenced model genomes and the emerging barley physical map.     

Molecular mapping and tagging of genes in crop plants

In India, molecular mapping and tagging of agronomically important genes using RFLP and RAPD markers have been carried out in three different crops: rice, mustard and chickpea. In rice, tagging of genes for resistance to gall midge and blast has been accomplished. Molecular mapping of cooking quality traits in rice is in progress. For fingerpringting rice cultivars, suitable probe enzyme combinations have been identified. In mustard, a partial RFLP linkage map has been constructed and one of the yellow seed-coat colour loci has been mapped. Significant associations of RFLP markers with quantitative traits have also been established. Potential use of RAPD markers to identify heterotic groups among mustard accessions has been demonstrated. In chickpea, the occurrence of considerable interspecific DNA polymorphism as revealed by RAPD analysis has facilitated construction of a partial linkage map.     

Glycerol concentrations in crop plants

A procedure has been developed for preparation of plant extracts for quantitation of their glycerol content using high performance liquid chromatography or enzymatic analysis. Fifteen crop plants grown under field conditions had leaf concentrations of glycerol between 10 and 39 μg/g wt weight of tissue. Approximately 12 h after relatively heavy rains leaves of maize, sugar beet, soybean, bean, pumpkin and alfalfa had several fold increases in concentrations of leaf glycerol. When barley plants were made anaerobic for 24 h, large increases in leaf glycerol concentrations were observed. It is proposed that part of the glycerol observed in anaerobic plants comes from glycerol synthesis in the root and transport to the leaves and part is produced in the leaves.     

Large SNP arrays for genotyping in crop plants

Genotyping with large numbers of molecular markers is now an indispensable tool within plant genetics and breeding. Especially through the identification of large numbers of single nucleotide polymorphism (SNP) markers using the novel high-throughput sequencing technologies, it is now possible to reliably identify many thousands of SNPs at many different loci in a given plant genome. For a number of important crop plants, SNP markers are now being used to design genotyping arrays containing thousands of markers spread over the entire genome and to analyse large numbers of samples. In this article, we discuss aspects that should be considered during the design of such large genotyping arrays and the analysis of individuals. The fact that crop plants are also often autopolyploid or allopolyploid is given due consideration. Furthermore, we outline some potential applications of large genotyping arrays including high-density genetic mapping, characterization (fingerprinting) of genetic material and breeding-related aspects such as association studies and genomic selection.     

Opportunities for improving phosphorus-use efficiency in crop plants

Limitation of grain crop productivity by phosphorus (P) is widespread and will probably increase in the future. Enhanced P efficiency can be achieved by improved uptake of phosphate from soil (P-acquisition efficiency) and by improved productivity per unit P taken up (P-use efficiency). This review focuses on improved P-use efficiency, which can be achieved by plants that have overall lower P concentrations, and by optimal distribution and redistribution of P in the plant allowing maximum growth and biomass allocation to harvestable plant parts. Significant decreases in plant P pools may be possible, for example, through reductions of superfluous ribosomal RNA and replacement of phospholipids by sulfolipids and galactolipids. Improvements in P distribution within the plant may be possible by increased remobilization from tissues that no longer need it (e.g. senescing leaves) and reduced partitioning of P to developing grains. Such changes would prolong and enhance the productive use of P in photosynthesis and have nutritional and environmental benefits. Research considering physiological, metabolic, molecular biological, genetic and phylogenetic aspects of P-use efficiency is urgently needed to allow significant progress to be made in our understanding of this complex trait.     

Coping mechanisms for crop plants in drought-prone environments

Background: Drought is a major limitation to plant productivity. Variousoptions are available for increasing water availability andsustaining growth of crop plants in drought-prone environments. Scope: After a general introduction to the problems of water availability,this review focuses on a critical evaluation of recent progressin unravelling mechanisms for modifying plant growth responsesto drought. Conclusions: Investigations of key regulatory mechanisms integrating plantgrowth responses to water deficits at the whole-organism, cellularand genomic levels continue to provide novel and exiting researchfindings. For example, recent reports contradict the widespreadconception that root-derived abscisic acid is necessarily involvedin signalling for stomatal and shoot-growth responses to soilwater deficits. The findings bring into question the theoreticalbasis for alternate-side root-irrigation techniques. Similarly,recent reports indicate that increased ABA production or increasedaquaporin expression did not lead to improved drought resistance.Other reports have concerned key genes and proteins involvedin regulation of flowering (FT), vegetative growth (DELLA),leaf senescence (IPT) and desiccation tolerance (LEA). Introgressionof such genes, with suitable promoters, can greatly impact onwhole-plant responses to drought. Further developments couldfacilitate the introduction by breeders of new crop varietieswith growth physiologies tailored to improved field performanceunder drought. Parallel efforts to encourage the introductionof supplementary irrigation with water made available by improvedconservation measures and by sea- or brackish-water desalination,will probably provide comprehensive solutions to coping withdrought-prone environments.     

Salt resistant crop plants

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Marker assisted selection in crop plants

Genetic mapping of major genes and quantitative traits loci (QTLs) for many important agricultural traits is increasing the integration of biotechnology with the conventional breeding process. Exploitation of the information derived from the map position of traits with agronomical importance and of the linked molecular markers, can be achieved through marker assisted selection (MAS) of the traits during the breeding process. However, empirical applications of this procedure have shown that the success of MAS depends upon several factors, including the genetic base of the trait, the degree of the association between the molecular marker and the target gene, the number of individuals that can be analyzed and the genetic background in which the target gene has to be transferred. MAS for simply inherited traits is gaining increasing importance in breeding programs, allowing an acceleration of the breeding process. Traits related to disease resistance to pathogens and to the quality of some crop products are offering some important examples of a possible routinary application of MAS. For more complex traits, like yield and abiotic stress tolerance, a number of constraints have determined severe limitations on an efficient utilization of MAS in plant breeding, even if there are a few successful applications in improving quantitative traits. Recent advances in genotyping technologies together with comparative and functional genomic approaches are providing useful tools for the selection of genotypes with superior agronomical performancies.     

Understanding CoQ evolution in plants for crop trait design

<正>The study of evolution is a fundamental pillar in our understanding of the natural world, providing critical insights into how species adapt to their environments through intricate genetic and molecular modifications. This research field not only elucidates the origins of biological traits and adaptation mechanisms but also reveals conserved genetic pathways and mutations that underpin biodiversity across different species.     

Anatomical anomalies in crop formation plants

Crop formations consist of geometrically organized regions ranging from 2 to 80 m diameter, in which the plants (primarily grain crops) are flattened in a horizontal position. Plants from crop formations display anatomical alterations which cannot be accounted for by assuming the formations are hoaxes. Near the soil surface the curved stems often form complex swirls with 'vortex' type patterns. In the present paper, evidence is presented which indicates that structural and cellular alterations take place in plants exposed within the confines of the 'circle' type formations, differences which were determined to be statistically significant when compared with control plants taken outside the formations. These transformations were manifested at the macroscopic-level as abnormal nodal swelling, gross malformations during embryogenesis. and charred epidermal tissue. Significant changes in seed germination and development were found, and at the microscopic level differences were observed in cell wall pit structures. Affected plants also have characteristics suggesting the involvement of transient high temperatures.