scholarly journals Importance of parental genome balance in the generation of novel yet heritable epigenetic and transcriptional states during doubled haploid breeding

2019 ◽  
Author(s):  
Jonathan Price ◽  
Javier Antunez-Sanchez ◽  
Nosheen Hussain ◽  
Anjar Wibowo ◽  
Ranjith Papareddy ◽  
...  
Keyword(s):  
Plant Breeding ◽  
Doubled Haploid ◽  
Computational Analysis ◽  
Epigenetic Modification ◽  
Phenotypic Variability ◽  
Doubled Haploids ◽  
Parental Genome ◽  
Crop Species ◽  
Epigenetic Manipulation ◽  
Doubled Haploid Breeding

AbstractBackgroundDoubling the genome contribution of haploid plants has accelerated breeding in most cultivated crop species. Although plant doubled haploids are isogenic in nature, they frequently display unpredictable phenotypes, thus limiting the potential of this technology. Therefore, being able to predict the factors implicated in this phenotypic variability could accelerate the generation of desirable genomic combinations and ultimately plant breeding.ResultsWe use computational analysis to assess the transcriptional and epigenetic dynamics taking place during doubled haploids generation in the genome of Brassica oleracea. We observe that doubled haploid lines display unexpected levels of transcriptional and epigenetic variation, and that this variation is largely due to imbalanced contribution of parental genomes. We reveal that epigenetic modification of transposon-related sequences during DH breeding contributes to the generation of unpredictable yet heritable transcriptional states. Targeted epigenetic manipulation of these elements using dCas9-hsTET3 confirms their role in transcriptional regulation. We have uncovered a hitherto unknown role for parental genome balance in the transcriptional and epigenetic stability of doubled haploids.ConclusionsThis is the first study that demonstrates the importance of parental genome balance in the transcriptional and epigenetic stability of doubled haploids, thus enabling predictive models to improve doubled haploid-assisted plant breeding.

Formation and composition of training flax collection

2020 ◽  
pp. 61-71
Author(s):  
L.M. Kryvosheieva ◽  
V.I. Chuchvaha ◽  
N.M. Kandyba
Keyword(s):  
Plant Breeding ◽  
Gene Pool ◽  
Phenotypic Variability ◽  
Plant Genetic Resources ◽  
Field Measurements ◽  
Educational Process ◽  
Educational Institutions ◽  
Economic Traits ◽  
Wide Range ◽  
History Of

Aim. Based on the results of multi-year research into the flax gene pool, to form a flax training collection to provide breeding scientific organizations and educational institutions with collection samples as well as with information about the bast crop gene pool. Results and Discussion. The studies were conducted in the crop rotation fields for breeding and seed production of the Institute of Bast Crops of the NAAS (Hlukhiv, Sumska Oblast) in 1992-2018. The field measurements and laboratory analyses were carried out in accordance with conventional methods of field and laboratory studies of collection flax samples.The article presents the results on the formation of a training collection of flax at the Institute of Bast Crops of the NAAS, which has 117 accessions (11 botanical species and three varieties) from 22 countries. In addition to species diversity, the collection includes accessions with different levels of expression of valuable economic and biological characteristics. It also includes accessions selected by phenotypic variability of individual characters or their combinations. The multi-year research into the flax collection accessions resulted in identification of sources of highly-expressed valuable economic traits, which are of interest for the plant breeding course. The history of flax breeding in Ukraine is shown, where breeding varieties that are most widespread or were significant breeding achievements in solving certain problems, are presented. The collection can be used as a visual aid for the plant breeding course in educational programs; in addition, it can provide starting material for scientific and educational institutions. The collection is registered with the National Center for Plant Genetic Resources of Ukraine (certificate No. 00273 dated 04/11/2019). Conclusions. The studies of accessions from the national flax collection allowed us to build up a training collection and register it with the NCPGRU. The collection represents a wide range of biological and economic features of the gene pool of this crop. The collection can be used in the educational process of educational agricultural and biological institutions. The multi-year research into the national flax collection resulted in identification of sources of highly-expressed valuable economic traits, which are of interest to the plant breeding course. The history of flax breeding in Ukraine got covered, and breeding varieties that are most widespread or were significant breeding achievements in solving certain problems are presented.

scholarly journals Comparison of methods for obtaining doubled haploids of carrot

2017 ◽  
Vol 86 (2) ◽  
Author(s):  
Waldemar Kiszczak ◽  
Urszula Kowalska ◽  
Agata Kapuścińska ◽  
Maria Burian ◽  
Krystyna Górecka
Keyword(s):  
Plant Regeneration ◽  
Doubled Haploid ◽  
Aspartate Aminotransferase ◽  
Doubled Haploids ◽  
The Other ◽  
Plant Production ◽  
Comparison Of Methods ◽  
Anther Cultures ◽  
Induction Stage ◽  
Main Factor

Doubled haploid lines of carrot can be obtained through androgenesis in anther cultures and in isolated microspore cultures. The two methods were compared using three carrot cultivars (‘Kazan F1’, ‘Feria F1’, and ‘Narbonne F1’) at the androgenesis induction stage, during plant regeneration from embryos, and during acclimatization of androgenetic plants as well as their characterization. It was found that cultivar was the main factor affecting the efficiency at each stage of plant production in both anther and isolated microspore cultures. The efficiency of androgenesis in anther cultures of ‘Feria F1’ was considerably higher in comparison with isolated microspore cultures, and more plants were obtained from the embryos of androgenesis-cultured plants. In ‘Kazan F1’ and ‘Narbonne F1’, more acclimatized androgenetic plants were produced from anther cultures. Ploidy assessment of acclimatized plants of ‘Narbonne F1’ showed that the majority of the plants in the population derived from anther cultures had a doubled chromosome (DH) set. On the other hand, the majority of plants obtained from isolated microspore cultures were haploids. When assessing homozygosity, it was found among plants obtained in anther cultures that the percentage of homozygotes for phosphoglucose isomerase (PGI) and aspartate aminotransferase (AAT) depended on the cultivar. In contrast, the majority of plants derived from isolated microspore cultures were homozygous regardless of cultivar.

COMPARAISON ENTRE DES LIGNEES PEDIGREES ET DES LIGNEES HAPLOIDES DOUBLEES CHEZ L’ORGE (HORDEUM VULGARE L.)

1980 ◽  
Vol 60 (1) ◽  
pp. 79-85 ◽  
Author(s):  
PIERRE TURCOTTE ◽  
C. A. ST-PIERRE ◽  
KEH MING HO
Keyword(s):  
Hordeum Vulgare ◽  
Doubled Haploid ◽  
Doubled Haploids ◽  
Block Design ◽  
Pure Line ◽  
Kernel Weight ◽  
Hordeum Vulgare L ◽  
Line Production ◽  
Doubled Haploid Lines ◽  
Time Required

Pedigree and doubled haploid lines from seven crosses of barley (Hordeum vulgare L.) were compared over 2 years. The lines were tested, in a randomized complete block design, in row plots at Ste-Foy in 1977 and in hill plots at Brawley, California in 1978. There are significant differences between the two methods of pure line production for grain yield, 1000-kernel weight, plant height, resistance to lodging and date of maturity. Furthermore, these significant differences between doubled haploid and pedigree lines seem to be tied to wide crosses. After showing that doubled haploids are superior for resistance to lodging, we conclude that the use of doubled haploid lines must be seriously considered in a barley breeding program on the basis of improved selection efficiency and the short time required to get homozygous lines.

Haploidy and plant breeding

1981 ◽  
Vol 292 (1062) ◽  
pp. 499-507 ◽  
Keyword(s):  
Plant Breeding ◽  
Doubled Haploids ◽  
Chromosome Complement ◽  
Basic Research ◽  
Breeding Value ◽  
Additive Variance ◽  
Ploidy Levels ◽  
Breeding Programmes ◽  
Dh Lines

A haploid is an organism that looks like a sporophyte, but has the chromosome complement of a reduced gamete. There are several ways in which haploids can occur or be induced in vivo : spontaneously, mostly associated with polyembryony, and through abnormal processes after crosses, like pseudogamy, semigamy, preferential elimination of the chromosomes of one parental species, and androgenesis. In the crops described, haploids are or are near to being used in basic research and plant breeding. The application of haploids in breeding self-pollinated crops is based on their potential for producing fully homozygous lines in one generation, which can be assessed directly in the field. Early generation testing of segregating populations is possible through haploids, because doubled haploids (DH) possess additive variance only. Haploids can also be applied in classical breeding programmes to make these more efficient through improved reliability of selection. The application of haploids in cross-pollinated crops is also based on a rapid production of DH-lines, which can be used as inbred lines for the production of hybrid varieties. By means of haploids all natural barriers to repeated selfing are bypassed. In autotetraploid crops there are two types of haploid. One cycle of haploidization leads to dihaploids; a second cycle produces monohaploids. The significance of dihaploids is in their greatly simplified genetics and breeding and in the possibility of estimation of the breeding value of tetraploid cultivars by assessing their dihaploids. The main drawback of dihaploids is their restriction to two alleles per locus. Also, after doubling, it is impossible to achieve tetra-allelism at many loci, the requirement for maximal performance of autotetraploid cultivars. Tetra-allelism can be obtained when improved dihaploids have a genetically controlled mechanism of forming highly heterozygous restitution gametes with the unreduced number of chromosomes. Monohaploids, after doubling or twice doubling, may lead to fully homozygous diploids and tetraploids. These are important for basic research, but not yet for practical application. Meiotic data of potato homozygotes at three ploidy levels are presented.

The genetic framework of plant breeding

1981 ◽  
Vol 292 (1062) ◽  
pp. 407-419 ◽  
Keyword(s):  
Plant Breeding ◽  
Recombinant Inbred ◽  
Recombinant Inbred Lines ◽  
Inbred Lines ◽  
Single Seed Descent ◽  
Crop Species ◽  
Biometrical Genetics ◽  
Mendelian Genetics ◽  
Linkage Disequilibria ◽  
Random Samples

The phenotypic variation that the breeder must manipulate to produce improved genotypes typically contains contributions from both heritable and non-heritable sources as well as from interactions between them. The totality of this variation can be understood only in terms of a methodology such as that of biometrical genetics - an extension of classical Mendelian genetics that retains all of its analytical, interpretative and predictive powers but only in respect of the net or summed effects of all contributing gene loci. In biometrical genetics the statistics that describe the phenotypic distributions are themselves completely described by heritable components based on the known types of gene action and interaction in combination with nonheritable components defined by the statistical properties of the experimental design. Biometrical genetics provides a framework for investigating the genetical basis and justification for current plant breeding strategies that are typified by the production of F 1 hybrids at one extreme and recombinant inbred lines at the other. From the early generations of a cross it can extract estimates of the heritable components of the phenotypic distributions that provide all the information required to interpret the cause of F 1 heterosis and predict the properties of any generation that can subsequently be derived from the cross. Applications to crosses in experimental and crop species show that true overdominance is not a cause of F 1 heterosis, although spurious overdominance arising from linkage disequilibria and non-allelic interactions can be. Predictions of the phenotypic distributions and ranges of recombinant inbred lines that should be extractable from these crosses are confirmed by observations made on random samples of inbred families produced from them by single seed descent. Within these samples, recombinant inbred lines superior to existing inbred lines and their F 1 hybrids are observed with the predicted frequencies.

Formation and composition of trait melon (Сucumis melo L.) collection

2021 ◽  
pp. 98-108
Author(s):  
OH Kholodniak ◽  
OO Kholodniak ◽  
SL Pavlova
Keyword(s):  
Plant Breeding ◽  
Land Reclamation ◽  
Abiotic Factors ◽  
Phenotypic Variability ◽  
Starting Material ◽  
Biological Traits ◽  
Economic Traits ◽  
Economically Valuable Traits ◽  
History Of ◽  
Water Problems

The aim of the article was to present the results on the formation of a trait collection of melons at the Southern State Agricultural Experimental Station of the Institute of Water Problems and Land Reclamation of NAAS of Ukraine, which contains 57 specimens (one botanical species, one subspecies and three varieties) from 11 countries. Results and Discussion. The collection includes specimens with 35 economically valuable traits, which can be useful for the lecture course Plant Breeding and as starting material for breeding research institutions. Each specimen was comprehensively studied and evaluated for performance and resistance to biotic and abiotic factors and described in terms of morphological features for three years. In addition to the species diversity, the trait collections included specimens with different levels of expression of valuable economic and biological traits. The collection also included specimens selected by phenotypic variability of individual traits or their combinations. The results of multi-year work with the melon collection specimens allowed us to identify sources of valuable economic traits with high levels of their expression, which are of interest for the lecture course Plant Breeding. Conclusion. The history of the melon breeding in Ukraine is shown; breeding varieties, which are most widespread or were a significant breeding achievement in solving certain problems, are presented. The collection can be used in plant breeding and as starting material in research and educational institutions.

scholarly journals Comparison and Application of Non-Destructive NIR Evaluations of Seed Protein and Oil Content in Soybean Breeding

Agronomy ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 77 ◽  
Author(s):  
Guo-Liang Jiang
Keyword(s):  
Plant Breeding ◽  
Oil Content ◽  
Near Infrared ◽  
Regression Equations ◽  
Single Plant ◽  
Crop Species ◽  
Soybean Breeding ◽  
Plant Breeding Program ◽  
Significant Difference ◽  
Non Destructive

A plant breeding program needs to evaluate a large number of materials for different traits within a limited time. Near-infrared (NIR) spectroscopy has been used to quickly determine seed composition in various crop species. In this study, we compared whole-seed evaluations of protein and oil content by NIR methods in soybean [Glycine max (L.) Merr.], and then discussed the application to plant breeding. The differences among the entries tested were highly significant in both traits for each method used. No significant difference but high correlation and consistency existed between DA 7250 and wet-chemistry methods. Compared with DA 7250, ZX-50 exhibited, to some extent, differences or errors. The differences of ZX-50 methods were found to be correlated with seed sizes and could be corrected using regression equations formulated for bias calculation. After correction, the differences in the predictions between DA 7250 and ZX-50 methods were insignificant. Similar to DA 7250, ZX-50 methods exhibited a high repeatability (> 98%) of the predictions. By validation with 760 bulk samples of different seed types and 240 single-plant samples, it further demonstrated that as a non-destructive, fast and cost-efficient method, ZX-50 NIR analysis with an appropriate bias correction could be used in soybean breeding, specifically suitable for single plant selection based on whole seeds.

scholarly journals Genome-Wide Differential DNA Methylation and miRNA Expression Profiling Reveals Epigenetic Regulatory Mechanisms Underlying Nitrogen-Limitation-Triggered Adaptation and Use Efficiency Enhancement in Allotetraploid Rapeseed

2020 ◽  
Vol 21 (22) ◽  
pp. 8453
Author(s):  
Ying-peng Hua ◽  
Ting Zhou ◽  
Jin-yong Huang ◽  
Cai-peng Yue ◽  
Hai-xing Song ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Epigenetic Modification ◽  
Lateral Roots ◽  
Regulatory Mechanisms ◽  
Crop Species ◽  
N Limitation ◽  
Genome Wide ◽  
Differentially Methylated Genes ◽  
N Metabolism ◽  
Use Efficiency

Improving crop nitrogen (N) limitation adaptation (NLA) is a core approach to enhance N use efficiency (NUE) and reduce N fertilizer application. Rapeseed has a high demand for N nutrients for optimal plant growth and seed production, but it exhibits low NUE. Epigenetic modification, such as DNA methylation and modification from small RNAs, is key to plant adaptive responses to various stresses. However, epigenetic regulatory mechanisms underlying NLA and NUE remain elusive in allotetraploid B. napus. In this study, we identified overaccumulated carbohydrate, and improved primary and lateral roots in rapeseed plants under N limitation, which resulted in decreased plant nitrate concentrations, enhanced root-to-shoot N translocation, and increased NUE. Transcriptomics and RT-qPCR assays revealed that N limitation induced the expression of NRT1.1, NRT1.5, NRT1.7, NRT2.1/NAR2.1, and Gln1;1, and repressed the transcriptional levels of CLCa, NRT1.8, and NIA1. High-resolution whole genome bisulfite sequencing characterized 5094 differentially methylated genes involving ubiquitin-mediated proteolysis, N recycling, and phytohormone metabolism under N limitation. Hypermethylation/hypomethylation in promoter regions or gene bodies of some key N-metabolism genes might be involved in their transcriptional regulation by N limitation. Genome-wide miRNA sequencing identified 224 N limitation-responsive differentially expressed miRNAs regulating leaf development, amino acid metabolism, and plant hormone signal transduction. Furthermore, degradome sequencing and RT-qPCR assays revealed the miR827-NLA pathway regulating limited N-induced leaf senescence as well as the miR171-SCL6 and miR160-ARF17 pathways regulating root growth under N deficiency. Our study provides a comprehensive insight into the epigenetic regulatory mechanisms underlying rapeseed NLA, and it will be helpful for genetic engineering of NUE in crop species through epigenetic modification of some N metabolism-associated genes.

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