scholarly journals Genetic mapping of genotype-by-ploidy effects in Arabidopsis thaliana

2021 ◽  
Author(s):  
Cris L. Wijnen ◽  
Frank F.M. Becker ◽  
Andries A. Okkersen ◽  
Bastiaan C. de Snoo ◽  
Martin P. Boer ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Genetic Variation ◽  
Ploidy Level ◽  
Genetic Factors ◽  
Doubled Haploids ◽  
Rapid Development ◽  
Ploidy Levels ◽  
Late Flowering ◽  
Large Populations ◽  
Phenotypic Responses

Plants can express different phenotypic responses following polyploidization, but ploidy-dependent phenotypic variation has so far not been assigned to specific genetic factors. To map such effects, segregating populations at different ploidy levels are required. The availability of an efficient haploid-inducer line in Arabidopsis thaliana allows for the rapid development of large populations of segregating haploid offspring. Because Arabidopsis haploids can be self-fertilised to give rise to homozygous doubled haploids, the same genotypes can be phenotyped at both the haploid and diploid ploidy level. Here, we compared the phenotypes of recombinant haploid and diploid offspring derived from a cross between two late flowering accessions to map genotype x ploidy (GxP) interactions. Ploidy-specific quantitative trait loci (QTLs) were detected at both ploidy levels. This implies that mapping power will increase when phenotypic measurements of monoploids are included in QTL analyses. A multi-trait analysis further revealed pleiotropic effects for a number of the ploidy specific QTLs as well as opposite effects at different ploidy levels for general QTLs. Taken together, we provide evidence of genetic variation between different Arabidopsis accessions being causal for dissimilarities in phenotypic responses to altered ploidy levels, revealing a GxP effect. Additionally, by investigating a population derived from late flowering accessions we revealed a major vernalisation specific QTL for variation in flowering time, countering the historical bias of research in early flowering accessions.

scholarly journals A 'Variant Viewer' for investigating population-level variation in Arabidopsis thaliana

2021 ◽  
Author(s):  
Matthew Cumming ◽  
Eddi Esteban ◽  
Vincent Lau ◽  
Asher Pasha ◽  
Nicholas J. Provart
Keyword(s):  
Arabidopsis Thaliana ◽  
Genetic Variation ◽  
High Throughput ◽  
Web Application ◽  
High Throughput Sequencing ◽  
Population Level ◽  
Gene Families ◽  
Level Variation ◽  
Splice Isoforms ◽  
Large Populations

High throughput sequencing has opened the doors for investigators to probe genetic variation present in large populations of organisms. In plants, the 1001 Genomes Project (1001genomes.org) is one such effort that sought to characterize the extant worldwide variation in Arabidopsis thaliana for future analyses to compare and draw upon. We developed a web application that accesses the 1001 Genomes database called The Variant Viewer, for investigators to view variants in any A. thaliana gene and within gene families. These variants may be visualized in the context of alignments of queried genes, across splice isoforms of these genes and in relation to conserved domains.

The effect of daylength on the transition to flowering in phytochrome-deficient, late-flowering and double mutants of Arabidopsis thaliana

1995 ◽  
Vol 95 (2) ◽  
pp. 260-266 ◽  
Author(s):  
Maarten Koornneef ◽  
Corrie Hanhart ◽  
Patty van Loenen-Martinet ◽  
Hetty Blankestijn de Vries
Keyword(s):  
Arabidopsis Thaliana ◽  
Late Flowering ◽  
Transition To Flowering

scholarly journals VTRNA2-1: Genetic Variation, Heritable Methylation and Disease Association

2021 ◽  
Vol 22 (5) ◽  
pp. 2535
Author(s):  
Pierre-Antoine Dugué ◽  
Chenglong Yu ◽  
Timothy McKay ◽  
Ee Ming Wong ◽  
Jihoon Eric Joo ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Dna Methylation ◽  
Genetic Variation ◽  
Genetic Factors ◽  
Disease Association ◽  
Country Of Birth ◽  
Cpg Site ◽  
Multiple Case ◽  
Metastable Epiallele ◽  
Methylation Quantitative Trait Loci

VTRNA2-1 is a metastable epiallele with accumulating evidence that methylation at this region is heritable, modifiable and associated with disease including risk and progression of cancer. This study investigated the influence of genetic variation and other factors such as age and adult lifestyle on blood DNA methylation in this region. We first sequenced the VTRNA2-1 gene region in multiple-case breast cancer families in which VTRNA2-1 methylation was identified as heritable and associated with breast cancer risk. Methylation quantitative trait loci (mQTL) were investigated using a prospective cohort study (4500 participants with genotyping and methylation data). The cis-mQTL analysis (334 variants ± 50 kb of the most heritable CpG site) identified 43 variants associated with VTRNA2-1 methylation (p < 1.5 × 10−4); however, these explained little of the methylation variation (R2 < 0.5% for each of these variants). No genetic variants elsewhere in the genome were found to strongly influence VTRNA2-1 methylation. SNP-based heritability estimates were consistent with the mQTL findings (h2 = 0, 95%CI: −0.14 to 0.14). We found no evidence that age, sex, country of birth, smoking, body mass index, alcohol consumption or diet influenced blood DNA methylation at VTRNA2-1. Genetic factors and adult lifestyle play a minimal role in explaining methylation variability at the heritable VTRNA2-1 cluster.

scholarly journals A Bibliometric Insight of Genetic Factors in ASD: Emerging Trends and New Developments

2020 ◽  
Vol 11 (1) ◽  
pp. 33
Author(s):  
Kang Wang ◽  
Weicheng Duan ◽  
Yijie Duan ◽  
Yuxin Yu ◽  
Xiuyi Chen ◽  
...  
Keyword(s):  
Genetic Factors ◽  
De Novo ◽  
Rapid Development ◽  
The United States ◽  
Research Area ◽  
Scientific Output ◽  
Autism Spectrum ◽  
De Novo Mutations ◽  
Emerging Trends ◽  
Genetic Abnormalities

Autism spectrum disorder (ASD) cases have increased rapidly in recent decades, which is associated with various genetic abnormalities. To provide a better understanding of the genetic factors in ASD, we assessed the global scientific output of the related studies. A total of 2944 studies published between 1997 and 2018 were included by systematic retrieval from the Web of Science (WoS) database, whose scientific landscapes were drawn and the tendencies and research frontiers were explored through bibliometric methods. The United States has been acting as a leading explorer of the field worldwide in recent years. The rapid development of high-throughput technologies and bioinformatics transferred the research method from the traditional classic method to a big data-based pipeline. As a consequence, the focused research area and tendency were also changed, as the contribution of de novo mutations in ASD has been a research hotspot in the past several years and probably will remain one into the near future, which is consistent with the current opinions of the major etiology of ASD. Therefore, more attention and financial support should be paid to the deciphering of the de novo mutations in ASD. Meanwhile, the effective cooperation of multi-research centers and scientists in different fields should be advocated in the next step of scientific research undertaken.

scholarly journals The physiological basis for genetic variation in water use efficiency and carbon isotope composition in Arabidopsis thaliana

2013 ◽  
Vol 119 (1-2) ◽  
pp. 119-129 ◽  
Author(s):  
Hsien Ming Easlon ◽  
Krishna S. Nemali ◽  
James H. Richards ◽  
David T. Hanson ◽  
Thomas E. Juenger ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Genetic Variation ◽  
Water Use Efficiency ◽  
Carbon Isotope ◽  
Water Use ◽  
Isotope Composition ◽  
Carbon Isotope Composition ◽  
Physiological Basis ◽  
Use Efficiency

A genetic and physiological analysis of late flowering mutants in Arabidopsis thaliana

1991 ◽  
Vol 229 (1) ◽  
pp. 57-66 ◽  
Author(s):  
M. Koornneef ◽  
C. J. Hanhart ◽  
J. H. van der Veen
Keyword(s):  
Arabidopsis Thaliana ◽  
Late Flowering ◽  
Physiological Analysis

scholarly journals Ploidy Levels of Hardy Actinidia Accessions in the U.S. Determined by Flow Cytometry

HortScience ◽  
1997 ◽  
Vol 32 (3) ◽  
pp. 439D-439 ◽  
Author(s):  
Mary Ann Start ◽  
James Luby ◽  
Robert Guthrie ◽  
Debby Filler
Keyword(s):  
Flow Cytometry ◽  
Ploidy Level ◽  
Interspecific Variation ◽  
Root Tip ◽  
Interspecific Crosses ◽  
Ploidy Levels ◽  
Haploid Chromosome Number ◽  
Tip Cells ◽  
Root Tip Cells ◽  
The U.S

The hardy Actinidia species represent a source of genetic diversity for improving A. deliciosa (kiwifruit) as well as for creating new economically important cultivars through intra- and interspecific crosses. Attempts at breeding in Actinidia have been complicated by the existence of intraspecific as well as interspecific variation in ploidy. The haploid chromosome number in Actinidia is 29 and diploid (2n=2x=58), tetraploid (2n=4x=116), and hexaploid (2n=6x=174) levels have been identified. Because of the problems encountered when crossing parents differing in ploidy level, it is desirable to know the ploidy levels of plants to be used in breeding. We determined the ploidy levels of 61 Actinidia accessions currently available in the U.S., including primarily accessions of relatively winter-hardy species. The 61 accessions, representing eight species and three interspecific hybrids, were screened for ploidy using flow cytometry. Mitotic root tip cells from one plant from each putative ploidy level were examined microscopically to confirm the ploidy level derived from flow cytometry. There were 17 diploids, 40 tetraploids, and 4 hexaploids. Intraspecific variation was not found among accessions of the species arguta, callosa, deliciosa, kolomikta, melanandra, polygama, or purpurea. All kolomikta and polygama accessions were diploid. All arguta, callosa, melanandra, and purpurea accessions were tetraploid. Actinidia deliciosa was hexaploid. One chinensis accession was tetraploid. Two accessions (NGPR 0021.14 and 0021.3), acquired as chinensis, were hexaploid and may, in fact, be A. deliciosa based on their morphology. `Issai' (arguta × polygama) was hexaploid and `Ken's Red' and `Red Princess' (both melanandra × arguta) were tetraploid.

scholarly journals Genetic Variation for Life History Sensitivity to Seasonal Warming in Arabidopsis thaliana

Genetics ◽  
2013 ◽  
Vol 196 (2) ◽  
pp. 569-577 ◽  
Author(s):  
Yan Li ◽  
Riyan Cheng ◽  
Kurt A. Spokas ◽  
Abraham A. Palmer ◽  
Justin O. Borevitz
Keyword(s):  
Arabidopsis Thaliana ◽  
Genetic Variation ◽  
Life History

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.

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