Tag Archives: #chromosome

Novel Haplotype-led Approach to Increase the Precision of Wheat Breeding (Botany)

Wheat researchers at the John Innes Centre are pioneering a new technique that promises to improve gene discovery for the globally important crop.

Crop breeding involves assembling desired combinations of traits that are defined by underlying genetic variation. Part of this genetic variation often stays the same between generations, with certain genes being inherited together. These blocks of genes – very rarely broken up in genetic recombination – are called haplotype blocks. These haplotypes are the units that breeders switch and select between plants to create new crop lines.

Novel haplotype-led approach will increase the precision of wheat breeding. ©John Innes Centre

In the new study which appears in Communications Biology John Innes Centre researchers led by the group of Professor Cristobal Uauy show that current platforms used by breeders do not provide the resolution needed to distinguish between haplotypes, potentially leading to inaccurate breeding decisions.

They defined shared haplotype-blocks across the 15 bread wheat cultivars assembled in the 10+ Wheat Genome Project a major international collaboration published today in Nature.

To illustrate the application of this haplotype-led approach to support crop improvement, they focused on a specific region of the wheat genome on chromosome 6A.

Through detailed genetic studies and extensive field experiments, they showed that UK breeders are maintaining multiple genes as an intact chromosome 6A haplotype to maximise the expression of desirable traits including flowering time and yield.

Given the low diversity on chromosome 6A, they tested the haplotype approach to discover and introduce novel haplotypes from wheat landraces not subjected to modern breeding.

Combining haplotype knowledge, genetics and field studies, they identified three novel haplotypes in the landraces associated with improved productivity traits in UK environments.

As these haplotypes are not present in modern germplasm, they represent novel variations that could be targeted for yield improvement in elite cultivars, using modern genomic tools.

Lead author Dr Jemima Brinton says: “We used strict criteria to distinguish these shared haplotype blocks from near-identical sequences. We argue that this stringency is essential for crop improvement. The breeding process is poised to undergo an improvement in precision and efficiency through haplotype-led breeding.”

The knowledge generated in the study directly affect the breeding and discovery process by allowing scientists to:

  • Perform focused discovery of novel haplotypes and use breeding strategies to introduce this genetic diversity into modern germplasm.
  • Prioritise research targets to understand the biological functions of sequences selected by breeders
  • Perform more precise selection of parents to maximise genetic gains within breeding programmes
  • Intentionally assemble optimised haplotype combinations

To make the work more accessible to readers, scientists and breeders, the group developed a new haplotype visualisation interface at http://www.crop-haplotypes.com.

The findings are set out in the study: ‘A haplotype-led approach to increase the precision of wheat breeding’ for publication in Communications Biology. Communications Biology https://www.nature.com/articles/s42003-020-01413-2

Reference: Jemima Brinton, Ricardo H. Ramirez-Gonzalez, James Simmonds, Luzie Wingen, Simon Orford, Simon Griffiths, Georg Haberer, Manuel Spannagl, Sean Walkowiak, Curtis Pozniak, Cristobal Uauy. A haplotype-led approach to increase the precision of wheat breeding. Communications Biology, 2020; 3 (1) DOI: 10.1038/s42003-020-01413-2

Provided by John Innes Center

Study Sheds Light On Abnormal Neural Function In Rare Genetic Disorder (Neuroscience)

Findings show deficits in the electrical activity of cortical cells; possible targets for treatment for 22q11.2 deletion syndrome.

A genetic study has identified neuronal abnormalities in the electrical activity of cortical cells derived from people with a rare genetic disorder called 22q11.2 deletion syndrome. The overexpression of a specific gene and exposure to several antipsychotic drugs helped restore normal cellular functioning. The study, funded by the National Institutes of Health (NIH) and published in Nature Medicine, sheds light on factors that may contribute to the development of mental illnesses in 22q11.2 deletion syndrome and may help identify possible targets for treatment development.

This stylistic diagram shows a gene in relation to the double helix structure of DNA and to a chromosome (right). The chromosome is X-shaped because it is dividing. Introns are regions often found in eukaryote genes that are removed in the splicing process (after the DNA is transcribed into RNA): Only the exons encode the protein. The diagram labels a region of only 55 or so bases as a gene. In reality, most genes are hundreds of times longer. Credit: Thomas Splettstoesser/Wikipedia/CC BY-SA 4.0

22q11.2 deletion syndrome is a genetic disorder caused by the deletion of a piece of genetic material at location q11.2 on chromosome 22. People with 22q11.2 deletion syndrome can experience heart abnormalities, poor immune functioning, abnormal palate development, skeletal differences, and developmental delays. In addition, this deletion confers a 20-30% risk for autism spectrum disorder (ASD) and an up to 30-fold increase in risk for psychosis. 22q11.2 deletion syndrome is the most common genetic copy number variant found in those with ASD, and up to a quarter of people with this genetic syndrome develop a schizophrenia spectrum disorder.

“This is the largest study of its type in terms of the number of patients who donated cells, and it is significant for its focus on a key genetic risk factor for mental illnesses,” said David Panchision, Ph.D., chief of the Developmental Neurobiology Program at the NIH’s National Institute of Mental Health. “Importantly, this study shows consistent, specific patient-control differences in neuronal function and a potential mechanistic target for developing new therapies for treating this disorder.”

While some effects of this genetic syndrome, such as cardiovascular and immune concerns, can be successfully managed, the associated psychiatric effects have been more challenging to address. This is partly because the underlying cellular deficits in the central nervous system that contribute to mental illnesses in this syndrome are not well understood. While recent studies of 22q11.2 deletion syndrome in rodent models have provided some important insights into possible brain circuit-level abnormalities associated with the syndrome, more needs to be understood about the neuronal pathways in humans.

To investigate the neural pathways associated with mental illnesses in those with 22q11.2 deletion syndrome, Sergiu Pasca, M.D.(link is external), associate professor of psychiatry and behavioral sciences at Stanford University, Stanford, California, along with a team of researchers from several other universities and institutes, created induced pluripotent stems cells — cells derived from adult skin cells reprogramed into an immature stem-cell-like state — from 15 people with 22q11.2 deletion and 15 people without the syndrome. The researchers used these cells to create, in a dish, three-dimensional brain organoids that recapitulate key features of the developing human cerebral cortex.

“What is exciting is that these 3D cellular models of the brain self-organize and, if guided to resemble the cerebral cortex, for instance, contain functional glutamatergic neurons of deep and superficial layers and non-reactive astrocytes and can be maintained for years in culture. So, there is a lot of excitement about the potential of these patient-derived models to study neuropsychiatric disease,” said Dr. Pasca.

The researchers analyzed gene expression in the organoids across 100 days of development. They found changes in the expression of genes linked to neuronal excitability in the organoids that were created using cells from individuals with 22q11.2 deletion syndrome. These changes prompted the researchers to take a closer look at the properties associated with electrical signaling and communication in these neurons. One way neurons communicate is electrically, through controlled changes in the positive or negative charge of the cell membrane. This electrical charge is created when ions, such as calcium, move into or out of the cell through small channels in the cell’s membrane. The researchers imaged thousands of cells and recorded the electrical activity of hundreds of neurons derived from individuals with 22q11.2 deletion syndrome and found abnormalities in the way calcium was moved into and out of the cells that were related to a defect in the resting electrical potential of the cell membrane.

A gene called DGCR8 is part of the genetic material deleted in 22q11.2 deletion syndrome, and it has been previously associated with neuronal abnormalities in rodent models of this syndrome. The researchers found that heterozygous loss of this gene was sufficient to induce the changes in excitability they had observed in 22q11.2-derived neurons and that overexpression of DGCR8 led to partial restoration of normal cellular functioning. In addition, treating 22q11.2 deletion syndrome neurons with one of three antipsychotic drugs (raclopride, sulpiride, or olanzapine) restored the observed deficits in resting membrane potential of the neurons within minutes.

“We were surprised to see that loss in control neurons and restoration in patient neurons of the DGCR8 gene can induce and, respectively, restore the excitability, membrane potential, and calcium defects,” said Pasca. “Moving forward, this gene or the downstream microRNA(s) or the ion channel/transporter they regulate may represent novel therapeutic avenues in 22q11.2 deletion syndrome.”

References: Khan, T.A., Revah, O., Gordon, A. et al. Neuronal defects in a human cellular model of 22q11.2 deletion syndrome. Nat Med (2020). https://doi.org/10.1038/s41591-020-1043-9 link: http://www.nature.com/articles/s41591-020-1043-9

Provided by NIH

How To Make A Replication Origin In Multicellular Eukaryotes? (Biology)

Loading of replicative helicases onto DNA is a key event during the initiation of chromosomal DNA replication. It takes place at specific chromosomal regions termed origins and is facilitated by the ORC protein complex. By resolving the cryo-EM structures of DNA-bound ORC, researchers from the Bleichert group (now at Yale) broaden our understanding of how DNA replication is initiated in animals.

Accurate replication of chromosomal DNA is essential for the survival and propagation of living organisms. Prior to cell division, many different proteins work together and duplicate genomes by semi-conservative replication so that copied chromosomes can be segregated into daughter cells. Genome integrity is sustained by highly efficient and accurate DNA replication exactly once per cell cycle. Failure to replicate DNA precisely can alter gene copy number and chromosome ploidy, which can give rise to genomic instability and a variety of human diseases.

Eukaryotic DNA replication initiation relies on the origin recognition complex (ORC), a DNA-binding ATPase that loads the Mcm2–7 replicative helicase onto replication origins. In yeast, origins are defined by a conserved consensus sequence that is recognized by ORC. By contrast, how replication origins are defined in animals (or metazoans) has remained unclear, but chromatin cues and local DNA structure are thought to help mediate the recognition of the origins. In a new paper, researchers reported cryo-electron microscopy (cryo-EM) structures of DNA-bound Drosophila ORC with and without the co-loader Cdc6.

These structures reveal that Orc1 and Orc4 constitute the primary DNA binding site in the ORC ring and cooperate with the winged-helix domains to stabilize DNA bending. A loop region near the catalytic Walker B motif of Orc1 directly contacts DNA, allosterically coupling DNA binding to ORC’s ATPase site.

Correlating structural and biochemical data showed that DNA sequence modulates DNA binding and remodeling by ORC, and that DNA bending promotes Mcm2–7 loading in vitro. Together, these findings explain the distinct DNA sequence-dependencies of metazoan and S. cerevisiae initiators in origin recognition and support a model in which DNA geometry and bendability contribute to Mcm2–7 loading site selection in metazoans.

References: Schmidt, J.M., Bleichert, F. Structural mechanism for replication origin binding and remodeling by a metazoan origin recognition complex and its co-loader Cdc6. Nat Commun 11, 4263 (2020). https://doi.org/10.1038/s41467-020-18067-7 link: https://www.nature.com/articles/s41467-020-18067-7