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(Bio) Genetics: The Mystery of Hybrid Vigor

 
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PostPosted: Wed May 17, 2006 7:44 am    Post subject: (Bio) Genetics: The Mystery of Hybrid Vigor Reply with quote






Iowa State University plant scientists begin to unravel the mystery of hybrid vigor
Iowa State University
8 May 2006

AMES, Iowa -- For nearly 80 years, corn breeders and producers have taken advantage of hybrid vigor to grow high-yielding crops. Yet this biological process remains a scientific mystery. No one really understands why crossing specific lines of corn that are genetically quite different can produce a hybrid that outperforms both parent lines.

That could change, however, thanks to ongoing research in Iowa State University's Plant Sciences Institute. Researchers have uncovered a key to understanding the complex molecular mechanisms of hybrid vigor, also known as heterosis, which affects most aspects of plant growth and development. Once the gene activity behind hybrid vigor is well understood, scientists could more rapidly create hybrids that confer desired traits like ethanol production into the germplasm.

The research team, led by Patrick Schnable, professor of agronomy and director of the Center for Plant Genomics, includes Dan Nettleton, associate professor of statistics; and graduate students Ruth Swanson-Wagner, Yi Jia, Rhonda DeCook and Lisa Borsuk.

Their research is published in the May 2 issue of the scientific journal, Proceedings of the National Academy of Science ("All Possible Modes of Gene Action are Observed in a Global Comparison of Gene Expression in a Maize F1 Hybrid and Its Parents").

For the two-year experiment, the researchers used the maize F1 hybrid and its inbred parents corn lines, B73 and Mo17. The F1 is taller, matures more quickly and produces higher grain yields than both parents.

"We analyzed global patterns of gene expression in these three genotypes because this hybrid and its relatives are widely grown in the Corn Belt," Schnable said. "Also, the genetic map of corn is based on recombinant inbreds developed from this hybrid."

The researchers grew seedlings of the three genotypes in growth chambers to tightly control environmental effects. They isolated RNA from each of the three genotypes, and used a maize gene chip to determine the amount of RNA that accumulates for each gene in each of the three genotypes.

"We used this gene expression information to understand how each of thousands of genes behave in the genetic background, " Schnable said.

Using microarray technology, the researchers observed the activity of nearly 14,000 genes at the same time. The technology enabled them to look simultaneously at the gene expression of the hybrid and its inbred parents. This is the first study that has looked at hybrid vigor in any crop on such a large scale.

They found that some genes are more active in the hybrid than in both of the parental inbred lines (overdominant), some genes are less active than both inbred lines (underdominant) and most genes --78 percent -- have activity levels in between the level of the inbreds (additive).

"Several molecular models have been proposed to explain the phenomena of hybrid vigor. Some models require that genes exhibit overdominance or underdominance. Others assume that overdominant and underdominant gene expression is not an important contributor to hybrid vigor," Schnable said.

The results of the Iowa State experiment provide support for multiple mechanistic explanations for hybrid vigor.

"Although this research does not explain hybrid vigor, it begins to uncover what happens on a molecular level in a hybrid compared to the inbred parents. It shows us that there are multiple molecular mechanisms at work and that hybrid vigor is complex," Schnable said.

"To understand this important biological process, we will need to apply cutting-edge, high-throughput genomic technologies. The Plant Sciences Institute at Iowa State is one of very few public-sector organizations in the world that has the technology and resources necessary to conduct this research," he said.

The research findings provide a foundation for the Iowa State scientists to explore specific genes of interest, or investigate the contributions of the different mechanisms resulting in the gene expression patterns found. Their next step is to determine the genetic control of overdominance.

"Ultimately, it is likely that we would be able to predict which specific inbreds when crossed would produce a strong heterotic response. To a large extent, this is now a matter of trial and error. Consequently, we might be able to develop favorable hybrids more quickly for less cost. This would result in faster genetic gain," Schnable said.

The research was funded by the state of Iowa, Iowa State University's Plant Sciences Institute and the Iowa Agriculture and Home Economics Experiment Station.

*************************************************************

Questions to explore further this topic:

A timeline for plant biotechnology

http://www.whybiotech.com/index.asp?id=2157

The Great Corn Adventure

http://www.urbanext.uiuc.edu/corn/

The story of corn

http://campsilos.org/mod3/index.shtml

An online lesson on biotechnology

http://www.childrensmuseum.org...../index.htm

How does corn grow?

http://maize.agron.iastate.edu/corngrows.html

A corn curriculum

http://www.ncga.com/education/main/index.html
http://www.ksgrains.com/corn/CornClass04.pdf

Popcorn lessons

http://www.popcorn.org/teacher.....rnav=flash

Images of cornfields

http://www.iowafarmertoday.com/corn_cam/

Images of cornfield mazes

http://cornmazes.com/photos.php

Ancients modified corn genes

http://www.cnn.com/2003/TECH/s.....index.html
http://www.nsf.gov/news/news_s....._id=104207

What are hybrid crops?

http://www.livinghistoryfarm.o.....ps_03.html

The science of seeds

http://www.ers.usda.gov/public.....ib786c.pdf

Who is Gregor Mendel?

http://www.physics.uoguelph.ca.....scor11.htm
http://www.accessexcellence.or.....endel.html
http://www.mnsu.edu/emuseum/in.....regor.html
http://mendel.imp.ac.at/mendel.....graphy.jsp

Mendel's Laws

http://www.purchon.com/biology/mendel.htm
http://www.ndsu.nodak.edu/inst.....endel1.htm

Mendel's Genetics

http://anthro.palomar.edu/mendel/mendel_1.htm

Probability of inheritance

http://anthro.palomar.edu/mendel/mendel_2.htm

Exceptions to simple inheritance

http://anthro.palomar.edu/mendel/mendel_3.htm

The Mendel Museum

http://www.mendel-museum.org/

Some of Mendel's scientific papers

http://www.mendelweb.org/MWpaptoc.html

What is a genotype?

http://en.wikipedia.org/wiki/Genotype

What is a phenotype?

http://en.wikipedia.org/wiki/Phenotype

What is hybrid vigor?

http://en.wikipedia.org/wiki/Hybrid_vigor
http://gears.tucson.ars.ag.gov/book/hybrid.html

Hybrid Vigor: The Transformation of a Scientific Racialist Idea

http://lumen.georgetown.edu/pr.....ulture.pdf

Classical Genetics

Children resemble their parents
http://www.dnaftb.org/dnaftb/12/concept/

Genes come in pairs
http://www.dnaftb.org/dnaftb/2/concept/index.html

Genes do not blend
http://www.dnaftb.org/dnaftb/3/concept/index.html

Some genes are dominant
http://www.dnaftb.org/dnaftb/4/concept/index.html

Genetic inheritance follows rules
http://www.dnaftb.org/dnaftb/5/concept/index.html

Genes are real things
http://www.dnaftb.org/dnaftb/6/concept/index.html

All cells arise from existing cells
http://www.dnaftb.org/dnaftb/7/concept/index.html

Sex cells have one set of chromosomes, body cells have two
http://www.dnaftb.org/dnaftb/8/concept/index.html

Specialized chromosomes determine gender
http://www.dnaftb.org/dnaftb/9/concept/index.html

Chromosomes carry genes
http://www.dnaftb.org/dnaftb/10/concept/index.html

Genes get shuffled when chromosomes exchange pieces
http://www.dnaftb.org/dnaftb/11/concept/index.html

Evolution begins with inheritance of gene variations
http://www.dnaftb.org/dnaftb/12/concept/index.html

Mendelian laws apply to humans
http://www.dnaftb.org/dnaftb/13/concept/index.html

Mendelian genetics cannot fully explain human health and behavior
http://www.dnaftb.org/dnaftb/14/concept/index.html

Molecular Genetics

DNA and proteins
http://www.dnaftb.org/dnaftb/15/concept/index.html

One gene makes one protein
http://www.dnaftb.org/dnaftb/16/concept/index.html

A gene is made of DNA
http://www.dnaftb.org/dnaftb/17/concept/index.html

Bacteria and viruses have DNA too
http://www.dnaftb.org/dnaftb/18/concept/index.html

DNA: A twisted ladder
http://www.dnaftb.org/dnaftb/19/concept/index.html

A half DNA ladder: A template for copying
http://www.dnaftb.org/dnaftb/20/concept/index.html

RNA
http://www.dnaftb.org/dnaftb/21/concept/index.html

Genetic code
http://www.dnaftb.org/dnaftb/22/concept/index.html

A gene is a discrete sequence
http://www.dnaftb.org/dnaftb/23/concept/index.html

Editing RNA
http://www.dnaftb.org/dnaftb/24/concept/index.html

Some viruses store genetic information in RNA
http://www.dnaftb.org/dnaftb/25/concept/index.html

RNA was the first genetic molecule?
http://www.dnaftb.org/dnaftb/26/concept/index.html

Mutations
http://www.dnaftb.org/dnaftb/27/concept/index.html

Some types of mutations are automatically repaired
http://www.dnaftb.org/dnaftb/28/concept/index.html

Corn hybrids and plant population

http://www.pioneer.com/usa/agronomy/corn/1106.htm

The basics of corn breeding

http://res2.agr.ca/CRECO/zea/zea01_e.htm

How do corn hybrids differ?

http://www.helenaconnects.com/.....082605.pdf

Examples of corn hybrids

http://res2.agr.ca/CRECO/zea/zea02_e.htm
http://res2.agr.ca/CRECO/corn-.....scer_e.htm
http://www.hylandseeds.com/new.....NMaritimes
http://www.urbanext.uiuc.edu/veggies/corn1.html

How are hybrids selected?

http://ohioline.osu.edu/agf-fact/0125.html
http://s142412519.onlinehome.us/uw/pdfs/A3265.PDF

Hybrid corn in the Philippines

http://www.newsflash.org/2003/05/si/si001700.htm

How does one track corn gene regulation?

http://ag.arizona.edu/pubs/gen.....rngene.pdf

Is there a difference between genetically modified and hybrid crops?

http://www.pbs.org/pov/pov2002.....ticle.html

GAMES

http://www.pbs.org/pov/pov2002.....rmore.html
http://www.fs4jk.org/games.html
http://www.ilcorn.org/index.htm


Last edited by adedios on Sat Jan 27, 2007 3:54 pm; edited 2 times in total
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PostPosted: Mon Jun 12, 2006 11:54 am    Post subject: Hybrid peppers developed at Hebrew University Reply with quote

The Hebrew University of Jerusalem
12 June 2006

Hybrid peppers developed at Hebrew University achieve sales success

Genetically enhanced hybrid peppers developed at the Hebrew University of Jerusalem that can be raised with minimal protection under moderate winter conditions have achieved worldwide commercial success. Pepper is one of the major vegetable crops in the world and in Israel.
The robust pepper varieties were developed by a research tem headed by Dr. Yonatan Elkind of the Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture at the Hebrew University's Faculty of Agricultural, Food and Environmental Quality Sciences in Rehovot. The research receives financial support from and is carried out in collaboration with the Zeraim Gedera company. For his work, Dr. Elkind is a recipient of one of this year's Kaye Innovation Awards, to be presented at the Hebrew University's 69th Board of Governors meeting on June 13.

The genetic improvements embodied in the peppers they have developed widen the ecological conditions under which they can be grown and also facilitate the use of simple greenhouses and netting instead of expensive structures.

The peppers, in various colors, have been raised to produce high yields under night-time conditions as low as 10 degrees celcius, which is much lower than previous hybrids that required temperatures higher than 18 degrees celcius and needed costly heating to grow and develop.

The new hybrids are characterized by high yields, a long growing season, resistance to viruses, firm fruit, good vine storage capacity, long shelf-life, and low sensitivity to cracking.

The breeding project involved large-scale experiments with more than 25,000 plants a year, grown in target areas, mainly in the Arava region of southern Israel and the south of Spain. Dr. Elkind noted that vegetable production under mild winter conditions and using simple plastic or net protection is one of the most rapidly expanding, protective cultivation systems worldwide. The major areas which use this production method, in addition to Israel and Spain, are Mexico and China.

The hybrids developed by the researchers – which to a large extent have replaced seed varieties formerly imported into Israel from Holland – have been commercialized through Yissum, the Hebrew University's technology transfer company, and are sold worldwide by the Zeraim Gedera seed company. In 2005, sales of the hybrid seeds amounted to $9.5 million and are expected to increase. In the Arava alone, 50 percent of red pepper seeds used are those developed at the Hebrew University, and have contributed significantly to the profitability of farmers in that region. Overall, in the 2004-05 growing season, pepper exports from Israel amounted to $80 million and constituted the leading vegetable export from the country.


###
The Kaye Innovation Awards at the Hebrew University have been awarded annually since 1994. Isaac Kaye of England, a prominent industrialist in the pharmaceutical industry, established the awards to encourage faculty, staff, and students of the Hebrew University to develop innovative methods and inventions with good commercial potential which will benefit the university and society.
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PostPosted: Thu Jul 20, 2006 7:37 am    Post subject: Nature vs. Nurture: Mysteries of Individuality Unraveled Reply with quote

Nature vs. Nurture: Mysteries of Individuality Unraveled

By Jeanna Bryner
Special to LiveScience
posted: 19 July 2006
10:38 am ET



Is it just coincidence that Bobby Bonds and his son Barry both made baseball history with their all-star power and speed?

Questions like this have long plagued psychologists, geneticists and philosophers.

Coined nature versus nurture, it is one of the great mysteries of the mind, and much research has focused on the relative role of genes and the environment in determining everything from athleticism to personality to a person's predisposition to obesity.


For the full article:

http://www.livescience.com/hum.....rture.html
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PostPosted: Wed Sep 13, 2006 5:57 am    Post subject: Since Mendel: From Counting Peas to Fluorescent Pigs Reply with quote

Since Mendel: From Counting Peas to Fluorescent Pigs

By Heather Whipps
Special to LiveScience
posted: 13 September 2006
12:28 am ET



The father of genetics was a monk who spent eight years counting 300,000 peas.

His modest story is a far cry from the work of modern geneticists who, in the past decade, have managed to concoct creatures fit for science fiction films, from fluorescent pigs to human-animal hybrids.

While those scientists get regular press, few outside the scientific community know much about the contributions of Gregor Mendel, who would eventually lay down the basic laws of inheritance. His methodical research in the 19th century should be recognized as the forerunner of even the most outlandish genetic experiments going on today, experts say.

An exhibition dedicated to Mendel and his work will open at the Field Museum in Chicago on Sept. 15.

For the full article:

http://www.livescience.com/his.....endel.html
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PostPosted: Tue Jan 30, 2007 7:19 am    Post subject: Genes behind animal growth discovered Reply with quote

University of Southern California
29 January 2007

Genes behind animal growth discovered

An advance in genomics, the ID of growth genes in oysters has relevance for farming and aquaculture
How many genes influence a complex trait, like weight, height or body type?

And why does the answer matter?

Among other reasons, because the "Green Revolution" that multiplied crop yields has to be followed by a "Blue Revolution" in ocean farming, according to marine biologists at the University of Southern California.

"We’re going to have to make future decisions as a society how to provide enough food for a growing population," said Donal Manahan, co-author of a study on oyster growth appearing online this week in Proceedings of the National Academy of Sciences Early Edition.

Currently a delicacy, oysters fed the masses in the past and could again become "the soy bean of the sea" as traditional fisheries collapse, Manahan predicted.

He and senior author Dennis Hedgecock linked growth rate in oysters to approximately 350 genes, or 1.5 percent of the more than 20,000 genes in the oyster genome.

To the authors’ knowledge, this is the first estimate of the number of genes that determine growth rate in any animal.

Specifically, the authors discovered the genes responsible for "hybrid vigor," or the ability of some children of crossbreeding to outgrow both parents. Hybrid vigor is of evolutionary as well as agricultural interest because it appears to favor biodiversity.

Many plants have hybrid vigor. Seed companies exploited this property to increase corn yields seven-fold from the 1920s to the present.

Most animals do not express hybrid vigor to such an extent, the authors said. That makes oysters particularly strong candidates for aquaculture.

"Their hybrids grow much faster than either of the parents. And this is exactly like corn," Manahan said.

The PNAS study may lead to improved breeding both on land and sea. The green revolution worked by trial and error, with companies trying every possible cross of corn strains to find the best hybrids.

"A century after its discovery in corn, we still don’t know why plants have hybrid vigor, despite the economic and evolutionary importance of this phenomenon," Hedgecock explained.

Knowing the genes for hybrid vigor may enable companies to develop the best cross of corn strains, or oyster types, without guesswork.

The lines would not be genetically modified, only screened and matched as in a dating service.

The goal is efficient and sustainable domestication of oysters and other promising ocean species, mostly shellfish. Oysters already are the number one farmed aquatic species worldwide.

Aquaculture of large fish remains environmentally challenging, Manahan and Hedgecock noted.

Another problem is the apparent lack of hybrid vigor in most fish. Even in oysters, the researchers found the rules of hybrid vigor to be more complicated than predicted by classical ideas in genetics and physiology.

For example, some genes were expressed much less in the offspring than in either parent, a pattern the authors call "underdominance." Very few genes were expressed as the average of the expression in their parents.

Hedgecock called the underdominance patterns "one of the more surprising findings" of the study.

###
Other authors on the study were USC graduate student Eli Meyer and biotechnology company Solexa Inc. researchers Ben Bowen, Christian Haudenschild, Jing-Zhong Lin and Shannon DeCola.

The U.S. Department of Agriculture, the W. M. Keck Foundation and the National Science Foundation funded the research.

OYSTERS.PNAS.CM --USC-- JAN. 26, 2007
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PostPosted: Wed Jun 06, 2007 2:05 pm    Post subject: Largest ever study of genetics of common diseases published Reply with quote

Wellcome Trust
6 June 2007

Largest ever study of genetics of common diseases published today

The Wellcome Trust Case Control Consortium, the largest ever study of the genetics behind common diseases such as diabetes, rheumatoid arthritis and coronary heart disease, today publishes its results in the journals Nature and Nature Genetics.

The £9 million study is one of the UK's largest and most successful academic collaborations to date. It has examined DNA samples from 17,000 people across the UK, bringing together 50 leading research groups and 200 scientists in the field of human genetics from dozens of UK institutions. Over two years, they have analysed almost 10 billion pieces of genetic information.

"Many of the most common diseases are very complex, part 'nature' and 'nurture', with genes interacting with our environment and lifestyles," says Professor Peter Donnelly, Chair of the Consortium, who is based at the University of Oxford. "By identifying the genes underlying these conditions, our study should enable scientists to understand better how disease occurs, which people are most at risk and, in time, to produce more effective, more personalised treatments."

The study has substantially increased the number of genes known to play a role in the development of some of our most common diseases. Many of these genes that have been found are in areas of the genome not previously thought to have been related to the diseases.

"Just a few years ago it would have been thought wildly optimistic that it would be possible in the near future to study a thousand genetic variants in each of a thousand people," says Dr Mark Walport, Director of the Wellcome Trust, the UK's largest medical research charity, which funded the study. "What has been achieved in this research is the analysis of half a million genetic variants in each of seventeen thousand individuals, with the discovery of more than ten genes that predispose to common diseases.

"This research shows that it is possible to analyse human variation in health and disease on an enormous scale. It shows the importance of studies such as the UK Biobank, which is seeking half a million volunteers aged between 40 and 69, with the aim of understanding the links between health, the environment and genetic variation. New preventive strategies and new treatments depend on a detailed understanding of the genetic, behavioural and environmental factors that conspire to cause disease."

Amongst the most significant new findings are four chromosome regions containing genes that can predispose to type 1 diabetes and three new genes for Crohn's disease (a type of inflammatory bowel disease). For the first time, the researchers have found a gene linking these two autoimmune diseases, known as PTPN2.

The study has also confirmed the importance of a process known as autophagy in the development of Crohn's disease. Autophagy, or "self eating", is responsible for clearing unwanted material, such as bacteria, from within cells. The may be key to the interaction of gut bacteria in health and in inflammatory bowel disease and could have clinical significance in the future.

"The link between type 1 diabetes and Crohn's disease is one of the most exciting findings to come out of the Consortium," says Professor John Todd from the University of Cambridge, who led the study into type 1 diabetes. "It is a promising avenue for us to understand how the two diseases occur. The pathways that lead to Crohn's disease are increasingly well understood and we hope that progress in treating Crohn's disease may give us clues on how to treat type 1 diabetes in the future."

Research from the Consortium has already played a major part in identifying the clearest genetic link yet to obesity and three new genes linked to type 2 diabetes, published in April in advance of the main study. It has found independently a major gene region on chromosome 9 identified by independent studies on coronary heart disease.

Researchers analysed DNA samples taken from people in the UK – 2,000 patients for each disease and 3,000 control samples – to identify common genetic variations for seven major diseases. These are bipolar disorder, Crohn's disease, coronary heart disease, hypertension, rheumatoid arthritis and type 1 and type 2 diabetes. For each disease, the researchers will study larger population samples to confirm their results.

Although the human genome is made up of more than three billion sub-units of DNA, called nucleotides (or bases), most of these show little in the way of differences between individuals. A substantial part of the variation in DNA sequence between individuals is due to single-nucleotide polymorphisms (differences), also known as SNPs. There are approximately 8 million common SNPs in European populations. Fortunately, because SNPs that lie close together on chromosomes often tell quite similar stories, researchers in the Consortium were able to explore this variation through analysing a subset of these SNPs (in fact approximately 500,000).

"Human genetics has a chequered history of irreproducible results, but this landmark collaboration of scientists in Britain has shown conclusively that the new approach of analysing a large subset of genetic variants in large samples of patients and healthy individuals works," says Professor Donnelly. "We are now able to effectively scan most of the common variation in the human genome to look for variants associated with diseases. This approach will undoubtedly herald major advances in how we understand and tackle disease in the future."

Further analysis as part of the Consortium will be looking at tuberculosis (TB), breast cancer, autoimmune thyroid disease, multiple sclerosis and ankylosing spondylitis. The results are expected later this year.

###
The Wellcome Trust Case Control Consortium, the largest ever study of the genetics behind common diseases such as diabetes, rheumatoid arthritis and coronary heart disease publishes its results in the journals Nature and Nature Genetics.

The £9 million study is one of the UK's largest and most successful academic collaborations to date. It has examined DNA samples from 17,000 people across the UK, bringing together 50 leading research groups and 200 scientists in the field of human genetics from dozens of UK institutions. Over two years, they have analysed almost 10 billion pieces of genetic information.

Researchers have uncovered genetic variations for seven major diseases: bipolar disorder, Crohn's disease, coronary heart disease, hypertension, rheumatoid arthritis and type 1 and type 2 diabetes.

Speakers:

Dr Mark Walport - Director, Wellcome Trust

Professor Peter Donnelly (University of Oxford) – Chair, Wellcome Trust Case Control Consortium

Professor John Todd (University of Cambridge) – Type 1 diabetes

Dr Miles Parkes (Addenbrooke's Hospital and University of Cambridge) – Crohn's disease
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