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New map of variation in maize genetics holds promise for developing new varieties
November 20, 2009ITHACA, N.Y. - A new study of maize has identified thousands of diverse genes in genetically inaccessible portions of the genome. New techniques may allow breeders and researchers to use this genetic variation to identify desirable traits and create new varieties that were not easily possible before.
Publishing in the Nov. 19 issue of Science, the researchers, whose senior and first author are at Cornell, have identified the first map of haplotypes - sets of closely linked gene variants known as alleles - in the maize genome. They have identified and mapped several million allele variants among 27 diverse inbred maize lines. The lines selected for study included a cross-section of maize types commonly used for breeding while also representing worldwide maize diversity.
The haplotype map "will help develop molecular markers and tools that breeders and geneticists around the world can use to study maize and improve maize varieties," said Ed Buckler, the paper's senior author, a USDA-ARS research geneticist in Cornell's Institute for Genomic Diversity and an adjunct professor of plant breeding and genetics. Michael Gore, a graduate student in Buckler's lab, is the paper's lead author.
The other co-authors are affiliated with the U.S. Department of Agriculture's Agricultural Research Service (USDA-ARS), Cold Spring Harbor Laboratory and University of California-Davis.
In the last century, maize breeders have found limitations in recombination (the ability to shuffle genetic variation), where large regions genetic material fail to recombine near the chromosome's center, called the centromere. To overcome this, breeders have crossed two complementary lines, resulting in a new line with higher yields and vigor.
However, because large regions of the maize chromosome are less accessible, breeders cannot arrive at optimal genetic combinations.
The study has revealed a great deal of genetic variation near the chromosomes' centromeres, which resist recombining. Now, breeders can use molecular markers to identify desirable genetic variants and new genetic technologies to move the desired variation onto the same chromosomes and create new, more productive lines with desired traits.
The study revealed more than 100 large regions (selective sweeps) on the genome where breeders selected for a gene during domestication. In doing so, genetic diversity was lost around those genes.
The study also identified regions of genes shared by all maize species as well as regions that are different based on the geographic adaptations of lines of plants. For example, the study identified almost 200 highly differentiated regions that result from adaptations in tropical and temperate maize.
"This survey of genetic diversity provides a foundation for uniting breeding efforts across the world and for dissecting complex traits through genomewide association studies," said Buckler.
The first complete sequence of the maize genome appears in the same issue of Science.
Cornell University
The other co-authors are affiliated with the U.S. Department of Agriculture's Agricultural Research Service (USDA-ARS), Cold Spring Harbor Laboratory and University of California-Davis.
In the last century, maize breeders have found limitations in recombination (the ability to shuffle genetic variation), where large regions genetic material fail to recombine near the chromosome's center, called the centromere. To overcome this, breeders have crossed two complementary lines, resulting in a new line with higher yields and vigor.
However, because large regions of the maize chromosome are less accessible, breeders cannot arrive at optimal genetic combinations.
The study has revealed a great deal of genetic variation near the chromosomes' centromeres, which resist recombining. Now, breeders can use molecular markers to identify desirable genetic variants and new genetic technologies to move the desired variation onto the same chromosomes and create new, more productive lines with desired traits.
The study revealed more than 100 large regions (selective sweeps) on the genome where breeders selected for a gene during domestication. In doing so, genetic diversity was lost around those genes.
The study also identified regions of genes shared by all maize species as well as regions that are different based on the geographic adaptations of lines of plants. For example, the study identified almost 200 highly differentiated regions that result from adaptations in tropical and temperate maize.
"This survey of genetic diversity provides a foundation for uniting breeding efforts across the world and for dissecting complex traits through genomewide association studies," said Buckler.
The first complete sequence of the maize genome appears in the same issue of Science.
Cornell University
Genetic Variation Current Events and Genetic Variation News RSSSome morbidly obese people are missing genes, shows new research
A small but significant proportion of morbidly obese people are missing a section of their DNA, according to research published today in Nature.
Genes that regulate maternal inflammatory response, bacterial vaginosis and preterm birth related
In a study to be presented today at the Society for Maternal-Fetal Medicine's (SMFM) annual meeting, The Pregnancy Meeting ™, in Chicago, researchers will show the use of haplotype tagging (hap-tag) single-nucleotide polymorphisms (SNPs) to study the relationship between genetic predispositions, an environmental factor - bacterial vaginosis, and preterm birth.
NIH scientists identify maternal and fetal genes that increase preterm birth risk
Researchers at the National Institutes of Health have identified DNA variants in mothers and fetuses that appear to increase the risk for preterm labor and delivery. The DNA variants were in genes involved in the regulation of inflammation and of the extracellular matrix, the mesh-like material that holds cells within tissues.
Animal behavioral studies can mimic human behavior
Studying animals in behavioral experiments has been a cornerstone of psychological research, but whether the observations are relevant for human behavior has been unclear.
Dog genome researchers track paw prints of selective breeding
From the Dachshund's stubby legs to the Shar-Pei's wrinkly skin, breeding for certain characteristics has left its mark on the dog genome. Researchers have identified 155 regions on the canine genome that appear to have been influenced by selective breeding.
New approach precisely tracks evolution's footprints in the human genome
Fossils may provide tantalizing clues to human history but they also lack some vital information, such as revealing which pieces of human DNA have been favored by evolution because they confer beneficial traits - resistance to infection or the ability to digest milk, for example.
Microcephaly genes associated with human brain size
A group of Norwegian and American researchers have shown that common variations in genes associated with microcephaly - a neuro-developmental disorder in which brain size is dramatically reduced - may explain differences in brain size in healthy individuals as well as in patients with neurological and psychiatric disorders.
New study links DHA type of omega-3 to better nervous-system function
The omega-3 essential fatty acids commonly found in fatty fish and algae help animals avoid sensory overload, according to research published by the American Psychological Association.
U-M study reveals lack of diversity in embryonic stem cell lines
The most widely used human embryonic stem cell lines lack genetic diversity, a finding that raises social justice questions that must be addressed to ensure that all sectors of society benefit from stem cell advances, according to a University of Michigan research team.
Some birds listen, instead of look, for mates
Looks can be deceiving, but certain bird species have figured out that a voice can tell them most of what they need to know to find the right mate.
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