Horse genome added to growing list of barnyard genetics projects

Shedding new light on chromosome structures, equines join pigs and cucumbers on roster of organisms to have DNA code spelled out letter by letter

Were Old McDonald in the genome sequencing business, he would be among the researchers who have announced decoding the complete genetic blueprints of the horse, pig and cucumber.

EQUINE VOLUNTEER A Thoroughbred grey mare named Twilight was the DNA donor for a project to decode the horse genome. Twilight lives at Cornell University in Ithaca, N.Y. Science/AAAS

BACK STORY : WHOLE GENOMES: ABOUT 5,000 DOWN, 10,000-PLUS TO GO Donald Danforth plant science center in St. Louis; Don Hamerman; Courtesy of Zhonghua Zhang of the Chinese Academy of Agricultural Sciences in Beijing

LITTLE PINK DOTS Centromeres (pink dots) sit at chromosome centers (human shown). The centromere on horse chromosome 11 evolved relatively recently. Institute for Genome Sciences and Policy/Duke Univ.

Knowing the details of these three genomes provides scientists with new information about the genetic makeup of economically useful animals and plants, but also helps answer some basic questions about biology and evolution.

A horse named Twilight, who lives at Cornell University, gave her DNA to the horse genome sequencing project. The complete picture of Twilight’s 2.5 billion to 2.7 billion DNA bases — the chemical building blocks that encode her genetic information — reveals that horses and humans share large blocks of DNA where genes are lined up in the same order, researchers involved in the sequencing project report in the November 6 Science.

Because horses have about 90 inherited conditions — such as inflammatory diseases, infertility and muscle disorders — that also affect humans, knowing the order of disease genes in horses could make pinpointing the genes in people easier, says Kerstin Lindblad-Toh, a geneticist at the Broad Institute of MIT and Harvard in Cambridge, Mass., and Uppsala University in Sweden. Lindblad-Toh and Claire Wade, a geneticist and computational biologist at the University of Sydney, led the horse sequencing effort.

Horses tend to have older versions of genes — closer to the form seen in the common ancestor of vertebrates — than those in humans or mice, so the horse genome “may be more indicative of where we came from,” says David Haussler, a geneticist and computational biologist at the University of California, Santa Cruz. Haussler and his colleagues propose to sequence 10,000 vertebrate genomes in order to put together a more detailed map of genetic changes that led to the modern forms of animals. The researchers detailed their proposal online November 6 in the Journal of Heredity.

Already the horse genome has helped to answer at least one fundamental question in biology: What is needed for proper centromere function? Centromeres are stretches of DNA often located near the center of chromosomes and are instrumental in the proper segregation of chromosomes during cell division. The centromere usually contains a core element surrounded by repetitive DNA sequences. Scientists know that the repetitive DNA helps stabilize the interaction of cellular machinery with the centromeres, but didn’t know the exact steps needed to build a centromere. Specifically, it has been unclear whether a core element could work without the surrounding repetitive sequences and vice versa.

On chromosome 11, horses have a relatively new centromere, one that evolved within the last 3 million years or so, the researchers report. The centromere is functional, but it isn’t wrapped in a blanket of repetitive DNA. The find suggests that the repetitive elements aren’t necessary for a centromere to function. “It’s really solved the chicken or egg problem,” says Lindblad-Toh.

Which doesn’t mean the repetitive DNA isn’t useful, says Wade. “It’s like moving house,” she says. “When you live somewhere for a long time, you accumulate a lot of stuff around you that makes you feel secure, but when you move, you clean house. This centromere has just moved.” In time, the centromere on horse chromosome 11, will acquire repetitive sequences around it making it more stable and settled, she says.

Horses are the latest barnyard animal to have its genome analyzed. The cow genome has also been completed and the pig isn’t far behind. Researchers from an international consortium have completed a rough draft of the genome of a red-haired Duroc pig housed at the University of Illinois at Urbana-Champaign, the team announced November 2 at a conference at the Wellcome Trust Sanger Institute in Hinxton, England. The sequence is about 98 percent complete. When finished, it may reveal genes important for meat production and also help find genes that are involved in diseases in people.

But animals aren’t the only farm dwellers giving up genetic secrets. The Chinese long cucumber is the latest crop plant to have its genome decoded. An international consortium led by researchers in China found that 10 chromosomes from the cucumber’s melon ancestor fused to form five of the seven modern cucumber chromosomes. The genome sequence also sheds new light on cucumber traits such as tendril formation and the source of cuke’s “fresh green” scent, the researchers report online November 1 in Nature Genetics.