Tag Archives: sequence

Wheat.

Wheat’s genetic secrets could lead to better, more resilient crops

Wheat has a genome five times longer than yours — and now, it’s been fully sequenced.

Wheat.

Image credits Brad Higham / Flickr.

Staying true to their name, researchers at the International Wheat Genome Sequencing Consortium have published a paper containing the complete sequence of the wheat (genus Triticum) genome, a dataset that could help breed new crops.

Food-nome

Having access to the plant’s genome should help speed up the breeding of more resilient, disease-resistant, and higher-yield crops. Wheat is currently the most widely grown crop, providing more protein than meat in the human diet, and supplying roughly one-fifth of the total calories people consume. It’s also surprisingly complex from a genetic standpoint: its genome includes some 16 million base pairs, over five times larger than yours or mine.

Despite its genetic beefiness, wheat is quite vulnerable to floods, droughts, and several diseases (such as wheat rust) that can claim whole crops at a time. Luckily, now that we know the structure of its genome, we can modify it to add a whole lot of desirable characteristics — resilience to pests, higher yields, more nutritional value — into our crops.

Actually sequencing the genome, however, proved to be a significant challenge. Not only was it huge, it also included three sub-genomes — a large part of which included repetitive elements. This makes long stretches of the genome identical or very similar to each other, making it difficult to distinguish individual chains and re-constructing the overall genome.

The sequencing effort is detailed in two papers. The first, published by researchers from the. International Wheat Genome Sequencing Consortium, details the sequence of the plant’s 21 chromosomes. It also lists the location of 107,891 genes, more than 4 million molecular markers, as well as sequence elements between the genes that regulate their expression.

The second paper, led by a team at the John Innes Centre (JIC), aims to help breeders and researchers understand what trait each gene affects. This work is largely based on a technique known as ‘speed breeding’, previously developed at the JIC. Speed breeding involves the use of glasshouses to shorten the breedings cycles of plants. Combined with the wealth of genome information from the first paper, this helped the team significantly shorten the time required to test what each gene does.

“Genomic knowledge of other crops has driven progress in selecting and breeding important traits,” says Cristobal Uauy, Project Leader in crop genetics at the John Innes Centre says.

“Tackling the colossal wheat genome has been a Herculean challenge, but completing this work means we can identify genes controlling traits of interest more rapidly. This will facilitate and make more effective the breeding for traits like drought or disease resistance. Where previously we had a broad view and could spot areas of interest, we can now zoom into the detail on the map.”

Uauy cites past research estimating that the world will need 60% more wheat by 2050 to meet global demand. The research his team performed can be instrumental towards reaching that goal.

It’s not the first time researchers have fully decoded the genome of a cereal: just last year, an international research team published the full genome of barley.

The first paper, “Shifting the limits in wheat research and breeding using a fully annotated reference genome”, has been published in the journal Science.

The second paper “The transcriptional landscape of polyploid wheat” has been published in the journal Science.

Complete Neanderthal genome sequenced

Yes ladies and gents, researchers have produced the whole genome sequence of the 3 billion “letters” (nucleotides) in the Neanderthalian genome, and the results are interesting to say the least. For starters, up to 2 percent of present day human DNA outside of Africa originated in Neanderthals; this result suggests that the Neanderthals, Homo neanderthalensis diverged from the same primate line that led to nowadays humans, homo sapiens.

neanderthal

However, some 400.000 years ago, they migrated to northern Eurasia, where they became genetically isolated and evolved differently than the other human line. Approximately 30.000 years ago however, the Neanderthals dissappeared. Still, they are our closest relative, considering we share an ancestor from some 800.000 years ago. For example, the chimpanzees diverged from the same line 5-7 million years ago.

“This sequencing project is a technological tour de force,” said NHGRI Director Eric D. Green, M.D., Ph.D. “You must appreciate that this international team has produced a draft sequence of a genome that existed 400 centuries ago. Their analysis shows the power of comparative genomics and brings new insights to our understanding of human evolution.”

In order to achieve their goals, researchers analyzed DNA from three females that lived some 40.000 years ago (pretty close to the extinction date). This provided the first “genome-wide look” at the similarities and unsimilarities between humans and our “relative”. They results showed that Neanderthal DNA is 99.7% identical to our own, and 98.8% identical to that of the chimpanzee (the same number is correct for human-chimp DNA comparison).

“The genomic calculations showed good correlation with the fossil record,” said coauthor Jim Mullikin, Ph.D., an NHGRI computational geneticist and acting director of the NIH Intramural Sequencing Center. “According to our results, the ancestors of Neanderthals and modern humans went their separate ways about 400,000 years ago.”

“It was a very unique series of events, with a founding population of modern humans of greatly reduced size — tens to hundreds of individuals,” Dr. Mullikin said.

They know this because geneticists can detect if the population constricts, identifying several genetic markers that are ore cnocentrated.

At that time,” Dr. Mullikin continued, “where the population was greatly reduced, the modern humans migrating out of Africa encountered Neanderthals and inter-breeding occurred between the two groups, leaving an additional, but subtle, genetic signature in the out-of-Africa group of modern humans.”

As homo sapiens spread across Europe and not only, they carried with them Neanderthal DNA – and spread it. So it’s no surprise then that 2 percent of the genomes of present-day humans living from Europe to Asia was inherited from them. The team however, did not find those traces of DNA in people in Africa.

“The data suggests that the genes flowed from Neanderthal to modern humans,” Dr. Mullikin said. “That had to have occurred at least once during the 20,000 to 30,000 years, in which modern humans and Neanderthal both lived on the Eurasian continent.”

However, the team said they need more samples in order to improve and expand their results.

“These are preliminary data based on a very limited number of samples, so it is not clear how widely applicable these findings are to all populations,” said Vence L. Bonham, Jr., J.D., senior advisor to the NHGRI Director on Societal Implications of Genomics. “The findings do not change our basic understanding that humans originated in Africa and dispersed around the world in a migration out of that continent.”

UPDATE: Researchers at the Max Plank Institute in Leipzig, Germany have recently released (2013) a high-detail genome of a Neanderthal specimen for open access. This will hopefully advance our understanding of Neanderthals and how they relate to modern man.