Barley and Wheat are pretty similar. After all they’re sisters… No really. In a flash of food-security related brilliance I named my guinea pigs Wheat and Barley. Let it never be said that I don’t take my PhD seriously…
But seriously: wheat and barley are both cereals; important food crops, important feed crops, vital for producing my two favourite beverages (20% of the worldwide narley yield goes for malting), not to mention bread… Wheat tends to get a lot more coverage though: the world grows around a quarter of the amount of barley that it does of wheat and the amount spent on barley-related science is therefore always likely to be a bit lower.
From a geneticist’s point of view though, barley is worth having around. It is a much simpler system than wheat (none of this pesky polyploid business) although it has nearly as much repeated sequence as its hexaploid cousin. So while last week British scientists (and a couple of Americans and Germans… but yey Britain!) released a draft assembled sequence for wheat, a few days later a barley map was published in Nature. Doing genetics is all very well, but without a reference sequence all of the bits of the jigsaw can’t be pinned together. A reference sequence allows you to say that Variety X differs from Variety Y at position Z and for that to be meaningful to the rest of the world. And so the International Barley Genome Sequencing Consortium came to be.
The paper outlines how the scientists produced a 5Gb physical map, of which just shy of 4 Gb are ‘anchored’ onto a high resolution genetic map. If you’re just starting to read about genomics you may be slightly confused by all of these maps floating around. What’s the difference between a physical map and a genetic map, I hear you ask? And why do we need both of them? And what about linkage maps?!
A physical map, as the name would suggest, is a map of genes or chromosomes made up of literally sequencing every last bit and then laying the pieces end to end. In this paper they used what we call BAC contigs. A BAC is a bacterial artificial chromosome: basically a plasmid with a really big insertion (usually a couple of hundred kilobases) to make sequencing easier. This is really useful, because it means that you can be sure that you have a perfect sequence for a really long stretch of DNA, but it’s not as cheap as some of the newer NextGen methods.
For large-scale projects like this one we can’t directly sequence individual genes, and doing the whole lot as BACs or YACs is time consuming and slightly problematic. we just shotgun sequence the entire lot. That means that we can’t say for certain that Piece 1 overlaps with Piece 2, and so any repeating sequences can make this assembly harder, but essentially the principle is the same. On average there will be a large number of sequences covering every point in the genome (e.g. the Chinese Spring shotgun data for wheat gives 5x coverage).
A linkage map, on the other hand, is a bit more cerebral. The idea is this: every time an organism reproduces it undergoes a process called crossing over, which reshuffles the genes. The more frequently two alleles are separated in a crossing over event, the further apart they must be. (So lots of children are born with brown hair and brown eyes, because the two genes are close to one another, so even when a brown eyed-brunette breeds with a blue-eyed blonde, it’s likely that the eye and hair colour genes will segregate together.
Because there are certain areas of the chromosome that are more or less likely to undergo crossing over (basically the middle and the ends of the chromosomes: the centromere and the telomeres are prone to not cross-over) a linkage map never perfectly matches a physical one. A linkage map is never as informative as a physical map can be, and is highly dependent on the number of markers you can put on it but it’s an awful lot cheaper to make.
There’s a lot more to this paper than I’ve talked about here, but I think rather than cramming it all into one post I’ll write another one about expression tomorrow!
A physical, genetic and functional sequence assembly of the barley genome
The International Barley Genome Sequencing Consortium