DNA – Page 118 – Agricultural Biodiversity Weblog

August 1, 2009July 30, 2009

Rice diversity measured and photographed

I did a quick nibble a few days ago about the OryzaSNP project, in which “[a]n international team of investigators used microarray-based resequencing to look for SNPs in 100 million bases of non-repetitive DNA in the genomes of 20 different rice varieties and landraces.”

They’ve come up with 159,879 single nucleotide polymorphisms, a “gold-standard set of curated polymorphisms” for rice.

As for the 20 varieties used…

“[t]hese varieties, the OryzaSNPset collection, are genetically diverse and actively used in international breeding programs because of their wide range of agronomic attributes,” the authors explained.

But what do they look like? Well, I just found this photograph of their seeds on IRRI’s Flickr page. A nice idea.

rice

http://www.flickr.com/photos/ricephotos/ / CC BY 2.0

July 24, 2009July 24, 2009

Nibbles: Camel, Maya forestry, Ancient barley, Cattle diversity, Poisons, Agroforestry Congress, Lactase persistence

Wild camel genetically distinct from the domesticated kind. Well I never.
Maya tapped into their “sacred groves” to build temples, which did not end well.
Boffins extract DNA from ancient barley in Upper Egypt, find it was 2-rowed, but derived from a 6-rowed ancestor. No word on whether it was used to make beer, but my guess is yes.
Large Y chromosome microsatellite study of Eurasian cattle does “not support the recent hypothesis on the origin of Y1 from the local European hybridization of cattle with male aurochsen.” This could run and run.
I like this idea: a garden of poisons.
Agroforestry’s coming-of-age party coming up. You going? Let us know.
Multiple explanations for lactase persistence.

July 15, 2009July 28, 2009

Nibbles: India, City chicks, Rooftop gardens, Black cherry, Prairie grasses, Oryza SNP

ICRISAT recommends diversity to cope with climate change in India.
US urban farmers “mad as wet hens“. City chicks?
US urban farmers with a view to die for.
CWR becomes nuisance when free of soil pathogen.
Convicts help with germplasm regeneration and multiplication.
The “gold-standard set of curated polymorphisms” for rice.

July 11, 2009July 11, 2009

Livestock genetics symposium online

DAD-Net informs us that the presentations given at the symposium on Statistical Genetics of Livestock for the Post-Genomic Era, held at the University of Wisconsin-Madison, USA, on May 4-6, 2009, are now available online in the form of both PDFs and videos. Quite a resource.

July 10, 2009July 10, 2009

Natural selection at work

“This new forage has great insect resistance”, effused a former colleague, “we just need to eliminate the toxins that keep sheep from eating it.”

Genetically engineered drought-tolerant crops are introduced with great fanfare, only to disappear when they turn out to have low yield under nondrought conditions.

Fascinating post from R. Ford Denison, about how silly old natural selection (apparently) fails to make simple changes that would “obviously” be good for the organism concerned. Denison is very clear, in this post and elsewhere on his blog, about just how hard it is for even clever people to improve on the countless experiments that natural selection has had to work on, especially in agriculture. That’s why I for one am not holding my breath waiting for anyone anywhere to transform a C3 plant into a C4 plant.