Monday 12 December 2011

War in a Bowl of Rice !: Story of BGI vs BIG both Chinese Genome Greats !

Welcome....

Well, to start up, please have a  sneak peak into the 2 articles:

1. Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm [Link: http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.1018.html#; Nature Genetics, Huang et al, 4th December, BIG; Beijing Institute of Genomics-Beijing ].

2. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes [ Link: http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2050.html#; Xu et al., 11th December, BGI, Beijing Genomics Institute-Shenzhen ]

Reminiscence goes back to the Pigeon Pea genome wars between 2 Indian ICAR [Indian Council for Agricultural Research] Institutions.

The 1st remains first, no matter where it is:

1. The first draft of the pigeon pea genome sequence [Link: http://www.springerlink.com/content/g78774q222672082/, Singh et al., 2011: Journal of Plant Biochemistry and Biotechnology]

And always the 2nd but the best one:

2. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers [Link: http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2022.html; Varshney et al., Nature Biotechnology, 2011]

But, I would not like to delve into the controversies and allow readers to go straight into the starchy-rice genomics !

BIG, clearly laid strong footholds on the largest ever pool of rice genotypes covering 950 worldwide accessions of oryza sativa indica and japonica varieties to perform GWAS ! No wonder, they end-up reporting 32 new loci associated with flowering time and 10 loci associated with grain-related traits. Admittedly, the authors claim a lowe-coverage sequencing data to frame a haplo-tpe-based de novo assembly for rice. Hence, they laid forth a novel approach to direct future research to do sequence-based GWAS and functional genome annotations to provide immensely useful tools to study complex traits and their polymorphisms. Clearly, a strong tool is developed to attain maximum advantage from low-coverage sequencing data when combined with detailed annotations.


BGI, on the other hand, report to have sequenced 40 cultivated and 10 wild ancestral progenitor genomes of rice up to >15 X data coverage, there by identifying 6.5 million SNPs, associated with many agronomic characters. Potentially they provide diagnostic markers and tools for future explorations in rice breeding programs for sure.

Hmm. So 2 big Giants on path for Rice Genome Explorations at the scale of loci and SNPs, ranging ina ccessions of 50's- to ~ 1000s, projecting tools to study basic polymorphic features to use of SNPs in breeding programmes.

Quite contrasting approaches, no doubt, but the end results are not blurred at all: all leading towards the "Application of Genomics for a Sustainable Human Society- Food and Health".

 Until finds a few more Mind-Churning News......

Signing Off,

Science-O-Nomist

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