- The Sorghum NAM population is designed to dissecting the genetic basis ("which genes and alleles?") and genetic architecture ("what distribution of effect sizes?") of diverse traits.
- The NAM was designed by Mitch Tuinstra and developed by Tuinstra, Jianming Yu, and Tesfaye Tesso
- The common (reference) parent, Tx430, is an admixed breeding line that is in many pedigree and has good grain quality characteristics.
- The other parents (Macia, Segeolane, Ajabsido, P898012 , SC1345, SC1103, SC35, SC971, SC283, SC265) are described in more detail in this table.
- A description of both the TAMU and KSU NAM founders is in this table.
- NAM Literature Review
- Overview: The two genotyping resources needed for NAM are (A) resequencing data for all the founder parental lines (11), to identify all segregating SNPs in the population and (B) genotyping-by-sequencing data on all the RILs (~2500) to identify recombination breakpoints.
- The resequencing of parental lines (A) has already been carried through the JGI Community Sequencing Program, on a project led by Andy Paterson. It is not clear what the status of this data is, as far as publication embargoes.
- The GBS on the RILs (B) will require about one flow cell of Illumina (assuming 384X multiplex; 2500/384=6.5)
- Genotyping results in hapmap format (Large file)
- Analysis scripts (Sophie)
- We need some easy phenotypes for quality control and preliminary mapping experiments. Flavonoid pigmentation traits seem like an excellent choice here (testa, pericarp color, adult plant color, seedling color). Other traits could be height, seed size, dry stem, [what else?].
- We can map traits with Joint Inclusive Composite Interval Mapping (JICIM) (Buckler et al. 2009 Science; Li H et al. 2011 PLoS ONE). Even with just three families in Arabidopsis, JICIM increased power compared in QTL mapping in the individual populations.