- Idea Corner -
Under acidic soil conditions, aluminum solubilizes and becomes highly toxic to plants. Aluminum toxicity is a limiting factor in crop productivity. In fact, about 30 to 50% of the world arable land is reported to have acidic soil conditions. For this reason, developing crops tolerant to aluminum toxicity is of paramount importance in coming years, in which population growth and land degradation are huge concerns.
I found interesting that aluminum tolerance in rice is under quantitative inheritance, as opposed to simple trait inheritance in sorghum, with 48 regions in the rice genome controlling this trait. Furthermore, none of the genes that have been cloned so far appeared to contribute with natural genetic variation in aluminum tolerance in rice. Similar results were confirmed for the newly characterized rice gene OsCDT3, which encodes a plasma membrane-localized small peptide that was shown to be involved in aluminum tolerance.
It occurred to me that a possible research strategy to increase the understanding behind the genetic architecture of natural variation in rice aluminum tolerance would combine Chip-seq analysis for ART1 and ASR5 proteins with bulk sergeant analysis (BSA) in a bi-parental mapping population (indica (IR64) x japonica(Azucena) RIL for example). I would expect there is natural genetic variation at the promoter level for downstream genes bound to ART1 and ASR5 proteins between indica (IR64) and japonica (Azucena) cultivars, with the binding activity of ART1 and ASR5 segregating with aluminum tolerance in selected F2s or RIL individuals. Thus, in F2/RIL plants displaying aluminum tolerance inherited by the japonica parent, ART1 and ASR5 proteins should bind genomic sequences not present in F2/RIL plants displaying aluminum sensitivity.
A Chip-seq analysis for ASR5 protein in rice was recently reported. Subsequently, the identified regions with differential ART1/ASR5 binding between indica (IR64) and japonica (Azucena) cultivars could be contrasted with recently described genomic regions identified by GWAS previously shown.
Furthermore, comparative genomics analysis of aluminum tolerance between rice, sorghum and maize could be performed by applying Chip-seq methodology using orthologous copies of ART1 and ASR5 proteins from sorghum and maize.
References:
Famoso et al. (2011). Genetic architecture of aluminum tolerance in rice (Oryza sativa) determined through genome-wide association analysis and QTL mapping. PLOS Genetics - DOI: 10.1371/journal.pgen.1002221
Xia et al. (2013). A plasma membrane-localized small peptide is involved in rice aluminum tolerance. Plant Journal - DOI: 10.1111/tpj.12296
Arenhart et al. (2014). New insights into aluminum tolerance in rice: the ASR5 protein binds the STAR1 promoter and other aluminum-responsive genes.Molecular Plant - DOI: 10.1093/mp/sst160