Long-term balancing selection at the Phosphorus Starvation Tolerance 1 (PSTOL1) locus in wild, domesticated and weedy rice (Oryza).
BACKGROUND
The ability to grow in phosphorus-depleted soils is an important trait for rice cultivation in many world regions, especially in the tropics. The Phosphorus Starvation Tolerance 1 (PSTOL1) gene has been identified as underlying the ability of some cultivated rice varieties to grow under low-phosphorus conditions; however, the gene is absent from other varieties. We assessed PSTOL1 presence/absence in a geographically diverse sample of wild, domesticated and weedy rice and sequenced the gene in samples where it is present.


RESULTS
We find that the presence/absence polymorphism spans cultivated, weedy and wild Asian rice groups. For the subset of samples that carry PSTOL1, haplotype sequences suggest long-term selective maintenance of functional alleles, but with repeated evolution of loss-of-function alleles through premature stops and frameshift mutations. The loss-of-function alleles have evolved convergently in multiple rice species and cultivated rice varieties. Greenhouse assessments of plant growth under low- and high-phosphorus conditions did not reveal significant associations with PSTOL1 genotype variation; however, the striking signature of balancing selection at this locus suggests that further phenotypic characterizations of PSTOL1 allelic variants is warranted and may be useful for crop improvement.


CONCLUSIONS
These findings suggest balancing selection for both functional and non-functional PSTOL1 alleles that predates and transcends Asian rice domestication, a pattern that may reflect fitness tradeoffs associated with geographical variation in soil phosphorus content.
Department of Biology, High Point University, High Point, NC, USA.
Cynthia C
CC
Vigueira
Department of Biology, Washington University, St. Louis, MO, USA.
Linda L
LL
Small
Department of Biology, Washington University, St. Louis, MO, USA. kolsen@wustl.edu.
Kenneth M
KM
Olsen
D000222:Adaptation, Physiological / Q000235:genetics*; D000483:Alleles; D018389:Codon, Nonsense; D019143:Evolution, Molecular; D016368:Frameshift Mutation; D017343:Genes, Plant / Q000235:genetics*; D005838:Genotype; D005843:Geography; D012275:Oryza / Q000145:classification / Q000235:genetics*; D010758:Phosphorus / Q000378:metabolism*; D010802:Phylogeny; D011110:Polymorphism, Genetic; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D012987:Soil / Q000737:chemistry; D013045:Species Specificity; D013997:Time Factors
D018389:Codon, Nonsense; D012987:Soil; D010758:Phosphorus
Abiotic stress; Balancing selection; Crop domestication; Gene presence/absence variation (PAV); Phosphorus Starvation Tolerance 1 (PSTOL1); Weedy rice