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1774992 
Journal Article 
Comparative sequence analyses of the major quantitative trait locus phosphorus uptake 1 (Pup1) reveal a complex genetic structure 
Heuer, S; Lu, X; Chin, JH; Tanaka, JP; Kanamori, H; Matsumoto, T; De Leon, T; Ulat, VJun; Ismail, AM; Yano, M; Wissuwa, M 
2009 
1 
Plant Biotechnology Journal
ISSN: 1467-7644
EISSN: 1467-7652 
7 
5 
456-471 
19422603 
WOS:000265936900007 
The phosphorus uptake 1 (Pup1) locus was identified as a
major quantitative trait locus (QTL) for tolerance of phosphorus deficiency in rice. Near-
isogenic lines with the Pup1 region from tolerant donor parent Kasalath typically show threefold
higher phosphorus uptake and grain yield in phosphorus-deficient field trials than the intolerant
parent Nipponbare. In this study, we report the fine mapping of the Pup1 locus to the long arm of
chromosome 12 (15.31-15.47 Mb). Genes in the region were initially identified on the basis of the
Nipponbare reference genome, but did not reveal any obvious candidate genes related to phosphorus
uptake. Kasalath BAC clones were therefore sequenced and revealed a 278-kbp sequence
significantly different from the syntenic regions in Nipponbare (145 kb) and in the indica
reference genome of 93-11 (742 kbp). Size differences are caused by large insertions or deletions
(INDELs), and an exceptionally large number of retrotransposon and transposon-related elements
(TEs) present in all three sequences (45%-54%). About 46 kb of the Kasalath sequence did not
align with the entire Nipponbare genome, and only three Nipponbare genes (fatty acid alpha-
dioxygenase, dirigent protein and aspartic proteinase) are highly conserved in Kasalath. Two
Nipponbare genes (expressed proteins) might have evolved by at least three TE integrations in an
ancestor gene that is still present in Kasalath. Several predicted Kasalath genes are novel or
unknown genes that are mainly located within INDEL regions. Our results highlight the importance
of sequencing QTL regions in the respective donor parent, as important genes might not be present
in the current reference genomes. 
abiotic stress tolerance; Kasalath; phosphorus; quantitative trait locus (QTL); rice; transposons