Comparative sequence analyses of the major quantitative trait locus phosphorus uptake 1 (Pup1) reveal a complex genetic structure

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dc.creatorHeuer, Sigrid
dc.creatorLu, Xiaochun
dc.creatorChin, Joong Hyoun
dc.creatorTanaka, Juan Pariasca
dc.creatorKanamori, Hiroyuki
dc.creatorMatsumoto, Takashi
dc.creatorDe Leon, Teresa
dc.creatorUlat, Victor Jun
dc.creatorIsmail, Abdelbagi M.
dc.creatorYano, Masahiro
dc.creatorWissuwa, Matthias
dc.date2009-06
dc.date2024-12-19T12:55:59Z
dc.date2024-12-19T12:55:59Z
dc.date.accessioned2026-06-27T04:16:22Z
dc.descriptionThe 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 α‐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.
dc.identifierhttps://hdl.handle.net/10568/166182
dc.identifier.urihttp://hdl.handle.net/123456789/27273
dc.languageen
dc.publisherWiley
dc.sourceHeuer, Sigrid; Lu, Xiaochun; Chin, Joong Hyoun; Tanaka, Juan Pariasca; Kanamori, Hiroyuki; Matsumoto, Takashi; De Leon, Teresa; Ulat, Victor Jun; Ismail, Abdelbagi M.; Yano, Masahiro and Wissuwa, Matthias. 2009. Comparative sequence analyses of the major quantitative trait locus phosphorus uptake 1 (Pup1) reveal a complex genetic structure. Plant Biotechnology Journal, Volume 7 no. 5 p. 456-471
dc.subjectabiotic stress
dc.subjectbacterial artificial chromosomes
dc.subjectgenes
dc.subjectgenomes
dc.subjectmineral deficiencies
dc.subjectmineral uptake
dc.subjectnutrient uptake
dc.subjectphosphorus
dc.subjectproteinases
dc.subjectquantitative trait loci
dc.subjecttransposable elements
dc.titleComparative sequence analyses of the major quantitative trait locus phosphorus uptake 1 (Pup1) reveal a complex genetic structure
dc.typeJournal Article

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Instituto Internacional de Investigación del Arroz (IRRI)