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Fine mapping SPP1, a QTL controlling the number of spikelets per panicle, to a BAC clone in rice (Oryza sativa)
- Liu, Touming, Mao, Donghai, Zhang, Shengpeng, Xu, Caiguo, Xing, Yongzhong
- Theoretical and applied genetics 2009 v.118 no.8 pp. 1509-1517
- Oryza sativa, bacterial artificial chromosomes, crop production, genes, genetic background, inbred lines, inflorescences, isogenic lines, open reading frames, quantitative trait loci, rice
- Near isogenic lines (NILs) can be used to efficiently handle a target quantitative trait locus (QTL) by blocking genetic background noise. One QTL, SPP1, which controls the number of spikelets per panicle (SPP), was located on chromosome 1, near Gn1a, a cloned gene for rice production in a recombinant inbred line population. NILs of the SPP1 regions were quickly obtained by self-crossing recombinant inbred line 30 which is heterozygous around SPP1. Using a random NIL-F₂ population of 210 individuals, we mapped SPP1 to a 2.2-cM interval between RM1195 and RM490, which explained 51.1% of SPP variation. The difference in SPP between the two homozygotes was 44. F₂-1456, one NIL-F₂ plant, was heterozygous in the SPP1 region but was fixed in the region of Gn1a gene. This plant F₃ family showed a very wide variation in SPP, which suggested that it was SPP1 but Gn1a affected the variation of SPP in this population. In a word, SPP1 is a novel gene distinct from Gn1a. Four newly developed InDel markers were used for high-resolution mapping of SPP1 with a large NIL-F₂ population. Finally, it was narrowed down to a bacterial artificial chromosome clone spanning 107 kb; 17 open reading frames have been identified in the region. Of them, LOC_Os01g12160, which encodes an IAA synthetase, is the most interesting candidate gene.