alexa RFLP analysis of genomic regions associated with cooked-kernel elongation in rice.
Bioinformatics & Systems Biology

Bioinformatics & Systems Biology

Journal of Phylogenetics & Evolutionary Biology

Author(s): Ahn SN, Bollich CN, McClung AM, Tanksley SD

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Abstract As a result of earlier breeding efforts, portions of the genome of "Basmati 370" have been introgressed into a rice breeding line, B8462T3-710. Cooked-kernel elongation was increased in this breeding line to a level equal to that of "Basmati 370". The objective of this study was to identify and locate quantitative trait loci (QTLs) associated with cooked-kernel elongation in an F3 population derived from a cross between B8462T3710 and the reduced-elongation recurrent parent variety, Dellmont. DNA from the parental lines and "Basmati 370" as a control, were screened for RFLPs using 170 clones chosen to cover the rice genome at intervals of 8 cM on average. Eighteen markers identified RFLPs common to Basmati 370 and B8462T3-710, but different from Dellmont, suggesting possible associations with kernel elongation. The B8462T3-710/Dellmont F3 population was analyzed for segregation of those RFLPs and for kernel elongation. Analysis of variance of the kernel elongation ratio revealed that two markers, 14.6 cM apart on chromosome 8, are significantly associated with this trait (RZ323 P ≤0.005, RZ562 P ≤0.05). Interval mapping suggests a single QTL with a close proximity to RZ323. This QTL was tested in F6 lines derived from the same cross and the presence of the B8462T3-710 segment detected by RZ323 caused a highly significant increase of the kernel elongation ratio (P ≤0.04). In addition, the QTL for kernel elongation and a gene for aroma, which are major components of the grain quality characteristics of Basmati-type rices, showed linkage. The availability of linked markers to the QTL may facilitate early selection for kernel elongation in rice breeding programs. This article was published in Theor Appl Genet and referenced in Journal of Phylogenetics & Evolutionary Biology

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