A molecular map based on an indica/indica recombinant inbred population and its comparison with an existing map derived from indica/japonica cross in rice

Li WeiMing; Tang DingZhong; Wu WeiRen; Lu HaoRan; Worland, A.J.

Chinese Journal of Rice Science 14(2): 71-78


ISSN/ISBN: 1001-7216
Accession: 003344257

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With the eventual purpose of precisely locating quantitative trait loci (QTLs) in indica rice, a molecular linkage map was constructed based on an indica x indica derived recombinant inbred (RI) population consisting of 131 (F6:7) lines. The map consists of 160 RFLP markers detected by 113 rice and 28 wheat probes and 78 AFLP markers revealed by five PstI/MseI primer combinations. The heterozygosity rate of the population was close to the expectation, indicating that the population had a normal genetic structure. Segregation distortion was observed in six chromosomal regions, suggesting that abnormal segregation could happen even in an intra-subspecies population. The map covers a length of 1435.8 cM, with an average distance of 6.38 cM between adjacent markers. A set of RFLP landmarks generated by the Japanese Rice Genome Program (RGP) was applied to allow comparison between this map and the RGP map. Both maps have nearly the same total map length regarding the coverage by common markers. Nine of 12 chromosomes showed complete linkage conservation in the two maps and rice chromosome 1 represented strong linearity to wheat group 3 chromosomes. Distinct organization between the two maps was evident. Four small inversions in chromosome arms 1S, 1L, 4L and 8L and nineteen additional loci mapping to all twelve chromosomes except chromosomes 5 and 6 were detected. Four regions on chromosome arms 2S, 7S, 10L and 11S exhibited no, or at least very low polymorphism resulting in obvious distal deficiencies in these regions of the indica map. The conservation of duplicated fragments between chromosome 11 and 12 was not detected in the indica map. Chromosome rearrangement involving in genome evolution in O. sativa is discussed.