Since the release of IR8 in 1966, 42 additional indica rice (Oryza sativa L.) cultivars developed by the International Rice Research Institute (IRRI) for the irrigated and favorable rainfed lowlands have been released in the Philippines. The maximum yield of IR8 has been reduced by about 2 Mg ha−1 during the past 30 yr. Empirical breeding for population improvement within the indica germplasm has resulted in the maintenance of rice yield potential in the tropics of about 10 Mg ha−1. To break the yield barrier, several approaches are being explored. These include development of a new plant type (NPT) with low tillering capacity and large panicles from tropical japonica germplasm and exploitation of heterosis through intervarietal and intersubspecific hybrids. Hybrid rice between indicas increased yield potential by about 9% under the tropical conditions. The higher yield potential of indica/indica hybrids compared with indica inbred cultivars was attributed to the greater biomass production rather than harvest index. New plant type breeding has not yet improved yield potential due to poor grain filling and low biomass production. Factors that cause poor grain filling and low biomass production of the NPT lines have been identified. Selecting parents with good grain filling traits, introduction of indica genes into NPT's tropical japonica background, and a refinement of the original NPT design are expected to improve the performance of the NPT lines. Further enhancement in yield potential may be possible from use of intersubspecific heterosis between indica and NPT lines.

One hundred and ninety three parental lines obtained from 26 countries for an international rice molecular breeding program were evaluated using 101 well-distributed simple sequence repeat (SSR) markers. An overall genetic diversity of 0.68 and an average of 6.3 alleles per locus were revealed, indicating a high level of genetic variation in these lines. Cluster analysis of the 193 accessions showed three major groups and nine subgroups. Group I corresponded to the classical indica subspecies, whereas groups II and III belong to the japonica subspecies. Indica and japonica differentiation accounted for only 6.5% of the total variation in the entire sample and 93.5% was due to within-subspecies diversity. Differentiation among eco-geographic regions accounted for 24% of the diversity within the subspecies. Larger amounts of the eco-geographical differentiation were resolved within japonica than within indica. The largest indica-japonica differentiation based on the single locus level was detected by markers on chromosomes 9 and 12, while the smallest differentiation was detected by markers on chromosomes 4 and 8. Furthermore, genetic differences at the single-locus and two-locus levels, as well as components due to allelic and gametic differentiation, were revealed between indica and japonica and among the main geographic regions. The multilocus analysis in genetic diversity showed a higher proportion of variation caused by predominant non-random associations of different loci within and among the classified subspecies and geographic subdivisions. The results suggest that selection for eco-geographical adaptation on multilocus associations was largely responsible for the maintenance of the extensive variation in the primary gene pool of rice.

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