| Abstract: | Increasing crop production is essential for securing the future food supply in developing countries in Asia and Africa as economies and populations grow. However, although the Green Revolution led to increased grain production in the 1960s, no major advances have been made in increasing yield potential in rice since then. In this study, we identified a gene, SPIKELET NUMBER (SPIKE), from a tropical japonica rice landrace that enhances the grain productivity of indica cultivars through pleiotropic effects on plant architecture. Map-based cloning revealed that SPIKE was identical to NARROW LEAF1 (NAL1), which has been reported to control vein pattern in leaf. Phenotypic analyses of a near-isogenic line of a popular indica cultivar, IR64, and overexpressor lines revealed increases in spikelet number, leaf size, root system, and the number of vascular bundles, indicating the enhancement of source size and translocation capacity as well as sink size. The near-isogenic line achieved 13–36% yield increase without any negative effect on grain appearance. Expression analysis revealed that the gene was expressed in all cell types: panicles, leaves, roots, and culms supporting the pleiotropic effects on plant architecture. Furthermore, SPIKE increased grain yield by 18% in the recently released indica cultivar IRRI146, and increased spikelet number in the genetic background of other popular indica cultivars. The use of SPIKE in rice breeding could contribute to food security in indica-growing regions such as South and Southeast Asia.The world’s population is expected to surpass 9 billion in 2050 (http://esa.un.org/unpd/ppp/index.htm). Most of this increase will occur in the developing countries of Asia and Africa. By 2035, a 26% increase in rice production will be essential to feed the rising population (1, 2). Rice (Oryza sativa L.) is a staple food of more than 3 billion people, mainly in Asia. Predominantly, indica cultivars are grown in southern China, Southeast Asia, and South Asia, occupying approximately 70% of the rice-producing area in the world, whereas japonica cultivars are grown mainly in East Asia (3, 4). Because of urbanization and industrialization, an increase in the yield of indica cultivars is a pressing need in Southeast and South Asia (5). Additionally, good grain quality (influencing market value) and high yield are essential for the adoption of new cultivars in local areas (6).The grain yield of rice is determined by spikelet number per panicle, panicle number per plant, grain weight, and spikelet fertility. Although many quantitative trait loci (QTLs) for yield components have been identified (www.gramene.org), few have so far been isolated. To date, at least nine genes or loci for yield-related traits in rice have been isolated from natural variation: Gn1a and APO1 for number of grains (7–9); GS3, GW2, and qSW5 for grain size (10–12); DEP1 and WFP for panicle architecture (13, 14); SCM2 for strong culm (15); and Ghd7 for late heading and number of grains (16). APO1, SCM2, and DEP1 increased grain yield in a japonica genetic background in field experiments (9, 13, 15). However, no novel cloned gene has been reported to increase grain yield in indica cultivars (17). Here, we identified a gene in a tropical japonica landrace and used the allele to increase the grain yield of modern indica cultivars at the crop level through a breeding concept developed by International Rice Research Institute (IRRI) breeders more than 20 y ago.In 1989, a breeding program for New Plant Type (NPT) rice was launched at IRRI to increase the yields of modern indica cultivars by using genetic material from tropical japonica landraces (18). Several Indonesian tropical japonica landraces—which are characterized by large panicles, large leaves, a vigorous root system, thick stems, and few unproductive tillers—have been used in international breeding programs. However, despite these features, the NPT cultivars yield less than modern indica cultivars, mainly because of low grain fertility and low panicle number (19, 20). To genetically dissect and elicit the valuable traits of NPT cultivars, we backcrossed the NPT cultivars including YP9 (IR68522-10-2-2) against modern indica cultivar IR64 to develop introgression lines (ILs) (Fig. S1). BC3-derived ILs, which had favorable yield-related traits and few undesirable traits, were selected by field observation (21). Using the ILs, we identified 21 QTLs for yield components such as total spikelet number per panicle (TSN), grain weight, and panicle number. Among the QTLs, qTSN4, for high TSN, was commonly detected on the long arm of chromosome 4 in five NPT lines derived from different tropical japonica cultivars (22). Additionally, a near-isogenic line (NIL) for qTSN4 from YP9, derived from tropical japonica landrace Daringan with an IR64 genetic background, had more spikelets per panicle and more branches than IR64.In this study, we isolated the gene for qTSN4 through map-based cloning to facilitate its use in breeding. The phenotypic effects of the gene were validated in transgenic plants and by expression analysis. To confirm the effect on practical grain yield in the field, we evaluated yield and related traits by using NILs with genetic backgrounds of popular indica cultivars. |
