Genetic mechanisms underlying yield potential in the rice high-yielding cultivar Takanari, based on reciprocal chromosome segment substitution lines

Abstract

BackgroundIncreasing rice yield potential is a major objective in rice breeding programs, given the need for meeting the demands of population growth, especially in Asia. Genetic analysis using genomic information and high-yielding cultivars can facilitate understanding of the genetic mechanisms underlying rice yield potential. Chromosome segment substitution lines (CSSLs) are a powerful tool for the detection and precise mapping of quantitative trait loci (QTLs) that have both large and small effects. In addition, reciprocal CSSLs developed in both parental cultivar backgrounds may be appropriate for evaluating gene activity, as a single factor or in epistatic interactions.ResultsWe developed reciprocal CSSLs derived from a cross between Takanari (one of the most productive indica cultivars) and a leading japonica cultivar, Koshihikari; both the cultivars were developed in Japan. Forty-one CSSLs covered most of the Takanari genome in the Koshihikari background and 39 CSSLs covered the Koshihikari genome in the Takanari background. Using the reciprocal CSSLs, we conducted yield trials under canopy conditions in paddy fields. While no CSSLs significantly exceeded the recurrent parent cultivar in yield, genetic analysis detected 48 and 47 QTLs for yield and its components in the Koshihikari and Takanari backgrounds, respectively. A number of QTLs showed a trade-off, in which the allele with increased sink-size traits (spikelet number per panicle or per square meter) was associated with decreased ripening percentage or 1000-grain weight. These results indicate that increased sink size is not sufficient to increase rice yield in both backgrounds. In addition, most QTLs were detected in either one of the two genetic backgrounds, suggesting that these loci may be under epistatic control with other gene(s).ConclusionsWe demonstrated that the reciprocal CSSLs are a useful tool for understanding the genetic mechanisms underlying yield potential in the high-yielding rice cultivar Takanari. Our results suggest that sink-size QTLs in combination with QTLs for source strength or translocation capacity, as well as careful attention to epistatic interactions, are necessary for increasing rice yield. Thus, our findings provide a foundation for developing rice cultivars with higher yield potential in future breeding programs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0295-2) contains supplementary material, which is available to authorized users.

Quantitative trait loci for large sink capacity enhance rice grain yield under free-air CO2 enrichment conditions

“…CSSL- GN1 was developed by repeated backcrossing with Koshihikari and marker-assisted selection 16 . NIL- APO1 was developed in the same way.…”

Detection of QTL for exudation rate at ripening stage in rice and its contribution to hydraulic conductance

“…Therefore, in a similar way of our previous successful trial [30], we screened frame SSR markers for linkage map construction from data of about 2000 SSRs [31] which are initial representative of the 18,000 [23]. Then, we selected 196 polymorphic SSR markers and one InDel marker (Gn1) [32] distributed evenly in the rice genome. Total genomic DNA was extracted from fresh leaves by the cetyltrimethylammonium bromide (CTAB) method [33] and amplification conditions for the selected SSR markers were as in [34].…”

Identification of a novel QTL for the number of spikelets per panicle using a cross between indica‐ and japonica‐type high‐yielding rice cultivars in Japan

“…An indica ‐type high‐yielding cultivar, ‘Takanari’, was developed in 1990 (Imbe et al., ). Takanari originates from high‐yielding indica cultivars including ‘IR8’; it has the sd1 gene and is shorter in plant stature than normal temperate japonica cultivars in Japan (Takai et al., ). Recent yield trials reported that Takanari produced the highest brown rice yield (11.7 t ha −1 ) on record in Japan (Nagata, Sasaki, Ohdaira, & Yoshinaga, ; Takai et al., ).…”

“…Takanari originates from high‐yielding indica cultivars including ‘IR8’; it has the sd1 gene and is shorter in plant stature than normal temperate japonica cultivars in Japan (Takai et al., ). Recent yield trials reported that Takanari produced the highest brown rice yield (11.7 t ha −1 ) on record in Japan (Nagata, Sasaki, Ohdaira, & Yoshinaga, ; Takai et al., ). The high yield was achieved because of large panicles, a high leaf photosynthetic ability, the high accumulation of non‐structural carbohydrates in the culm and leaf sheath at the full heading stage, and the translocation of many of these carbohydrates into panicles during grain filling (Kanemura, Homma, Ohsumi, Shiraiwa, & Horie, ; Ohsumi et al., ; Takai et al., ).…”

“…The high yield was achieved because of large panicles, a high leaf photosynthetic ability, the high accumulation of non‐structural carbohydrates in the culm and leaf sheath at the full heading stage, and the translocation of many of these carbohydrates into panicles during grain filling (Kanemura, Homma, Ohsumi, Shiraiwa, & Horie, ; Ohsumi et al., ; Takai et al., ). At least two quantitative trait loci (QTLs), GN1a and APO1 , contribute to the large panicles (Takai et al., ), and another QTL, GPS , underlies the high chlorophyll content and, therefore, the high leaf photosynthetic ability in Takanari (Takai et al., ). The causal gene of GPS is identical to that of SPIKE , which controls the number of spikelets per panicle, which indicates an allelic relationship between GPS and SPIKE (Fujita et al., ; Takai et al., , ).…”