Landraces of temperate japonica rice have superior alleles for improving culm strength associated with lodging resistance

Abstract

Lodging can reduce grain yield and quality in cereal crops including rice (Oryza sativa L.). To achieve both high biomass production and lodging resistance, the breeding of new cultivars with strong culms is a promising strategy. However, little is known about the diversity of culm strength in temperate japonica rice and underlying genetic factors. Here, we report a wide variation of culm strength among 135 temperate japonica cultivars, and some landraces having the strongest culms among these cultivars. The genome-wide association study (GWAS) identified 55 quantitative trait loci for culm strength and morphological traits, and revealed several candidate genes. The superior allele of candidate gene for culm thickness, OsRLCK191, was found in many landraces but had not inherited to the modern improved cultivars. Our results suggest that landraces of temperate japonica rice have unutilized superior alleles for contributing future improvements of culm strength and lodging resistance.

Potential of rice landraces with strong culms as genetic resources for improving lodging resistance against super typhoons

“…2L and 3S identified in this study were not detected in that previous study 28 . Unlike that previous study 28 , the panel used in the present study included temperate japonica varieties from the rice core collection of Japanese landraces composed by National Agriculture and Food Research Organization (NARO) and landraces from Okinawa, which may have unique genetic variations due to geographical factors. Therefore, it is possible that a novel QTL that was not previously detected was identified in this study.…”

“…A QTL for culm diameter on chr. 5L was identified in a previous study on 135 temperate japonica varieties from different panels 28 , but was not detected in this study. Conversely, the QTLs on chr.…”

“…To date, few studies have evaluated the traits associated with strong culms of landraces 13 , 28 . However, in this study, by comprehensively analysing the lodging resistance of a large number of varieties, we found that some landraces showed very high culm strength (Fig.…”

“…In our previous studies, superior alleles of STRONG CULM 1 and 2 ( SCM1 and SCM2 ) QTLs, which increase culm strength, were detected in an indica variety Habataki 16 , similarly STRONG CULM 3 and 4 ( SCM3 and SCM4 ) QTLs were detected in a tropical japonica variety Chugoku 117 17 , and the genes responsible for SCM2 and SCM3 were identified as APO1 ABERRANT PANICLE ORGANIZATION 1 ( APO1 ) 16 , 18 and FINE CULM 1 ( FC1 ) 17 , 19 , 20 , respectively. In addition, many other QTLs associated with strong culms have been identified 21 – 28 .…”

“…For instance, under phosphorus-limiting conditions, the japonica landrace Akamai developed an extensive root system compared with that of the japonica breeding variety Koshihikari to obtain more phosphorus and efficiently redistributed it within the plant 29 . However, few studies have comprehensively compared various varieties for culm-associated traits among Japanese genetic resources 13 , 28 .…”