Dissecting the molecular basis of spike traits by integrating gene regulatory networks and genetic variation in wheat

Spike architecture influences both grain weight and grain number per spike,which are the two major components of grain yield in bread wheat(Triticum aestivum L.).However,the complex wheat genome and the influence of various environmental factors pose challenges in mapping the causal genes that affect spike traits.Here,we systematically identified genes involved in spike trait formation by integrating information on genomic variation and gene regulatory networks controlling young spike development in wheat.We identified 170 loci that are responsible for variations in spike length,spikelet number per spike,and grain number per spike through genome-wide association study and meta-QTL analyses.We constructed gene regulatory networks for young inflorescences at the double ridge stage and thefloret primordium stage,in which the spikelet meristem and thefloret meristem are predominant,respec-tively,by integrating transcriptome,histone modification,chromatin accessibility,eQTL,and protein–pro-tein interactome data.From these networks,we identified 169 hub genes located in 76 of the 170 QTL regions whose polymorphisms are significantly associated with variation in spike traits.The functions of TaZF-B1,VRT-B2,and TaSPL15-A/D in establishment of wheat spike architecture were verified.This study provides valuable molecular resources for understanding spike traits and demonstrates that combining genetic analysis and developmental regulatory networks is a robust approach for dissection of complex traits.

RNA-Directed DNA Methylation Is Involved in Regulating Photoperiod-Sensitive Male Sterility in Rice

Photoperiod-sensitive male sterility （PSMS） is a valuable germplasm for hybrid rice breeding. Recently, we cloned pros3, a locus controlling PSMS, which encodes a long non-coding RNA called LDMAR required for normal male fertility of the rice plant under long-day conditions. Increased methylation in the promoter of LDMAR in the PSMS rice （Nongken 58S） relative to the wild-type （Nongken 58） reduced expression of LDMAR leading to male sterility under long-day conditions. In this study, we identified a siRNA named Psi-LDMAR in the LDMAR promoter region that was more abundant in Nongken 58S than in Nongken 58. We showed that Psi-LDMAR was likely derived from AKl11270, a transcript obtained from the sense strand of the LDMAR promoter with its 3＇-end having a 110-base overlap with the 5＇-end of LDMAR. Overexpressing AKl11270 in Nongken 58S greatly enriched Psi-LDMAR, which induced RNA-directed DNA methylation in the LDMAR promoter and repressed the expression of LDMAR. Reduction of LDMAR in Nongken 58S changed the critical day length for fertility recovery and delayed the fertility recovery under short-day conditions. This result added to our understanding of the molecular mechanism for PSMS.