Understanding how numerous quantitative trait loci (QTL) shape phenotypic variation is an important question in genetics. To address this, we established a permanent population of 18,421 (18K) rice lines with reduced population structure. We generated reference-level genome assemblies of the founders and genotyped all 18K-rice lines through whole-genome sequencing. Through high-resolution mapping, 96 high-quality candidate genes contributing to variation in 16 traits were identified, including OsMADS22 and OsFTL1 verified as causal genes for panicle number and heading date, respectively. We identified epistatic QTL pairs and constructed a genetic interaction network with 19 genes serving as hubs. Overall, 170 masking epistasis pairs were characterized, serving as an important factor contributing to genetic background effects across diverse varieties. The work provides a basis to guide grain yield and quality improvements in rice.

Protecting haploid pollen and spores against ultraviolet-B (UV-B) light and high temperature, two major stresses inherent to the terrestrial environment, is critical for plant reproduction and dispersal. Here, we show flavonoids play an indispensable role in this process. Firstly, we identified the flavanone naringenin, which serves to defend against UV-B damage, in the sporopollenin wall of all vascular plants tested. Secondly, we found that flavonols are present in the spore/pollen protoplasm of all euphyllophyte plants tested and that these flavonols scavenge ROS to protect against environmental stresses, particularly heat. Genetic and biochemical analyses showed that these flavonoids are sequentially synthesized in both the tapetum and microspores during pollen ontogeny in Arabidopsis (Arabidopsis thaliana). We show that stepwise increases in the complexity of flavonoids in spores/pollen during plant evolution mirrors their progressive adaptation to terrestrial environments. The close relationship between flavonoid complexity and phylogeny and its strong association with pollen survival phenotypes suggests that flavonoids played a central role in the progression of plants from aquatic environments into progressively dry land habitats.

The subcellular events occurring in cells of legume plants as they form transcellular symbiotic-infection structures have been compared with those occurring in premitotic cells. Here, we demonstrate that Aurora kinase 1 (AUR1), a highly conserved mitotic regulator, is required for intracellular infection by rhizobia inMedicago truncatula. AUR1 interacts with microtubule-associated proteins of the TPXL and MAP65 families, which, respectively, activate and are phosphorylated by AUR1, and localizes with them within preinfection structures. MYB3R1, a rhizobia-induced mitotic transcription factor, directly regulatesAUR1through two closely spaced, mitosis-specific activatorciselements. Our data are consistent with a model in which the MYB3R1-AUR1 regulatory module serves to properly orient preinfection structures to direct the transcellular deposition of cell wall material for the growing infection thread, analogous to its role in cell plate formation. Our findings indicate that the eukaryotically conserved MYB3R1-TPXL-AUR1-MAP65 mitotic module was conscripted to support endosymbiotic infection in legumes.

Photoperiod- and thermo-sensitive genic male sterility (P/TGMS) lines are widely used in crop breeding. The fertility conversion of Arabidopsis thaliana TGMS lines including cals5-2, which is defective in callose wall formation, relies on slow development under low temperatures. In this study, we discovered that cals5-2 also exhibits PGMS. Fertility of cals5-2 was restored when pollen development was slowed under short-day photoperiods or low light intensity, suggesting that slow development restores the fertility of cals5-2 under these conditions. We found that several other TGMS lines with defects in pollen wall formation also exhibited PGMS characteristics. This similarity indicates that slow development is a general mechanism of PGMS fertility restoration. Notably, slow development also underlies the fertility recovery of TGMS lines. Further analysis revealed the pollen wall features during the formation of functional pollens of these P/TGMS lines under permissive conditions. We conclude that slow development is a general mechanism for fertility restoration of P/TGMS lines and allows these plants to take different strategies to overcome pollen formation defects.

The specific partnership between legumes and rhizobia relies on a chemical dialogue. Plant flavonoids activate the bacterial transcription factor NodD, which triggers production of Nod factors that are recognized by the plant. Structural studies of the Pisum sativum (pea) symbiont Rhizobium leguminosarum NodD revealed two pockets that are essential for its activation by flavonoids. Comparative studies with NodD1 of Sinorhizobium medicae , the symbiont of Medicago truncatula , revealed that this specificity is determined by the shape of the pocket and by specific amino acids. A chimeric NodD containing the flavonoid recognition residues from S. medicae NodD1 in the R. leguminosarum NodD backbone was sufficient to complement nitrogen fixation in M. truncatula by an S. medicae nodD1 mutant, confirming the critical role of flavonoid recognition in host range.