Rice (Oryza sativa L.) is a chilling-sensitive staple food crop, and thus, low temperature significantly affects rice growth and yield. Many studies have focused on the cold shock of rice although chilling acclimation is more likely to happen in the field. In this paper, a genome-wide association study (GWAS) was used to identify the genes that participated in cold stress and chilling accumulation. A total of 235 significantly associated single-nucleotide polymorphisms (SNPs) were identified. Among them, we detected 120 and 88 SNPs for the relative shoot fresh weight under cold stress and chilling acclimation, respectively. Furthermore, 11 and 12 quantitative trait loci (QTLs) were identified for cold stress and chilling acclimation, respectively, by integrating the co-localized SNPs. Interestingly, we identified 10 and 15 candidate genes in 11 and 12 QTLs involved in cold stress and chilling acclimation, respectively, and two new candidate genes (LOC_Os01g62410, LOC_Os12g24490) were obviously up-regulated under chilling acclimation. Furthermore, OsMYB3R-2 (LOC_Os01g62410) that encodes a R1R2R3 MYB gene was associated with cold tolerance, while a new C3HC4-type zinc finger protein-encoding gene LOC_Os12g24490 was found to function as a putative E3 ubiquitin-protein ligase in rice. Moreover, haplotype, distribution, and Wright’s fixation index (FST) of both genes showed that haplotype 3 of LOC_Os12g24490 is more stable in chilling acclimation, and the SNP (A > T) showed a difference in latitudinal distribution. FST analysis of SNPs in OsMYB3R-2 (LOC_Os01g62410) and LOC_Os12g24490 indicated that several SNPs were under selection in rice indica and japonica subspecies. This study provided new candidate genes in genetic improvement of chilling acclimation response in rice.

Cellulose crystallinity is a crucial factor influencing stem strength and, consequently, wheat lodging. However, the genetic dissection of cellulose crystallinity is less reported due to the difficulty of its measurement. In this study, VIS/NIR spectra and cellulose crystallinity were measured for a wheat accession panel with diverse genetic backgrounds. We developed a reliable VIS/NIR model for cellulose crystallinity with a high determination coefficient (R²) (0.95) and residual prediction deviation (RPD) (4.04), enabling the rapid screening of wheat samples. A GWAS of the cellulose crystallinity in 326 wheat accessions revealed 14 significant SNPs and 13 QTLs. Two candidate genes, TraesCS4B03G0029800 and TraesCS5B03G1085500, were identified. In summary, this study establishes an efficient method for the measurement of cellulose crystallinity in wheat stems and provides a genetic basis for enhancing lodging resistance in wheat.