Genome-wide association studies (GWASs) encounter limitations from population structure and sample size, restricting their efficacy. Though meta-analysis mitigates these issues, its application in rice research remains limited. Here, we report a large-scale meta-analysis of six independent GWAS experiments in rice to mine genes for key agronomic traits. By integrating a rice pan-genome graph to identify structural variants, we obtained 6,604,898 SNP and 42,879 PAV variants for the six panels (7765 accessions). Meta-analysis significantly improved quantitative trait loci (QTLs) detection and hidden heritability by up to 43 and 37.88%, respectively. Among 156 QTLs identified for six agronomic traits, 116 were exclusively detected through meta-analysis, highlighting its superior resolution. Two novel QTLs governing grain width and length were functionally validated through CRISPR/Cas9, confirming their candidate genes. Our findings underscore the utility and potential advantages of this pan-genome-based meta-GWAS approach, providing a scalable model for efficiently gene mining from diverse rice germplasms.

A new wheat-Thinopyrum translocation line CH13-21 was selected from the progenies derived from a cross between wheat-Th. intermedium partial amphiploid TAI7047 and wheat line Mianyang11. CH13-21 was characterized by using genomic in situ hybridization (GISH), multicolor-GISH (mc-GISH), multicolor-fluorescence in situ hybridization (mc-FISH) and chromosome-specific molecular markers. When inoculated with stripe rust and powdery mildew isolates, CH13-21 displayed novel resistance to powdery mildew and stripe rust which inherited from its Thinopyrum parent. The chromosomal counting analyses indicated that CH13-21 has 42 chromosomes, with normal bivalent pairing at metaphase I of meiosis. GISH probed by Th. intermedium genomic DNA showed that CH13-21 contained a pair of wheat-Th. intermedium translocated chromosomes. Sequential mc-FISH analyses probed by pSc119.2 and pAs1 clearly revealed that chromosome arm 6BS of CH13-21 was replaced by Thinopyrum chromatin in the translocation chromosome. The molecular markers analysis further confirmed that the introduced Th. intermedium chromatin in CH13-21 belonged to the long arm of homoeologous group 6 chromosome. Therefore, CH13-21 was a new T6BS.6Ai#1L compensating Robertsonian translocation line. It concludes that CH13-21 is a new genetic resource for wheat breeding programs providing novel variation for disease resistances.

Background: The identification of chromosomes among Avena species have been studied by C-banding and in situ hybridization. However, the complicated results from several cytogenetic nomenclatures for identifying oat chromosomes are often contradictory. A universal karyotyping nomenclature system for precise chromosome identification and comparative evolutionary studies would be essential for genus Avena based on the recently released genome sequences of hexaploid and diploid Avena species. Results: Tandem repetitive sequences were predicted and physically located on chromosomal regions of the released Avena sativa OT3098 genome assembly v1. Eight new oligonucleotide (oligo) probes for sequential fluorescence in situ hybridization (FISH) were designed and then applied for chromosome karyotyping on mitotic metaphase spreads of A. brevis, A. nuda, A. wiestii, A. ventricosa, A. fatua, and A. sativa species. We established a high-resolution standard karyotype of A. sativa based on the distinct FISH signals of multiple oligo probes. FISH painting with bulked oligos, based on wheat-barley collinear regions, was used to validate the linkage group assignment for individual A. sativa chromosomes. We integrated our new Oligo-FISH based karyotype system with earlier karyotype nomenclatures through sequential C-banding and FISH methods, then subsequently determined the precise breakage points of some chromosome translocations in A. sativa. Conclusions: This new universal chromosome identification system will be a powerful tool for describing the genetic diversity, chromosomal rearrangements and evolutionary relationships among Avena species by comparative cytogenetic and genomic approaches.

Common oat (Avena sativa L.) is one of the important minor grain crops in China, and drought stress severely affects its yield and quality. To investigate the drought resistance characteristics of oat seedlings, this study used Baiyan 2, an oat cultivar at the three-leaf stage, as the experimental material. Drought stress was simulated using polyethylene glycol (PEG) to treat the seedlings. The photosynthetic parameters and physicochemical indices of the treatment groups at 6 h and 12 h were measured and compared with the control group at 0 h. The results showed that drought stress did not significantly change chlorophyll content, but it significantly reduced net photosynthetic rate and other photosynthetic parameters while significantly increasing proline content. Transcriptome analysis was conducted using seedlings from both the control and treatment groups, comparing the two treatment groups with the control group using Tbtool software (v2.136). This analysis identified 344 differentially expressed genes. Enrichment analysis of these differentially expressed genes revealed significant enrichment in physiological pathways such as photosynthesis and ion transport. Ten differentially expressed genes related to the physiological process of photosynthetic carbon assimilation were identified, all of which were downregulated. Additionally, seven differentially expressed genes were related to ion transport. Through gene co-expression analysis combined with promoter region structure analysis, 11 transcription factors (from MYB, AP2/ERF, C2C2-dof) were found to regulate the expression of 10 genes related to photosynthetic carbon assimilation. Additionally, five transcription factors regulate the expression of two malate transporter protein-related genes (from LOB, zf-HD, C2C2-Dof, etc.), five transcription factors regulate the expression of two metal ion transporter protein-related genes (from MYB, zf-HD, C2C2-Dof), five transcription factors regulate the expression of two chloride channel protein-related genes (from MYB, bZIP, AP2/ERF), and two transcription factors regulate the expression of one Annexin-related gene (from NAC, MYB). This study provides a theoretical foundation for further research on the molecular regulation of guard cells and offers a molecular basis for enhancing drought resistance in oats.

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a globally serious disease adversely affecting wheat production. The Bgt-resistant wheat breeding line CH09W89 was derived after backcrossing a Bgt resistant wheat-Thinopyrum intermedium partial amphiploid TAI7045 with susceptible wheat cultivars. At the seedling stage, CH09W89 exhibited immunity or high resistance to Bgt pathotypes E09, E20, E21, E23, E26, Bg1, and Bg2, similar to its donor line TAI7045 and Th. intermedium. No Th. intermedium chromatin was detected based on genomic in situ hybridization of mitotic chromosomes. To determine the mode of inheritance of the Bgt resistance and the chromosomal location of the resistance gene, CH09W89 was crossed with two susceptible wheat cultivars. The results of the genetic analysis showed that the adult resistance to Bgt E09 in CH09W89 was controlled by a single recessive gene, which was tentatively designated as pmCH89. Two polymorphic SSR markers, Xwmc310 and Xwmc125, were linked to the resistance gene with genetic distances 3.1 and 2.7 cM, respectively. Using the Chinese Spring aneuploid and deletion lines, the resistance gene and its linked markers were assigned to chromosome arm 4BL in the bin 0.68–0.78. Due to its unique position on chromosome 4BL, pmCH89 appears to be a new locus for resistance to powdery mildew. These results will be of benefit for improving powdery mildew resistance in wheat breeding programs.

Hemerocallis citrina is a popular vegetable crop. Its eatable flower buds contain abundant nutrients, especially lecithin (Guo et al., 2022). In March 2021, leaf spot disease was observed on 90% cu...