Common gene mapping approaches mainly include QTL-mapping, BSA-seq (QTL-seq) and GWAS. BSA-seq is designed to facilitate the mapping of quantitative trait loci (QTL) in a cost-effective and high-efficiency manner. In order to accommodate the diverse species-specific traits and population genetic architectures, researchers have developed a series of tailored BSA methodologies. In this study, using six wild rices (Oryza rufipogon) as donors and the elite cultivated rice Youzhan 8 (YZ8) as the recipient, we constructed a BC4F8 population through hybridization and backcrossing. These six wild rice introgression lines together constitute a nested association mapping (NAM) population. Upon genotyping 1819 lines of the NAM population for the Sd1 gene, we found that among lines harboring the 383 bp deletion, 98.5–99.3% exhibited a low plant height (LP) phenotype, whereas 0.7–1.5% showed a high plant height (HP) phenotype. Based on this phenotypic segregation, we selected a total of 20 HP lines and 20 LP lines from six BC4F8 populations to form the H-bulk and L-bulk, respectively. Using BSA-seq, we identified a total of 33 significantly associated candidate intervals. One candidate interval located on chromosome 1 contains D18, a previously reported gene that regulates plant height. Furthermore, we preliminarily identified two major candidate genomic regions on chromosome 8 (4.60–5.76 Mb and 7.29–7.33 Mb). Integrating RNA-seq data, CAFRI-Rice online functional prediction and RT-qPCR validation, two key candidate genes, LOC_Os08g09900 and LOC_Os08g09000, were selected for subsequent functional characterization. The results of this study indicate that the NAM-BSA technology has great potential to detect QTL associated with complex traits, which can provide a novel technical strategy for the genetic dissection of complex traits in rice.

Black rice contains substantial levels of anthocyanins, a class of bioactive compounds recognized for their health-promoting properties that constitute an important determinant of nutritional and functional quality. In this study, we cloned rice TRANSPARENT TESTA 2 (OsTT2), a regulatory gene for anthocyanin biosynthesis that is located on chromosome 3 with a 331 bp segmental duplication in its promoter region. OsTT2 encodes an R2R3-MYB transcription factor that localizes to the nucleus. Interestingly, OsTT2 significantly influences plant height, panicle length, total grain number per plant, grain length, and grain width. Although no significant differences were detected in the number of panicles per plant or 1000-grain weight, the presence of a functional OsTT2 gene substantially increases overall rice yield. We found that OsTT2 binds to the promoter region of OsMED15a, which activates the OsMED15a-OsNAC024 pathway, thereby modulating grain length and width. Our findings provide new resources and novel approaches for the genetic improvement of rice anthocyanin biosynthesis, quality, and yield.

WRKY transcription factors are important plant regulators that participate in diverse biotic and abiotic stress responses. However, their roles in resistance to Southern rice black-streaked dwarf virus (SRBSDV) remain unknown. Previous work demonstrated that the histone deacetylase gene OsHDA706 (LOC_Os06g37420) enhances SRBSDV resistance by promoting jasmonic acid (JA) biosynthesis. In this study, we first confirmed that the rice line GR216 exhibits strong resistance to SRBSDV through artificial inoculation. Knockout of OsHDA706 in GR216 led to typical SRBSDV symptoms, including dwarfing, dark-green wrinkled leaves, and inverted fibrous roots, confirming its role in antiviral defense. Using the RiceTFtarget database and yeast one-hybrid experiments, we identified OsWRKY30 (LOC_Os08g38990) as a potential upstream regulator of OsHDA706. Co-expression analysis based on the CARFI-Rice database revealed that the expression pattern of OsWRKY30 closely resembles that of several disease-resistance–related WRKY genes under biotic stress and hormone treatments. CRISPR-Cas9 knockout of OsWRKY30 in GR216 resulted in strong symptoms after inoculation with SRBSDV, supporting its involvement in antiviral immunity. RNA sequence (RNA-seq) analysis further showed that OsWRKY30 expression was significantly down-regulated in mutants after SRBSDV infection, and that defense response, stress response, and salicylic acid signaling pathways were significantly enriched in both wild-type and mutant plants. Hormone quantification revealed that JA levels were markedly higher in wild-type than in oswrky30 mutants. Collectively, these results demonstrate that OsWRKY30 positively regulates rice resistance to SRBSDV, likely by modulating JA biosynthesis. This study provides new insights into the molecular mechanisms of rice antiviral defense and offers valuable genetic resources for breeding SRBSDV-resistant cultivars.

Background: The passion fruit (Passiflora edulis Sims) is a diploid plant (2n = 2x = 18) and is a perennial scrambling vine in Southern China. However, the occurrence and spread of stem rot in passion fruit severely impact its yield and quality. Methods: In this study, we re-sequenced a BC1F1 population consisting of 158 individuals using whole-genome resequencing. We constructed a high-density genetic linkage map and identified the quantitative trait locus (QTL), and analyzed candidate genes associated with stem rot resistance in passion fruit. Results: Based on the passion fruit reference genome (MER), a high-density genetic linkage map was constructed with 1,180,406 single nucleotide polymorphisms (SNPs). The map contains nine linkage groups, covering a total genetic distance of 1559.03 cM, with an average genetic distance of 311.81 cM. The average genetic distance between 4206 bins was 0.404 cM, and the average gap length was 10.565 cM. The collinearity correlation coefficient between the genetic map and the passion fruit genome was 0.9994. Fusarium solani was used to infect the BC1F1 population, and the resistance to stem rot showed a continuous distribution. A QTL, qPSR5, was mapped to the 113,377,860 bp–114,811,870 bp genomic region on chromosome 5. We performed RNA sequencing (RNA-seq) and real-time quantitative polymerase chain reaction (RT-qPCR) to analyze the expression levels of predicted genes in the candidate region and identified ZX.05G0020740 and ZX.05G0020810 as ideal candidate genes for stem rot resistance in passion fruit. Conclusions: The findings in this study not only lay the foundation for cloning the qPSR5 responsible for stem rot resistance but also provide genetic resources for the genetic improvement of passion fruit.

Stem rot disease poses a significant challenge in passion fruit production, necessitating the identification of resistant genes for the development of stem rot resistant varieties. In this study, we conducted artificial inoculation of Fusarium solani on leaves of two passion fruit varieties, `Huangjinguo' and `Ziguo 7'. Leaf samples were collected at 0 h, 24 h, and 48 h post-inoculation for RNA-sequenc ing (RNA-seq) analysis, and 3 370, 4 464, and 3 974 differentially expressed genes (DEGs) were identified at these stages. Gene Ontology (GO) analysis revealed associations with functions such as response to reactive oxygen species (ROS), response to hydrogen peroxide, and protein complex oligomerisation. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis highlighted the enrichment of DEGs in the phenylpropanoid biosynthesis pathway, including genes such as ZX.06G0025070, ZX.01G0064640, ZX.04G0011040, ZX.05G0011380, all implicated in lignin biosynthesis. Weighted gene co-expression network analysis (WGCNA) identified three modules significantly associated with passion fruit stem rot resistance. Network analysis highlighted ZX.08G0013660 as the gene with the highest connectivity in these modules, featuring a leucine-rich repeat domain. Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) analysis further validated ZX.08G0013660 and other genes as potential candidates for passion fruit stem rot resistance. Overall, genes related to ROS, phenylpropanoid biosynthesis and leucine-rich repeat domain protein likely play critical roles in passion fruit stem rot resistance. This study provides new insights for breeding passion fruit varieties resistant to stem rot disease.

Seed size is a critical factor affecting seed yield and has been one of the primary objectives of plant breeders since the domestication of crop plants. In Arabidopsis (Arabidopsis thaliana (L.) Heynh.), TRANSPARENT TESTA GLABRA1 (AtTTG1, At5G24520) has been confirmed to be associated with seed size. However, whether Oryza sativa TRANSPARENT TESTA GLABRA 1 (OsTTG1, LOC_Os02g45810) affects seed size has not been reported. In this study, we obtained A. thaliana transgenic lines expressing OsTTG1 via the floral dip method. We found that OsTTG1 effectively restored the defective phenotypes of small seeds and short siliques exhibited by this mutant. Compared with the ttg1 mutant, A. thaliana seeds from the OsTTG1-OE lines showed significantly increased grain length (2-56 %), grain width (3-55 %), 100-grain weight (19-58 %), silique length (15-33 %), and the number of seeds per silique (11-73 %) compared with the ttg1 mutant. In contrast, there were no significant differences between the OsTTG1-OE strain and the wild type for any of the traits, except for slightly smaller grain length and width. These results suggest that OsTTG1 plays an important role in the regulation of seed and silique development. To further investigate the mechanism by which OsTTG1 influences seed size and silique length, we performed RNA-seq analysis on samples from the early, middle, and late pod-setting stages of the three genotypes. In |log2 (Fold Change) | ≥ 1 and the adjusted P-value < 0.05, we identified multiple DEGs (CYP72C1, CYP78A5, CYP78A9, ABI5, STK, TTG2, MEA, MET1, RR21, AP2) that may be related to seed size and silique length. OsTTG1 may directly or indirectly affect the expression of the above genes, which in turn affects seed size. Altogether, our results demonstrate that OsTTG1 can positively regulate seed size and silique length.

Wild rice, as the ancestor of cultivated rice, has accumulated a wide range of beneficial traits through prolonged natural selection and evolution. Oryza officinalis, belonging to the CC genome, differs significantly from the AA genome. In this study, we utilized second- and third-generation sequencing, along with Hi-C technology, to assemble the genome of MT10 (O. officinalis). The assembled genome is 552.58 Mb, with contigs and scaffold N50 values of 40.04 and 44.48 Mb, respectively, and 96.73% of the sequences anchored to 12 chromosomes. A total of 33,813 genes were annotated, and repetitive sequences account for 54.24% of the MT10 genome. The number of unique genes in MT10 exceeds that in the O. officinalis genome from Thailand, and their divergence time is estimated at 1.6 million years ago. The MT10 genome exhibits fewer expanded gene families compared to contracted ones, with the expanded families predominantly associated with disease and pest resistance. Comparative genomic analysis of MT10 and Nipponbare reveals sequence variations in biotic and abiotic resistance-related genes. In particular, the presence of R genes and cystatin gene families in MT10 may contribute to its unique insect resistance. Transcriptome analyses indicate that flavonoid biosynthesis and MAPK-related genes are expressed in response to brown planthopper infestation. This study represents the first chromosome-level genome assembly of MT10, providing a reference sequence for the efficient cloning of beneficial genes from O. officinalis, which holds significant potential for the genetic improvement of cultivated rice.

A total of 4006 tropical and subtropical rice germplasms were screened for brown planthopper resistance, and the resistance mechanisms of 63 highly resistant accessions were characterized. This led to the designation of three novel resistance QTLs: Bph47, Bph48, and Bph49. The brown planthopper (BPH) is a significant piercing-sucking pest of rice plants that causes widespread destruction globally. Discovering new germplasms and genes for BPH resistance is essential for enhancing genetic diversity in rice breeding. In this study, 4006 rice accessions from tropical and subtropical regions were screened for BPH resistance at the seedling stage, and 63 accessions with high-resistant were identified. Of these, 59 accessions exhibited high resistance to BPH at the adult stage. The 63 accessions displayed widespread variation in key agronomic traits, though most were generally unsatisfactory. Assessments of antixenosis, antibiosis, and tolerance indicated diverse resistance mechanisms in the 63 accessions, with the majority (39/63) demonstrating both antixenosis and antibiosis. Microscopic observations and physiological assessments revealed significant differences in vascular bundle structure, fiber content, and activity of defense-related enzymes between the 63 high-resistance and 27 susceptible ones. Furthermore, correlation analysis highlighted a substantial positive relationship between BPH resistance and parameters such as rice trypsin inhibitor (RTI) levels and width of the sclerenchyma layer (WSL). Genetic analysis of F2:3 segregating populations from four resistant accessions crossed with the susceptible rice variety 9311 identified three novel major-effect quantitative-trait loci (QTLs) located on chromosome 1L (690 kb and 1.84 Mb) and 5S (295 kb). This study significantly enriched the BPH-resistant germplasm sources and genes, highlighting the varied resistance mechanisms of rice against BPH.

Nitrogen (N) is an essential nutrient for rice ( Oryza sativa L.) growth and development. However, the lower nitrogen use efficiency (NUE) results in an N fertilizer surplus, which causes many environmental problems. In this study, genome‐wide association studies were used to detect nitrate reductase (NR)‐related loci in 419 rice landraces. Using the general linear model (GLM), mixed linear model (MLM), linear model (LM), and linear mixed model (LMM), we found six, nine, seven, and six significant single‐nucleotide polymorphisms (SNPs) associated ( p < 1 × 10 −5 ) for three traits. Moreover, 98 significant SNPs were associated (logarithm of odds ≥ 3) with three traits through 3 V multi‐locus random‐SNP‐effect mixed linear model. Interestingly, we found that Chr1_15896481 was significantly associated in the GLM, MLM, LM, and LMM models. Meanwhile, this significant locus overlapped with a candidate region in bulked segregant RNA sequencing. Through integrated analysis, we identified a most likely candidate genomic region 15,627,420–16,084,761 bp on chromosome 1. By performing functional annotation, RNA sequencing, and real‐time quantitative polymerase chain reaction (RT‐qPCR) analysis for the genes within this interval, we identified five candidate genes that may affect NR activity. Os01g0378400 exhibits a gene expression pattern highly similar to that of OsNR1.2 . It belongs to the NAC transcription factor family, which is involved in plant N metabolism. Os01g0377700 is homologous to an ammonium transporter gene ( Cre06g293051 ). Os01g0383700 encodes a WD40 domain protein, Os01g0379400 encodes an F‐box protein, and Os01g0382800 encodes a DYW‐type PPR domain protein. These findings will provide valuable genetic resources for NUE genetic improvement in rice breeding.

Temperature is a critical abiotic factor affecting rice (Oryza sativa L.) yields, and cold stress at the seedling stage can inhibit plant growth or even be fatal. Antioxidants such as anthocyanins accumulate in a variety of plants during cold stress, but the underlying mechanisms are not well understood. Here, we report that rice TRANSPARENT TESTA GLABRA 1 (OsTTG1), a major regulator of anthocyanin biosynthesis in rice, responds to short- and long-term cold stress at both the transcriptional and protein levels. Metabolomic and transcriptomic data indicate that OsTTG1 activates the expression of anthocyanidin synthase (OsANS) genes under cold stress. Our data also suggest that OsTTG1 forms a MYB-bHLH-WD (MBW) complex with Basic helix-loop-helix 148 (OsbHLH148) and Myb-related S3 (OsMYBS3), and this complex activates the expression of Dehydration-responsive element-binding protein 1 (OsDREB1) and OsANS genes. Together, our findings reveal the mechanisms by which OsTTG1 coordinates both anthocyanin biosynthesis and the expression of cold-responsive genes in colored rice, providing genetic resources for future cold resistance breeding in rice.

Fragrance is a valuable trait in rice varieties, with its aroma significantly influencing consumer preference. In this study, we conducted comprehensive metabolome and transcriptome analyses to elucidate the genetic and biochemical basis of fragrance in the Shangsixiangnuo (SSXN) variety, a fragrant indica rice cultivated in Guangxi, China. Through sensory evaluation and genetic analysis, we confirmed SSXN as strongly fragrant, with an 806 bp deletion in the BADH2 gene associated with fragrance production. In the metabolome analysis, a total of 238, 233, 105 and 60 metabolic compounds exhibited significant changes at the seedling (S), reproductive (R), filling (F), and maturation (M) stages, respectively. We identified four compounds that exhibited significant changes in SSXN across all four development stages. Our analyses revealed a significant upregulation of 2-acetyl-1-pyrroline (2AP), the well-studied aromatic compound, in SSXN compared to the non-fragrant variety. Additionally, correlation analysis identified several metabolites strongly associated with 2AP, including ethanone, 1-(1H-pyrrol-2-yl)-, 1H-pyrrole, and pyrrole. Furthermore, Weighted Gene Co-expression Network Analysis (WGCNA) analysis highlighted the magenta and yellow modules as particularly enriched in aroma-related metabolites, providing insights into the complex aromatic compounds underlying the fragrance of rice. In the transcriptome analysis, a total of 5582, 5506, 4965, and 4599 differential expressed genes (DEGs) were identified across the four developmental stages, with a notable enrichment of the common pathway amino sugar and nucleotide sugar metabolism in all stages. In our correlation analysis between metabolome and transcriptome data, the top three connected metabolites, phenol-, 3-amino-, and 2AP, along with ethanone, 1-(1H-pyrrol-2-yl)-, exhibited strong associations with transcripts, highlighting their potential roles in fragrance biosynthesis. Additionally, the downregulated expression of the P4H4 gene, encoding a procollagen-proline dioxygenase that specifically targets proline, in SSXN suggests its involvement in proline metabolism and potentially in aroma formation pathways. Overall, our study provides comprehensive insights into the genetic and biochemical mechanisms underlying fragrance production in rice, laying the foundation for further research aimed at enhancing fragrance quality in rice breeding programs.

The cultivated passion fruit (Passiflora edulis) is a diploid plant (2n=2x=18) and is an important fruit tree in southern China. However, the occurrence and spread of stem rot in passion fruit severely impact its yield and quality. This study aims to construct a high-density genetic linkage map and identify the quantitative trait locus (QTL) and candidate genes associated with stem rot resistance in passion fruit. In this study, we used an HG and ZG7 hybrid to develop a BC1F1 population consisting of 158 individuals. Take a previously published passion fruit genome as reference, a high-density genetic linkage map was constructed with 1,180,406 single nucleotide polymorphisms (SNPs). The map contains 9 linkage groups, covering a total genetic distance of 1559.03 cM, with an average genetic distance of 311.81 cM. The average genetic distance between 4206 bins was 0.404 cM, and the average gap length was 10.565 cM. The collinearity correlation coefficient between the genetic map and the passion fruit genome was 0.9994. Fusarium solani was used to infect the BC1F1 population, and the resistance to stem rot showed a continuous distribution. A QTL, qPSR5, was identified in the 145.878-152.951 cM region on the 5th linkage group. We performed RNA-seq and RT-qPCR to analyze the expression levels of predicted genes in the candidate region and identified ZX.05G0020740 and ZX.05G0020810 as ideal candidate genes for stem rot resistance in passion fruit. The findings in this study not only lay the foundation for cloning the qPSR5 responsible for stem rot resistance but also provide genetic resources for the genetic improvement of passion fruit.

Nitrogen is essential for crop production. It is a critical macronutrient for plant growth and development. However, excessive application of nitrogen fertilizer is not only a waste of resources but also pollutes the environment. An effective approach to solving this problem is to breed rice varieties with high nitrogen use efficiency (NUE). In this study, we performed a genome-wide association study (GWAS) on 419 rice landraces using 208,993 single nucleotide polymorphisms (SNPs). With the mixed linear model (MLM) in the Tassel software, we identified 834 SNPs associated with root surface area (RSA), root length (RL), root branch number (RBN), root number (RN), plant dry weight (PDW), plant height (PH), root volume (RL), plant fresh weight (PFW), root fractal dimension (RFD), number of root nodes (NRN), and average root diameter (ARD), with a significant level of p < 2.39×10–7. In addition, we found 49 SNPs that were correlated with RL, RBN, RN, PDW, PH, PFW, RFD, and NRN using genome-wide efficient mixed-model association (GEMMA), with a significant level of p < 1×10–6. Additionally, the final results for eight traits associated with 193 significant SNPs by using multi-locus random-SNP-effect mixed linear model (mrMLM) model and 272 significant SNPs associated with 11 traits by using IIIVmrMLM. Within the linkage intervals of significantly associated SNP, we identified eight known related genes to NUE in rice, namely, OsAMT2;3, OsGS1, OsNR2, OsNPF7.4, OsPTR9, OsNRT1.1B, OsNRT2.3, and OsNRT2.2. According to the linkage disequilibrium (LD) decay value of this population, there were 75 candidate genes within the 150-kb regions upstream and downstream of the most significantly associated SNP (Chr5_29804690, Chr5_29956584, and Chr10_17540654). These candidate genes included 22 transposon genes, 25 expressed genes, and 28 putative functional genes. The expression levels of these candidate genes were measured by real-time quantitative PCR (RT-qPCR), and the expression levels of LOC_Os05g51700 and LOC_Os05g51710 in C347 were significantly lower than that in C117; the expression levels of LOC_Os05g51740, LOC_Os05g51780, LOC_Os05g51960, LOC_Os05g51970, and LOC_Os10g33210 were significantly higher in C347 than C117. Among them, LOC_Os10g33210 encodes a peptide transporter, and LOC_Os05g51690 encodes a CCT domain protein and responds to NUE in rice. This study identified new loci related to NUE in rice, providing new genetic resources for the molecular breeding of rice landraces with high NUE.

Grain qualities including milling quality, appearance quality, eating and cooking quality, and nutritional quality are important indicators in rice breeding. Significant achievements in genetic improvement of rice quality have been made. In this study, we analyzed the variation patterns of 16 traits in 1570 rice varieties and found significant improvements in appearance quality and eating and cooking quality, particularly in hybrid rice. Through genome-wide association study and allelic functional nucleotide polymorphisms analysis of quality trait genes, we found that ALK, FGR1, FLO7, GL7/GW7, GLW7, GS2, GS3, ONAC129, OsGRF8, POW1, WCR1, and Wx were associated with the genetic improvement of rice quality traits in Southern China. Allelic functional nucleotide polymorphisms analysis of 13 important rice quality genes, including fragrance gene fgr, were performed using the polymerase chain reaction amplification refractory mutation system technology. The results showed that Gui516, Gui569, Gui721, Ryousi, Rsimiao, Rbasi, and Yuehui9802 possessed multiple superior alleles. This study elucidates the phenotypic changes and molecular basis of key quality traits of varieties in Southern China. The findings will provide guidance for genetic improvement of rice quality and the development of new varieties.

Plant height (PH) is a complex trait regulated by the environment and multiple genes. PH directly affects cropyield, harvest index, and lodging resistance. From plant dwarf mutants, many genes related to PH have been identified anddescribed. Nonetheless, the molecular mechanism of height regulation in high-culm rice mutants has not been wellstudied. By using transcriptome and weighted gene co-expression network analysis (WGCNA), we identified thedifferentially expressed genes (DEGs) between high-culm rice mutants (MUT) and wild-type (WT) and explored thekey pathways and potential candidate genes involved in PH regulation. Transcriptome analysis identified a total of2,184 DEGs, of which 1,317 were identified at the jointing stage and 1,512 were identified at the heading stage. KyotoEncyclopedia of Genes and Genomes enrichment showed that the enrichment pathways were mainly involved inplant hormone signal transduction, ABC transportation, and steroid hormone biosynthesis. Among these metabolicpathways,LOC_Os05g43910andLOC_Os01g35030were auxin (IAA)-related genes, up-regulated in MUT andLOC_Os02g08500(LEPTO1),LOC_Os11g04720, andLOC_Os12g04500were cytokinin (CK)-related genes, down-regulated in MUT. The WGCNA identified four modules (light cyan, dark grey, grey, and pale turquoise) closelyrelated to PH, and seven key genes were screened from these modules, of which two were up-regulated cell wall-related genes (LOC_Os01g26174(OsWAK5),LOC_Os06g05050) in MUT, and one gibberellic acid (GA) gene(LOC_Os06g37364, OsKO2) was also up-regulated. These genes might be closely related to PH regulation. Thesefindings help us better understand the transcriptional regulation of rice plant growth and development and provide atheoretical basis for mapping and cloning the PH regulatory genes.

The analysis of the genetic diversity of aromatic rice varieties and clarification of the genetic relationship of aromatic rice varieties can provide references for breeding high-quality aromatic rice varieties. 24 conventional aromatic rice varieties approved in Guangxi was used in the study. The genetic diversity of the varieties was analyzed by SSR fluorescence labeled capillary electrophoresis in this study. The results showed that a total of 170 alleles were detected by 48 SSR primers. The number of alleles（Na） varied from 1 to 9, with an average of 3.54. The range of effective allele number（Ne） ranged from 1 to 4.5534, with an average of 2.0736. The highest effective allele number was RM21, followed by RM481, RM493 and RM258. Four pairs of primers had high detection efficiency. Shannon’s index（I） ranged from 0 to 1.7942 with an average of 0.7726. The variation range of polymorphic information content（PIC） ranged from 0 to 0.7541 with an average value of 0.3732, indicating that the 24 varieties had certain genetic variation. The genetic similarity coefficient of the 24 varieties ranged from 0.3299 to 0.9600, among which the genetic similarity coefficient of ‘Sanxiang 628’ and ‘Nongxiang 32’ was the lowest, indicating that the genetic basis difference of the two varieties was the greatest and the genetic relationship was the furthest. The genetic similarity coefficient of ‘Wanxiang 696’ and ‘Guangliangxiang 2’ was the greatest, indicating that the genetic basis difference of the two varieties was small and the genetic relationship was close. Cluster analysis showed that the 24 cultivars could be divided into three large groups and four subgroups at the similarity coefficient of 0.504. There were two varieties in theⅠcategory, 19 varieties in theⅡcategory and 3 varieties in theⅢcategory. CategoryⅡcould be divided into 4 subclasses at the similarity coefficient of 0.624, including 1 variety in Subclassⅰ, 14 varieties in subclass ⅱ, 3 varieties in subclass ⅲ, and 1 variety in subclass ⅳ. The results showed that there was a certain genetic diversity in the 24 varieties, but it was not rich enough.The DNA fingerprints of the 24 varieties were constructed in the form of digital coding. The results could provide references for breeding and identification of conventional aromatic rice varieties in Guangxi.

The overuse of nitrogen (N) fertilizer in fields has increased production costs and raised environmental concerns. Increasing the N use efficiency (NUE) of rice varieties is crucial for sustainable agriculture. Here we report the cloning and characterization of OsNPF3.1, a gene that controls rice NUE. An amino acid mutation in the OsNPF3.1 coding region caused different NUEs in wild and cultivated rice. OsNPF3.1, which is expressed mainly in the aerial parts of rice, also affects rice plant height, heading date, and thousand-grain weight. The OsNPF3.1 protein is located in the plasma membrane. When OsNPF3.1 was subjected to artificial selection, two naturally varying loci were associated with NUE, of which OsNPF3.1Chr6_8741040 differed between indica and japonica rice. OsNPF3.1 can be used as a new target gene for breeding rice varieties with high NUE.

BACKGROUND:Cold damage stress significantly affects rice growth (germination and seedling) and causes serious losses in yield in temperate and high-altitude areas around the globe. OBJECTIVE:This study aimed to explore the cold tolerance (CT) locus of rice and create new cold-tolerant germplasm. We constructed a chromosome segment substitution line (CSSL) with strong CT and fine mapped quantitative trait loci (QTLs) associated with CT by performing the whole-genome resequencing of CSSL with phenotypes under cold treatment. METHODS:A chromosome CSSL, including 271 lines from a cross between the cold-tolerant wild rice Y11 (Oryza rufipogon Griff.) and the cold-sensitive rice variety GH998, was developed to map QTLs conferring CT at the germination stage. The whole-genome resequencing was performed on CSSL for mapping QTLs of associated with CT at the germination stage. RESULTS:A high-density linkage map of the CSSLs was developed using the whole-genome resequencing of 1484 bins. The QTL analysis using 615,466 single-nucleotide polymorphisms (SNPs) led to the identification of 2 QTLs related to germination rate at low-temperature on chromosome 8 (qCTG-8) and chromosome 11 (qCTG-11). The qCTG-8 and qCTG-11 explained 14.55% and 14.31% of the total phenotypic variation, respectively. We narrowed down qCTG-8 and qCTG-11 to 195.5 and 78.83-kb regions, respectively. The expression patterns of important candidate genes in different tissues, and of RNA-sequencing (RNA-seq) in CSSLs, were identified based on gene sequences in qCTG-8 and qCTG-11 cold-induced expression analysis. LOC_Os08g01120 and LOC_Os08g01390 were identified as candidate genes in qCTG-8, and LOC_Os11g32880 was identified as a candidate gene in qCTG-11. CONCLUSIONS:This study demonstrated a general method that could be used to identify useful loci and genes in wild rice and aid in the future cloning of candidate genes of qCTG-8 and qCTG-11. The CSSLs with strong CT were supported for breeding cold-tolerant rice varieties.

Information of the Passiflora genome is still very limited. Understand the evolutionary relationship between different species of Passiflora , and develop a large number of SSR markers to provide a basis for the genetic improvement of Passiflora . Applying restriction site associated DNA sequencing (RAD-Seq) technology, we studied the phylogeny, simple sequence repeat (SSR) and marker transferability of 10 accessions of 6 species of Passiflora . Taking the partial assembly sequence of accessions P4 as the reference genome, we constructed the phylogenetic tree using the detected 46,451 high-quality single nucleotide polymorphisms (SNPs), showing that P6, P7, P8 and P9 were a single one while P5 and P10 were clustered together, and P1, P2, P3 and P4 were closer in genetic relationship. Using P8 as the reference genome, a total of 12,452 high-quality SNPs were used to construct phylogenetic tree. P3, P4, P7, P8, P9 and P10 were all single branch while P1 and P2 were clustered together, and P5 and P6 were clustered into one branch. A principal component analysis (PCA) revealed a similar population structure, which four cultivated passion fruits forming a tight cluster. A total of 2,614 SSRs were identified in the genome of 10 Passiflora accessions. The core motifs were AT, GA, AAG etc., 2-6 bases, 4-16 repeats, and 2,515 pairs of SSR primer were successfully developed. T the SSR transferability in cultivated passion fruits is the best. These results will contribute to the study of genomics and molecular genetics in passion fruit.