Oryza rufipogon Griff., the wild progenitor of cultivated rice, contains essential genetic resources for rice improvement and global food security. Preserving the integrity of its germplasm has therefore become a critical conservation priority. In this study, we applied GIS-based spatial analysis and the MaxEnt model, integrating global occurrence data of O. rufipogon with 20 environmental variables to predict suitable habitats during the Last Interglacial (LIG, 130-115 ka before present [BP]), the Last Glacial Maximum (LGM, 26-19 ka BP), and the present. Model performance was evaluated using the area under the receiver operating characteristic curve, and spatial clustering was conducted based on the contributions of environmental factors. The results identified three current core ecological zones: the tropical monsoon region of Southeast and East Asia; the tropical grassland-monsoon region of South Asia; and the tropical rainforest region spanning northern Australia, the Philippines, and Indonesia. During the LGM, colder and drier climates led to a more fragmented distribution, whereas the LIG showed a clearer expansion into broader tropical and subtropical zones. Priority regions for O. rufipogon germplasm collection were identified across Southeast, East, and South Asia, as well as northern Australia. This study proposes a targeted sampling strategy that incorporates elevation, soil properties, and water availability, providing a solid scientific basis for global O. rufipogon surveys and the conservation of high-quality germplasm resources.

BACKGROUND:Toxic heavy metal elements in soils are major global environmental issues and easily migrate to crop grains to cause severe problems in human health, whereas moderately essential elements such as selenium are beneficial for human health. The accumulation of heavy metals and essential elements in rice grains and their genetic mechanisms are still poorly understood. RESULTS:We conducted genetic dissection of four toxic heavy metal elements (lead, cadmium, mercury, and chromium), one quasi metallic element (arsenic), and one essential element (selenium) in grains of 290 Xian and 308 Geng rice accessions through a genome-wide association study (GWAS) based on three statistical models and assays of element concentrations from three environments. A total of 99 quantitative trait loci (QTLs) were identified. Among these QTLs, 18.2% overlapped between/among two or more elements, indicating that some QTLs related to the accumulation of certain elements may depend on other heavy metal elements or be involved in the collaborative transport of other elements. Moreover, at least 14 QTLs/regions were identified in the same regions, containing 12 cloned genes reported to be associated with element accumulation or tolerance-related traits, while the remaining 85 were new QTLs. A total of 62 promising candidate genes were identified from 50 major QTLs, of which 25 genes were newly discovered in this study. More importantly, population genetic analysis revealed 26 and 15 intraspecies divergent regions affecting element concentrations in the Xian and Geng subspecies, respectively, including 25 QTLs identified in this study and 13 previously reported and cloned genes. CONCLUSIONS:Our findings will facilitate further gene cloning and dissection of the genetic mechanisms of element accumulation in rice grains to improve grain quality.

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.

Tiller number per plant-a cardinal component of ideal plant architecture-affects grain yield potential. Thus, alleles positively affecting tillering must be mined to promote genetic improvement. Here, we report a Tiller Number 1 (TN1) protein harbouring a bromo-adjacent homology domain and RNA recognition motifs, identified through genome-wide association study of tiller numbers. Natural variation in TN1 affects its interaction with TIF1 (TN1 interaction factor 1) to affect DWARF14 expression and negatively regulate tiller number in rice. Further analysis of variations in TN1 among indica genotypes according to geographical distribution revealed that low-tillering varieties with TN1-hap(L) are concentrated in Southeast Asia and East Asia, whereas high-tillering varieties with TN1-hap(H) are concentrated in South Asia. Taken together, these results indicate that TN1 is a tillering regulatory factor whose alleles present apparent preferential utilization across geographical regions. Our findings advance the molecular understanding of tiller development.

Lodging is one of the major abiotic stresses, affecting the total crop yield and quality. The improved lodging resistance and its component traits potentially reduce the yield losses. The section modulus (SM), bending moment at breaking (M), pushing resistance (PR), and coefficient of lodging resistance (cLr) are the key elements to estimate the lodging resistance. Understanding the genetic architecture of lodging resistance–related traits will help to improve the culm strength and overall yield potential. In this study, a natural population of 795 globally diverse genotypes was further divided into two (indica and japonica) subpopulations and was used to evaluate the lodging resistance and culm strength–related traits. Significant diversity was observed among the studied traits. We carried out the genome-wide association evaluation of four lodging resistance traits with 3.3 million deep resolution single-nucleotide polymorphic (SNP) markers. The general linear model (GLM) and compressed mixed linear model (MLM) were used for the whole population and two subpopulation genome-wide association studies (GWAS), and a 1000-time permutation test was performed to remove the false positives. A total of 375 nonredundant QTLs were observed for four culm strength traits on 12 chromosomes of the rice genome. Then, 33 pleiotropic loci governing more than one trait were mined. A total of 4031 annotated genes were detected within the candidate genomic region of 33 pleiotropic loci. The functional annotations and metabolic pathway enrichment analysis showed cellular localization and transmembrane transport as the top gene ontological terms. The in silico and in vitro expression analyses were conducted to validate the three candidate genes in a pleiotropic QTL on chromosome 7. It validated OsFBA2 as a candidate gene to contribute to lodging resistance in rice. The haplotype analysis for the candidate gene revealed a significant functional variation in the promoter region. Validation and introgression of alleles that are beneficial to induce culm strength may be used in rice breeding for lodging resistance.

In situ conserved wild rice (Oryza rufipogon Griff.) is a promising source of alleles for improving rice production worldwide. In this study, we conducted a genomic analysis of an in situ conserved wild rice population (Guiping wild rice) growing at the center of wild rice genetic diversity in South China. Differences in the plant architecture in this population were investigated. An analysis using molecular markers revealed the substantial genetic diversity in this population, which was divided into subgroups according to the plant architecture. After resequencing representative individuals, the Guiping wild rice population was compared with other O. rufipogon and Oryza sativa populations. The results indicated that this in situ conserved wild rice population has a unique genetic structure, with genes that were introgressed from aromatic and O. sativa ssp. indica and japonica populations. The QTLs associated with plant architecture in this population were detected via a pair-wise comparison analysis of the sequencing data for multiple DNA pools. The results suggested that a heading date-related gene (DHD1) might be associated with variations in plant architecture and may have originated in cultivated rice. Our findings provide researchers with useful insights for future genomic analyses of in situ conserved wild rice populations.

[目的]为水稻紫色叶舌标记性状在分子标记辅助育种、品种鉴定、制种除杂和植物新品种权保护等方面的应用提供参考.[方法]以日本晴(叶舌为绿色)与WPB-1(叶舌为紫色)作为亲本,通过系列杂交、自交与回交构建BC1F4代群体,通过表型统计与遗传分析,结合表型混样池的GSR 40 K SNP芯片检测,筛选存在差异的分子标记位点,进而定位目标基因可能存在的区段.[结果]水稻叶舌颜色性状至少受2个基因控制.当2个基因均为显性时叶舌表现为紫色,否则表现为绿色,且2个控制基因为显性互补效应;筛选出与叶舌颜色性状相关的差异位点27个,分别位于第2、3、4和8染色体上.[结论]研究群体中位于第4染色体目标区段上的1个目标基因有可能是Os04g0557500,该基因控制花色苷的积淀;另1个基因可能是未被发现的新基因,需进行后续研究确定.

[目的]筛选镉低积累型水稻品种并开展镉超标稻田表现评价研究,为广西中低度镉污染稻田生产安全稻米提供品种和数据参考.[方法]以114份(V1～V114)水稻低镉品种育种材料为试验对象,从中筛选综合性状优良且籽粒表现为镉低积累的目标材料;对目标材料进行大田试验和盆栽试验验证,测定其在广西不同试验点的农艺性状和精米镉含量.[结果]初步筛选试验的114份参试材料中,除V102的精米镉含量低于最低检测值外,其余113份水稻育种材料的精米镉含量范围在0.01～0.35 mg/kg,平均值为0.10 mg/kg,筛选得到综合性状优良且精米镉含量较低的材料V111(审定后名称为桂育12).桂育12在中低度镉污染区大田验证种植时,精米镉含量(0.01～0.10 mg/kg)未超出国家标准GB 2762—2017《食品安全国家标准食品中污染物限量》规定的限值(0.20 mg/kg).盆栽试验结果表明,在pH为5.0,土壤镉含量3.0 mg/kg条件下,桂育12精米镉含量(0.34 mg/kg)有超标风险;各试验中土壤镉含量对桂育12部分农艺性状指标影响显著(P<0.05),但属于品种种植的正常波动范围,对米质和产量的综合影响有限.[结论]从114份水稻材料中筛选出的镉低积累品种桂育12,经多年多点试验验证,在中低度镉污染稻田产出的稻米镉含量不超标,籽粒镉低积累性状较稳定,综合性状表现受土壤镉含量影响较小,可在广西中低度镉污染稻田推广应用.

The yield of rice is mostly affected by three factors, namely, panicle number, grain number and grain weight. Variation in panicle and grain numbers is mainly caused by tiller and panicle branches generated from axillary meristems (AMs). MOC1 encodes a putative GRAS family nuclear protein that regulates AM formation. Although several alleles of MOC1 have been identified, its variation in germplasm resources remains unclear. In the present study we characterized a novel moc1 allele named gnp6 which has a thymine insertion in the coding sequence of the SAW motif in the GRAS domain. This mutation causes arrested branch formation. The SAW motif is necessary for nuclear localization of GNP6/MOC1 where it functions as a transcription factor or co-regulator. Haplotype analysis showed that the coding region of GNP6/MOC1 was conserved without any non-synonymous mutations in 240 rice accessions. However, variation in the promoter region might affect the expression of it and its downstream genes. Joint haplotype analysis of GNP6/MOC1 and MOC3 showed that haplotype combinations H9, H10 and H11, namely MOC1-Hap1 in combination with MOC3-Hap3, MOC3-Hap4 or MOC3-Hap5 could be bred to promote branch formation. These findings will enrich the genetic resources available for rice breeders.

Although morphology and grain size are important to rice growth and yield, the identity of abundant natural allelic variations that determine agronomically important differences in crops is unknown. Here, we characterized the function of mitogen-activated protein kinase 3 from Oryza officinalis Wall. ex Watt encoded by OrMKK3. Different alternative splicing variants occurred in OrMKK3. Green fluorescent protein (GFP)–OrMKK3 fusion proteins localized to the cell membrane and nuclei of rice protoplasts. Overexpression of OrMKK3 influenced the expression levels of the grain size-related genes SMG1, GW8, GL3, GW2, and DEP3. Phylogenetic analysis showed that OrMKK3 is well conserved in plants while showing large amounts of variation between indica, japonica, and wild rice. In addition, OrMKK3 slightly influenced brassinosteroid (BR) responses and the expression levels of BR-related genes. Our findings thus identify a new gene, OrMKK3, influencing morphology and grain size and that represents a possible link between mitogen-activated protein kinase and BR response pathways in grain growth.

Cultivated rice varieties are all diploid, and polyploidization of rice has long been desired because of its advantages in genome buffering, vigorousness, and environmental robustness. However, a workable route remains elusive. Here, we describe a practical strategy, namely de novo domestication of wild allotetraploid rice. By screening allotetraploid wild rice inventory, we identified one genotype of Oryza alta (CCDD), polyploid rice 1 (PPR1), and established two important resources for its de novo domestication: (1) an efficient tissue culture, transformation, and genome editing system and (2) a high-quality genome assembly discriminated into two subgenomes of 12 chromosomes apiece. With these resources, we show that six agronomically important traits could be rapidly improved by editing O. alta homologs of the genes controlling these traits in diploid rice. Our results demonstrate the possibility that de novo domesticated allotetraploid rice can be developed into a new staple cereal to strengthen world food security.

[目的]收集鉴定广西地方稻种资源,为广西地方稻种资源保护和利用提供科学依据.[方法]2015─2019年,通过"第三次全国农作物种质资源普查与收集行动"项目的实施,对广西61个县(区、市)188个乡(镇)265个村(屯)的地方稻种资源进行系统调查和收集,对收集资源的分布特点和种质类型进行分析,对各表型性状进行鉴定评价.[结果]从广西各地收集地方稻种资源476份.从水平分布来看,广西地方稻种资源在广西四大稻作区均有分布,稻种资源主要集中分布于融水、上思、凤山、资源、隆林和东兰等6个经济相对不发达的边远地区.从垂直分布上分析,稻种资源主要分布在0～400 m的低海拔地区,收集资源232份,占收集总数的48.74％.广西地方稻种资源多样性丰富,包含籼稻、粳稻、早稻、中晚稻、粘稻、糯稻、水稻、陆稻、深水稻及有色稻等类型,且多数的农艺性状具有较丰富的变异类型.收集及鉴定评价出香糯、米粉特用、大穗、大粒等珍稀特异地方稻种资源9份.[结论]广西地方稻种资源多样性丰富,且普遍具有株高较高、穗粒数多、结实率高的特点.收集、鉴定评价出珍稀特异地方稻种资源9份,可用于产业开发及育种.

Background Low temperature is a limiting factor of rice productivity and geographical distribution. Wild rice ( Oryza rufipogon Griff.) is an important germplasm resource for rice improvement. It has superior tolerance to many abiotic stresses, including cold stress, but little is known about the mechanism underlying its resistance to cold. Results This study elucidated the molecular genetic mechanisms of wild rice in tolerating low temperature. Comprehensive transcriptome profiles of two rice genotypes (cold-sensitive ce 253 and cold-tolerant Y12–4) at the germinating stage under cold stress were comparatively analyzed. A total of 42.44–68.71 million readings were obtained, resulting in the alignment of 29,128 and 30,131 genes in genotypes 253 and Y12–4, respectively. Many common and differentially expressed genes (DEGs) were analyzed in the cold-sensitive and cold-tolerant genotypes. Results showed more upregulated DEGs in the cold-tolerant genotype than in the cold-sensitive genotype at four stages under cold stress. Gene ontology enrichment analyses based on cellular process, metabolic process, response stimulus, membrane part, and catalytic activity indicated more upregulated genes than downregulated ones in the cold-tolerant genotype than in the cold-sensitive genotype. Quantitative real-time polymerase chain reaction was performed on seven randomly selected DEGs to confirm the RNA Sequencing (RNA-seq) data. These genes showed similar expression patterns corresponding with the RNA-Seq method. Weighted gene co-expression network analysis (WGCNA) revealed Y12–4 showed more positive genes than 253 under cold stress. We also explored the cold tolerance gene LTG5 (Low Temperature Growth 5) encoding a UDP-glucosyltransferase. The overexpression of the LTG5 gene conferred cold tolerance to indica rice. Conclusion Gene resources related to cold stress from wild rice can be valuable for improving the cold tolerance of crops.

Additional file 6: Table S1. genes were significantly differentially expressed in 253.

美国是水稻出口大国,水稻科研能力与生产水平位居世界前列.本文对美国特别是路易斯安那州的水稻生产和科研情况进行考察,目的是为了给国内水稻科研与生产提供参考及借鉴.路易斯安那州水稻种植面积在美国位居第3,达到17.20万hm2,种植的水稻类型分为长粒稻、中粒稻及特种稻,其中,长粒稻的种植面积最大,占89％;2019年水稻单产为7.15 t/hm2,总产达到119.78万t,总售价3.09亿美元.栽培管理技术先进,广泛使用洁田技术和机械化种植技术.高通量的分子标记辅助选择技术深度应用到水稻育种工作中.

AbstractBackgroundThe grain number per panicle (GNP), which is one of three grain yield components, is an important trait for the genetic improvement of rice. Although theNAL1andGNP1genes regulating the rice GNP and grain yield have been cloned, their allelic diversity, functional differences in rice germplasms, and effects of their combination on GNP and grain yield remain unclear.ResultsBased on DNA sequences of these two genes in 198 cultivated rice (Oryza sativa) and 8–10 wild rice (Oryza rufipogon) germplasms, 16 and 14 haplotypes were identified forNAL1andGNP1, respectively. TheNAL1gene had the strongest effects on GNP inindica(xian) andjaponica(geng) subpopulations. In contrast,GNP1had no significant effects in thegengsubpopulation and was rare in thexianbackground, in which the superiorGNP1allele (GNP1–6) was detected in only 4.0% of the 198 germplasms. Compared with the transgenic lines withGNP1orNAL1, the transgenic lines with both genes had a higher GNP (15.5%–25.4% and 11.6%–15.9% higher, respectively) and grain yield (5.7%–9.0% and 8.3%–12.3% higher, respectively) across 3 years. The two genes combined in the introgression lines in Lemont background resulted in especially favorable effects on the GNP.ConclusionsOur results indicated that theGNP1andNAL1exhibited obvious differentiation and their combinations can significantly increase the grain yield ingengrice cultivars. These observations provide insights into the molecular basis of the GNP and may be useful for rice breeding of high yield potential by pyramidingGNP1andNAL1.

Additional file 7: Table S2. genes were significantly differentially expressed in Y12–4.

Callus browning, a common trait derived from the indica rice cultivar ( Oryza sativa L.), is a challenge to transformation regeneration. Here, we report the map-based cloning of BROWNING OF CALLUS1 ( BOC1 ) using a population derived from crossing Teqing, an elite indica subspecies exhibiting callus browning, and Yuanjiang, a common wild rice accession ( Oryza rufipogon Griff.) that is less susceptible to callus browning. We show that BOC1 encodes a SIMILAR TO RADICAL-INDUCED CELL DEATH ONE (SRO) protein. Callus browning can be reduced by appropriate upregulation of BOC1 , which consequently improves the genetic transformation efficiency. The presence of a Tourist -like miniature inverted-repeat transposable element ( Tourist MITE) specific to wild rice in the promoter of BOC1 increases the expression of BOC1 in callus. BOC1 may decrease cell senescence and death caused by oxidative stress. Our study provides a gene target for improving tissue culturability and genetic transformation.

SummaryRice (Oryza sativa L.) cultivars harbour morphological and physiological traits different from those of wild rice (O. rufipogon Griff.), but the molecular mechanisms underlying domestication remain controversial. Here, we show that awn and long grain traits in the near‐isogenic NIL‐GLA are separately controlled by variations within the GLA (Grain Length and Awn Development) gene, a new allele of GAD1/RAE2, which encodes one member of the EFPL (epidermal patterning factor‐like protein) family. Haplotype analyses and transgenic studies revealed that InDel1 (variation for grain length, VGL) in the promoter region of GLA (GLAVGL) increases grain length by promoting transcription of GLA. Absence of InDel3 (variation for awn formation, VA) in the coding region (CDS) of GLA (GLAva) results in short awn or no awn phenotypes. Analyses of minimum spanning trees and introgression regions demonstrated that An‐1, an important gene for awn formation, was preferentially domesticated and its mutation to an‐1 was followed by GLA and An‐2. Gene flow then occurred between the evolved japonica and indica populations. Quality analysis showed that GLA causes poor grain quality. During genetic improvement, awnlessness was selected in ssp. indica, whereas short–grained and awnless phenotypes with good quality were selected in japonica. Our findings facilitate an understanding of rice domestication and provide a favourable allele for rice breeding.

The occurrence of parallel speciation strongly implies the action of natural selection. However, it is unclear how general a phenomena parallel speciation is since it was only shown in a small number of animal species. In particular, the adaptive process and mechanisms underlying the process of parallel speciation remain elusive. Here, we used an integrative approach incorporating population genomics, common garden, and crossing experiments to investigate parallel speciation of the wild rice species Oryza nivara from O. rufipogon. We demonstrated that O. nivara originated multiple times from different O. rufipogon populations and revealed that different O. nivara populations have evolved similar phenotypes under divergent selection, a reflection of recurrent local adaptation of ancient O. rufipogon populations to dry habitats. Almost completed premating isolation was detected between O. nivara and O. rufipogon in the absence of any postmating barriers between and within these species. These results suggest that flowering time is a "magic" trait that contributes to both local adaptation and reproductive isolation in the origin of wild rice species. Our study thus demonstrates a convincing case of parallel ecological speciation as a consequence of adaptation to new environments.