Rice (Oryza sativa) production underpins food security in many rice-consuming nations. As a critical developmental transition that directly determines yield and grain quality, flowering dates and timing are genetically complex and highly sensitive to environmental fluctuations. This complexity requires new methods to quantify diurnal floral characteristics, which are essential to hybrid breeding in cereals. Here, we present BloomSight, an ultra-high-frequency and deep-learning (DL) powered framework for phenotyping and measuring minute-level flowering dynamics in japonica and indica rice. After monitoring 172 rice accessions selected from the Chinese Rice Mini-Core Collection using cost-effective time-lapse imaging platforms for 16 days, we acquired over 530,000 accession-level images and established the Open Rice Flowering Training (ORFT) dataset, with over 39,000 panicles and 350,000 anthers annotated. Next, a two-stage customised DL model (i.e. YOLACT-Panicle for panicle segmentation and UNet-Anther for anther identification) was trained using the ORFT set, enabling ultra-high-frequency measures of anther extrusion at the minute level. Based on trait analysis, we further fitted curves to dynamically identify diurnal flowering patterns, including key timepoints such as the initial flowering timepoint (TIni.), quickest flowering timepoint (TQck.), and peak flowering time (TPeak), and novel traits such as the duration of rapid flowering phase (PRpd.) and flowering density across key phases. After validating BloomSight-derived traits against manual observations, we classified the japonica and indica accessions into three patterns: Slow, Moderate, and Fast, all of which had distinct flowering windows. These analyses helped us integrate phenotypic variations into a genome-wide association study (GWAS), revealing many significant single nucleotide polymorphisms (SNPs) associated with known (e.g. EMF1, OsMYB8, and PME42) and several repeatedly identified unknown loci (one of these loci has been recently verified by other groups), demonstrating the value of the BloomSight framework. Taken together, we believe that BloomSight provides an ultra-high-frequency framework for diurnal flowering phenotyping, enabling the measurement of biological meaningful floral traits with minute-level resolution that can enable flowering-related developmental studies and hybrid-breeding applications in rice and more broadly benefit the plant and crop research community.

Asian cultivated rice is one of the most important cereal crops globally,feeding approximately 50％ of the world's population.Increasing rice nitrogen use efficiency(NUE)is crucial for achieving high yields with low nitrogen inputs(Xu et al.,2012;Hu et al.,2023).However,modern cultivars are typically bred for high yields through excessive nitrogen fertilizer use,leading to the loss of bene-ficial alleles associated with high NUE during the breeding process(Wang and Peng,2017;Hu et al.,2023).

Dissecting the mechanism of drought resistance (DR) and designing drought-resistant rice varieties are promising strategies to address the challenge of climate change. Here, we selected a typical droughtavoidant (DA) variety, IRAT109, and a drought-tolerant (DT) variety, Hanhui15, as parents to develop a stable recombinant inbred line (RIL) population (F8, 1262 lines). The de novo assembled genomes of both parents were released. By resequencing of the RIL population, a set of 1 189 216 reliable SNPs were obtained and used to construct a dense genetic map. Using above- and belowground phenomic platforms and multi- modal cameras, we captured 139 040 image-based traits (i-traits) of whole-plant phenotypes in response to drought stress throughout the entire rice growth period and identified 32 586 drought-responsive quantitative trait loci (QTLs), including 2097 unique QTLs. QTLs associated with panicle i-traits occurred more than 600 times on the middle of chromosome 8, and QTLs associated with leaf i-traits occurred more than 800 times on the 50 end of chromosome 3, indicating the potential effects of these QTLs on plant phenotypes. We selected three candidate genes (OsMADS50, OsGhd8, OsSAUR11) related to leaf, panicle, and root traits, respectively, and verified their functions in DR. OsMADS50 was found to negatively regulate DR by modulating leaf dehydration, grain size, and downward root growth. A total of 18 and 21 composite QTLs significantly related to grain weight and plant biomass were also screened from 597 lines in the RIL population under drought conditions in field experiments, and the composite QTL regions showed substantial overlap (76.9%) with known DR gene regions. Based on three candidate DR genes, we proposed a haplotype design suitable for different environments and breeding objectives. This study provides a valuable reference for multimodal and time-series phenomic analyses, deciphers the genetic mechanisms of DA and DT rice varieties, and offers a molecular navigation map for breeding of DR varieties.

Mesocotyl elongation of rice seedlings is a key trait for deep sowing tolerance and well seedling establishment in dry direct sowing rice (DDSR) production. Subsets of the Rice Diversity Panel 1 (RDP1, 294 accessions) and Hanyou 73 (HY73) recombinant inbred line (RIL) population (312 lines) were screened for mesocotyl length (ML) via dark germination. Six RDP1 accessions (Phudugey, Kasalath, CA902B21, Surjamkuhi, Djimoron, and Goria) had an ML longer than 10 cm, with the other 19 accessions being over 4 cm. A GWAS in RDP1 detected 118 associated SNPs on all 12 chromosomes using a threshold of FDR-adjusted p < 0.05, including 11 SNPs on chromosomes 1, 4, 5, 7, 10, and 12 declared by -log10(P) > 5.868 as the Bonferroni-corrected threshold. Using phenotypic data of three successive trials and a high-density bin map from resequencing genotypic data, four to six QTLs were detected on chromosomes 1, 2, 5, 6, and 10, including three loci repeatedly mapped for ML from two or three replicated trials. Candidate genes were predicted from the chromosomal regions covered by the associated LD blocks and the confidence intervals (CIs) of QTLs and partially validated by the dynamic RNA-seq data in the mesocotyl along different periods of light exposure. Potential strategies of donor parent selection for seedling establishment in DDSR breeding were discussed.

Phosphate (Pi) is indispensable for the growth and development of plant, and low-Pi stress is a major limitation for crop growth and yield worldwide. The tolerance to low-Pi stress varied among rice germplasm resources. However, the mechanisms underlying the tolerance of rice to low-Pi stress, as a complex quantitative trait, are not clear. We performed a genome-wide association study (GWAS) through a diverse worldwide collection of 191 rice accessions in the field under normal-Pi and low-Pi supply in two years. Twenty and three significant association loci were identified for biomass and grain yield per plant under low-Pi supply respectively. The expression level of OsAAD as a candidate gene from a associated locus was significantly up-regulated after low-Pi stress treatment for five days and tended to return to normal levels after Pi re-supply in shoots. Suppression of OsAAD expression could improve the physiological phosphorus use efficiency (PPUE) and grain yields through affecting the expression of several genes associated with GA biosynthesis and metabolism. OsAAD would be a promising gene for increasing PPUE and grain yield in rice under normal- and low-Pi supply via genome editing.

Plant height is an important morphological trait that affects crop yield. Several genes related to plant height and yield have been reported in rice (Oryza sativa L.), however, the molecular mechanism underlying the regulation of these traits is still not completely understood. VP64 is widely used as a transcriptional activator to investigate the biological function of genes encoding transcription factors. Here, we identified a novel bZIP transcription factor OsbZIP62 that is involved in modulating agronomic traits in rice. Overexpression of OsbZIP62-VP64 (OsbZIP62V) significantly increases the plant height and yield per plant in rice. RNA-seq analysis showed that some plant height and panicle development related genes (i.e., OsEATB, OsDSS1 and OsGA3ox2) were up-regulated in OsbZIP62V overexpressing rice plants. Besides, OsbZIP62 could also bind to the promoters of several putative target genes. These results suggested that OsbZIP62 plays a role as transcriptional regulator in regulating the expression of genes associated with agronomic traits, and OsbZIP62 fused with VP64 would be useful in crop genetic modification with improved plant architecture and yield.

根系是植物吸收水分和养分的主要器官,培育发达的深根系统是水稻抗旱育种的重要目标。该文系统介绍了水稻根系生长角度、根系向重力性、根系穿透力、深层土壤根系分布特征等深根性相关性状的遗传研究进展,指出今后需针对目标环境开展水稻深根性QTL发掘与利用、加快主效深根性QTL的验证及其在水稻抗旱分子育种的应用。

The increasing concentration of greenhousegases(GHGs)in Earth's atmosphere leads to global warming,which further causes a series of climate changes and does great harm to both human society and natural ecosystems.Agricultural GHG emissions,mainly in the form of methane(CH4)and nitrous oxide(N2O),are a significant source of GHGs,accounting for～14％ to-tal global GHGs(Zhang et al.,2022).

Since gravitropism is one of the primary determinants of root development, facilitating root penetration into soil and subsequent absorption of water and nutrients, we studied this response in rice. The gravitropism of 226 Chinese rice micro-core accessions and drought-resistant core accessions were assessed through the modified gravity-bending experiment and genome-wide association analysis (GWAS) was used to map the associated QTLs. The average value of gravitropic response speed of seminal roots was 41.05°/h, ranging from 16.77°/h to 62.83°/h. The gravity response speed of Indica (42.49°/h) was significantly (P < 0.002) higher than Japonica (39.71°/h) subspecies. The gravitational response speed of seminal roots was significantly positively correlated with the number of deep roots (r = 0.16), the growth speed of seminal roots (r = 0.21) and the drought resistance coefficient (r = 0.14). In total, 3 QTLs (quantitative traits) associated with gravitropic response speed were identified on chromosome 4, 11 and 12. There are some known QTLs relating to roots traits and drought resistance located nearby the QTLs identified here, which confirms the close relationship between radicle gravitropism and the drought resistance. From within these intervals, 5 candidate genes were screened and verified by qPCR in a few rice varieties with extreme phenotypic values, demonstrating that gene LOC_Os12g29350 may regulate gravitropism negatively. This may be a promising candidate to be confirmed in further studies.

首先,利用30份水稻品种资源,观测淹水萌发过程中胚芽鞘长度的动态变化,确定水稻淹水发芽相关性状的鉴定方法;然后,对一套250个品种的水稻自然变异群体,分别在淹水和正常条件下开展发芽试验,观测其发芽率和幼苗胚芽鞘长度.结果表明:大部分参试品种不具备淹水发芽成苗能力,胚芽鞘长度差值的变异系数达到28.5％,提示参试群体的淹水发芽能力存在较为丰富的遗传变异;粳稻品种的淹水发芽能力优于籼稻品种.模拟直播淹水试验表明,淹水发芽胚芽鞘长度与成苗率密切相关;筛选出'隆化毛葫'丽江新团黑谷'高阳淀稻'黄皮糯'4个高成苗率的优异种质,可用作耐水直播水稻育种的亲本材料.

The resource and environmental challenges faced by rice production call for resource-saving and environment-friendly rice varieties. Water-saving and drought-resistance rice (WDR) is a new type of cultivated rice combining both high yield potential and acceptable grain quality as a current lowland paddy rice, as well as water-saving and drought resistance as a traditional upland rice. The lowland and upland rice are two ecotypes adapted to contrasting soil water status, originating mainly because of their differentiated drought resistance. Upland rice, domesticated in a water–limited environment and experiencing a bidirectional selection process, has better drought resistance and especially better drought avoidance. Though the potential tradeoff between drought resistance and productivity is very common in rice, the bidirectional selection could overcome this tradeoff and accumulate recombination genotypes. It is very important to choose elite parents on the basis of studies on the great genetic diversity of rice yield and drought resistance among the rice germplasm resources and adapt the bidirectional selection strategies to especially integrate drought avoidance, drought tolerance, high water use efficiency, and productivity in WDR breeding. The breeding history and genomic studies indicated that lowland paddy rice and upland rice hybridization breeding with suitable selection in different environments is an effective approach to improving complex traits such as yield potential and drought resistance. Meanwhile, molecular technology shows higher efficiency on value-added breeding such as transferring and pyramiding pest- and disease-resistant genes, which helps WDR obtain other green characters. Twenty-two WDR varieties were registered and distributed to farmers in recent years and could be planted in both irrigated and rainfed ecosystems, thus showing promising application prospects. The major crop management technology of WDR in lowland paddy fields with water-saving cultivation and in rainfed fields by dry seeding with aerobic cultivation were also discussed in this article.

[目的]本文基于幼苗图像分析建立鉴定水稻耐深播相关特性的方法,鉴定旱直播条件下水稻耐深播的农艺性状.[方法]以不同中胚轴伸长能力的18份水稻品种和稗草、 马唐的种子,设置3cm、5cm、7cm、9cm和11cm深度的砂培试验,观察出苗情况并在播种后第15天摄取幼苗照片,采用图像分析技术提取幼苗生长相关的表型指标.[结果]在人工标记幼苗胚芽鞘节等部位前提下,通过图像分析可一次性测定中胚轴长度和累积绿叶投射面积;当播种深度为3cm时,短中胚轴水稻品种能在播后第6天前后出苗,长中胚轴品种能在播后第5天出苗;播种深度为5-7cm时,短中胚轴品种不能正常出苗,长中胚轴品种能在播后第7-10天出苗;在同等播种深度下长中胚轴品种第15天幼苗叶面积高于短中胚轴品种,在7cm以上播种深度下差异极为明显;稗草和马唐都具有幼苗中胚轴伸长能力,种子能从5cm或3cm深度下正常出苗.[结论]基于幼苗图像分析技术,本试验建立了水稻旱直播耐深播相关指标的表型检测方法,识别幼苗中胚轴和叶片等部位,提取中胚轴长度和累积绿叶投射面积指标.水稻差异性代表品种和常见禾本科杂草的观察结果表明中胚轴伸长能力是深播后快速、 整齐出苗并较早形成自养能力的关键.

Increasing agricultural productivity is one of the most important goals of plant science research and imperative to meet the needs of a rapidly growing population. Rice (Oryza sativa L.) is one of the most important staple crops worldwide. Grain size is both a major determinant of grain yield in rice and a target trait for domestication and artificial breeding. Here, a genome-wide association study of grain length and grain width was performed using 996,722 SNP markers in 270 rice accessions. Five and four quantitative trait loci were identified for grain length and grain width, respectively. In particular, the novel grain size gene OsSNB was identified from qGW7, and further results showed that OsSNB negatively regulated grain size. Most notably, knockout mutant plants by CRISPR/Cas9 technology showed increased grain length, width, and weight, while overexpression of OsSNB yielded the opposite. Sequencing of this gene from the promoter to the 3'-untranslated region in 168 rice accessions from a wide geographic range identified eight haplotypes. Furthermore, Hap 3 has the highest grain width discovered in japonica subspecies. Compared to other haplotypes, Hap 3 has a 225 bp insertion in the promoter. Based on the difference between Hap 3 and other haplotypes, OsSNB_Indel2 was designed as a functional marker for the improvement of rice grain width. This could be directly used to assist selection toward an improvement of grain width. These findings suggest OsSNB as useful for further improvements in yield characteristics in most cultivars.

Mesocotyl elongation is an important trait influencing seedling emergence and establishment in rice direct-seeding cultivation and is immediately inhibited after light exposure. Detailed researches on the molecular basis and biological processes underlying light repression of mesocotyl growth could probably provide useful information for key factors controlling this trait. Here we monitored the transcriptome and endogenous phytohormone changes specifically in the elongating mesocotyl in response to light exposure with a time-course. It was revealed that 974 transcripts were significantly differentially expressed (FDR < 0.05, |log2 (L/D) | ≥2) after light exposure. Most of the differential expression genes associated with the responses to hormone. Metabolic pathway analysis using the KEGG system suggested plant hormone signal transduction, α-linolenic acid metabolism and diterpenoid biosynthesis were critical processes of mesocotyl growth inhibited by light. Consistent with DEGs, the endogenous IAA, tZ and GA3 content was significantly reduced while JA level was dramatically increased, which indicated that light inhibited rice mesocotyl growth through decreasing IAA, tZ and GA3 content and/or increasing JA level. The present results enriched our knowledge about the genes and phytohormones regulating mesocotyl elongation in rice, which may help improve future studies on associated genes and develop new varieties tolerance to deep sowing.

Drought is the most serious abiotic stress limiting rice production, and deep root is the key contributor to drought avoidance. However, the genetic mechanism regulating the development of deep roots is largely unknown. In this study, the transcriptomes of 74 root samples from 37 rice varieties, representing the extreme genotypes of shallow or deep rooting, were surveyed by RNA-seq. The 13,242 differentially expressed genes (DEGs) between deep rooting and shallow rooting varieties (H vs. L) were enriched in the pathway of genetic information processing and metabolism, while the 1,052 DEGs between the deep roots and shallow roots from each of the plants (D vs. S) were significantly enriched in metabolic pathways especially energy metabolism. Ten quantitative trait transcripts (QTTs) were identified and some were involved in energy metabolism. Forty-nine candidate DEGs were confirmed by qRT-PCR and microarray. Through weighted gene co-expression network analysis (WGCNA), we found 18 hub genes. Surprisingly, all these hub genes expressed higher in deep roots than in shallow roots, furthermore half of them functioned in energy metabolism. We also estimated that the ATP production in the deep roots was faster than shallow roots. Our results provided a lot of reliable candidate genes to improve deep rooting, and firstly highlight the importance of energy metabolism to the development of deep roots.

Mesocotyl elongation of rice seedlings is an important characteristics influencing seedling establishment and early seedling vigor after dry direct sowing.An F2∶3 population was developed from the cross between the parental lines of ‘ Zhaxima’ and ‘ Hanhui No.3 ’.The mesocotyl lengths of dark germinated seedlings had continuous distribution and transgression on both sides.One or two seedlings were selected from each F3 line with extremely long or short mesocotyl length.Two bulked DNA pools were prepared from DNA samples isolated from mesocotyl tissues of 70 seedlings with the longest(59-102 mm)or the shortest mesocotyls (2-20 mm),respectively.The pooled DNA samples were sequenced by about 70 × coverage using the next generation genome sequencing platform.A total of 18 putative regions were declared on chromosome 1,3,6,7,8,9,11 and 12.Based on differential expression between parental lines and in seedlings of long-mesocotyl parent after light treatment,two putative candidate genes(LOC_Os01g08220 and LOC_Os08g15296)were found to negatively regulate mesocotyl elongation.

Drought is a major environmental factor that limits grain yield in rice. In order to understand the proteomic changes in response to drought at reproductive stage, proteins expressed in the young panicles were compared between two varieties of rice with contrasting tolernace to drought. The identified 36 differentially expressed proteins are involved in energy production, metabolism, stress defense, protein destination and cell structure. A coordinative up-regulation of triosephosphate isomerase, glycin decarboxylase complex H-protein, glyoxylase I and cytosolic ascorbate peroxidase was obseved in the drought tolerant variety Zhonghan 3, which may contribute to higher tolerance by increasing the energy production and maintaining redox homeostasis. Two-dimensional Western blotting experiments identified three APX1 and three APX2 isoforms up-regulated during drought stress in drought-tolerant varieties (Zhonghan 3, IRAT109 and PRATAO). However, in drought-suceptible varieties (IR29, Zhengshan 97B and CATUNA), expression of the six isoforms was unchanged or even down-regulated. Under normal growth conditions, expression level of the six APX isoforms showed negative correlation with drought tolerance of rice. Our data suggested that APX isoforms may be considered as indicators of the redox status that related to drought tolerance in rice.

Drought is one of the vitally critical environmental stresses affecting both growth and yield potential in rice. Drought resistance is a complicated quantitative trait that is regulated by numerous small effect loci and hundreds of genes controlling various morphological and physiological responses to drought. For this study, 270 rice landraces and cultivars were analyzed for their drought resistance. This was done via determination of changes in plant height and grain yield under contrasting water regimes, followed by detailed identification of the underlying genetic architecture via genome-wide association study (GWAS). We controlled population structure by setting top two eigenvectors and combining kinship matrix for GWAS in this study. Eighteen, five, and six associated loci were identified for plant height, grain yield per plant, and drought resistant coefficient, respectively. Nine known functional genes were identified, including five for plant height (OsGA2ox3, OsGH3-2, sd-1, OsGNA1, and OsSAP11/OsDOG), two for grain yield per plant (OsCYP51G3 and OsRRMh) and two for drought resistant coefficient (OsPYL2 and OsGA2ox9), implying very reliable results. A previous study reported OsGNA1 to regulate root development, but this study reports additional controlling of both plant height and root length. Moreover, OsRLK5 is a new drought resistant candidate gene discovered in this study. OsRLK5 mutants showed faster water loss rates in detached leaves. This gene plays an important role in the positive regulation of yield-related traits under drought conditions. We furthermore discovered several new loci contributing to the three investigated traits (plant height, grain yield, and drought resistance). These associated loci and candidate genes significantly improve our knowledge of the genetic control of these traits in rice. In addition, many drought resistant cultivars screened in this study can be used as parental genotypes to improve drought resistance of rice by molecular breeding.

In this study, the elite major rice varieties were used as recieptor and rice germplasm around the world were used as donors for developing in large scale the introgressed lines which were applied for pyramiding green traits of Green Super Rice, e.g. tolerant to disease and pests, high utilization effiency of N and P, drough tolerance, high yield and good quality. The practical molecular markers were developed to assist the selection for multiple traits pyramiding, which overcame the low effiency by single gene introgression in traditional molecular marker assisted breeding and broken the linkage drag as well as developing the propestive parents of Green Super Rice. The Green Super Rice varieties have been developed by pyramiding different favorable genes of multiple traits.