Status and Perspectives on the Researches of Rice Glutelin Mutants

Rice (Oryza sativa L. ) is one of the model plants for genomics research. As the raising of functional rice breeding for special usage, glutelin mutants play a more and more important role in the functional rice breeding as well as eukaryotic gene expression and regulation research materials. For example, the rice cultivar special for the patients suffering from kidney disease and diabetes could be developed from the rice glutelin mutants. In this paper, current researches on characterization, mutation mechanism and breeding usage of various rice glutelin mutants, especially the low glutelin content cultivars, were all discussed with perspectives on the trends of the glutelin mutant researches in the era of post-genomics.

Effort and Contribution of T-DNA Insertion Mutant Library for Rice Functional Genomics Research in China:Review and Perspective

With the completion of the rice （Oryza sativa L.） genome-sequencing project, the rice research community proposed to characterize the func- tion of every predicted gene in rice by 2020. One of the most effective and high-throughput strategies for studying gene function is to employ genetic mutations induced by insertion elements such as T-DNA or transposons. Since 1999, with support from the Ministry of Science and Technology of China for Rice Functional Genomics Programs, large-scale T-DNA insertion mutant populations have been generated in Huazhong Agricultural University, the Chinese Academy of Sciences and the Chinese Academy of Agricultural Sciences. Currently, a total of 372,346 mutant lines have been generated, and 58,226 T-DNA or Tos17 flanking sequence tags have been isolated. Using these mutant resources, more than 40 genes with potential applications in rice breeding have already been identified. These include genes involved in biotic or abiotic stress responses, nutrient metabolism, pollen development, and plant architecture. The functional analysis of these genes will not only deepen our understanding of the fundamental biological questions in rice, but will also offer valuable gene resources for developing Green Super Rice that is high-yielding with few inputs even under the poor growth conditions of many regions of Africa and Asia.

Functional genomics in the rice blast fungus to unravel the fungal pathogenicity

A rapidly growing number of successful genome sequencing projects in plant pathogenic fungi greatly increase the demands for tools and methodologies to study fungal pathogenicity at genomic scale. Magnaporthe oryzae is an economically important plant pathogenic fungus whose genome is fully sequenced. Recently we have reported the development and application of functional genomics platform technologies in M. oryzae. This model approach would have many practical ramifications in design and implementation of upcoming functional genomics studies of filamentous fungi aimed at understanding fungal pathogenicity.

From Green Super Rice to green agriculture:Reaping the promise of functional genomics research

Producing sufficient food with finite resources to feed the growing global population while having a smaller impact on the environment has always been a great challenge.Here,we review the concept and practices of Green Super Rice(GSR)that have led to a paradigm shift in goals for crop genetic improvement and models of food production for promoting sustainable agriculture.The momentous achievements and global deliveries of GSR have been fueled by the integration of abundant genetic resources,functional gene discoveries,and innovative breeding techniques with precise gene and whole-genome selection and efficient agronomic management to promote resource-saving,environmentally friendly crop production systems.We also provide perspectives on new horizons in genomic breeding technologies geared toward delivering green and nutritious crop varieties to further enhance the development of green agricul-ture and better nourish the world population.

Rice Functional Genomics Research： Past Decade and Future

Rice （Oryza sativa） is a major staple food crop for more than 3.5 billion people worldwide. Under- standing the regulatory mechanisms of complex agronomic traits in rice is critical for global food security. Rice is also a model plant for genomics research of monocotyledonso Thanks to the rapid development of functional genomic technologies, over 2000 genes controlling important agronomic traits have been cloned, and their molecular biological mechanisms have also been partially char- acterized. Here, we briefly review the advances in rice functional genomics research during the past 10 years, including a summary of functional genomics platforms, genes and molecular regulatory networks that regulate important agronomic traits, and newly developed tools for gene identification. These achievements made in functional genomics research will greatly facilitate the development of green super rice. We also discuss future challenges and prospects of rice functional genomics research.

Twenty years of rice genomics research: From sequencing and functional genomics to quantitative genomics

Since the completion of the rice genome sequencing project in 2005,we have entered the era of rice genomics,which is still in its ascendancy.Rice genomics studies can be classified into three stages:structural genomics,functional genomics,and quantitative genomics.Structural genomics refers primarily to genome sequencing for the construction of a complete map of rice genome sequence.This is fundamental for rice genetics and molecular biology research.Functional genomics aims to decode the functions of rice genes.Quantitative genomics is large-scale sequence-and statistics-based research to define the quantitative traits and genetic features of rice populations.Rice genomics has been a transformative influence on rice biological research and contributes significantly to rice breeding,making rice a good model plant for studying crop sciences.

Mutant Resources for the Functional Analysis of the Rice Genome

Rice is one of the most important crops worldwide, both as a staple food and as a model system for genomic research. In order to systematically assign functions to all predicted genes in the rice genome, a large number of rice mutant lines, including those created by T-DNA insertion, Ds/dSpm tagging, Tos17 tagging, and chemical/irradiation mutagenesis, have been generated by groups around the world. In this study, we have reviewed the current status of mutant resources for functional analysis of the rice genome. A total of 246 566 flanking sequence tags from rice mutant libraries with T-DNA, Ds/dSpm, or Tos17 insertion have been collected and analyzed. The results show that, among 211 470 unique hits, inserts located in the genic region account for 68.16%, and 60.49% of nuclear genes contain at least one insertion. Currently, 57% of non-transposable-element-related genes in rice have insertional tags. In addition, chemical/irradiation-induced rice mutant libraries have contributed a lot to both gene identification and new technology for the identification of mutant sites. In this review, we summarize how these tools have been used to generate a large collection of mutants. In addition, we discuss the merits of classic mutation strategies. In order to achieve saturation of mutagenesis in rice, DNA targeting, and new resources like RiceFox for gene functional identification are reviewed from a perspective of the future generation of rice mutant resources.

Genome editing enables defense-yield balance in rice

This brief article highlights the key findings of the study conducted by Sha et al.(Nature,doi:10.1038/s41586-023-06205-2,2023),focusing on the cloning of the RBL1 gene from rice,which is associated with lesion mimic mutant(LMM)traits.The RBL1 gene encodes a cytidine diphosphate diacylglycerol(CDP-DAG)synthase and plays a crucial role in regulating cell death and immunity by controlling phosphatidylinositol biosynthesis.The rbl1 mutant shows autoimmunity with multi-pathogen resistance but with severe yield penalty.Using genome editing techniques,the research team successfully generated an elite allele of RBL1 that not only restores rice yield but also provides broad-spectrum resistance against both bacterial and fungal pathogens.These findings demonstrate the potential of utilizing genome editing to enhance crop productivity and pathogen resistance.

Isolation and Identification of a Functional Centromere Element in the Wild Rice Species Oryza granulata with the GG Genome

The centromere of eukaryotic chromosomes is the crucial locus responsible for sister chromatid cohesion and for correct segregation of chromosomes to daughter cells during cell division. In the structural genomics era, centromeres represent the last frontiers of higher eukaryotic genomes because of their densely methylated, highly repetitive and, heterochromatic DNA （Hall et al., 2004）. Although these functions are conserved among all eukaryotes, centromeric DNA sequences are evolving rapidly （Jiang et al., 2003）.

An Exome-seq Based Tool for Mapping and Selection of Candidate Genes in Maize Deletion Mutants

Despite the large number of genomic and transcriptomic resources in maize, there is still much to learn about the function of genes in developmental and biochemical processes. Some maize mutants that were generated by gamma-irradiation showed clear segregation for the kernel phenotypes in B73 ? Mo17 F2 ears. To better understand the functional genomics of kernel development,we developed a mapping and gene identi?cation pipeline, bulked segregant exome sequencing(BSEx-seq), to map mutants with kernel phenotypes including opaque endosperm and reduced kernel size. BSEx-seq generates and compares the sequence of the exon fraction from mutant and normal plant F2 DNA pools. The comparison can derive mapping peaks, identify deletions within the mapping peak, and suggest candidate genes within the deleted regions. We then used the public kernel-speci?c expression data to narrow down the list of candidate genes/mutations and identi?ed deletions ranging from several kb to more than 1 Mb. A full deletion allele of the Opaque-2 gene was identi?ed in mutant 531, which occurs within a $200-kb deletion. Opaque mutant 1486 has a 6248-bp deletion in the mapping interval containing two candidate genes encoding RNA-directed DNA methylation 4(RdDM4) and AMP-binding protein, respectively. This study demonstrates the ef?-ciency and cost-effectiveness of BSEx-seq for causal mutation mapping and candidate gene selection,providing a new option in mapping-by-sequencing for maize functional genomics studies.

伽玛射线诱变群体选育的两个粒型变异系的基因组变异分析

哈粳稻7号(HG7)是一个清香型大粒优质粳稻品种,在哈尔滨种植时植株较高、熟期较晚。为培育半矮杆、早熟HG7突变体,利用γ射线辐射HG7种子培育了1个M2群体,但只鉴定到2个粒型变异株。对两个M3变异系进行观察发现,两个变异系内粒型不再分离,一个粒型细长,粒长较HG7增加2.6%,粒宽减小18.7%;另一个呈短圆粒,粒长缩短26.0%,粒宽增加4.1%,两者分别被命名为HG7-TG、HG7-SG。与HG7相比,HG7-TG和HG7-SG的株高、穗型等也存在一定差异。为确定HG7-TG和HG7-SG与HG7之间的亲缘关系,首先利用NY/T 1433-2014《水稻品种鉴定技术规程SSR标记法》的48个简单序列重复(SSR)标记对三者进行了分析。结果发现,HG7-TG与HG7之间存在24个SSR位点差异,而HG7-SG与HG7之间仅有1个位点差异。利用基因组重测序分析三者在全基因组水平上的遗传变异,结果表明HG7-TG与HG7之间存在约2.8 M个遗传变异,变异率高达7.5×10^(-3);HG7-SG与HG7之间约存在0.02 M个变异,变异率仅为5.2×10^(-5)。遗传分析结果表明,长粒性状为不完全显性。本研究结果表明,在诱变育种实践中,诱变群体中所鉴定到的变异株可能并非由原品种突变而来,采用SSR标记和基因组重测序的方法先对材料进行甄别,可确保突变体的真实性。本研究采用基因组重测序方法甄别真假突变体,对诱变育种研究具有一定的指导意义。

Recent Progress on Rice Genetics in China

Through thousands of years of evolution and cultivation, tremendously rich genetic diversity has been accumulated in rice （Oryza sativa L.）, developing a large germplasm pool from which people can select varieties with morphologies of Interest and other important agronomic traits. With the development of modern genetics, scientists have paid more attention to the genetic value of these elite varieties and germplasms, and such rich rice resources provide a good foundation for genetic research in China. Approximately 100 000 accessions of radiation-, chemical- or insertion-induced mutagenesis have been generated since the 1980s, and great progress has been made on rice molecular genetics. So far at least 16 variant/mutant genes Including MOC1, BC1, SKC1, and Rfgenes have been isolated and characterized in China. These achievements greatly promote the research on functional genomics, understanding the mechanism of plant development and molecular design breeding of rice in China. Here we review the progress of three aspects of rice genetics in China： moving forward at the molecular level, genetic research on elite varieties and germplasms, and new gene screening and genetic analysis using mutants. The prospects of rice genetics are also discussed.

Genetic and Physiological Analysis of a Novel Type of Interspecific Hybrid Weakness in Rice

Hybrid weakness is an important reproductive barrier that hinders genetic exchange between different species at the post-zygotic stage. However, our understanding of the molecular mechanisms underlying hybrid weakness is limited. In this study, we report discovery of a novel interspecific hybrid weakness in a rice chromosome segment substitution line （CSSL） library derived from a cross between the indica variety Teqing （Oryza sativa） and common wild rice （O. rufipogon）. The dominant Hybrid weakness il （Hwil） gene from wild rice is genetically incompatible with Teqing and induced a set of weakness symptoms, including growth suppression, yield decrease, impaired nutrient absorption, and the retardation of crown root initiation. Phytohormone treatment showed that salicylic acid （SA） could restore the height of plants expressing hybrid weakness, while other phytohormones appear to have little effect. Fine mapping indicated that Hwil is located in a tandem leucine-rich repeat receptor-like kinase （LRR-RLK） gene cluster. Within the 13.2-kb candidate region on the short arm of chromosome 11, there are two annotated LRR-RLK genes, LOC_Osllg07230 and LOC_Osllg07240. The Teqing allele of LOCOsllg07230 and the wild rice allele of LOC_Osllg07240 encode predicted functional proteins. Based on the genetic inheritance of hybrid weakness, LOC_Osllg07240 is implicated as the candidate gene for Hwil. Functional analysis of Hwil will expand our knowledge of the regulation of hybrid weakness in rice.

High-resolution melting-based TILLING of γ ray-induced mutations in rice

Targeting Induced Local Lesions IN Genomes （TILLING） is a reverse genetics strategy for the high-throughput screening of induced mutations.γ, radiation, which often induces both insertion/deletion （Indel） and point mutations, has been widely used in mutation induction and crop breeding. The present study aimed to develop a simple, high-throughput TILLING system for screening γ ray-induced mutations using high-resolution melting （HRM） analysis. Pooled rice （Oryza sativa） samples mixed at a 1：7 ratio of Indel mutant to wild-type DNA could be distinguished from the wild-type controls by HRM analysis. Thus, an HRM-TILLING system that analyzes pooled samples of four M2 plants is recommended for screening γ, ray-induced mutants in rice. For demonstration, a γ, ray-mutagenized M2 rice population （n=4560） was screened for mutations in two genes, OsLCT1 and SPDT, using this HRM-TILLING system. Mutations including one single nucleotide substitution （G→A） and one single nucleotide insertion （A） were identified in OsLCT1, and one tdnucleotide （TTC） deletion was identified in SPDT. These mutants can be used in rice breeding and genetic studies, and the findings are of importance for the application of γ, ray mutagenesis to the breeding of rice and other seed crops.

水稻窄叶突变体nrl2新等位基因的鉴定与功能分析

以籼型两系不育系Y58S的窄叶突变体nrl2(1)为试验材料,对nrl2(1)突变体材料进行表型、组织学分析,发现该突变体主要表现为叶片变窄且卷曲,维管束发育异常,大、小叶脉数显著减少;遗传分析结果表明,该窄叶表型受1对隐性核基因控制;通过基因精细定位,发现NRL2(1)定位在第3染色体46000 bp区间内;图位克隆及候选基因验证结果表明该基因是NRL2的等位基因;测序比对结果显示,突变体的第17个外显子由碱基C变为T,对应的氨基酸由谷氨酰胺变为终止密码子,造成翻译提前终止。以nrl2(1)为亲本材料,选育两系不育系,预期可选育出叶片较窄、株型紧凑、分蘖多的新型两系不育系。

一株稻黄单胞菌ZX002的基因组完成图及分析

水稻白叶枯病是一种严重的细菌性病害,对浙江省乃至全国的水稻生产造成了严重影响,其病原菌为水稻黄单胞菌水稻致病变种(Xanthomonas oryzae pv.oryzae,Xoo),因此分析稻黄单胞菌的基因组信息有利于该病菌致病机制的研究和水稻白叶枯病的防控.2020年从浙江省温州市水稻白叶枯重病区采集的发病叶片中分离到一株稻黄单胞菌,并将其命名为ZX002.采用高通量测序技术对ZX002菌株进行全基因组测序,并利用生物信息学方法对其进行基因组组分和功能分析,结果表明该菌株的全基因组总长度为4749798 bp,预测到4440个编码基因,编码基因总长度为4031775 bp,同时还包括253个非编码RNA,分别为:53个tRNA,194个sRNA,2个5s rRNA,2个16s rRNA和2个23s rRNA.全基因组共检测到23个基因岛,并检测到1个非核糖体肽合成酶(non-ribosomal peptide synthetase,NRPS)基因簇.全基因组功能注释表明,ZX002菌株的预测基因主要富集在氨基酸、碳水化合物、辅助因子及维生素代谢和能量代谢等途径中.

水稻突变体与功能基因组学

突变体是功能基因组学研究的重要材料。本文综述了水稻突变体的创制方法、变异的机制、水稻突变体/基因分类和数量、克隆的水稻重要基因的研究进展,包括1698个水稻突变体/基因的分类和43个克隆的水稻突变体基因,并提出了利用水稻突变体的展望。

水稻谷蛋白突变体的研究现状与展望

水稻 (OryzasativaL .)是基因组研究的模式植物。随着培育功能性专用品种日渐成为水稻育种的重要目标 ,作为研究真核生物基因表达调控理想材料的谷蛋白突变体也为功能性专用水稻品种的选育提供了优良的遗传资源。利用低谷蛋白突变体可以培育肾脏病和糖尿病患者专用的低谷蛋白水稻品种。笔者在概述水稻谷蛋白突变体的主要类型及其突变的遗传规律的基础上 ,结合其它作物中的成功范例着重介绍了低谷蛋白突变体的研究现状 ,探讨了后基因组学时代适用于功能性育种的水稻谷蛋白突变体的相关研究方向。

水稻条纹病毒的分子生物学

综述了近年来国内外有关水稻条纹病毒在基因组结构、功能、复制、转录、表达策略及其分类地位、病毒分子变异和病害控制策略以及进化上的亲缘关系等方面的最新研究进展 。

籼稻9311辐射突变体的分离与鉴定

利用350Gy的60Co-γ对籼稻9311进行辐射处理,以诱导产生大量的农艺与发育性状突变体,为水稻遗传研究和功能基因组学研究提供基础材料。M1代单本栽插并实行单株收获;M2代种植5000个家系,根据各个生育阶段形态性状表现进行初步鉴定,共有1665个家系的4136个单株发生形态变异,并筛选出各类形态突变体2001份;M3代按系谱种植进行重复鉴定获得包括叶、茎、穗、育性和熟期变化等各类突变体1996份。形态性状的突变频率按M2代种植家系中突变家系的百分比计算为33.3%,表明9311对γ射线是十分敏感的。本研究还发现辐射突变表现为单基因突变和多基因突变同时发生。同时,还筛选到一些优良农艺性状的突变体,可以直接应用于育种及生产当中。