Genetic analysis and fine-mapping of a dwarfing with withered leaf-tip mutant in rice

A dwarf mutant of rice （Oryza sativa L.） by mutagenesis of ethylene methylsulfonate （EMS） treatment from Nipponbare was identified. The mutant exhibited phenotypes of dwarfism and withered leaf tip （dwll）. Based on the intemode length of dwll, this mutant belongs to the dm type of dwarfing. Analysis of elongation of the second sheath and m-amylase activity in endosperm showed that the phenotype caused by dwll was insensitive to gibberellin acid treatment. Using a large F2 population derived from a cross between the dwll and an indica rice variety, TN1, the DWL1 gene was mapped to the terminal region of the long arm of chromosome 3. Fine-mapping delimited it into a 46 kb physical distance between two STS markers, HL921 and HL944, where 6 open reading frames were predicted. Cloning of DWL1 will contribute to dissecting molecular mechanism that regulates plant height in rice, which will be beneficial to molecular assisted selection of this important trait.

WRKY72 Negatively Regulates Seed Germination Through Interfering Gibberellin Pathway in Rice

Seed germination is associated with grain yield and quality in crop production.Gibberellic acid(GA)serves as a major phytohormone in the promotion of seed germination.It is synthesized in the embryos and transmitted to the aleurone layers,where GA triggers the synthesis and secretion of a set of hydrolases,especiallyα-amylase.Subsequently,the storage nutrients such as starch in the endosperm are digested by these hydrolases and absorbed by the embryo to sustain seed germination and early seedling establishment(Kaneko et al,2002).The detailed GA biosynthesis process has been well studied and thoroughly reviewed in several literatures(Sakamoto et al,2004;Reinecke et al,2013).Briefly,geranylgeranyl diphosphate(GGDP)is turned into ent-kaurene by two terpene synthases,ent-copalyl diphosphate synthase(CPS)and ent-kaurene synthase(KS).Subsequently,the conversion of GA precursor ent-kaurene to ent-kaurenoic acid is catalyzed by ent-kaurene oxidase(KO),and that from ent-kaurenoic acid to GA12 is catalyzed by ent-kaurenoic acid oxidase(KAO).Ultimately,GA12 is converted to various GA intermediates and bioactive GAs by GA20-oxidase(GA20ox)and GA3-oxidase(GA3ox),respectively.

OsPPR9 encodes a DYW-type PPR protein that affects editing efficiency of multiple RNA editing sites and is essential for chloroplast development

Photosynthesis occurs mainly in chloroplasts,whose development is regulated by proteins encoded by nuclear genes.Among them,pentapeptide repeat(PPR)proteins participate in organelle RNA editing.Although there are more than 450 members of the PPR protein family in rice,only a few affect RNA editing in rice chloroplasts.Gene editing technology has created new rice germplasm and mutants,which could be used for rice breeding and gene function study.This study evaluated the functions of OsPPR9 in chloroplast RNA editing in rice.The osppr9 mutants were obtained by CRISPR/Cas9,which showed yellowing leaves and a lethal phenotype,with suppressed expression of genes associated with chloroplast development and accumulation of photosynthetic-related proteins.In addition,loss of OsPPR9 protein function reduces the editing efficiency of rps8-C182,rpoC2-C4106,rps14-C80,and ndhB-C611 RNA editing sites,which affects chloroplast growth and development in rice.Our data showed that OsPPR9 is highly expressed in rice leaves and encodes a DYW-PPR protein localized in chloroplasts.Besides,the OsPPR9 protein was shown to interact with OsMORF2 and OsMORF9.Together,our findings provide insights into the role of the PPR protein in regulating chloroplast development in rice.

Mapping QTLs for heading synchrony in a doubled haploid population of rice in two environments

Simultaneous heading of plants within the same rice variety, also refer to heading synchrony, is an important factor that affects simultaneous ripening of the variety. Understanding of the genetic basis of heading synchrony may contribute to molecular breeding of rice with simultaneous heading and ripening. In the present study, a doubled haploid （DH） population, derived from a cross between Chunjiang 06 and TN1 was used to analyze quantitative trait locus （QTL） for heading synchrony related traits, i.e., early heading date （EHD）, late heading date （LHD）, heading asynchrony （HAS）, and tiller number （PN）. A total of 19 QTLs for four traits distributed on nine chromosomes were detected in two environments. One QTL, qHAS-8 for HAS, explained 27.7% of the phenotypic variation, co-located with the QTLs for EHD and LHD, but it was only significant under long-day conditions in Hangzhou, China. The other three QTLs, qHAS-6, qHAS-9, and qHAS-10, were identified under short-day conditions in Hainan, China, each of which explained about 11% of the phenotypic variation. Two of them, qHAS-6 and qHAS-9, were co-located with the QTLs for EHD and LHD. Two QTLs, qPN-4 and qPN-5 for PN, were detected in Hangzhou, and qPN-5 was also detected in Hainan. However, none of them was co-located with QTLs for EHD, LHD, and HAS, suggesting that PN and HAS were controlled by different genetic factors. The results of this study can be useful in marker assisted breeding for improvement of heading synchrony.

The OsNAC23-Tre6P-SnRK1 a feed-forward loop regulates sugar homeostasis and grain yield in rice

Tre6P(trehalose-6-phosphate)mediates sensing of carbon availability to maintain sugar homeostasis in plants,which underpins crop yield and resilience.However,how Tre6P responds to fluctuations in sugar levels and regulates the utilization of sugars for growth remains to be addressed.Here,we report that the sugar-inducible rice NAC transcription factor OsNAC23 directly represses the transcription of the Tre6P phosphatase gene TPP1 to simultaneously elevate Tre6P and repress trehalose levels,thus facilitating carbon partitioning from source to sink organs.Meanwhile,OsNAC23 and Tre6P suppress the transcription and enzyme activity of SnRK1a,a low-carbon sensor and antagonist of OsNAC23,to prevent the SnRK1a-mediated phosphorylation and degradation of OsNAC23.Thus,OsNAC23,Tre6P,and SnRK1a form a feed-forward loop to sense sugar and maintain sugar homeostasis by transporting sugars to sink organs.Importantly,plants over-expressing OsNAC23 exhibited an elevated photosynthetic rate,sugar transport,and sink organ size,which consistently increased rice yields by 13%–17%in three elite-variety backgrounds and two locations,suggesting that manipulation of OsNAC23 expression has great potential for rice improvement.Collectively,these findings enhance our understanding of Tre6P-mediated sugar signaling and homeostasis,and provide a new strategy for genetic improvement of rice and possibly also other crops.

LRG1 maintains sterile lemma identity by regulating OsMADS6 expression in rice

Dear Editor,Spikelet is the unique structural unit of grass panicles with florets and diverse glume-like organs.In rice,a normal spikelet usually has two pairs of glume-like organs,including a pair of sterile lemmas and a pair of rudimentary glumes.Generally,the sterile lemma is considered to be the severely degenerated bract,but its origin is still controversial.

bZIP71 delays flowering by suppressing Ehd1 expression in rice

Flowering time is a fundamental factor determining the global distribution and final yield of rice(Oryza sativa).Although diverse flowering time genes have been reported in this crop,the transcriptional regulation of its key flowering genes are poorly understood.Here,we report that a basic leucine zipper transcription factor,bZIP71,functions as a flowering repressor.The overexpression of bZIP71 delays flowering,while the bzip71 mutant flowers early in both long-day and short-day conditions.A genetic analysis showed that the regulation of flowering by bZIP71 might be independent of Heading date 2(Hd2),Hd4,and Hd5.Importantly,bZIP71 directly associates with the Early heading date 1(Ehd1)promoter and represses its transcription,and genetically the function of bZIP71 is impaired in the ehd1 mutant.Moreover,bZIP71 interacts with major components of polycomb repressive complex 2(PRC2),SET domain group protein 711(SDG711),and Fertilization independent endosperm 2(FIE2),through which bZIP71 regulates the H3K27me3 level of Ehd1.Taken together,we present a transcriptional regulatory mechanism in which bZIP71 enhances the H3K27me3 level of Ehd1 and transcriptionally represses its expression,which not only offers a novel insight into a flowering pathway,but also provides a valuable putative target for the genetic engineering and breeding of elite rice cultivars.

LSL1 controls cell death and grain production by stabilizing chloroplast in rice

Lesion mutants can be valuable tools to reveal the interactions between genetic factors and environmental signals and to improve grain production.Here we identified a rice(Oryza sativa)mutant,lesion spotleaf1(lsl1),which produces necrotic leaf lesions throughout its life cycle.LSL1 encodes a protein of unknown function and belongs to a grass-specific clade.The lesion phenotype of the lsl1 mutant was sharply induced by shading,and its detached leaves incubated in 6-benzylamino purine similarly formed lesions in the dark.In addition,the lsl1 mutant exhibited reactive oxygen species accumulation and cell death.The terminal deoxynucleotidyl transferase d UTP nick end-labeling(TUNEL)and comet assays revealed that the lsl1 mutant contained severe DNA damage,resulting in reduced grain yield and quality.RNA sequencing,gene expression,and protein activity analyses indicate that LSL1 is required for chloroplast function.Furthermore,LSL1 interacts with Psa D and PAP10 to form a regulatory module that functions in chlorophyll synthesis and chloroplast development to maintain redox balance.Our results reveal that LSL1 maintains chloroplast structure,redox homeostasis,and DNA stability,and plays important roles in the interaction between genetic factors and environmental signals and in regulating grain size and quality.

Rice Breeding:A Long Noncoding Locus with Great Potential

Rice is one of the most widely consumed cereal crops and staple food for more than half of the world's population,especially in Asian countries(Li and Cui,2014).The growth period of rice is an important agronomic trait,which determines the planting regions or adaptabilities of rice varieties.In breeding practice,there is often a contradiction between high yield and early maturity(Wang et al.,2018a),meaning that a variety with higher yield usually has a longer growth period.Thus,breeding varieties with early maturity and high yield has been one of the main directions of genetic breeding programs.

C2H2锌指蛋白LRG1调控水稻小穗的发育

水稻小穗是一种独特的花序结构,其发育直接决定种子的大小和产量.一个正常的水稻小穗包含一个可育小花(1个外稃、1个内稃、2个浆片、6个雄蕊和1个雌蕊)、一对护颖及一对副护颖.通过EMS诱变,本研究分离得到了一个新的隐性水稻小穗突变体lacking rudimentary glume 1(lrg1).lrg1的小穗仅仅只有一个副护颖,且其与护颖一起被同源转化为外稃状器官.细胞学和分子生物学研究发现,LRG1基因在水稻小穗副护颖中显著表达,证明了LRG1是副护颖的特征基因.此外,lrg1突变体谷粒表型异常是由颖壳细胞数目和大小决定的,说明LRG1还参与调控谷粒大小.进一步的实验发现,LRG1基因编码的ZOS4-06-C2H2锌指结构转录因子可能是与TPRs蛋白相互作用来抑制下游基因表达.本研究一方面证实了副护颖、护颖和外稃是同源器官,另一方面LRG1基因参与调控种子大小,为分子设计育种提供了新的基因资源.