OsVP1 activates Sdr4 expression to control rice seed dormancy via the ABA signaling pathway

Pre-harvest sprouting(PHS)is a disadvantageous trait in cereal production worldwide,causing large economic losses each year.Its regulation mechanism is still unclear.We generated the Oryza sativa Viviparous1(OsVP1)mutant using gene editing technique,which shows increased PHS compared with that of the wild type Nipponbare.OsVP1 is localized mainly in the nucleus and expressed in various tissues and organs.Expression of Seed dormancy 4(Sdr4),a key gene controlling PHS,was sharply reduced in OsVP1 mutants.OsVP1 bound to the specific motif CACCTG in the promoter of Sdr4 and activated its expression in rice protoplasts.Overexpression of Sdr4 reduced the high seed germination rate of OsVP1 mutant cr-osvp1-1,showing that Sdr4 acts as a downstream target of OsVP1.Both OsVP1 and Sdr4 loss-of-function mutants were insensitive to exogenous ABA and employed the ABA signaling pathway in regulating seed dormancy.These findings shed light on the control of seed dormancy aimed at preventing PHS in rice.

Correlation Between Parents and F_1 and Combining Ability of Parents on Seed Dormancy in indica Rice (Oryza sativa)

Dormancy indices of hulled and dehulled seeds were investigated by using 19 cytoplasmic male sterile （CMS） lines, 9 restorer lines and their 109 F1 hybrids of indica hybrid rice. The seeds of each F1 and the parents were harvested on 35 days after flowering. Combining ability was analyzed in 25 combinations made by 5 CMS lines and 5 restorer lines （North Carolina II mating design）. The seed dormancy index of F1 was positively and highly significantly correlated with those of their parents and mid-parent value. Out of the 109 combinations, 82 combinations showed mid-parent heterosis, and 43 heterobeltiosis. Seed dormancy indices of F1s and their parents declined dramatically in dehulled seeds compared with hulled seeds, indicating that the hull played an important role in seed dormancy. However, the trends were similar in hulled seeds and dehulled seeds in terms of relationships between the seed dormancy indicices in F1 and their parents. The influence of hull on seed dormancy mainly depended on F1 genotype, not on the hull from maternal parent. The variances of general combining ability （GCA） in female and male parents occupied 59.2% and 31.1% of total variance, respectively. The variance of specific combining ability （SCA） in combinations occupied 9.7% of total variance, indicating that gene additive effects were principal. Among the 5 CMS lines, II112A had the highest GCA effect for seed dormancy, followed by D62A. Among the 5 restorer lines, IRl12 had the highest GCA effect for seed dormancy, followed by 2786. These lines are elite parental materials for breeding F1 hybrid rice with stronger seed dormancy.

Mapping of three QTLs for seed setting and analysis on the candidate gene for qSS-1 in rice(Oryza sativa L.)

The lower seed setting is one of the major hindrances which face grain yield in rice. One of the main reasons to cause low spikelet fertility （seed setting） is male sterility or pollen abortion. Notably, pollen abortion has been frequently observed in advanced progenies of rice. In the present study, 149 BC2F6 individuals with significant segregation in spikelet fertility were generated from the cross between N040212 （indica） and Nipponbare （japonica） and used for primary gene mapping. Three QTLs, qSS-1, qSS-7 and qSS-9 at chromosomes 1, 7 and 9, respectively, were found to be associated with seed setting. The recombinant analysis and the physical mapping information from publicly available resources exhibited that the qSS-1, qSS-7 and qSS-9 loci were mapped to an interval of 188, 701 and 3741 kb, respectively. The seed setting responsible for QTL qSS-1 was further fine mapped to 93.5 kb by using BC2F7 population of 1 849 individuals. There are 16 possible putative genes in this 93.5 kb region. Pollen vitality tests and artificial pollination indicated that the male gamete has abnormal pollen while the female gamete was normal. These data showed that low seed setting rate relative to qSS-1 may be caused by abnormal pollen grains. These results will be useful for cloning, functional analysis of the target gene governing spikelet fertility （seed setting） and understanding the genetic bases of pollen sterility.

Analysis of QTL for Seed Dormancy and Their Response to Dry Heat Treatment in Rice (Oryza sativa L.)

Quantitative trait loci (QTL) controlling seed dormancy in rice were identified usingrecombinant inbred lines (RILs) population derived from the cross between a japonicavariety Kinmaze and an indica variety DV85. Seeds of two parental cultivars and each RILwere harvested in 35d after heading. The germination percentage of these seeds at 30℃for 7 days were measured as the degree of seed dormancy. QTL analysis was performed withWindows QTL Cartographer 1.13a program by composite interval mapping. A total of four QTLfor seed dormancy were detected on chromosome 2 (two regions), 5 and 11, respectively.Phenotypic variation explained by each QTL ranged from 8.37 to 17.40%. Responses of suchloci to a dormancy-breaking treatment with dry heat were further detected. The resultsshowed that two alleles of qDOR-2-1 and qDOR-5 from DV85 as well as the allele of qDOR-11 from Kinmaze increased the seed dormancy, which seemed to be easily broken by dry heattreatment. Such loci of seed dormancy may be applied to rice genetic improvement. Theallele of qDOR-2-2 from DV85 increased the seed dormancy, which could not be broken bydry heat treatment.

Mapping and Analysis of Quantitative Trait Loci Controlling Seed Dormancy in Rice

Seed dormancy is one of the most important traits related to the rice grain quality and seeds application, because it is associated with pre-harvest sprouting, resulting in a downgrading of quality and severe limitations in end-use application. The recent development of DNA markers and linkage maps of rice has made possible mapping of individual genes associated with complex seed dormancy traits, analyzing the genetics effects of individual genes and genotype-by- environment interactions. Up to now, numerous quantitative trait loci (QTLs) associated with seed dormancy in rice have been identified and mapped in the molecular genetic map by different populations. In this review, we focus on the genetic base of seed dormancy in rice, especially compare QTLs controlling seed dormancy reported up to now, analyze the expression and stability of QTLs controlling seed dormancy, and discuss the present problems. Finally we show a new pathway to further research on seed dormancy.

Effects of Artificial Aging on Physiological Characteristics of Rice Seeds with Different Dormancy Characteristics

In this study,two indica varieties with different dormancy characteristics [4 K58( II-32 B dormant),4 K59( II-32 B) ] and their F2 seeds( C178,C179) obtained through hybridization with sterile line( II-32 A) were used as materials. Different aged seeds( 0,3,6 and 9 d) of these four varieties were acquired by artificial accelerated aging method. Effects of artificial aging on malondialdehyde( MDA) content and catalase( CAT),ascorbate peroxidase( APX),peroxidase( POD) and superoxide dismutase( SOD) activity were investigated. The results showed that with the prolongation of aging time,MDA contents of these four rice varieties increased significantly,while the activity of antioxidant enzymes decreased dramatically. Besides,MDA contents and SOD,CAT and APX activity of the two inbred lines were significantly lower than those of the hybrid varieties. In addition,the activity of antioxidant enzymes in 4 K58 and C178 was significantly lower than that in 4 K59 and C179,respectively. This study indicated that artificial aging treatment significantly inhibited the activity of antioxidant system in seeds,improved membrane lipid peroxidation degree,and thus aggravated the deterioration of seeds. In addition,it also suggested that rice seeds with dormant property were more intolerant to storage.

Molecular Dissection of Relationship Between Seedling Characteristics and Seed Size in Rice

Seedling characteristics such as leaf emergency, chlorophyll content, and height are important for early growth and also associated with seed size. Quantitative trait loci (QTLs) for rice (Oryza sativa L.) seedling characteristics (leaf length, chlorophyll content, seedling height) and seed size were identified with an attempt to explore the relationship between seedling characteristics and seed size, using a recombinant inbred population derived from a cross between Zhenshan 97A and Minghui 63. Two, one, five, four, four, and nine QTLs were detected for chlorophyll a content, total chlorophyll, length of the second seedling leaf, length of the third seedling leaf, seedling height, and seed size, respectively. The results indicated that four QTLs for seed size and four QTLs for seedling characteristics shared several similar regions (G359-RG532, C567-RG236, RZ403-R19, C371-C405a), respectively, suggesting a close association between seedling characteristics and seed size. Several chromosomal regions influencing seed size, however, had no effects on seedling characteristics, suggesting that it was possible to improve seedling vigor without increasing grain size.

Advances in Physiological-biochemical and Genetic Mechanisms of Seed Aging in Rice(Oryza sativa L.)

Reasons causing or accelerating seed aging are mainly damage of mem- branes, DNA and proteins, decline of protein synthesis capacity and excessive ac- cumulation of reactive oxygen species. With the application of natural aging or artifi- cial aging methods, it was reported that quantitative trait loci （QTLs） of seed stora- bility in rice were widely distributed on the chromosomes except the 10th chromo- some. In this paper, we reviewed the progresses in the research on physiological- biochemical and genetic mechanisms of seed aging, and analyzed the existing problems and developing prospect in molecular breeding of rice with improved seed storability, in order to provide reference for the basic research and genetic improve- ment of rice seed storabUity.

Genetic Analysis and QTL Mapping of Mature Seed Culturability in Indica Rice

Genetic segregation analysis for mature seed culturability was conducted using recombinant inbred lines derived from a cross of indica rice, Yangdao 6 and Pei＇ai 64s. Three indices of seed culturability, the frequency of callus induction, the frequency of brown callus and the increase of callus weight were investigated. A combined genetic map constructed with simple sequence repeat （SSR）, sequence tag site （STS）, cleaved amplified polymorphic sequences （CAPS） and single nucleotide polymorphism （SNP） markers covered a total distance of 1 732.5 cM, averaging approximately 12 cM between two neighboring loci. Three QTLs on chromosomes 7, 7 and 10 were detected for the frequency of callus induction; three QTLs on chromosomes 6, 7 and 9 were detected for the frequency of brown callus; and two QTLs on chromosomes 5 and 7 were detected for the increase of callus weight. Common QTLs mapped at the interval flanking RM5481 and RM6835 on chromosome 7 were identified to be involved in the frequency of callus induction and the frequency of brown callus, explaining 7.29% and 12.52% of phenotypic variation, respectively. A total of 14 epistatic effects were detected for the three indices of mature seed culturability. ~

Research Progress of Molecular Regulation Mechanism of Seed Dormancy

Dormancy is the biological adaptation behavior for seed, and it is regulated by many factors. A lot of studies have been done on various aspects of seed dormancy, and the breadth and width of these studies are in constant expanding and deepening. With the wide application of means of quantitative genetics method and mutant in the study on seed dormancy, a large number of quantitative trait loci（QTL） and mutant genes related with dormancy have been identified, which is of great significance for the further revelation of the detail mechanisms of plant seed dormancy and germination. This paper briefly introduced the genetic variation of seed dormancy in recent years, described the inductive formation of plant seed dormancy from the four aspects of dormancy specific gene, chromatin, seed growth development and hormone, and stated the action mechanism of environmental factors on seed dormancy from genetic and molecular levels, as well as the regulation and control mechanism of dormancy release, with the aim to provide certain references for the study on seed dormancy.

Identification of a major quantitative trait locus and its candidate underlying genetic variation for rice stigma exsertion rate

Stigma exsertion in male sterile lines of hybrid rice is important for seed yield.In the present study, ZS616 [Oryza sativa subsp.Xian(indica)], a male sterile line with a stigma exsertion rate(SER) as high as 94.5%, was crossed to DS552, a japonica line with almost no exserted stigmas.F3 plants with extremely low and high SER were sequenced to identify SER-associated quantitative trait loci(QTL).A major QTL for SER, qSER-3.1, was identified along with other QTL on chromosome 3 in a 3.9 Mb region.A total of 307 nonsynonymous single-nucleotide polymorphisms(SNPs) and 27 frame-shift insertion/deletions(InDels)differentiating ZS616 and DS552 were identified in the region containing qSER-3.1.Most SNPs(294) and InDels(25) were excluded after further analysis because they were shared by ZS616 and low(<2.0%) SER accessions in the Huazhong Agricultural University(HAU) core rice collection.Association analysis using the full HAU collection identified a 17-bp InDel in OS03 G0689400 as the most likely causal genetic variant underlying qSER-3.1.ZS616-type accessions(n = 54, with the 17-bp insertion) in the HAU collection had minimum(16.5%)and mean(39.6%) SERs significantly greater than those(n = 424) without the insertion(with minimum and mean SERs of 0.2% and 20.6%, respectively).Thus, this study identified a major QTL for stigma exsertion and revealed the mutation in a candidate gene for the QTL.

Identification of Quantitative Trait Loci for Lipid Metabolism in Rice Seeds

Plant seed oil is important for human dietary consumption and industrial application. The oil trait is controlled by quantitative trait loci （QTLs）, but no QTLs for fatty acid composition are known in rice, the monocot model plant. QTL analysis was performed using F2 and F2：3 progeny from a cross of an indica variety and a japonica variety. Gas chroma- tography-mass spectrometry （GC-MS） analysis revealed significant differences between parental lines in fatty acid com- position of brown rice oil, and 29 associated QTLs in F2 and/or F2：3 populations were identified throughout the rice genome, except chromosomes 9 and 10. Eight QTLs were repeatedly identified in both populations across different envi- ronments. Five loci pleiotropically controlled different traits, contributing to complex interactions of oil with fatty acids and between fatty acids. Nine rice orthologs of Arabidopsis genes encoding key enzymes in lipid metabolism co-localized with 11 mapped QTLs. A strong QTL for oleic （18：1） and linoleic （18：2） acid were associated with a rice ortholog of a gene encoding acyI-CoA：diacylglycerol acyltransferase （DGAT）, and another for palmitic acid （16：0） mapped similarly to the acyl- ACP thioesterase （FatB） gene ortholog. Our approach rapidly and efficiently identified candidate genes for mapped QTLs controlling fatty acid composition and oil concentration, providing information for improving rice grain quality by marker assisted selection.

Quantitative trait loci analysis for rice seed vigor during the germination stage

Seed vigor is an important characteristic of seed quality,and rice cultivars with strong seed vigor are desirable in direct-sowing rice production for optimum stand establishment.In the present study,the quantitative trait loci (QTLs) of three traits for rice seed vigor during the germination stage,including germination rate,final germination percentage,and germination index,were investigated using one recombinant inbred line (RIL) population derived from a cross between japonica Daguandao and indica IR28,and using the multiple interval mapping (MIM) approach.The results show that indica rice presented stronger seed vigor during the germination stage than japonica rice.A total of ten QTLs,and at least five novel alleles,were detected to control rice seed vigor,and the amount of variation (R2) explained by an individual QTL ranged from 7.5% to 68.5%,with three major QTLs with R2>20%.Most of the QTLs detected here are likely to coincide with QTLs for seed weight,seed size,or seed dormancy,suggesting that the rice seed vigor might be correlated with seed weight,seed size,and seed dormancy.At least five QTLs are novel alleles with no previous reports of seed vigor genes in rice,and those major or minor QTLs could be used to significantly improve the seed vigor by marker-assisted selection (MAS) in rice.

成熟期水稻种子脱水速率全基因组关联分析

[目的]籽粒脱水速率直接影响种子的安全收获和快速干燥。选育成熟期籽粒含水量低、脱水速率快的品种,可保障种子质量,降低生产成本。[方法]采用来自82个不同国家和地区的165份水稻核心种质作为试验材料,将成熟期种子脱水速率表型与基因型相结合进行GWAS分析,挖掘调控种子脱水的关键基因,为培育和创制脱水快速品种奠定基础。[结果]1)对165份水稻核心种质群体脱水速率性状进行描述性统计分析,结果显示2年脱水速率性状均呈连续性偏正态分布,2年快速脱水的脱水速率性状在年际间具有显著相关性。不同亚群之间快速脱水与慢速脱水速率正相关。2)GWAS关联分析共获得与脱水速率显著关联的SNP 170个,QTL 36个。通过LD分析定位到6个与脱水速率密切相关的QTL,分别为qGDR2.3、qGDR4.1、qGDR4.2、qGDR6.1、qGDR6.4、qGDR10.1。[结论]这些QTL区间内主要候选基因OsPIP1;1、Os TIFY9、Osb ZIP48、Os ATG8b、OsDREB1C、Os SCP46与水分转运活性、信号转导、转录调控、抗氧化防御密切相关,推测它们与成熟期水稻种子脱水速率相关,可作为候选基因。

近年我国水稻种子休眠与萌发调控机制研究进展

水稻种子的休眠与萌发是维持水稻产量和品质的重要农艺性状。水稻种子收获前较低的休眠水平易引起穗发芽,导致水稻产量和品质降低。另一方面,较高的休眠程度易引起水稻播种期的低发芽率和出苗不整齐,严重制约水稻的高产稳产。综述了2020年以来国内在水稻种子休眠与萌发遗传调控领域取得的一系列重要进展,具体从植物激素、非生物胁迫和穗发芽调控机制展开,并对国外相关领域的研究作简要介绍,提出研究趋势和展望,以期阐明调控种子萌发的遗传特性和作用机理,为适宜休眠度的水稻新品种培育提供理论依据和优良基因资源。

绿豆种子休眠性和百粒重的QTLs和互作分析

利用绿豆Berken/ACC41重组自交系在北京种植得到的121个F10家系和79个RFLP分子标记,采用改进复合区间作图法对绿豆种子休眠性和百粒重进行数量性状基因定位及上位性互作分析。检测到与发芽势有关的QTL3个,与发芽率有关的QTL4个,分别位于第1、11连锁群,解释表型变异的8.17%～12.14%和4.34%～12.69%。检测到与百粒重有关的QTL5个,分别位于第2、8、9、11连锁群,解释表型变异的4.58%～10.36%。增加发芽率和百粒重的基因效应均来自母本Berken。分别检测到发芽势、发芽率和百粒重的加性×加性上位性互作8、9、9对,对这3个性状的总表型贡献率分别达到66.58%、47.91%、39.90%。本文初步分析了休眠性和百粒重的关系,并与前人的研究结果作了比较,旨在通过分子标记辅助选择,培育适度休眠的优良绿豆品种,进而解决绿豆收获前的荚上子粒发芽问题。

Sdr4 dominates pre-harvest sprouting and facilitates adaptation to local climatic condition in Asian cultivated rice

Pre-harvest sprouting(PHS),which reduces grain yield and quality,is controlled by seed dormancy genes.Because few dormancy-related genes have been cloned,the genetic basis of seed dormancy in rice(Oryza sativa L.)remains unclear.Here,we performed a genome-wide association study and linkage mapping to dissect the genetic basis of seed dormancy in rice.Our findings suggest that Seed Dormancy4(Sdr4),a central modulator of seed dormancy,integrates the abscisic acid and gibberellic acid signaling pathways at the transcriptional level.Haplotype analysis revealed that three Sdr4 alleles in rice cultivars already existed in ancestral Oryza rufipogon accessions.Furthermore,like the semi-dwarf 1(SD1)and Rc loci,Sdr4 underwent selection during the domestication and improvement of Asian cultivated rice.The distribution frequency of the Sdr4-n allele in different locations in Asia is negatively associated with local annual temperature and precipitation.Finally,we developed functional molecular markers for Sdr4,SD1,and Rc for use in molecular breeding.Our results provide clues about the molecular basis of Sdr4-regulated seed dormancy.Moreover,these findings provide guidance for utilizing the favorable alleles of Sdr4 and Rc to synergistically boost PHS resistance,yield,and quality in modern rice varieties.

水稻种子休眠遗传调控机制研究进展

种子休眠可确保种子在最适宜的条件下萌发,对植物的生存和环境适应具有重要意义。种子休眠的强弱关系到种子穗发芽、萌发率、整齐度及后续生长,对作物的产量和品质十分重要。种子休眠受内源激素、环境和复杂遗传网络等多种因素的调控。其中植物激素脱落酸(abscisic acid,ABA)和赤霉素(gibberellic acid,GA)是水稻休眠调控网络中最重要的2个激素,大多数休眠相关基因通过直接或间接调控ABA和GA相关基因来介导种子的休眠。过去几十年,育种家对水稻种子休眠进行了一些数量性状座位(Quantitative trait locus,QTL)定位研究,并结合一系列水稻穗发芽的突变体,初步揭示了种子休眠的分子机制。该研究归纳总结近几年控制水稻休眠的关键基因及其调控机制,以期为该方向的研究以及水稻抗穗发芽分子育种提供帮助。

Identification and mapping of quantitative trait loci controlling cold-tolerance of Chinese common wild rice (O. rufipogon Griff.) at booting to flowering stages

An advanced backcross population of rice was used to identify the quantitative trait locus (QTL) controlling the cold-tolerance at booting to flowering stages. The recipient, Guichao 2 (GC2), was a commercial Indica rice; the donor Dongxiang common wild rice, was an accession of common wild rice (DXCWR, Oryza rufipogon Griff.). Three QTLs for cold-tolerance were detected on chromosomes 1, 6 and 11. Two of them coming from DXCWR could enhance the cold-tolerance of the backcross progenies. Moreover, one sterility QTL that could reduce the seed set rate of the backcross progenies by 78% was mapped on chromosome 5.

利用高密度遗传图谱定位水稻耐低氧萌发QTL

【目的】耐低氧萌发能力是水稻直播适应性的核心性状之一。采用直播型温带粳稻品种Francis和多穗型优质恢复系R998衍生的重组自交系群体开展水稻耐低氧萌发QTL定位研究,旨在为直播稻品种培育提供新的有价值的基因资源,促进直播稻新品种培育和直播稻生产方式的推广。【方法】以28℃淹水10 cm暗培养7 d的水稻胚芽鞘长、芽长和最大根长作为耐低氧萌发能力指标,通过低倍基因组重测序构建含有3106个bin标记的高密度遗传图谱,采用WinQTL Cart 2.5进行QTL扫描。【结果】低氧萌发条件下,Francis的胚芽鞘长度和根长显著高于R998,但是两者芽长差异不显著。构建的遗传图谱总图距为3646.2 cM,其中12号染色体标记数最少,1号染色体标记数最多,分别为174个和389个。遗传图谱的标记平均图距为1.21 cM,各染色体的平均图距范围为0.68~1.84 cM,5 cM以上的Gap比例为0.36%。采用复合区间作图法(CIM),共检测到分布于5条染色体上的6个耐低氧萌发相关QTL。其中,控制胚芽鞘长度、芽长和根长的QTL个数分别为3、1、2个。表型贡献率超过10%的2个QTL是胚芽鞘长度位点qCL9和芽长位点qSL5,二者分别解释群体表型变异的13.39%和10.78%。qCL9与根长QTL qRL2-1的增效等位基因均来自亲本Francis,其余4个QTL的增效等位基因来自亲本R998。6个QTL中有3个暂未见报道,可能是新的QTL。【结论】Francis和R998低氧萌发特性存在显著差异,双亲中均含有耐低氧萌发的增效等位基因。qCL9和qSL5是分别影响胚芽鞘长和芽长的主效QTL,在直播稻分子育种中具有潜在应用价值。