水稻耐淹涝性状的遗传分析和SSR标记的研究

淹涝胁迫对水稻生产造成了严重影响, 发掘可应用于耐淹涝辅助选择的分子标记(MAS), 将有助于水稻耐淹涝性状的遗传改良。应用耐淹涝材料FR13A和淹涝敏感材料IR39595-503-2-1-2为亲本做正反交获得F₁和F₂代群体。对正反交的F₁群体的耐淹涝性状进行遗传分析, 发现正反交的F₁代群体在耐淹涝性状上没有显著差异, 说明耐淹涝性状是核基因控制。从两次淹涝处理中F₂代群体的分离情况来看, 来源于FR13A的耐淹特性表现出数量-质量性状遗传的特点。当淹涝胁迫压力比较轻时表现为数量性状遗传, 具有微效多基因的作用。当淹涝胁迫压力增大时, 表现为主效基因控制的质量性状。在SSR分析中, 187对SSR引物中有73对引物在两亲本间有明显的差异, 差异率为39%。用这73对差异引物, 对F2群体进行多态筛选, 结果筛选到一个与耐淹涝性状连锁的标记RM219, 验证了耐淹涝性状确实由主效基因Sub1控制, 因此, RM219在水稻耐淹涝育种中具有利用价值。     

我国水稻功能基因研究获重大进展

中科院上海生科院植物生理生态所植物分子遗传国家重点实验室研究员林鸿宣及其博士生任仲海、高继平等与美国加州大学伯克利分校教授栾升及其助手李乐攻博士进行合作,在水稻重要农艺性状功能基因研究上取得突破性进展,成功克隆了与水稻耐盐相关的数量性状基因SKC1,并阐明了该基因的生物学功能和作用机理。相关论文已在线发表于国际顶级遗传学杂志《自然——遗传学》(Nature Genetics),并将刊登在10月份的《自然——遗传学》上。林鸿宣领导的研究组多年来潜心于水稻耐盐数量性状基因的克隆研究并取得了突破,成功克隆了盐胁迫下控制水稻地上…     

外源调节剂对淹涝水稻幼苗株高及碳水化合物消耗的影响

为研究淹涝条件下水稻幼苗株高及碳水化合物消耗对不同外源生长调节剂的响应,本试验选用籼型常规稻IR64和导入耐淹涝基因Sub1的IR64-Sub1为试验材料,秧龄20 d时喷施1-氨基环丙烷-1-羧酸(ACC)、多效唑(PB)、赤霉素(GA)3种外源生长调节剂,以喷施清水为对照(CK).喷施处理2 d后进行0、4、8、12、16 d没顶淹涝胁迫,淹涝胁迫结束后常温恢复7 d,取样分析不同外源生长调节剂对水稻成活率、株高、叶绿素降解及恢复、地上部非结构性碳水化合物(NSC)消耗的影响.结果表明:淹涝导致水稻幼苗株高显著增长,叶片SPAD值快速下降,叶片可溶性糖迅速消耗,但耐淹涝品种IR64-Sub1淹水前茎鞘NSC含量明显高于IR64,淹涝中NSC消耗速率低于IR64,淹水结束后地上部淀粉含量高于IR64.外源PB处理显著抑制水稻幼苗株高增长、叶绿素降解及NSC消耗,提高存活率,且对IR64-Sub1效果更为显著.外源GA处理水稻幼苗叶绿素降解、株高增长和NSC消耗最快,植株恢复能力最低,耐淹涝能力最差,但与IR64相比,GA对IR64-Sub1淹涝耐性的抑制明显减弱.外源ACC促进伸长效果明显低于外源GA处理.淹水前喷施PB可有效抑制植株水下伸长,延缓叶绿素降解,减缓NSC消耗,保留更多NSC,为淹水胁迫解除后水稻快速恢复提供有利条件,这对于易涝地区减轻涝渍危害具有重要意义.     

水稻萌发耐淹性的遗传分析

水稻(Oryza sativa)萌发耐淹性受到复杂的网络调控, 其分子机制不同于苗期耐淹性的相关机制, 萌发耐淹性的强弱影响着直播稻的成苗率。通过对256份水稻核心种质的萌发耐淹性评估, 发现粳稻和籼稻之间的萌发耐淹性差异并不显著, 都存在广泛的遗传变异。利用以粳稻R0380为供体亲本, 籼稻RP2334为轮回亲本的170个高代回交自交系构建含146个分子标记的连锁图谱, 以低氧胚芽鞘长度为性状指标, 通过复合区间作图法检测到影响萌发耐淹性的4个QTLs(quantitative trait loci), 分别定位于第2(2个)、3(1个)和8号(1个)染色体。贡献率最大的QTL为qGS2.2, 其值为17.34%, 增效等位基因来自轮回亲本籼稻RP2334; 其余3个QTLs的增效等位基因均来自供体亲本粳稻R0380, 贡献率分别为12.86%、9.37%和14.60%。     

水稻种子耐淹特性研究

水稻直播的面积虽然呈逐年增加的趋势,但产量不稳定,其主要原因是水稻种子不耐淹导致直播种子成苗率低.本研究以445份水稻种子为材料,通过大田淹水和量筒淹深水两种模式开展水稻种子发芽和苗期的耐淹特性比较,筛选耐淹水稻品种.结果 表明,在大田淹水处理条件下,不同水稻种子耐淹特性差异明显,根据相对成苗率可分为耐淹、较耐淹、较敏...     

水稻RIL群体苗期耐冷性QTL分析

水稻苗期冷害是影响早春季节和高纬度地区水稻成苗和秧苗生长的重要限制因素之一。为了鉴定控制水稻苗期耐冷性的QTL,研究采用了1个水稻“粳籼交”重组自交系(RIL)群体,结合1张高密度分子遗传图谱,对3叶期幼苗经过10℃冷处理3d、恢复培养2d和4d时的秧苗存活率进行复合区间作图。亲本Lemont和特青的苗期耐冷性具有极显著差异,Lemont的苗期耐冷性很强,而特青对低温敏感。在重组自交系群体中,苗期耐冷性表现为连续变异,在两个方向上均出现大量超亲分离。共检测到5个水稻苗期耐冷性QTL,分别位于水稻1、3、8和11号染色体上,单个QTL对性状的贡献率为7％～21％。其中,4个QTL的增效基因来源于亲本Lemont,另1个QTL的增效基因来源于亲本特青。2个主效QTL(qSCT-3和qSCT-8)分别位于3号染色体标记区间RM282-RM156和8号染色体标记区间RM230—RM264,对性状的贡献率达到或接近20％,被检测到的LOD值显著较高,其增效基因均来自于耐冷性亲本Lemont。研究结果进一步揭示了水稻苗期耐冷性QTL具有丰富的位点多样性,表明耐冷性普遍较强的粳稻是发掘苗期耐冷性优异基因的主要稻种资源。     

长江下游不同类型水稻分蘖期耐淹能力比较

在分蘖期对长江下游稻作区主栽的9个水稻品种进行大田模拟没顶淹涝处理,研究淹涝胁迫对水稻植株农艺性状、生理指标和产量性状的影响,比较分析了常规粳稻、杂交籼稻和杂交粳稻对淹水胁迫环境适应性的差异.结果表明:淹水胁迫4d后,水稻株高及顶部全展3片叶长均比对照有不同程度的增加,伸长程度为杂交粳稻＞杂交籼稻＞常规粳稻.杂交粳稻的茎蘖数、绿叶数和地上部干质量损失率分别为18.0％、41.4％、13.2％,显著小于常规粳稻;杂交籼稻则介于杂交粳稻和常规粳稻之间,且整株死亡率显著低于常规粳稻.常规粳稻叶片中丙二醛(MDA)含量比对照增加1.91 μmol·g-1 FM,超氧化物歧化酶(SOD)和过氧化氢酶(CAT)活性明显降低;杂交粳稻和杂交籼稻MDA含量分别降低2.32和2.10 μmol·g-1 FM,SOD和CAT活性显著提高.不同类型品种的减产程度差异显著,常规粳稻的产量损失率达到38.5％,显著高于杂交粳稻和杂交籼稻,杂交粳稻产量损失率仅为4.1％.长江下游水稻分蘖期的耐淹涝能力为杂交粳稻强于杂交籼稻,常规粳稻的耐淹能力最低.     

水稻粒形遗传的研究进展

水稻（Oryza sativa）粒形性状包括粒长、粒宽、粒厚、粒重和长宽比等,是构成水稻产量的重要因素之一。因此,阐明水稻粒形遗传控制的机理,对提高水稻产量具有十分重要的意义。水稻粒形的遗传是多基因共同作用的数量性状遗传,相对于单一基因控制的性状,研究要相对复杂。该文综述了水稻粒形的遗传特点、QTL定位和基因克隆,并展望了粒形遗传的研究前景。     

水稻苗期耐低钾品种筛选及相关性状的QTL定位

对159份遗传差异较大的水稻品种进行耐低钾筛选,根据综合指数筛选出18份耐低钾和10份低钾敏感的水稻品种。利用筛选得到的耐低钾水稻品种台农67和低钾敏感品种制西构建重组自交系,对耐低钾相关性状进行QTL分析和定位,共检测到27个耐低钾相关性状的QTL,LOD值为2.52～9.23,可解释表型变异为2.22%～7.25%,其中贡献率最高的QTL是qKC-2,该QTL定位在水稻2号染色体上,可能是1个控制水稻钾含量的未知基因,可进一步通过构建次级群体对该基因进行精细定位和克隆。本研究中设计的Indel标记可快速筛选水稻育种材料中的耐低钾基因型,缩短育种时间,而且重组自交系中可以选出农艺性状好又耐低钾的株系直接应用于育种。     

亚洲栽培稻主要驯化性状研究进展

水稻是研究谷类作物驯化的良好材料, 其中种子落粒性消失、休眠性减弱和株型上的变化是水稻驯化过程中的3个关键事件, 造就了高产、发芽整齐及可密植的现代水稻。落粒性丧失一直被认为是野生稻驯化形态学上的最直接证据, 而控制落粒的主要基因Sh4和qSH1分别暗示不同的水稻驯化历史。种子休眠性的减弱适应了现代农业生产上同步发芽的需求, Sdr4、qSD7-1和qSD12基因是目前已知的调控种子休眠性的3个关键位点。野生稻匍匐生长等特点与其长期所在的易变生境有关, 而栽培稻的直立生长形态则适应了农业上密植生产的需要, 受PROG1等基因控制。野生稻的异交特性促进了驯化基因在群体间传播, 而自花授粉则使驯化基因得以稳定遗传, 从而加快人工选择的累积。目前的水稻驯化研究侧重于单基因或一些中性标记, 而对控制驯化性状的网络化通路的进化研究却相对缺乏。随着功能基因组研究的深入, 驯化性状的分子机理将会被全面揭示, 而基于此的网络化通路研究必将更加真实地反应水稻驯化过程。文章综述了水稻关键驯化性状分子机理的研究进展, 为驯化基因网络的研究提供参考, 也为水稻分子设计改良提供新的思路。     

A high-resolution linkage map of the vicinity of the rice submergence tolerance locus Sub1

Resistance to submergence stress is an important breeding objective in areas where rice cultivars are subjected to complete inundation for a week or more. The present study was conducted to develop a high-resolution map of the region surrounding the submergence tolerance gene Sub1 in rice, which derives from the Indian cultivar FR13A. Submergence screening of 8-day-old plants of F₃ families kept for 14 days submerged in 60 cm of water allowed an accurate classification of Sub1 phenotypes. Bulked segregant analysis was used to identify AFLP markers linked to Sub1. A population of 2950 F₂ plants segregating for Sub1 was screened with two RFLP markers flanking the Sub1 locus, 2.4 and 4.9 cM away. Submergence tolerance was measured in the recombinant plants, and AFLP markers closely linked to Sub1 were mapped. Two AFLP markers cosegregated with Sub1 in this large population, and other markers were localized within 0.2 cM of Sub1. The high-resolution map should serve as the basis for map-based cloning of this important locus, as it will permit the identification of BAC clones spanning the region. Received: 15 December 1999 / Accepted: 18 February 2000     

Regulatory interplay of the Sub1A and CIPK15 pathways in the regulation of α-amylase production in flooded rice plants

Rice (Oryza sativa L.) can successfully germinate and grow even when flooded. Rice varieties possessing the submergence 1A (Sub1A) gene display a distinct flooding-tolerant phenotype, associated with lower carbohydrate consumption and restriction of the fast-elongation phenotype typical of flooding-intolerant rice varieties. Calcineurin B-like interacting protein kinase 15 (CIPK15) was recently indicated as a key regulator of α-amylases under oxygen deprivation, linked to both rice germination and flooding tolerance in adult plants. It is still unknown whether the Sub1A- and CIPK15-mediated pathways act as complementary processes for rice survival under O(2) deprivation. In adult plants Sub1A and CIPK15 may perhaps play an antagonistic role in terms of carbohydrate consumption, with Sub1A acting as a starch degradation repressor and CIPK15 as an activator. In this study, we analysed sugar metabolism in the stem of rice plants under water submergence by selecting cultivars with different traits associated with flooding survival. The relation between the Sub1A and the CIPK15 pathways was investigated. The results show that under O(2) deprivation, the CIPK15 pathway is repressed in the tolerant, Sub1A-containing, FR13A variety. CIPK15 is likely to play a role in the up-regulation of Ramy3D in flooding-intolerant rice varieties that display fast elongation under flooding and that do not possess Sub1A.     

Evolutionary analysis of the Sub1 gene cluster that confers submergence tolerance to domesticated rice

BACKGROUND AND AIMS: Tolerance of complete submergence is recognized in a small number of accessions of domesticated Asian rice (Oryza sativa) and can be conferred by the Sub1A-1 gene of the polygenic Submergence-1 (Sub1) locus. In all O. sativa varieties, the Sub1 locus encodes the ethylene-responsive factor (ERF) genes Sub1B and Sub1C. A third paralogous ERF gene, Sub1A, is limited to a subset of indica accessions. It is thought that O. sativa was domesticated from the gene pools of the wild perennial species O. rufipogon Griff. and/or the annual species O. nivara Sharma et Shastry. The aim of this study was to evaluate the orthologues of the Sub1 locus in the closest relatives of O. sativa to provide insight into the origin of the gene and allelic variation of the Sub1 locus. METHODS: Orthologues of the Sub1 genes were isolated from O. rufipogon and O. nivara by use of oligonucleotide primers corresponding to the most highly conserved regions of the Sub1 genes of domesticated rice. The phylogenetic relatedness of Sub1 genes of O. sativa and its wild relatives was evaluated. KEY RESULTS AND CONCLUSIONS: Both O. rufipogon and O. nivara possess two Sub1 gene orthologues with strong sequence identity to the Sub1B and Sub1C alleles of cultivated rice. The phylogeny of the Sub1 genes of the domesticated and wild rice suggests that Sub1A arose from duplication of Sub1B. Variation in Sub1B alleles is correlated with the absence or presence of Sub1A. Together, the results indicate that genetic variation at the Sub1 locus is due to gene duplication and divergence that have occurred both prior to and after rice domestication.     

Introgression of dual abiotic stress tolerance QTLs (Saltol QTL and Sub1 gene) into Rice (Oryza sativa L.) variety Aiswarya through marker assisted backcross breeding

Salinity and submergence are two very prominent abiotic stress conditions affecting rice yield adversely in the coastal agro ecosystem. Marker Assisted Backcross Breeding (MABB) is an efficient and fast track molecular tool to incorporate a desired stress tolerant QTL/gene into an improved cultivar. The present study was carried out for the introgression of Saltol QTL responsible for salinity tolerance and Sub1 gene responsible for submergence tolerance into the high yielding rice variety Aiswarya independently through MABB. Final objective of the study is to develop dual stress tolerant (tolerance to salinity and submergence) Aiswarya rice variety by pyramiding the both target QTLs introgressed BC₂F₂ progenies having maximum background homozygosity. The donors of Saltol QTL and Sub1 gene used in the present study were FL478 and Swarna Sub1, respectively. Based on the background genome analysis of the introgressed plants, the plants with > 85–90% background similarity were selected for pyramiding of Saltol QTL and Sub1 gene into the elite background of rice variety Aiswarya. Those selected introgressed lines with Saltol QTL and Sub1 gene will be again crossed to pyramid both Saltol QTL and Sub1 gene into the rice variety Aiswarya. Such a mega rice variety pyramided with dual stress tolerant QTLs is the expected outcome of this study and can be recommended for cultivation in the flood prone saline coastal agroecosystem.     

A marker-assisted backcross approach for developing submergence-tolerant rice cultivars

Submergence stress regularly affects 15 million hectares or more of rainfed lowland rice areas in South and Southeast Asia. A major QTL on chromosome 9, Sub1, has provided the opportunity to apply marker assisted backcrossing (MAB) to develop submergence tolerant versions of rice cultivars that are widely grown in the region. In the present study, molecular markers that were tightly linked with Sub1, flanking Sub1, and unlinked to Sub1 were used to apply foreground, recombinant, and background selection, respectively, in backcrosses between a submergence-tolerant donor and the widely grown recurrent parent Swarna. By the BC₂F₂ generation a submergence tolerant plant was identified that possessed Swarna type simple sequence repeat (SSR) alleles on all fragments analyzed except the tip segment of rice chromosome 9 that possessed the Sub1 locus. A BC₃F₂ double recombinant plant was identified that was homozygous for all Swarna type alleles except for an approximately 2.3–3.4 Mb region surrounding the Sub1 locus. The results showed that the mega variety Swarna could be efficiently converted to a submergence tolerant variety in three backcross generations, involving a time of two to three years. Polymorphic markers for foreground and recombinant selection were identified for four other mega varieties to develop a wider range of submergence tolerant varieties to meet the needs of farmers in the flood-prone regions. This approach demonstrates the effective use of marker assisted selection for a major QTL in a molecular breeding program. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Genes/QTLs affecting flood tolerance in rice

The adaptation of deepwater rice to flooding is attributed to two mechanisms, submergence tolerance and plant elongation. Using a QTL mapping study with replicated phenotyping under two contrasting (water qualities) submergence treatments and AFLP markers, we were able to identify several genes/QTLs that control plant elongation and submergence tolerance in a recombinant inbred rice population. Our results indicate that segregation of rice plants in their responses to different flooding stress conditions is largely due to the differential expression of a few key elongation and submergence tolerance genes. The most important gene was QIne1 mapped near sd-1 on chromosome 1. The Jalmagna (the deepwater parent) allele at this locus had a very large effect on internal elongation and contributed significantly to submergence tolerance under flooding. The second locus was a major gene, sub1(t), mapped to chromosome 9, which contributed to submergence tolerance only. The third one was a QTL, QIne4, mapped to chromosome 4. The IR74 (non-elongating parent) allele at this locus had a large effect for internal elongation. An additional locus that interacted strongly with both QIne1 and QIne4 appeared near RG403 on chromosome 5, suggesting a complex epistatic relationship among the three loci. Several QTLs with relatively small effects on plant elongation and submergence tolerance were also identified. The genetic aspects of these flooding tolerance QTLs with respect to patterns of differential expression of elongation and submergence tolerance genes under flooding are discussed. Received: 13 December 1999 / Accepted: 14 March 2000<@head-com-p1a.lf>Communicated by G. Wenzel     

Development of submergence-tolerant rice cultivars: the Sub1 locus and beyond

Background and Aims

Submergence is a recurring problem in the rice-producing rainfed lowlands of south and south-east Asia. Developing rice cultivars with tolerance of submergence and with agronomic and quality traits acceptable to farmers is a feasible approach to address this problem. The objectives of this study were to (a) develop mega varieties with Sub1 introgression that are submergence tolerant, (b) assess the performance of Sub1 in different genetic backgrounds, (c) determine the roles of the Sub1A and Sub1C genes in conferring tolerance, and (d) assess the level of tolerance in F₁ hybrids heterozygous for the Sub1A-1-tolerant allele.

Methods

Tolerant varieties were developed by marker-assisted backcrossing through two or three backcrosses, and their performance was evaluated to determine the effect of Sub1 in different genetic backgrounds. The roles of Sub1A and Sub1C in conferring the tolerant phenotype were further investigated using recombinants identified within the Sub1 gene cluster based on survival and gene expression data.

Key Results

All mega varieties with Sub1 introgression had a significantly higher survival rate than the original parents. An intolerant Sub1C allele combined with the tolerant Sub1A-1 allele did not significantly reduce the level of tolerance, and the Sub1C-1 expression appeared to be independent of the Sub1A allele; however, even when Sub1C-1 expression is completely turned off in the presence of Sub1A-2, plants remained intolerant. Survival rates and Sub1A expression were significantly lower in heterozygotes compared with the homozygous tolerant parent.

Conclusions

Sub1 provided a substantial enhancement in the level of tolerance of all the sensitive mega varieties. Sub1A is confirmed as the primary contributor to tolerance, while Sub1C alleles do not seem important. Lack of dominance of Sub1 suggests that the Sub1A-1 allele should be carried by both parents for developing tolerant rice hybrids.Key words: Oryza sativa, Sub1, marker-assisted backcrossing, mega varieties, submergence tolerance, recombinant, hybrid, abiotic stress