水稻灌浆期耐热害的数量性状基因位点分析

 利用由98个家系组成的Nipponbare / Kasalath // Nipponbare回交重组自交系群体及其分子连锁图谱，以粒重感热指数\[（适温粒重-高温粒重）/适温粒重×100\]为评价指标，采用混合线性模型的QTL定位方法，对水稻灌浆期耐热性的主效、上位性数量性状基因位点及其与环境的互作进行分析。共检测到3个灌浆期耐热性主效QTL，分别位于第1、4和7染色体上，LOD值为8.16、11.08和12.86，贡献率8.94%、17.25%和13.50%。其中位于第4染色体标记C1100-R1783之间的QTL，没有显著的上位性和环境互作效应，表明在不同环境和遗传背景中的表达较为稳定，在水稻耐热性育种中可能具有较大的利用价值，其耐热性等位基因来自亲本Kasalath，高温热害时可减少粒重损失3.31%。位于第1染色体标记R1613-C970之间的QTL和第7染色体标记C1226-R1440之间的QTL，耐热性等位基因来自亲本Nipponbare，分别可减少粒重损失2.38%和2.92%。这两个QTL均具有与环境的互作效应，其中第7染色体上的QTL还和其他基因位点有互作。检测到8对加性×加性上位性互作QTL，分布于第1、2、3、5、7、8、10和12染色体上。没有检测到上位性QTL与环境的互作效应。     

稻米直链淀粉含量和胶稠度对高温耐性的QTL分析

利用由98个家系组成的Nipponbare/Kasalath//Nipponbare回交重组自交系群体,以直链淀粉含量耐热指数（高温下直链淀粉含量/适温下直链淀粉含量×100）和胶稠度耐热指数（高温下胶稠度/适温下胶稠度×100）为评价指标,采用混合线性模型的QTL定位方法,在南昌和南京两个试验地点对水稻蒸煮食用品质性状的高温耐性QTL进行了检测。两个性状在两个试验地点共检测到9个QTLs,其中直链淀粉含量高温耐性QTL 3个,胶稠度高温耐性QTL 6个。两个性状中共有3个QTLs在两个地点同时被检测到。其中位于第6染色体上与Wx基因相同的染色体区域和第8染色体G1073-R727区域分别是控制直链淀粉含量和胶稠度高温耐性的重要区域。     

水稻抽穗期基因的精细定位、克隆和生物学功能分析

介绍了水稻抽穗期QTL研究的进展,在相同亲本日本晴/Kasalath衍生的不同类型的多个群体中,共检测到15个QTL;应用高世代回交后代,精细定位了其中8个QTL;将在初步定位时同一区间检测到的1个控制种子休眠期QTL(Sdr1)和1个抽穗期QTL (Hd8),分解为两个紧密连锁的基因;将经过精细定位表明可能具有双重功能的单个孟德尔因子Hd3,分解为两个功能不同的紧密连锁的基因Hd3a和Hd3b;根据QTL近等基因系的光周期反应以及这些座位间上位性互作的研究,明确了其中6个QTL的生物学功能;应用图位法克隆了其中3个QTL,研究了它们的表达和调控,并与拟南芥的同源基因进行比较。为水稻其他数量性状以及其他作物数量性状的遗传学研究,提供了一个范例。     

利用染色体片段置换系群体定位和分析水稻粒重和粒型QTL

[目的]挖掘水稻粒重和粒型相关性状QTL,对于解析水稻籽粒遗传机理具有重要作用.[方法]本研究以籼稻9311为受体、粳稻日本晴为供体构建的染色体片段置换系(Chromosome Segment Substitution Lines,CSSLs)群体为材料,在4个环境下对控制稻谷与糙米的粒重和粒型QTL进行了定位分析.[...     

Identification of QTLs for Cooking and Eating Quality of Rice Grain

Rice is one of the major crops served as the staple food of more than 50% of the world’s population. Recently, more attention has been paid to rice quality, especially the cooking and eating quality than achieving the higher yield. The amylose content (AC), gelatinization temperature (GT) and gel consistency (GC) are the three major rice characteristics directly related to cooking and eating quality, responsible for the physical and chemical characteristics of the starch in the endosperm [1…     

利用回交重组自交系定位稻米赖氨酸含量的基因座位

利用日本晴（粳稻）/Kasalath（籼稻）//日本晴组合衍生的98个回交重组自交系（BILs）株系和具有245个RFLP标记的遗传图谱,在浙江和海南2个环境条件下,开展了精米赖氨酸含量的QTL定位。精米赖氨酸含量在浙江和海南均表现连续变异和超亲分离。在第6染色体发现2个具有显著遗传主效应的QTL(qLYS6 1和qLYS6 2）,表型贡献率分别为2708%和4756%。qLYS6 1 还具有显著的环境互作效应。qLYS6 1的增效基因来自Kasalath,而qLYS6 2的增效基因来自日本晴。未检测到显著的上位性效应。     

Confirmation of Novel Quantitative Trait Loci for Seed Dormancy at Different Ripening Stages in Rice

Seed dormancy contributes resistance to pre-harvest sprouting.Effects on respective quantitative trait loci (QTLs) for dormancy should be assessed by using fresh seeds before germinability altered through storage.We investigated QTLs related to seed dormancy using backcross inbred lines derived from a cross between Nipponbare and Kasalath.Four putative QTLs for seed dormancy were detected immediately after harvest using composite interval mapping.These putative QTLs were mapped near C1488 on chromosome 3 (qSD-3.1),R2171 on chromosome 6 (qSD-6.1),R1245 on chromosome 7 (qSD-7.1) and C488 on chromosome 10 (qSD-10.1).Kasalath alleles promoted dormancy for qSD-3.1,qSD-6.1 and qSD-7.1,and the respective proportions of phenotypic variation explained by each QTL were 12.9%,9.3% and 8.1%.We evaluated the seed dormancy harvested at different ripening stages during seed development using chromosome segment substitution lines (CSSLs) to confirm gene effects.The germination rates of CSSL27 and CSSL28 substituted with the region including qSD-6.1 were significantly lower than those of Nipponbare and other CSSLs at the late ripening stage.Therefore,qSD-6.1 is considered the most effective novel QTL for pre-harvest sprouting resistance among the QTLs detected in this study.     

Genetic and physiological analysis of tolerance to acute iron toxicity in rice

Background

Fe toxicity occurs in lowland rice production due to excess ferrous iron (Fe²⁺) formation in reduced soils. To contribute to the breeding for tolerance to Fe toxicity in rice, we determined quantitative trait loci (QTL) by screening two different bi-parental mapping populations under iron pulse stresses (1,000 mg L⁻¹ = 17.9 mM Fe²⁺ for 5 days) in hydroponic solution, followed by experiments with selected lines to determine whether QTLs were associated with iron exclusion (i.e. root based mechanisms), or iron inclusion (i.e. shoot-based mechanisms).

Results

In an IR29/Pokkali F₈ recombinant inbred population, 7 QTLs were detected for leaf bronzing score on chromosome 1, 2, 4, 7 and 12, respectively, individually explaining 9.2-18.7% of the phenotypic variation. Two tolerant recombinant inbred lines carrying putative QTLs were selected for further experiments. Based on Fe uptake into the shoot, the dominant tolerance mechanism of the tolerant line FL510 was determined to be exclusion with its root architecture being conducive to air transport and thus the ability to oxidize Fe²⁺ in rhizosphere. In line FL483, the iron tolerance was related mainly to shoot-based mechanisms (tolerant inclusion mechanism). In a Nipponbare/Kasalath/Nipponbare backcross inbred population, 3 QTLs were mapped on chromosomes 1, 3 and 8, respectively. These QTLs explained 11.6-18.6% of the total phenotypic variation. The effect of QTLs on chromosome 1 and 3 were confirmed by using chromosome segment substitution lines (SL), carrying Kasalath introgressions in the genetic background on Nipponbare. The Fe uptake in shoots of substitution lines suggests that the effect of the QTL on chromosome 1 was associated with shoot tolerance while the QTL on chromosome 3 was associated with iron exclusion.

Conclusion

Tolerance of certain genotypes were classified into shoot- and root- based mechanisms. Comparing our findings with previously reported QTLs for iron toxicity tolerance, we identified co-localization for some QTLs in both pluse and chronic stresses, especially on chromosome 1.     

水稻顶部三叶与穗重的关系及其QTL分析

 摘要: 对水稻汕优63重组自交系群体顶部3张叶片的长、宽、重和单穗重等10个性状进行了相关分析和QTL定位。穗重与9个叶片性状存在极显著的正相关，其中与倒2叶重的相关系数最大，剑叶重次之。所有性状在重组自交系群体中均存在双向超亲分离，接近正态分布。共检测到44个主效QTL和43对双位点互作影响上述10个性状。主效QTL分布于水稻的除第8染色体外的其余11条染色体上，贡献率介于3.19%~26.23%；互作分布于水稻的12条染色体上，贡献率变幅为2.03%~8.93%。第2染色体的R2510-RM211标记区间同时检测到控制单穗重和倒2叶重的QTL，该QTL对超级稻株型育种具有应用价值。     

稻米垩白性状对高温耐性的QTL分析

【目的】本研究旨在筛选与稻米外观品质高温耐性连锁的分子标记,为稻米品质育种提供参考。【方法】以耐热水稻品系996和热敏感水稻品系4628为亲本构建的重组自交系为材料,采用垩白粒率耐热指数、垩白大小耐热指数和垩白度耐热指数为评价指标,对水稻垩白性状的高温耐性QTL进行检测。【结果】采用复合区间作图法两年共检测到垩白性状高温耐性QTL 24个,包括垩白粒率高温耐性QTL 8个,垩白大小高温耐性QTL 12个,垩白度高温耐性QTL 4个。其中,第6染色体上的2个垩白粒率高温耐性QTL和第7染色体上的2个垩白度高温耐性QTL在两年中重复检测到,且这2个稳定表达的垩白度位点与2015年检测到的第7染色体上的垩白粒率位点重合。另外,发现有4个QTL一因多效,同时影响垩白粒率、垩白大小及垩白度。【结论】控制垩白粒率耐热指数的q HTCGR6.1和控制垩白度耐热指数的q HTCD7.1是新的QTL。     

Mapping Quantitative Trait Loci for Palatability of Milled Rice

Quantitative trait loci (QTLs) controlling palatability in rice were identified using a set of 98 backcross inbred lines (BILs) population derived from a cross between a japonica variety Nipponbare and an indica variety Kasalath. The palatability scores of the population measured by RQ1/Plus Rice Analyzer, showed a continuous and transgressive segregative distribution with a range from 66 to 92. Four putative QTLs for palatability, qPAL-5, qPAL-7, qPAL-8a and qPAL-8b, were detected on chromosome 5, 7 and 8, and they accounted 7.83, 7.03, 11.58 and 7.19% of the total phenotypic variation, respectively. Three alleles qPAL-5, qPAL-7 and qPAL-8b from Kasalath increased the palatability score, whereas only one Nipponbare allele qPAL-8a increased the score. Eight transgressive lines in palatability were selected to make a comparison between phenotypic and genotypic classes. The result explained the possibility of positive QTLs pyramiding through marker-assisted selection of highly palatable rice.     

Characterization of physicochemical qualities and starch structures of two indica rice varieties tolerant to high temperature during grain filling

An extreme high temperature during grain filling is an important environmental factor that reduce the yield and quality of rice. In this study, we compared the grain appearance, composition and starch structure of four rice varieties response to high temperature during grain filling. The results obviously revealed that two indica AUS varieties Halwa and Jamir showed more tolerance to high temperature during grain filling than either the japonica Nipponbare or another AUS rice DJ24. The data showed that Halwa and Jamir presented less chalkiness, less grain weight loss, less change of endosperm components as well as starch structure than Nipponbare and DJ24 under high temperature treatment. Hence, the results implied that Halwa and Jamir might be useful targets to further identify genetic mechanism response to high temperature, at least during grain filling and endosperm development. Moreover, these AUS varieties have potential application value in further breeding of rice with good quality and heat tolerance.     

The QTL Analysis of RuBisCO in Flag Leaves and Non-Structural Carbohydrates in Leaf Sheaths of Rice Using Chromosome Segment Substitution Lines and Backcross Progeny F2 Populations

Abstract

In rice (Oryza sativa L.), the maintenance of high photosynthetic rate of flag leaves and the carbon remobilization from leaf sheaths after heading is a critical physiological component affecting the yield. To clarify the genetic basis of RuBisCO content of the flag leaf, a major determinant of photosynthetic rate, and non-structural carbohydrate (NSC) concentration in the third leaf sheath at heading, we carried out quantitative trait loci (QTL) analysis with 39 Koshihikari/Kasalath chromosome segment substitution lines (CSSLs) and backcross progeny F₂ population derived from target CSSL holding the QTL/Koshihikari in the field. QTLs for RuBisCO content and NSC concentration at heading were detected between R2447-C1286 and R2447-R716 on chromosome 10, respectively, by comparing Koshihikari with four CSSLs for chromosome 10 (SL-229, -230, -231 and -232). The progeny QTL for RuBisCO content and for NSC concentration at heading qRCH-10 and qNSCLSH-10-1, respectively, were detected at similar marker intervals between RM8201 and RM5708. In addition, QTLs for RuBisCO content at 14 d after heading, qRCAH-10-1 and qRCAH-10-2, were detected in regions different from that of qRCH-10. No QTL for NSC concentration at 14 d after heading was detected between RM8201 and R716, the region analyzed in this study. The QTLs qRCH-10 and qRCAH-10-1 for RuBisCO content would have additive effects. These QTLs for RuBisCO content and NSC concentration newly found using CSSLs and their backcross progeny F₂ population should be useful for better understanding the genetic basis of source and temporary-sink functions in rice and for genetic improvement of Koshihikari in terms of their functions.     

Identification of QTLs for Improvement of Plant Type in Rice (Oryza sativa L.) Using Koshihikari / Kasalath Chromosome Segment Substitution Lines and Backcross Progeny F2 Population

Abstract

Thirty-nine chromosome segment substitution lines (CSSLs) population derived from a Koshihikari / Kasalath cross was used for quantitative trait locus (QTL) analysis of plant type in rice (Oryza sativa L.). Putative rough QTLs (26.2～60.3cM of Kasalath chromosomal segments) for culm length, plant height, panicle number, chlorophyll content of flag leaf blade at heading and specific leaf weight, were mapped on the several chromosomal segments based on the comparison of CSSLs with Koshihikari in the field experiment for 3 years. In order to verify and narrow QTLs detected in CSSLs, we conducted QTL analyses using F₂ populations derived from a cross between Koshihikari and target CSSL holding a putative rough QTL. The qPN-2, QTL for panicle number was mapped on chromosome 2. In traits of flag leaf, the qCHL-4-1 and qCHL-4-2 for chlorophyll content was mapped on chromosome 4, and the qSLW-7 for specific leaf weight on chromosome 7. All QTLs were detected in narrow marker intervals, compared with rough QTLs in CSSLs. The qPN-2, qCHL-4-1 and qCHL-4-2 had only additive effect. On the other hand, the qSLW-7 showed over-dominance. It could be emphasized that QTL analysis in the present study with the combination of CSSLs and backcross progeny F₂ population can not only verify the rough QTLs detected in CSSLs but also estimate allelic effects on the QTL.     

非洲栽培稻垩白粒率耐热性QTL的定位

【目的】本研究旨在定位一个稻米垩白粒率高温耐性QTL,为外观品质育种及解析垩白粒率高温耐性的遗传机制提供依据。【方法】以非洲栽培稻耐热品种IRGC102309(Oryza glaberrima Steud.)和籼稻品种R9311(O. sativa L. subsp. indica Kato.)为亲本构建的栽培稻种间染色体片段导入系CSIL05-23为材料构建次级分离群体,结合人工气候室模拟灌浆期高温胁迫处理,采用垩白粒率高温钝感值为评价指标,对非洲栽培稻垩白粒率高温耐性 QTL 进行检测。【结果】 在BC₆F₂分离群体,利用单标记分析,发现第5染色体上的SSR标记RM1200与垩白粒率耐热性状极显著正相关（P=0.0005）。进一步利用BC₆F₃和BC₆F₄分离群体,采用QTL Cartographer 2.5软件和复合区间作图法在水稻第5染色体上的SSR标记RM1200-RM5796区间重复检测到一个灌浆期垩白粒率耐热性QTL, 命名为qHTCGR5,分别解释11.4%和17.5%表型变异。根据BC₆F₄分离群体的纯合重组体表型分组,利用置换作图方法将目标QTL同样定位在SSR标记RM1200-RM5796之间,遗传图距为1.3 cM,物理图距约为333.4 kb。【结论】 控制垩白粒率耐热性的qHTCGR5是一个能够用于稻米外观品质育种的新QTL。     

小麦抽穗期QTL及其与环境的互作

为筛选稳定表达的小麦抽穗期QTL用于辅助选择,以旱选10号×鲁麦14的DH群体为试材,在四种环境下对抽穗期进行QTL。结果表明,该DH群体抽穗期呈连续性分布,表现为多基因控制的数量性状。四种环境下共检测到6个抽穗期加性QTLs,分别位于1B、1D、4D、6B、7B、7D染色体上,LOD值为3.13~10.88,贡献率在1.57%~6.72%之间,其中QHd-1D-1和QHd-7B与环境具有互作效应。共检测到10对上位性QTL位点,互作效应值为-0.39~0.423,表型贡献率在1.39%~4.86%之间,其中4对上位性位点与环境具有互作效应。     

利用近等基因系研究3个抗水稻纹枯病QTL的聚合效应

利用特青/Lemont组合的回交群体,证实了特青第7染色体上存在抗纹枯病QTL qSB7Tq。以Lemont为轮回亲本,通过分子标记辅助连续回交结合性状鉴定,构建了qSB7Tq与另外两个抗水稻纹枯病QTL qSB9Tq（位于特青第9染色体）和qSB11Le（位于Lemont第11染色体）的一套近等基因系,对各抗性QTL的单个效应及其聚合效应进行了研究。3个抗性QTL单独存在或在聚合状态下均能显著提高水稻品种对纹枯病的抗性水平。但是,不同抗性QTL之间可能普遍存在一定的负向互作关系。讨论了一致的遗传背景对QTL研究的重要性,以及不同QTL的聚合效应及互作关系对育种实践的意义。     

Mapping quantitative trait loci (QTLs) for seedling-vigor using recombinant inbred lines of rice (Oryza sativa L.)

Seedling-vigor is important for optimum stand establishment and increasing weed competitive ability in rice cropping systems. In the current study, three seedling-vigor-related traits, seed germination rate, seedling shoot length and dry matter weight, were investigated by the paper-roll tests with rice recombinant inbred lines derived from a cross between Lemont (japonica) and Teqing (indica). The phenotype data, together with a linkage map consisting of 198 marker loci, was used to conduct composite interval mapping by QTLMapper 1.0 to simultaneously map both main-effect and epistatic QTLs for seedling-vigor in rice. Totally, 13 putative main-effect QTLs and 19 pairs of epistatic loci with R² ≥ 5% were identified. Almost all of these QTLs or interactions individually explained only around 5–10% of the phenotypic variation. The majority (68%) of these main-effect and epistatic loci were clustered in seven chromosome regions, each spanning 12–28 cM (centi-Morgan) and containing three or more detectable loci. When detectable for the multiple seedling-vigor-related traits, either the main-effect QTLs or the epistatic interactions sharing the same map location had their additive or epistatic effects in the same direction, which agreed well with the positive correlations among the traits. The results demonstrated that seedling-vigor in rice could be controlled by many loci, most of which had small effects, but, relatively, epistasis as a genetic factor was much more important than main-effects of QTLs. Along with the results reported previously, this study revealed the extensive genetic diversity for seedling-vigor in rice. In addition, the QTL q^SV-7 on chromosome 7 was found to have the largest main-effects on multiple seedling-vigor-related traits and therefore could be used as a potential target to be genetically manipulated by marker-assisted selection in rice seedling-vigor breeding programs.     

水稻苗期耐热种质资源筛选及QTL定位

[目的]鉴定和筛选水稻极端耐热种质或基因,为培育耐高温水稻新品种提供技术支撑.[方法]以耐热等级和幼苗存活率为指标对不同类型水稻苗期耐热性进行鉴定评价,以筛选和鉴定耐热种质资源及主效QTL.[结果]不同类型水稻品种苗期耐热性存在明显差异,籼稻品种耐热性明显强于粳稻品种,籼稻和粳稻品种均存在极端耐热和极端敏感种质资源;共...     

特大粒水稻材料粒型性状的QTL检测

 利用特大粒粳稻TD70（2011年千粒重达80 g）和籼稻品种Kasalath杂交,经单粒传法获得的240个重组自交系（RIL）为作图群体,分别于2010年和2011年对粒长、粒宽、粒厚性状进行鉴定,用完备区间作图法,以均匀分布于12条染色体的141个SSR标记对粒型性状进行QTL检测。共检测到粒型性状的 QTL 18 个,分布于第2、3、5、7、9和12染色体上。其中,控制粒长的QTL 5个,控制粒宽的QTL 6个,控制粒厚的QTL 7个。两年间均能检测到的QTL有7个,分别为粒长QTL qGL3.1,粒宽QTL qGW2.1、qGW2.2、qGW5.1、qGW5.2,粒厚QTL qGT2.3、qGT3.1;其平均贡献率分别为56.19%、4.42%、29.41%、10.37%、7.61%、21.19%和17.06%。第2染色体RM1347-RM5699区间是粒长、粒宽、粒厚的共同标记区间。第3染色体RM6080-RM6832区间为粒长qGL3.1、粒厚qGT3.1共同标记区间。18 个QTL的增效等位基因均来源于大粒亲本TD70,且增效作用显著。定位的大部分位点包含已报道的精细定位和克隆的主要粒型基因;除第2染色体的qGW2.1（qGT2.1）、qGW2.3、qGL2.2和第12染色体的qGT12等位点已有粒型性状相关报道外,定位的qGT22,qGW9 和qGT9可能是新的QTL。