利用染色体片段置换系定位水稻赖氨酸含量的QTL

 以籼稻品种9311为受体、粳稻品种日本晴为供体构建95个染色体片段置换系, 对水稻控制赖氨酸含量的QTL进行了定位。结果显示, 共有7个染色体片段置换系（chromosome segment substitution line, CSSL）的稻米赖氨酸含量与亲本9311差异显著。利用代换作图法共鉴定了4个与赖氨酸含量相关的QTL, 分别位于水稻第8、9和12染色体上。其中qHLY8和qHLY9.2来自高赖氨酸含量籼稻品种9311, 正向加性效应百分率分别为9.6%和8.5%;而qHLY9.1和qHLY12则来自低赖氨酸含量粳稻品种日本晴, 负向加性效应百分率分别为-16.0%和-21.3%。     

水稻米粒延伸性QTLs定位和基因型与环境互作分析

 利用协青早B/密阳46所构建的重组自交系群体及其相应分子遗传图谱，在海南和杭州两地试验，以延伸率作为米粒延伸性考察指标，检测QTL主效应、上位性效应和基因型×环境互作效应的遗传分析方法，进行联合检测分析。结果表明，该性状两地间的平均表现和群体分布特征较为相似，但两地间表型值相关系数却较小。试验检测到1个控制该性状的QTL基因qCRE 6,其增效基因来自于父本，提高3.99%的米粒延伸率，可解释5.30%的表型变异，它不存在与环境间显著互作。另外，还检测到2对上位性互作基因，即qCRE 2与qCRE 5 1、qCRE 5 2与qCRE 7,前者与环境间存在有显著的基因型×环境互作，在杭州有增加米粒延伸性的效果。     

利用三倍体胚乳遗传模型定位爆裂玉米子粒蛋白含量QTL

在两种环境条件下种植以普通玉米自交系丹232和爆裂玉米自交系N04为亲本构建的259个F23∶家系群体,采用SSR标记构建了包含183个标记的爆裂玉米遗传连锁图谱,覆盖玉米基因组1762.2cM,标记间平均距离为9.6cM。利用三倍体胚乳遗传模型和区间作图方法对子粒蛋白含量进行了QTL定位和效应分析。在春、夏播条件下均检测到6个QTL,分别位于第1、3、4、6、7和第8染色体上,其中春、夏播条件下都检测到的QTL有3个,可解释的表型总变异分别为42.85%和53.19%,单个QTL可解释的表型变异为4.50%～17.70%。表现为加性、部分显性、显性和超显性的QTL数目分别为2、2、2和6。3个QTL的增效基因均来自丹232,其余QTL的增效基因均来自N04。     

利用贝叶斯法进行水稻籽粒植酸含量性状的QTL定位及互作分析

 利用水稻植酸含量差异较大的品种中花11(粳型)和LPA（籼型）为亲本杂交获得F2群体的172个单株,构建了含126个SSR和4个STS标记的遗传连锁图谱,利用贝叶斯（Bayesian）法对水稻籽粒植酸含量性状进行了主效应QTL定位和上位性互作分析。共检测到 3 个与水稻籽粒植酸含量性状有关的主效QTL,分布在第3、5和6 染色体的相应区间内,表型贡献率分别为538%、802%和462%,降低籽粒植酸含量的等位基因均来自亲本LPA。检测到10对上位性互作影响籽粒植酸含量, 分布于水稻第1、3、5、6、11染色体上,互作效应值为169～518,其表型变异的解释率为867%～2473%。     

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。     

超级杂交稻协优9308重组自交系群体的穗部性状QTL分析

 将281个株系组成的超级杂交稻协优9308重组自交系群体种植在海南陵水（2006年和2007年）和浙江富阳（2006年）,采用Windows QTL Cartographer 2.5的复合区间作图法进行QTL检测。共检测到控制7个穗部性状的52个QTL,其中包括7个控制穗长的QTL,8个控制一次枝梗数的QTL,9个控制二次枝梗数的QTL,6个控制着粒密度的QTL, 7个控制每穗总粒数的QTL,11个控制每穗实粒数的QTL,4个控制结实率的QTL。单个QTL对群体性状表型变异的贡献率为23%~312%。控制穗部性状的QTL基本上以加性效应为主,上位性效应和环境互作效应不大。在3组试验中都检测到控制3个穗部性状的8个QTL：qPL-1,qPL-6-1;qTNSP-1,qTNSP-2,qTNSP-3;qNFGP-1,qNFGP-3-2,qNFGP-6-2。这些QTL,尤其是第3染色体RM168-RM143区间控制每穗总粒数的qTNSP-3和控制每穗实粒数的qNFGP-3-2,其加性效应值和贡献率均较大,可以考虑下一步进行QTL精细定位和克隆。研究发现多个重要QTL聚集区间,在同一QTL聚集区间,控制相关性状的QTL效应方向基本上相同,利用这些QTL紧密连锁的分子标记进行辅助选择,可望同时针对多个性状进行遗传改良。     

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。     

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。     

酸刺激和谷氨酸处理对不同粳稻品种稻谷γ-氨基丁酸积累的影响

以常优94 1、浙湖9423、R717、中超123、赚钱1号和日本晴6个粳稻品种为材料,比较研究了种子萌发时间、酸刺激和L 谷氨酸（L-Glu）浸泡处理对不同品种稻谷中GABA积累的影响。萌发活化4～6 d、pH 6.0缓冲液浸泡2 h及50 mmol/L的L Glu 浸泡12 h能显著促进萌发稻谷中GABA的积累,使萌发稻谷中GABA含量较萌发前增加0.8～5.9倍; 不同品种稻谷GABA初始含量不同,萌发活化、酸刺激和L-Glu浸泡处理对稻谷积累GABA的促进效应具有很大的品种差异。经处理后中超123和日本晴两个品种GABA含量高,分别达到1.1236 mg/g和0.9064 mg/g,是萌发前的5.6和22倍。     

水稻剑叶全氮含量及其变化的遗传分析

 以籼稻品种IR24 和粳稻品种Asominori 及其染色体片段置换系（CSSLs）群体为遗传研究材料, 在抽穗后5个不同时期分别测定剑叶全氮含量，并结合水稻RFLP分子标记连锁图谱,对水稻剑叶全氮含量性状进行QTL的动态定位，探讨了控制剑叶全氮含量基因在水稻发育过程中的时序表达方式。在抽穗后各时期共检测到7个QTL, 位于第2和第11染色体上的2个QTL（QN 2、QN 11）增效基因来自粳稻品种Asominori，其他QTL的增效基因来自籼稻IR24；抽穗后2周内检测到2个QTL，即QN 3和QN 8b, 其加性效应值较大, 解释表型变异的贡献率较高；后期检测到的QTL加性效应和贡献率较低，位于第2染色体上R3393的QN 2位点的基因在抽穗后第3周内表达, 位于第8染色体上G1149的QN 8位点的基因在抽穗后第4周内表达，位于第11染色体上G1465的QN 11位点的基因在抽穗后４周和５周持续表达。控制剑叶全氮含量的基因在抽穗后早期表达较为活跃，可以应用于改良水稻品种的剑叶光合功能；在测定末期检测到的控制剑叶全氮含量的QTL，则可以用于延缓叶片早衰的育种改良。     

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。     

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.     

Mapping QTL for Heat-Tolerance at Grain Filling Stage in Rice

A mapping population of 98 lines (backcross inbred lines, BILs) derived from a backcross of Nipponbare/Kasalath// Nipponbare was planted at two experimental sites, Nanjing and Nanchang, and treated with high and optimal temperature during grain filling, respectively. The grain weight heat susceptibility index [GWHSI= (grain weight at optimum temperature-grain weight at high temperature) / grain weight at optimum temperature ×100] was employed to evaluate the tolerance of rice to heat stress. A genetic linkage map with 245 RFLP markers and a mixed linear-model approach was used to detect quantitative trait loci (QTLs) and their main effects, epistatic interactions and QTL×environment interactions (Q×E). The threshold of LOD score=2.0 was used to detect the significance of association between marker and trait. A total of 3 QTLs controlling heat tolerance during grain filling were detected, on chromosomes 1, 4 and 7, with LOD scores of 8.16, 11.08 and 12.86, respectively, and they explained the phenotypic variance of 8.94, 17.25 and 13.50 %, correspondingly. The QTL located in the C1100-R1783 region of chromosome 4 showed no QTL×environment interaction and epistatic effect, suggesting that it could be stably expressed in different environments and genetic backgrounds, and thus it would be valuable in rice breeding for heat tolerance improvement. This QTL allele, derived from Kasalath reduced 3.31% of the grain weight loss under heat stress. One located between R1613-C970 on chromosome 1 and the other between C1226-R1440 on chromosome 7, with additive effect 2.38 and 2.92%, respectively. The tolerance alleles of both these QTLs were derived from Nipponbare. Both of these QTLs had significant QTL×environment interactions, and the latter was involved in epistatic interaction also. Eight pairs of epistatic effect QTLs were detected, one pair each on chromosomes 1,2,3, 5, 7, 8, 10 and 12. The results could be useful for elucidating the genetic mechanism of heat-tolerance and the development of new rice varieties with heat tolerance during grain filling phase.     

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.     

Root plasticity under fluctuating soil moisture stress exhibited by backcross inbred line of a rice variety,Nipponbare carrying introgressed segments from KDML105 and detection of the associated QTLs

In rainfed lowland rice ecosystem, rice plants are often exposed to alternating recurrences of waterlogging and drought due to erratic rainfall. Such soil moisture fluctuation (SMF) which is completely different from simple or progressive drought could be stressful for plant growth, thereby causing reduction in yield. Root plasticity is one of the key traits that play important roles for plant adaptation under such conditions. This study aimed to evaluate root plasticity expression and its functional roles in dry matter production and yield under SMF using Nipponbare, KDML 105 and three backcross inbred lines (BILs) and to identify QTL(s) associated with root traits in response to SMF at two growth stages using Nipponbare/KDML105 F₂ plants. A BIL, G3-3 showed higher shoot dry matter production and yield than Nipponbare due to its greater ability to maintain stomatal conductance concomitant with greater root system development caused by promoted production of nodal and lateral roots under SMF. QTLs were identified for total nodal root length, total lateral root length, total root length, number of nodal roots, and branching index under SMF at vegetative and reproductive stages. The QTLs detected at vegetative and reproductive stages were different. We discuss here that relationship between root system of G3-3 and the detected QTLs. Therefore, G3-3 and the identified QTLs could be useful genetic materials in breeding program for improving the adaptation of rice plants in target rainfed lowland areas.     

稻米淀粉RVA谱特征值与直链淀粉、蛋白含量的相关性及QTL定位分析

【目的】检测到新的控制稻米品质性状相关的QTL并分析各性状间的相关性,为了解控制水稻品质的遗传机理和培育优质水稻品种奠定基础。【方法】利用Sasanishiki×Habataki回交重组自交系(backcross inbred lines,BILs)群体在两个环境下种植的结果,检测与稻米直链淀粉含量、蛋白质含量及RVA谱特征值相关的加性QTL。【结果】表型分析结果显示,Habataki的蛋白含量明显高于Sasanishiki;而除消减值以外其余的稻米品质性状指标,Sasanishiki均高于Habataki。利用BIL群体共检测到加性QTL 42个,其中10个QTL位点在2个环境中均能被检测到,即q PC8、q AC4、q AC10、q PKV2、q PKV7、q HPV7、q CPV1、q BDV4、q BDV7、q SBV7,且q CPV1、q BDV4、q PKV7、q HPV7和q AC10等5个QTL尚未见报道。同时,我们还利用Sasanishiki×Habataki染色体片断置换系(Chromosome segment substitution lines,CSSLs)验证了10个稳定表达的QTL位点。【结论】稻米RVA谱特征值与直链淀粉含量、蛋白质含量之间呈现一定相关性,且控制不同品质性状的QTL之间具有共定位现象。