水稻第1染色体短臂粒长和粒宽QTL的精细定位

以第1染色体短臂RM1-RM3746和RM151-RM243区间内呈杂合、背景基本纯合的2个水稻剩余杂合体（RHL）衍生两个F6群体,将控制水稻粒长和粒宽的2个粒形QTL（qGL 1和qGW 1）定位于RM3746-RM243区间内。在此基础上,应用SSR标记检测,从其中1个群体中筛选到杂合区间分别为RM151-RM10404、RM10398-RM5359、RM10435-RM259和RM10381-RM243的4个单株,应用SSR标记进一步检测4套F2群体,从每套F2群体中分别筛选到母本珍汕97B和父本密阳46纯合型材料各10株,自交获得4套近等基因系材料并考查其粒长和粒宽。利用交迭重组染色体片段代换系分析法,将控制粒长和粒宽的QTL （qGL 1和qGW 1）界定于437.5 kb的RM10390-RM1344区间和392.9 kb的RM10376-RM10398区间,增效等位基因均来自母本珍汕97B,表明qGL 1和qGW 1是紧密连锁的不同座位。     

QTL Mapping for Grain Size Traits Based on Extra-Large Grain Rice Line TD70

Grain size traits, including grain length, grain width and grain thickness, are controlled by quantitative trait loci （QTLs）. Many QTLs relating to rice grain size traits had been reported, but their control mechanisms have not yet been elucidated. A recombinant inbred line （RIL） population of 240 lines, deriving from a cross between TD70, an extra-large grain size japonica line with 80 g of 1000-grain weight, and Kasalath, a small grain size indica variety, were constructed and used to map grain size QTLs to a linkage map by using 141 SSR markers in 2010 and 2011. Five QTLs for grain length, six for grain width and seven for grain thickness were detected distributing over chromosomes 2, 3, 5, 7, 9 and 12. Seven QTLs, namely qGL3.1, qGW2, qGW2.2, qGW5.1, qGW5.2, qGT2.3 and qGT3.1, were detected in either of the two years and explained for 56.19%, 4.42%, 29.41%, 10.37%, 7.61%, 21.19% and 17.06% of the observed phenotypic variances on average, respectively. The marker interval RM1347-RM5699 on chromosome 2 was found common for grain length, grain width and grain thickness; qGL3.1 and qGT3.1 were mapped to the same interval RM6080-RM6832 on chromosome 3. All 18 QTL alleles were derived from the large grain parent TD70. Most of the QTLs mapped in the present study were found the same as the genes previously cloned （GW2, GS3 or qGL3, GW5 and GS5）, and several were the same as the QTLs （GS7 and qGL-7） previously mapped. Three QTLs, qGL2.2 on chromosome 2, qGW9 and qGT9 on chromosome 9, were first detected. These results laid a foundation for further fine mapping or cloning of these QTLs.     

水稻种子低氧发芽力的QTL定位和上位性分析

利用35份水稻品种资源,评价了在不同水深、温度等低氧条件下的种子萌发情况,表明水温30℃、水深0.2 m下黑暗萌发5 d为最佳鉴定方法,并以此条件下水稻种子萌发的芽长为鉴定指标,评价了359份水稻品种低氧发芽力地区间、籼粳间的差异。进一步利用81个Kinmaze/DV85 重组自交系群体进行了水稻低氧发芽力数量性状位点分析, 在第1、2、5、7染色体上检测到5 个低氧发芽力QTL,其中第5染色体上存在2个QTL,各QTL的贡献率为10.5%～19.6%。同时进行上位性分析,检测到3对互作位点,分别位于第2、3、5、11染色体上,其中位于第3染色体上标记C563-X182之间的位点与第5染色体上标记R830-X208之间的位点的互作贡献率高达48.78%。     

粳稻垩白性状的QTL检测

 利用大粒粳稻DL115与小粒粳稻XL005杂交获得的F2群体200个单株为作图群体,采用复合区间作图方法,利用SSR标记对稻米垩白性状进行了数量性状基因座(QTL)检测。研究结果表明,稻米垩白粒率、垩白大小和垩白度在F3株系均呈连续分布,表现为由多基因控制的数量性状。检测到与稻米垩白性状相关的QTL 8个,分别位于第3（5个）、第5（2个）和第6（1个）染色体上,包括与垩白粒率有关的QTL 3个,与垩白大小相关的QTL 2个,与垩白度有关的QTL 3个。其中位于第3染色体RM6832-RM411、RM15456-RM6832和RM6266-RM15456区间的qPGWC3、qACE3b和qDEC3b,分别解释垩白粒率、垩白大小和垩白度表型变异的43.89%、18.83%和19.57%,为主效QTL。上述3个主效QTL所在染色体上的位置与前人研究结果均不一致,认为是新的QTL。所检测到的8个QTL中,除qPGWC6的增效等位基因来自无垩白亲本XL005外,其他7个QTL的增效等位基因均来自垩白性状值较大的亲本DL115。垩白粒率和垩白大小基因作用表现为部分显性,垩白度基因作用表现为加性。     

稻米出饭特性QTL分析及遗传研究

 米粒长、饭粒长和饭粒延伸系数等性状与米饭品质密切相关。以籼稻台中本地1号（TN1）与粳稻春江06为亲本构建的加倍单倍体群体为材料,利用全基因饱和分子标记连锁遗传图谱对多个稻米出饭特性相关的性状进行QTL定位, 共检测到14个QTL。其中,米粒长和米粒浸长QTL各1个,均位于第2染色体上,分别可以解释性状变异的15.20% 和1850%;1个米粒浸泡膨胀率QTL,位于第6染色体上,可解释性状变异的1339%;1个煮饭粒长QTL,位于第9染色体上,可解释性状变异的1360%; 3个蒸饭粒长QTL,分别位于第1、3和12染色体上,共解释性状变异4500%;4个煮饭延伸率QTL, 分别位于第3、6、9和10染色体上,共解释性状变异6130%; 3个蒸饭延伸率QTL分别位于第1、3和6染色体上,共解释性状变异4910%。在已知的Wx和ALK基因所在区域都检测到了米饭延伸性相关的QTL。相比较而言,覆盖ALK基因的QTL对出饭特性的影响更大,LOD值达到了635。该研究结果可为稻米出饭特性相关调控基因的克隆奠定基础,同时对稻米品质的改良及高产优质稻品种的分子标记辅助选育提供理论参考。     

Quantitative Trait Loci for Mercury Tolerance in Rice Seedlings

Mercury (Hg) is one of the most toxic heavy metals to living organisms and its conspicuous effect is the inhibition of root growth.However,little is known about the molecular genetic basis for root growth under excess Hg2+ stress.To map quantitative trait loci (QTLs) in rice for Hg2+ tolerance,a population of 120 recombinant inbred lines derived from a cross between two japonica cultivars Yuefu and IRAT109 was grown in 0.5 mmol/L CaCl2 solution.Relative root length (RRL),percentage of the seminal root length in +HgCl2 to-HgCl2,was used for assessing Hg2+ tolerance.In a dose-response experiment,Yuefu had a higher RRL than IRAT109 and showed the most significant difference at the Hg2+ concentration of 1.5 μmol/L.Three putative QTLs for RRL were detected on chromosomes 1,2 and 5,and totally explained about 35.7% of the phenotypic variance in Hg2+ tolerance.The identified QTLs for RRL might be useful for improving Hg2+ tolerance of rice by molecular marker-assisted selection.     

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.     

Identification of New Resistance Loci Against Sheath Blight Disease in Rice Through Genome-Wide Association Study

Sheath blight (SB) caused by the soil borne pathogen Rhizoctonia solani is one of the most serious global rice diseases. Breeding resistant cultivar is the most economical and effective strategy to control the disease. However, no rice varieties are completely resistant to SB, and only a few reliable quantitative trait loci (QTLs) linked with SB resistance have been identified to date. In this study, we conducted a genome-wide association study (GWAS) of SB resistance using 299 varieties from the rice diversity panel 1 (RDP1) that were genotyped using 44 000 high-density single nucleotide polymorphism (SNP) markers. Through artificial inoculation, we found that only 36.5% of the tested varieties displayed resistance or moderate resistance to SB. In particular, the aromatic and aus sub-populations displayed higher SB resistance than the tropical japonica (TRJ), indica and temperate japonica sub-populations. Seven varieties showed similar resistance levels to the resistant control YSBR1. GWAS identified at least 11 SNP loci significantly associated with SB resistance in the three independent trials, leading to the identification of two reliable QTLs, qSB-3 and qSB-6, on chromosomes 3 and 6. Using favorable alleles or haplotypes of significantly associated SNP loci, we estimated that both QTLs had obvious effects on reducing SB disease severity and can be used for enhancing SB resistance, especially in improving SB resistance of TRJ sub-population rice varieties. These results provided important information and genetic materials for developing SB resistant varieties through breeding.     

Quantitative Trait Loci for Heading Date and Their Relationship with Genetic Control of Yield Traits in Rice (Oryza sativa)

Grain yield and heading date are key factors determining the commercial potential of a rice variety. Mapping of quantitative trait loci (QTLs) in rice has been advanced from primary mapping to gene cloning, and heading date and yield traits have always attracted the greatest attention. In this review, genomic distribution of QTLs for heading date detected in populations derived from intra-specific crosses of Asian cultivated rice (Oryza sativa) was summarized, and their relationship with the genetic control of yield traits was analyzed. The information could be useful in the identification of QTLs for heading date and yield traits that are promising for the improvement of rice varieties.     

水稻抽穗期QTL及其与产量性状遗传控制的关系

 产量和抽穗期是评价水稻品种应用价值的基本性状。水稻QTL分析已经历了从初定位到基因克隆的发展过程,并以抽穗期和产量性状最受重视。总结了亚洲栽培稻抽穗期QTL的基因组分布,分析了这些QTL与产量性状遗传控制的关系,为进一步筛选和鉴定具有较高育种应用潜力的水稻抽穗期QTL和产量性状QTL提供参考。     

用培矮64S/日本晴F2群体对水稻6个农艺性状的QTL定位

 用水稻测序品种培矮64S和日本晴配组建立了由180个单株组成的F2群体，构建了含137个SSR标记的连锁遗传图谱，对水稻的分蘖数、有效分蘖数、分蘖率、株高、剑叶长和穗长等6个相关农艺性状进行了QTL定位分析。共检测到14个QTL，分布在第1、2、4、5、6、7染色体的11个区间。检测到1个控制株高的主效QTL(qPH1 2),位于第1染色体，其表型贡献率为24.0%；1个控制剑叶长的主效QTL(qFL4）,位于第4染色体，其表型贡献率为30.5%。对所定位QTL的价值、QTL在染色体上的区域分布等进行了探讨。     

Quantitative Trait Loci Associated with Pollen Fertility under High Temperature Stress at Flowering Stage in Rice (Oryza sativa)

High temperature stress (HTS), an increasingly important problem in rice production, significantly reduces rice yield by reducing pollen fertility and seed setting rate. Breeding rice varieties with tolerance to HTS at the flowering stage is therefore essential for maintaining rice production as the climate continues to become warm. In this study, two quantitative trait loci (QTLs) underlying tolerance to HTS were identified using recombinant inbred lines derived from a cross between an HTS-tolerant rice cu...     

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.     

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。     

水稻抗条纹叶枯病数量性状座位分析

为探明水稻品种窄叶青8号抗条纹叶枯病的数量性状座位,构建了窄叶青8号/武育粳3号F2群体的分子图谱,采用人工接种和田间自然接种两种鉴定方法,以病情指数比率为表型值,对每个F2单株衍生的F2∶3家系进行了抗条纹叶枯病鉴定。整个群体的病情指数比率均呈偏向于抗性亲本的连续性分布,表明条纹叶枯病抗性受数量性状基因的控制。进一步的QTL分析发现,两种鉴定方法所检测到的QTL完全不同,人工接种（强迫饲毒）方法仅检测到1个抗性基因位点qSTV7,其增强抗性的等位基因来源于窄叶青8号,而田间自然接种方法检测到2个抗性基因位点qSTV5和qSTV1,其增强抗性的等位基因分别来源于窄叶青8号和武育粳3号,暗示抗性亲本窄叶青8号可能携带耐病毒基因和抗灰飞虱基因,而感病亲本武育粳3号经遗传重组后,其抗性基因也得以表现。比较前人研究结果,发现检测到的QTL为新的抗条纹叶枯病基因位点,这些基因不同于抗条纹叶枯病主基因Stvb i,可为防止单一基因广泛使用造成的遗传脆弱性,提供新的抗性基因资源。     

水稻单穗重和千粒重的QTL定位

用基于混合线性模型的统计方法对一套来源于亲本IR64/Azucena的加倍单倍体群体在两个生产季节的水稻单穗重和千粒重进行了分析,各检测到15个QTL分别控制这两个性状,其中有6个QTL同时与这两个性状有关。所有QTL分布在除第11、12染色体以外的其余10条染色体的相应标记区间内。在控制千粒重的QTL中,12个QTL有加性效应,6对QTL带有加加上位性效应,它们不受环境条件的影响。在控制单穗重的QTL中,7个QTL具有加性效应,但其中4个QTL的表达随环境而异;6对QTL具有加加上位性,但其中1对对环境敏感。qTGW2的加性效应对千粒重的贡献率超过10%;3个QTL（qGW1、qGW7和 qGW8 1）在早季环境的加性效应对单穗重的贡献率亦都大于10%,但对环境敏感。     

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。     

小麦籽粒WSC含量QTL的整合与元分析

在干旱胁迫条件下,小麦营养器官暂贮性可溶性碳水化合物(Water-soluble carbohydrates,WSC)是小麦籽粒灌浆所需的重要碳源。为发掘控制小麦籽粒WSC含量的真实主效数量性状位点(Quantitative trait loci,QTL),利用生物信息学方法,借助小麦高密度分子标记遗传图谱,对来自不同遗传作图群体的控制小麦籽粒WSC含量的168个QTL位点进行图谱映射和元分析。结果发现,142个QTL定位区间与参考图谱有共有标记,其中92个QTL对籽粒WSC含量的表型变异具有增效效应,50个QTL具有减效效应。建立控制小麦籽粒WSC含量的QTL一致性图谱,获得16个"一致性"QTL(Meta quantitative trait loci,MQTL)位点及其连锁标记,MQTL置信区间最小达到0.77cM。     

A General Method for QTL Mapping in Multiple Related Populations Derived from Multiple Parents

It’s well known that incorporating some existing populations derived from multiple parents may improve QTL mapping and QTL-based breeding programs. However, no general maximum likelihood method has been available for this strategy. Based on the QTL mapping in multiple related populations derived from two parents, a maximum likelihood estimation method was proposed, which can incorporate several populations derived from three or more parents and also can be used to handle different mating designs. Taking a c...