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。     

QTL Analysis of Al Tolerance in Recombinant Inbred Lines of Arabidopsis thaliana

In the December issue of Plant and Cell Physiology     

利用重组自交系群体检测水稻条纹叶枯病抗性基因及QTL分析

利用81个株系组成的Kinmaze(japonica)／DV85(indica)重组自交系(recombinant inbred lines,RIL)群体,采用苗期强迫饲毒的鉴定方法,以病情指数作为条纹叶枯病的表型值,鉴定亲本及81个RILs对水稻抗条纹叶枯病毒(rice stripe virus,RSV)的抗性。利用QTL Cartographer软件,对水稻条纹叶枯病抗性基因进行检测分析。检测到3个QTL位点：qStv1、qStv7、qStv11分别位于第1、7、11染色体上,各QTL的LOD值为2．44～3．83,贡献率为19．8％～30．9％。根据抗性基因加性效应的方向,在qStv7、qStv11位点上,亲本DV85存在抗条纹叶枯病增效基因,Kinmaze具有抗条纹叶枯病减效基因,而qStv1位点抗性基因效应来源正好相反。     

QTL mapping of physiological traits associated with salt tolerance in Medicago truncatula Recombinant Inbred Lines

In this study, QTL mapping of physiological traits in the model Legume (Medicago truncatula) was performed using a set of RILs derived from LR5. Twelve parameters associated with Na+ and K+ content in leaves, stems and roots were measured. Broad-sense heritability of these traits was ranged from 0.15 to 0.83 in control and from 0.14 to 0.61 in salt stress. Variation among RILs was dependent on line, treatment and line by treatment effect. We mapped 6 QTLs in control, 2 in salt stress and 5 for sensitivity index. No major QTL was identified indicating that tolerance to salt stress is governed by several genes with low effects. Detected QTL for leaf, stem and root traits did not share the same map locations, suggesting that genes controlling transport of Na+ and K+ may be different. The maximum of QTL was observed on chromosome 1, no QTL was detected on chromosomes 5 and 6.     

QTL Mapping of Agronomic Waterlogging Tolerance Using Recombinant Inbred Lines Derived from Tropical Maize (Zea mays L) Germplasm

Waterlogging is an important abiotic stress constraint that causes significant yield losses in maize grown throughout south and south-east Asia due to erratic rainfall patterns. The most economic option to offset the damage caused by waterlogging is to genetically incorporate tolerance in cultivars that are grown widely in the target agro-ecologies. We assessed the genetic variation in a population of recombinant inbred lines (RILs) derived from crossing a waterlogging tolerant line (CAWL-46-3-1) to an elite but sensitive line (CML311-2-1-3) and observed significant range of variation for grain yield (GY) under waterlogging stress along with a number of other secondary traits such as brace roots (BR), chlorophyll content (SPAD), % stem and root lodging (S&RL) among the RILs. Significant positive correlation of GY with BR and SPAD and negative correlation with S&RL indicated the potential use of these secondary traits in selection indices under waterlogged conditions. RILs were genotyped with 331 polymorphic single nucleotide polymorphism (SNP) markers using KASP (Kompetitive Allele Specific PCR) Platform. QTL mapping revealed five QTL on chromosomes 1, 3, 5, 7 and 10, which together explained approximately 30% of phenotypic variance for GY based on evaluation of RIL families under waterlogged conditions, with effects ranging from 520 to 640 kg/ha for individual genomic regions. 13 QTL were identified for various secondary traits associated with waterlogging tolerance, each individually explaining from 3 to 14% of phenotypic variance. Of the 22 candidate genes with known functional domains identified within the physical intervals delimited by the flanking markers of the QTL influencing GY and other secondary traits, six have previously been demonstrated to be associated with anaerobic responses in either maize or other model species. A pair of flanking SNP markers has been identified for each of the QTL and high throughput marker assays were developed to facilitate rapid introgression of waterlogging tolerance in tropical maize breeding programs.     

利用回交导入系群体定位大豆蛋白质含量与脂肪含量QTL

对大豆的蛋白质含量和脂肪含量进行QTL定位,可为其分子标记辅助育种提供依据。以回交导入系群体中黄13×中黄20的BC2F5的100个家系为材料,分析群体的SSR标记多态性,采用近红外光谱分析技术测定群体蛋白质含量和脂肪含量。构建了一张涵盖大豆20个连锁群、总长为948.01 c M、平均遗传距离为8.78 c M、包含108个SSR标记的大豆遗传连锁图谱。共检测到与蛋白质含量相关的QTL 5个,与脂肪含量相关的QTL 9个,其中Satt445~Sat_303连续2年被检测到与脂肪含量相关,Satt445~Sat_303与Satt543~Satt574均被检测到与蛋白质含量和脂肪含量相关,Sat_389~Satt590、Satt238~Satt388及Satt685~Sat_381均与脂肪含量相关。     

A Set of Lotus japonicus Gifu x Lotus burttii Recombinant Inbred Lines Facilitates Map-based Cloning and QTL Mapping

Model legumes such as Lotus japonicus have contributed significantly to the understanding of symbiotic nitrogen fixation. This insight is mainly a result of forward genetic screens followed by map-based cloning to identify causal alleles. The L. japonicus ecotype 'Gifu' was used as a common parent for inter-accession crosses to produce F2 mapping populations either with other L. japonicus ecotypes, MG-20 and Funakura, or with the related species L. filicaulis. These populations have all been used for genetic studies but segregation distortion, suppression of recombination, low polymorphism levels, and poor viability have also been observed. More recently, the diploid species L. burttii has been identified as a fertile crossing partner of L. japonicus. To assess its qualities in genetic linkage analysis and to enable quantitative trait locus (QTL) mapping for a wider range of traits in Lotus species, we have generated and genotyped a set of 163 Gifu × L. burttii recombinant inbred lines (RILs). By direct comparisons of RIL and F2 population data, we show that L. burttii is a valid alternative to MG-20 as a Gifu mapping partner. In addition, we demonstrate the utility of the Gifu × L. burttii RILs in QTL mapping by identifying an Nfr1-linked QTL for Sinorhizobium fredii nodulation.     

Two-Locus Linkage Analysis Using Recombinant Inbred Strains and Bayes'' Theorem

Recombinant inbred (RI) strains are useful in linkage analysis and gene mapping. The currently available statistical tests of linkage using data derived from the study of RI strains, including a previous Bayesian analysis, have not been stringent enough guides for conclusions about linkage. In this paper, the probability of linkage was estimated using Bayes' theorem. Tables are presented that give the probability of linkage in sets of up to 30 RI strains and the critical values of i (the number of recombinants) in sets of up to 100 RI strains. Several means of increasing the power of RI strains in linkage analysis are discussed.     

粳稻糙米钙含量QTL分析

以'十和田'为轮回亲本,'丽粳2号'为供体,培育出糙米钙含量近等基因系下的重组近交系261个BC_5F_6株系,采用BSA法从遍布水稻12条染色体上的600对SSR引物中筛选到1个与糙米钙含量有关联的SSR标记RM5536.进一步据其在水稻染色体上的位置,结合PCR找到了与糙米钙含量有关的3个SSR标记(RM5794、RM5362和RM12178).用MAPMAKER/EXP3.0软件做出了这4个标记的连锁群,最后采用混合线性模型找到了糙米钙含量QTL位点.QTL分析结果显示:该位点位于1号染色体引物RM12178和RM5362之间,贡献率为9.62%,为新发现的糙米钙含量QTL位点,暂命名为qBRCA-1.并发现与糙米锶含量有关的QTL位点,其位于标记RM5362和RM5794之间,贡献率为3.93%.同时本试验首次从分子水平上验证了偏相关比简单相关更准确解释元素间的相关性.     

QTL Mapping in New Arabidopsis thaliana Advanced Intercross-Recombinant Inbred Lines

Background

Even when phenotypic differences are large between natural or domesticated strains, the underlying genetic basis is often complex, and causal genomic regions need to be identified by quantitative trait locus (QTL) mapping. Unfortunately, QTL positions typically have large confidence intervals, which can, for example, lead to one QTL being masked by another, when two closely linked loci are detected as a single QTL. One strategy to increase the power of precisely localizing small effect QTL, is the use of an intercross approach before inbreeding to produce Advanced Intercross RILs (AI-RILs).

Methodology/Principal Findings

We present two new AI-RIL populations of Arabidopsis thaliana genotyped with an average intermarker distance of 600 kb. The advanced intercrossing design led to expansion of the genetic map in the two populations, which contain recombination events corresponding to 50 kb/cM in an F₂ population. We used the AI-RILs to map QTL for light response and flowering time, and to identify segregation distortion in one of the AI-RIL populations due to a negative epistatic interaction between two genomic regions.

Conclusions/Significance

The two new AI-RIL populations, EstC and KendC, derived from crosses of Columbia (Col) to Estland (Est-1) and Kendallville (Kend-L) provide an excellent resource for high precision QTL mapping. Moreover, because they have been genotyped with over 100 common markers, they are also excellent material for comparative QTL mapping.     

Limitation of Number of Strains and Persistence of False Positive Loci in QTL Mapping Using Recombinant Inbred Strains

While the identification of causal genes of quantitative trait loci (QTL) remains a difficult problem in the post-genome era, the number of QTL continues to accumulate, mainly identified using the recombinant inbred (RI) strains. Over the last decade, hundreds of publications have reported nearly a thousand QTL identified from RI strains. We hypothesized that the inaccuracy of most of these QTL makes it difficult to identify causal genes. Using data from RI strains derived from C57BL/6J (B6) X DBA/2J (D2), we tested the possibility of detection of reliable QTL with different numbers of strains in the same trait in five different traits. Our results indicated that studies using RI strains of less than 30 in general have a higher probability of failing to detect reliable QTL. Errors in many studies could include false positive loci, switches between QTL with small and major effects, and missing the real major loci. The similar data was obtained from a RI strain population derived from a different pair of parents and a RI strain population of rat. Thus, thousands of reported QTL from studies of RI strains may need to be double-checked for accuracy before proceeding to causal gene identification.     

以回交重组自交系定位水稻萌芽期耐镉胁迫相关QTLs

水稻是世界上最主要的粮食作物之一,目前农用耕地存在土壤重金属污染的问题,而水稻对镉（Cd）等重金属的耐受性较低,进而使水稻产量和质量受到影响。定位稻种耐Cd胁迫相关数量性状基因座(quantitative trait loci, QTLs),对于指导水稻耐Cd育种具有重要意义。为发掘Cd胁迫相关基因,以粳稻02428和籼稻昌恢891衍生的124个回交重组自交系群体（backcross recombinant inbred ines,BILs）为材料,对水稻萌芽期的根长、芽长进行了分析,并对萌芽期与Cd胁迫相关的QTLs进行了定位分析。结果显示：Cd胁迫处理下,02428和昌恢891根长和芽长均受到显著抑制（P＜0.01）,其中Cd对根长的抑制强于芽长;QTL分析共检测到5个萌芽期与Cd胁迫相关的QTLs：qCdBL3、qCdRL7、qCdBL8.1、qCdBL8.2和qCdBL9分别位于水稻第3、7、8、8和9号染色体上,贡献率为6.45%~19.46%。其中,qCdBL3、qCdBL8.1、qCdBL8.2和qCdBL9与芽长相关,qCdRL7与根长相关。同时,检测到2个在对照条件下（水溶液）影响根长和芽长的QTLs：qCKBL8、qCKRL4,分别位于第8和4号染色体上,贡献率为10.53%和10.89%。比较显示,对照和Cd处理条件下控制水稻萌芽期根长或芽长的QTLs均不相同,说明Cd胁迫条件下,控制水稻根长和芽长的遗传机制可能不同于非Cd胁迫条件。研究结果为耐Cd基因的克隆和耐Cd水稻新品种的选育提供了参考。     

十和田/丽粳2号回交重组自交系糙米Zn含量与其他元素和农艺性状间相关性

用ICP-AES法测定了十和田/丽粳2号/十和田BC4F5回交重组自交系264个株系糙米Zn含量及其在株型间的遗传变异,分析了糙米Zn含量与16种元素(K、P、S、Mg、Ca、Mo、Ni、Fe、Cr、Na、Al、Cu、Sn、B、Mn和Sr)、9个农艺性状(结实率、实粒数、秕粒数、穗长、有效穗、花药长度、花药宽度、穗茎节间长和倒2叶长)、MDA(丙二醛)含量、3种酶(POD、SOD、CAT)活性间相关性,旨在揭示糙米Zn与其他元素、稻米产量、稻耐冷性等关联性。结果表明:回交重组自交群体糙米Zn含量为正态分布,有超亲优势株系;糙米Zn含量与8种元素(K、S、P、Mg、Ca、Fe、B、Mn)含量呈极显著相关,与5种元素(S、Mg、Ni、Cr、Al)含量呈显著偏相关;初步认为糙米Zn含量与稻米产量及耐冷性为负相关,与酶活性相关性不显著。     

Genetics of Glucocorticoid Receptor Levels in Recombinant Inbred Lines of Mice

Hepatic glucocorticoid receptor binding activity was measured in A/J, C57BL/6J, their F1 reciprocal crosses and their F1 recombinant inbred (RI) lines. The glucocorticoid binding capacity was measured in Hepes buffer and Hepes buffer plus dithiothreitol (DTT). The A/J parental strain showed higher levels, and a greater increase of glucocorticoid binding in the presence of DTT, than did the C57BL/6J strain. The response of binding in the presence of DTT to that without DTT was expressed as a ratio. The levels and distribution of these measurements among the RI lines and F1 reciprocal crosses suggested that there was a maternal effect on glucocorticoid receptor binding capacity. The data on RI lines suggested epistatic interactions, but could fit a two-gene model. beta 2-Microglobulin, beta-glucuronidase and H-2 (located on chromosomes 2, 5, and 17, respectively) were chosen to analyze any association to glucocorticoid receptor binding, because they have been considered to be related to glucocorticoid-induced cleft palate or glucocorticoid receptors. No significant associations were found.     

Mapping Quantitative Trait Loci for Grain Appearance Traits of Rice Using a Recombinant Inbred Line Population

A linkage map consisting of 221 markers was constructed based on a recombinant inbred line (RIL) population from the cross between Zhenshan 97 and Minghui 63. Quantitative trait loci (QTL) mapping was carried out for grain appearance traits such as grain length, grain width and grain shape in rice in 1998 and 1999. Based on interval mapping method at the threshold LOD≥2.4, six, two and two QTLs were detected for grain length, grain width and grain shape, respectively, in 1998; In 1999, three, two and two QTLs were identified for the three traits, respectively. Of them, seven QTLs were simultaneously identified in both of the years. The QTL with large effects located in the interval RG393-C1087 on chromosome 3 not only controlled the grain length, but also influenced the grain shape. It explained 57.5%, 61.4% and 26.7%, 29.9% of phenotypic variation of the grain length and the grain shape in two years, respectively. The QTL with large effects located in the interval RG360-C734B on chromosome 5 affected the grain width and the grain shape. It explained 44.2%, 53.2% and 32.1%, 36.0% of phenotypic variation of the grain width and the shape in two years, respectively. Eight, five and five QTLs were identified for the grain length, width and shape, respectively, based on mixed linear-model composite interval mapping method at P =0.005. Their general contributions were 58.81%, 44.75%, and 57.47%. One QTL for the grain length was found to be significant interaction with environment.     

利用水稻重组自交系群体定位谷粒外观性状的数量性状基因

用区间作图和混合线性模型的复合区间作图两种方法,对水稻（Oryza sativa L）珍汕97和明恢63组合的重组自交系群体的谷粒外观性状－粒长,粒宽和粒形进行了数量性状基因（QTL）定位,用区间作图法在LOD≥2．4水平上（近拟于a=0.005),1998年对粒长,粒宽和粒形分别检测到6,2放2个QTLs,1999年对以上3个性状分别检测到3,2和2个QTLs,其中7个QTLs在两年均检测到,位于第3染色体RG393－C1087区间的QTL效应大,同时影响粒长和粒形,两年贡献分别为57．5％,61．4％和26．7％,29．9％,位于第5染色体RG360－C734B区间的QTL效应大,同时影响粒宽和粒形,两年贡献率分别为44．2％,53．2％和32．1％和36．0％,用混合线性模型的复合区间作图法在P＝0．005水平上,对粒长,粒宽和粒形分别检测到8,5和5个QTLs,共解释各自性状变异的58．81％,44．75％和57．47％,只检测到1个QTL与环境之间存在的显互作。     

Endosperm Protein Quality and Kernel Modification in the Quality Protein Maize Inbred Lines

Twenty-two selected quality protein maize (QPM) lines, including 13 lines developed in India (DMRQPM series) and nine lines released by CIMMYT, Mexico (CML series), were evaluated for their endosperm protein content and quality, besides kernel modification in terms of vitreousness. Endosperm protein contents in 13QPMlines were on par or better than that of the normal maize ‘checks’ (Trishulata and Parkash). The QPM endosperm proteins showed significantly higher % tryptophan as well as EF-1α (a multifunctional protein with a positive and highly significant correlation with lysine content in the endosperm) contents, in comparison with the normal maize genotypes. Evaluation of kernel modification revealed considerable scope for accumulation of endosperm modifiers in some of the QPM lines. Positive and highly significant correlation was revealed between tryptophan and EF-1α contents in the endosperm proteins, whereas the correlations between the quality parameters with kernel modification in the QPM genotypes were found to be non-significant. The study led to the identification of some promising QPM lines, such as DMRQPM-37, DMRQPM-44, CML176, CML142 and CML149, which could be effectively deployed in the QPM breeding programmes.     

水稻籽粒锌含量的QTL 定位

锌元素的营养失衡已成为影响人类健康的最重要因素之一, 籽粒锌含量的QTL(quantitative trait loci)定位对研究富锌水稻的遗传育种具有重要的意义。以水稻(Oryza sativa L.)亲本奉新红米和明恢100杂交的145个株系的F2群体为实验材料, 利用92个SSR(simple sequence repeat)标记对水稻籽粒锌含量进行了QTL定位, 共检测到3个QTLs , 分别定位于第3、6和11染色体上, 对表型变异的贡献率分别为4.97%、12.75%和7.74%。其中位于第3染色体上的分子标记RM186和RM168之间的QZN3对表型变异的贡献率最大, 其增效等位基因来自亲本明恢100, 表现为部分显性。3个QTLs 的联合贡献率为25.46%, 具有基因累加效应。该研究结果有利于深入理解水稻锌含量的遗传基础, 为锌含量的QTL精细定位、基因克隆和分子标记辅助选择提供依据。     

水稻籽粒锌含量的QTL定位

锌元素的营养失衡已成为影响人类健康的最重要因素之一,籽粒锌含量的QTL（quantitative trait loci）定位对研究富锌水稻的遗传育种具有重要的意义。以水稻（Oryzasativa L．）亲本奉新红米和明恢100杂交的145个株系的F2群体为实验材料,利用92个SSR（simple sequence repeat）标记对水稻籽粒锌含量进行了QTL定位,共检测到3个QTLs,分别定位于第3、6和11染色体上,对表型变异的贡献率分别为4．97％、12．75％和7．74％。其中位于第3染色体上的分子标记RM186和RM168之间的QZN3对表型变异的贡献率最大,其增效等位基因来自亲本明恢100,表现为部分显性。3个QTLs的联合贡献率为25．46％。具有基因累加效应。该研究结果有利于深入理解水稻锌含量的遗传基础,为锌含量的QTL精细定位、基因克隆和分子标记辅助选择提供依据。     

利用水稻重组自交系群体对一些重要农艺性状进行基因定位和互作分析

对水稻（OryzasativaL．）籼（indica）、粳（Japonica）交（窄叶青8号×京系17）通过一粒传获得了一个自交9代的重组自交系（RIL）群体,该群体含有107个稳定纯合的株系,通过构建分子连锁图谱,对水稻播抽期、株高、每穗颖花数、每穗实粒数、200粒重和结实率进行数量性状基因座位（QTL）分析,定位了影响播抽期的2个QTLs、株高的2个QTLs、每穗颖花数的2个QTLs和每穗实粒数的1个QTL。其中,控制播抽期的1个QTL即qHD－8为主效基因,控制株高的1个QTL即qPH－1为主效基因,其余为微效基因。同时分析了影响水稻生产力的数量性状基因座位间的互作。结果表明,影响播抽期、株高、每穗颖花数、每穗实粒数和结实率的互适型互作共有24个,对性状有6．2％～10．9％的贡献率。