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。     

应用重组自交系群体定位大豆根重QTL

应用构建的NJRIKY(科丰1号×1138-2)大豆重组自交家系群体,对大豆根重QTL进行8次重复的随机区组分析;以该群体所构成的遗传连锁图谱为基础,采用复合区间作图法(Cartographer V.1.21)检测到3个与根重有关的QTL位于连锁群N3-B1和N6-C2上。其中rw1在N3-B1的端距离是66.31cM,位于A520T～ACCCA-GO5区间,rw2和rw3分别在N6-C2的端距离是169.91cM和179.71cM,并与OPW13和ACGCATO6重叠。LOD值分别是10.34、4.01和3.15,可以解释26.3％、9.2％和6.8％的遗传变异。加性效应估计值分别为-0.514、-0.303和-0.260。     

Molecular marker dissection of rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) plant architecture under temperate and tropical climates

Rice (Oryza sativa L.) plants develop vertically with shoot elongation and horizontally with tillering. The purpose of this study was to identify and characterize genomic regions influencing the rice plant architecture by quantitative trait locus (QTL) analysis for the component traits: culm length (CL), panicle length (PnL), panicle number (PnN) and tiller number (TN). For this QTL analysis, 191 recombinant inbred lines (F₇) derived from a cross of Milyang 23 (M23) and Akihikari (AK) were grown in 1995, 1996 and 1997 (May–Oct) in Joetsu, Japan (temperate climate), and in the 2000 dry season (Jan–Apr), the 2000 wet season (Jun–Oct) and the 2001 dry season in Los Baños, The Philippines (tropical climate). Results showed that rice plant architecture was influenced by 19 genomic regions categorized into five groups. In Group I, two regions (on chrs. 6 and 11) affected shoot elongation (CL and PnL) and tillering (PnN and TN) in opposite directions more significantly in Los Baños than in Joetsu. In Group II, two regions (chrs. 3 and 12) affected shoot elongation, whereas in Group III, five regions [chrs. 1 (two), 2, 3 and 9] affected only culm length (CL). Expressions of four regions of Group III were influenced by either tropical or temperate environments. In Group IV, seven regions (chrs. 1, 2, 4, 5, 6, 8 and 9) controlled panicle development (PnN or PnL), and in Group V, three regions (chrs. 1, 2 and 3) regulated tillering (PnN or TN). Characterizing these 19 genomic regions provided a detailed analysis of rice plant architecture with emphasis on the multiple effect and environmental responsive regions.Communicated by D. Mackill     

Marker-based mapping of quantitative trait loci using replicated progenies

Summary When heritability of the trait under investigation is low, replicated progenies can bring about a major reduction in the number of individuals that need to be scored for marker genotype in determining linkage between marker loci and quantitative trait loci (QTL). Savings are greatest when heritability of the trait is low, but are much reduced when heritability of the quantitative trait is moderate to high. Required numbers for recombinant inbred lines will be greater than those required for a simple F₂ population when heritabilities are moderate to high and the proportion of recombination between marker locus and quantitative trait locus is substantial.Contribution No. 2613-E of the Agricultural Research Organization, 1989 series     

Fine mapping of QTLs of chromosome 2 affecting the fruit architecture and composition of tomato

Negative correlations between quality traits and fruit size may hamper the breeding of fresh market tomato varieties for better organoleptic qualities. In a recent QTL analysis, QTLs with large effects on fruit weight, locule number and several quality traits were detected in the distal 50 cM of chromosome 2, but favorable alleles for fruit weight and locule number were unfavorable to quality traits. Substitution mapping was undertaken to determine whether the effects were due to a single QTL or to several tightly linked QTLs. Several chromosomal segments were characterized using near-isogenic lines. Five of them appeared to be involved in one or several traits. Considering the five segments from the top to the bottom of the region, the QTLs detected in each segment controlled the variation of: (1) fruit weight, (2) soluble solids content and dry matter weight, (3) fruit weight, (4) locule number and (5) fruit weight, dry matter weight, total sugars, titratable acidity and soluble solids content. This last cluster illustrates an antagonism between fruit weight and four quality traits, as favorable alleles are not conferred by the same parent in both cases. Nevertheless, several antagonistic QTLs were separated from each other in the first four segments, holding the promise for marker-assisted improvement of fruit quality traits without compromising the fruit size.     

Identification of QTLs for root characteristics in maize grown in hydroponics and analysis of their overlap with QTLs for grain yield in the field at two water regimes

We investigated the overlap among quantitative trait loci (QTLs) in maize for seminal root traits measured in hydroponics with QTLs for grain yield under well-watered (GY-WW) and water-stressed (GY-WS) field conditions as well as for a drought tolerance index (DTI) computed as GY-WS/GY-WW. In hydroponics, 11, 7, 9, and 10 QTLs were identified for primary root length (R1L), primary root diameter (R1D), primary root weight (R1W), and for the weight of the adventitious seminal roots (R2W), respectively. In the field, 7, 8, and 9 QTLs were identified for GY-WW, GY-WS, and DTI, respectively. Despite the weak correlation of root traits in hydroponics with GY-WW, GY-WS, and DTI, a noticeable overlap between the corresponding QTLs was observed. QTLs for R2W most frequently and consistently overlapped with QTLs for GY-WW, GY-WS, and/or DTI. At four QTL regions, an increase in R2W was positively associated with GY-WW, GY-WS, and/or DTI. A 10 cM interval on chromosome 1 between PGAMCTA205 and php20644 showed the strongest effect on R1L, R1D, R2W, GY-WW, GY-WS, and DTI. These results indicate the feasibility of using hydroponics in maize to identify QTL regions controlling root traits at an early growth stage and also influencing GY in the field. A comparative analysis of the QTL regions herein identified with those described in previous studies investigating root traits in different maize populations revealed a number of QTLs in common.     

Stability over genetic backgrounds, generations and years of quantitative trait locus (QTLs) for organoleptic quality in tomato

The efficiency of marker-assisted backcross for the introgression of a quantitative trait locus (QTL) from a donor line into a recipient line depends on the stability of QTL expression. QTLs for six quality traits in tomato (fruit weight, firmness, locule number, soluble solid content, sugar content and titratable acidity) were studied in order to investigate their individual effect and their stability over years, generations and genetic backgrounds. Five chromosome regions carrying fruit quality QTLs were transferred following a marker-assisted backcross scheme from a cherry tomato line into three modern lines with larger fruits. Three sets of genotypes corresponding to three generations were compared: (1) an RIL population, which contained 50% of each parental genome, (2) three BC3S1 populations which segregated simultaneously for the five regions of interest but were almost fully homozygous for the recipient genome on the eight chromosomes carrying no QTL and (3) three sets of QTL-NILs (BC3S3 lines) which differed from the recipient line only in one of the five regions. QTL detection was performed in each generation, in each genetic background and during 2 successive years for QTL-NILs. About half of the QTLs detected in QTL-NILs were detected in both years. Eight of the ten QTLs detected in RILs were recovered in the QTL-NILs with the genetic background used for the initial QTL mapping experiment, with the exception of two QTLs for fruit firmness. Several new QTLs were detected. In the two other genetic backgrounds, the number of QTLs in common with the RILs was lower, but several new QTLs were also detected in advanced generations.     

小麦旗叶长、宽及面积的QTL分析

以小麦品种‘小偃81’和‘西农1376’构建的含236个家系的自交重组系(RIL)群体(F2:7、F2:8代)为研究材料,采用完全随机区组设计,连续2年在陕西杨陵、河南驻马店和山东济南于灌浆期(花后20d)随机取每个株系10株测量旗叶长、宽,并利用172个SSR标记构建了遗传连锁图谱,通过基于完备区间作图法的QTL IciMapping V3.2软件,对控制小麦旗叶长、宽和面积的数量性状位点(QTL)进行了加性效应分析。结果发现:(1)9个旗叶长QTLs位于1A、4A、3B、5D和7D染色体上,单个QTL可解释5.10%~16.44%的表型变异;10个旗叶宽QTLs位于1A、3A、5A、7A、3B和5D染色体上,单个QTL可解释4.63%~14.24%的表型变异;12个旗叶面积QTLs位于1A、4A、3B、2D和5D染色体上,单个QTL可解释4.25%~22.67%的表型变异。(2)控制小麦旗叶长、宽和面积的QTLs存在差异,同一QTL在不同性状中的遗传贡献率也不同。(3)同一性状在同一年份,不同地点和在不同年份,相同地点下检测到的QTLs有的相同,但有的差异明显。(4)有些控制不同性状的QTLs在染色体的同一标记区间,表现一因多效。研究表明:位于1A和5D染色体上的2个加性QTLs都同时控制旗叶长、宽和面积,且前者为主效基因,后者遗传贡献率也较大,可用于标记辅助育种和分子聚合育种。     

Improving QTL Mapping Resolution Based on Genotypic Sampling—a Case Using a RIL Population

The QTL mapping results were compared with the genotypically selected and random samples of the same size on the base of a RIL population. The results demonstrated that there were no obvious differences in the trait distribution and marker segregation distortion between the genotypically selected and random samples with the same population size. However, a significant increase in QTL detection power, sensitivity, specificity, and QTL resolution in the genotypically selected samples were observed. Moreover, the highly significant effect was detected in small size of genotypically selected samples. In QTL mapping, phenotyping is a more sensitive limiting factor than genotyping so that the selection of samples could be an attractive strategy for increasing genome-wide QTL mapping resolution. The efficient selection of samples should be more helpful for QTL maker assistant selection, fine mapping, and QTL cloning.     

基于基因型选择提高QTL作图的精度——以一个RIL群体为例

以PCR为基础的分子标记以及其他检测技术的发展,使得大规模的标记分析成为现实。这也为通过大群体标记分析,然后基于基因型选择挑选合适的小群体,从而提高QTL定位准确性和精度提供了可能。以一个包含294个家系的重组自交系（RIL）群体为例,通过基因型选择和随机选择的办法产生了一系列大小不等的亚群体,比较了两类群体QTL定位的结果。分析表明：相同大小的基因型选择群体与随机群体相比性状的表型分布都符合正态分布;标记的偏分离情况也没有明显的差别,都随着群体大小的增大,偏分离的比例也逐渐增大。但同等大小的基因型选择群体比随机群体的交换富集率（CE）要大,且随着选择强度的增大不断增大,如群体大小为270时,CE=1．04,群体大小为30时,CE=1．45。总体上,随着群体大小的增加,不管是随机群体还是选择群体,其QTL检测能力、灵敏性和特异性也随之增加,但选择群体的检测能力、灵敏性和特异性总体上要好于随机群体。当群体大于或等于240时,其QTL检测能力基本没有差别;群体大小大于或等于210时,其QTL检测的灵敏性和特异性也没有什么差别。这也说明：选择强度越大,效果越明显。以QTLI—LOD区间作为衡量QTL精度的一个指标,结果显示所有基因型选择群体都比相同大小随机群体的QTL定位精度高。目前QTL定位研究中,基因型数据较表型数据而言更容易准确获得,因此通过基因型选择可以更好的优化群体结构,减少田间实验的工作量,提高全基因组水平QTL作图的精度,为随后的QTL辅助选择和精细定位以及克隆提供帮助。     

直播条件下水稻6个穗部性状的QTL分析

在大田直播条件下,利用来源于＂Lemont/特青＂的重组自交系群体,对水稻6个穗部性状及其相互间遗传相关的分子基础进行了QTL分析,共检测到19个QTL,各性状QTL数为2～4个,单个QTL贡献率为4%～22%。共检测到3个染色体区段能同时影响多个穗部性状,其中第1染色体RM212-RM104和第2染色体RM263-RM221区段的QTL能同时影响单株产量、每穗颖花数、着粒密度和二次枝梗数中的3个或4个性状,且这2个区段的QTL对各性状的效应方向相同,增效等位基因均来自‘特青’,为各性状间表型正相关提供了重要的遗传解释。第11染色体RG1022附近的QTL对着粒密度的效应值为负,来自‘特青’的等位基因增加性状值,而对穗长的效应值为正,来自‘特青’的等位基因降低性状值,为这2个性状间表型负相关也提供了一定的遗传解释。此外,对水稻穗部性状QTL在多种环境和遗传背景下的稳定表达及其在分子标记辅助育种中的应用进行了讨论。     

A new approach for mapping quantitative trait loci using complete genetic marker linkage maps

A new approach based on nonlinear regression for the mapping of quantitative trait loci (QTLs) using complete genetic marker linkage maps is advanced in this paper. We call the approach joint mapping as it makes comprehensive use of the information from every marker locus on a chromosome. With this approach, both the detection of the existence of QTLs and the estimation of their positions, with corresponding confidence intervals, and effects can be realized simultaneously. This approach is widely applicable because only moments are used. It is simple and can save considerable computer time. It is especially useful when there are multiple QTLs and/or interactions between them on a chromosome.     

小麦萌发期抗旱和耐盐性状的QTL分析

该研究以‘山农0431×鲁麦21’RIL群体及其父母本为材料,用20%PEG-6000溶液和100 mmol·L-1 NaCl溶液分别模拟干旱和盐环境,对12个小麦萌发期抗旱耐盐相关性状进行测定,结合已构建的分子标记遗传图谱对小麦萌发期抗旱、耐盐的相关性状进行QTL分析,为小麦抗旱、耐盐基因的克隆和分子标记辅助选择提供参考。结果表明:(1)正常、干旱和盐胁迫3种处理下共检测到143个QTL。检测到相对高频QTL(RHF-QTL)29个,平均贡献率范围为4.39%~13.28%,贡献率在10%以上的主效RHF-QTL有10个。(2)检测到胁迫下特异表达的RHF-QTL共17个,正常处理下特异表达的RHF-QTL为8个,稳定表达的RHF-QTL为4个。(3)QTL分析结果表明,7个RHF-QTL形成了3个QTL簇,且分布在2D、4D和5B等3条染色体上,其中:QC1位于2D染色体的wPt-6847~D-1172783区间,包括3个QTL(QRl-2D.2、QSdw-2D.3、QTdw-2D);QC2位于4D染色体短臂的D-2245724~D-1108531区间,包括2个QTL(QSl-4D、QShl-4D);QC3位于5B染色体的D-982263~S-1083095区间,包括2个QTL(QSl-5B.2、QTdw-5B.1)。     

两种肥力水平下水稻苗高QTL的比较分析

利用一个来源于粳／籼交组合的水稻重组自交系群体进行盆栽试验,设正常肥力(对照CK)和低肥力(不施肥)2个处理,分别在播种后25d(时期Ⅰ)和50d(时期Ⅱ)取样测定秧苗的苗高。结合一张含有198个标记的高密度分子遗传图谱,对性状进行复合区间作图。共检测到8个水稻苗高QTL,分别位于第1、3、5、6、8和10号染色体上,各QTL对性状的贡献率为4％～12％。通过对2种肥力水平下水稻苗高QTL的比较分析,发现大多数QTL只在1种肥力水平下表达,QTL与不同肥力水平之间存在着显著的互作。唯一一个在2种肥力水平下均能稳定起作用、而且加性效应的方向一致的QTL是qSH-3-2,该QTL位于3号染色体标记区间RM156-RM16,其加性效应值为正,增效基因来自于亲本Lemont。此外,有3个QTL(qSH-1、qSH-3-3和qSH-5)在2个抽样时期均起作用,且加性效应的方向一致。对利用分子标记辅助选择改良水稻品种的耐低肥特性的育种策略进行了讨论。     

RFLP analysis of soybean seed protein and oil content

Summary The objectives of this study were to present an expanded soybean RFLP map and to identify quantitative trait loci (QTL) in soybean [Glycine max (L.) Merr.] for seed protein and oil content. The study population was formed from a cross between a G. max experimental line (A81-356022) and a G. soja Sieb. and Zucc. plant introduction (PI 468916). A total of 252 markers was mapped in the population, forming 31 linkage groups. Protein and oil content were measured on seed harvested from a replicated trial of 60 F₂-derived lines in the F₃ generation (F₂₃ lines). Each F₂₃ line was genotyped with 243 RFLP, five isozyme, one storage protein, and three morphological markers. Significant (P<0.01) associations were found between the segregation of markers and seed protein and oil content. Segregation of individual markers explained up to 43% of the total variation for specific traits. All G. max alleles at significant loci for oil content were associated with greater oil content than G. soja alleles. All G. soja alleles at significant loci for protein content were associated with greater protein content than G. max alleles.     

Genomic Regions Associated with Amino Acid Composition in Soybean

Soybean [Glycine max (L.) Merr.] is the single largest source of protein in animal feed. However, few studies have been conducted to evaluate genomic regions controlling amino acid composition in soybean. It is important to study the genetics of amino acid composition to achieve improvements through breeding. The objectives of this study were to determine the ratios between essential to non-essential (E:NE) and essential to total (E:T) amino acids, and to identify genomic regions controlling essential and non-essential amino acid composition in soybean seed. To achieve these objectives, 101 F₆-derived recombinant inbred lines (RIL) developed from a cross of N87-984-16 × TN93-99 were used. Ground soybean seed samples were analyzed for amino acids using a near infrared spectroscopy (NIRS) instrument. A significant (p < 0.01) difference among the RIL was found for amino acid composition. Heritability estimates on an entry mean basis ranged from 0.13 for His to 0.67 for Tyr. A total of 94 polymorphic simple sequence repeat (SSR) molecular genetic markers were screened in DNA from progenies. Single factor ANOVA was used to identify candidate quantitative trait loci (QTL), which were then confirmed by QTL Cartographer. At least one QTL for each amino acid was detected in this population. QTL linked to molecular markers Satt143, Satt168, Satt203, Satt274 and Satt495 were associated with most of the amino acids. Phenotypic variation explained by an individual QTL ranged from 9.4 to 45.3%. QTL detected for amino acids in soybean in this experiment are expected to be useful for future breeding programs targeting development of improved soybean amino acid composition for human and animal nutrition.     

应用重组自交系群体定位大豆抗虫QTL

以大豆组合科丰1号×南农1138-2衍生的重组自交系(RIL)群体为材料构建遗传连锁图谱, 利用软件 Cartographer V.2.5 采用复合区间作图法检测定位大豆抗虫QTL。以斜纹夜蛾幼虫重为抗性指标, 检测到 1 个与抗虫性有关的 QTL, 位于G20-O连锁群上, 其端距离为31.91 cM, 加性效应估计值为0.0408, 对性状变异的解释率为 11.74％; 以蛹重为抗性指标, 检测到 2 个与抗虫性有关的 QTL, 分别位于G8-D1b+W和G17-L连锁群上, 其端距离分别为 14.71 cM和0.01 cM, 加性效应估计值分别为-0.0139和0.0103, 对性状变异的解释率分别为 11.30％和6.36％。     

绿豆产量相关农艺性状的QTL定位

绿豆育种的目标性状大多是受多基因控制的数量性状,表现型受环境影响很大。为深入分析绿豆复杂数量性状的遗传特征,本试验以绿豆Berken/ACC41 F10重组近交系群体为作图群体,利用该群体已经构建的包含79个RFLP标记的分子连锁图谱对北京和广西2个种植环境下考察的11个绿豆产量相关农艺性状进行QTL定位。结果表明,2个环境下共检测到产量相关性状QTL 63个（其中北京25个,广西38个）,分布于除第13连锁群以外的12条连锁群。大部分QTL只在单一环境下被检测到,说明产量相关QTLs与环境之间存在明显的互作。2个环境均能检测到的QTL仅有6个,分别为控制荚长、百粒重、生育期的QTLs,这6个在不同生态环境下同时发挥效应的QTLs对于绿豆分子标记辅助育种具有特殊的意义。研究还发现2个QTLs富集区域和若干成束分布的QTLs,它们可能是发掘通用QTL的候选位点。     

Cold Tolerance of the Photosynthetic Apparatus: Pleiotropic Relationship between Photosynthetic Performance and Specific Leaf Area of Maize Seedlings

The objective of this study was to elucidate the genetic relationship between the specific leaf area (SLA) and the photosynthetic performance of maize (Zea mays L.) as dependent on growth temperature. Three sets of genotypes: (i) 19 S₅ inbred lines, divergently selected for high or low operating efficiency of photosystem II (Φ_PSII) at low temperature, (ii) a population of 226 F_2:3 families from the cross of ETH-DL3 × ETH-DH7, and (iii) a population of 168 F_2:4 families from the cross of Lo964 × Lo1016 were tested at low (15/13 °C day/night) or at optimal (25/22 °C day/night) temperature. The latter cross was originally developed to study QTLs for root traits. At 15/13 °C the groups of S₅ inbred lines selected for high or low Φ_PSII differed significantly for all the measured traits, while at optimal temperature the groups differed only with regard to leaf greenness (SPAD). At low temperature, the SLA of these inbred lines was negatively correlated with Φ_PSII (r = − 0.56, p < 0.05) and SPAD (r = − 0.80, p < 0.001). This negative relationship was confirmed by mapping quantitative trait loci (QTL) in the two mapping populations. A co-location of three QTLs for SLA with QTLs for photosynthesis-related traits was detected in both populations at 15/13 °C, while co-location was not detected at 25/22 °C. The co-selection of SLA and Φ_PSII in the inbred lines and the co-location of QTL for SLA, SPAD, and Φ_PSII at 15/13 °C in the QTL populations strongly supports pleiotropy. There was no evidence that selecting for high Φ_PSII at low temperature leads to a constitutively altered SLA.     

Stability of Soybean Recombinant Plastome Over Six Generations

The stability of a plastid transgene has been evaluated in soybean transformants over six generations. These transformants had integrated the aadA selection cassette in the intergenic region between the rps12/7 and trnV genes. Three independent homoplasmic T0 transformation events were selected and ten plants from each event propagated to generation T5 in the absence of selection pressure. No transgene rearrangement nor wild-type plastome were detected in generation T5 by Southern blot analysis. All tested progenies were uniformly resistant to spectinomycin. Therefore, soybean transformants of generations T0 and T5 appear to be genetically and phenotypically identical.