分子标记增效座位在不同生长环境下预测籼型杂交稻籽粒外观性状的效应

以两套杂交水稻不完全双列组合(按NCⅡ设计)及其亲本为材料,在重庆和泸州两个环境条件下种植,利用SSR和AFLP技术分析32个亲本材料的1 085个标记座位,并从这1 085个标记座位中筛选出与F1粒形性状相关的阳性位点和增效位点,分别用此两类座位计算的遗传差异对F1谷粒、糙米和整精米的长、宽和厚共9个籽粒外形性状进行了预测.结果表明,增效位点的亲本遗传距离与相应F1粒形性状的相关系数在0.321～0.892间,平均0.736,高于阳性位点的相关系数.对不同亲本组合(套间)的预测结果表明,增效位点的预测效果明显好于阳性位点,其预测值为0.138～0.805,平均0.451,其中对谷宽、糙米宽和整精米宽预测值分别为0.704、0.707和0.654,达到了可预测水平.同一套组合在不同环境下(环境间)预测结果表明,增效位点的预测效果明显好于阳性位点,预测值平均达0.653,除谷厚、糙米厚和整精米厚外的6个粒形性状其预测值均在0.640以上,达到了可预测水平.部分性状在组合间和环境间达到可预测水平,这将为育种家们对这些性状进行早期选择具有一定指导意义.     

Using of AFLP Marker to Predict the Hybrid Yield and Yield Heterosis in Rice

利用AFLP分子标记对46个水稻品种进行遗传多样性分析,继而研究分子标记遗传距离与按照NC设计获得的195个杂交组合的产量及特殊配合力的相关性,探讨预测杂种优势的可能性。结果表明:(1)通过UPGMA聚类分析(图3),可将供试材料分为16个类群,并把来源不明的品种(系)划分到相应类群中,从而对这些材料进行初步鉴定。可见,AFLP分子标记是检测类内品种间遗传差异的有效方法,为水稻品种(系)亲本选配提供理论依据。(2)分子标记遗传距离与杂种产量优势、F1产量、特殊配合力之间都呈显著正相关,相关系数介于0.3235-0.7713之间。但相关程度还不足以预测杂种优势。增效座位和减效座位以及使用与杂种优势有关的QTL连锁标记位点可能提高杂种优势的预测能力,但最终解决,将依赖于杂种优势遗传机理的研究。     

中国野生大豆群体农艺加工性状与SSR关联分析和特异材料的遗传构成

选用204对SSR标记对全国野生大豆群体(174份代表性样本)的基因组扫描,采用TASSEL软件的GLM (general linear model)方法对百粒重、开花期、成熟期、干豆腐得率、干豆乳得率和耐淹性性状值关联分析,解析与性状关联位点的优异等位变异,鉴别出一批与农艺、加工性状关联的优异等位变异及携带优异等位变异的载体材料;进一步分析极值表型材料的遗传构成。结果表明: (1)累计51个位点(次)与性状关联,有些标记同时与2个或多个性状相关联,可能是性状相关的遗传基础;关联位点中累计16位点(次)与连锁分析定位的QTL一致;(2)与地方品种群体和育成品种群体的关联位点比较,发现野生群体关联位点只有少数与之相同,群体间育种性状的遗传结构有明显差异。(3)与多性状关联的位点其等位变异对不同性状的效应方向可相同可不同,如GMES5532a-A332对百粒重和耐淹性的相对死苗率都是增效效应,而GMES5532a-A344对百粒重是减效效应,对相对死苗率是增效效应;(4)极值表型材料间的遗传构成有很大差异。表型值大的材料携带较多增效效应大的位点等位变异,例如N23349的百粒重是9.08 g,含有4个增效效应较大的位点等位变异;表型值小的材料携带较多减效效应大的位点等位变异,如N23387的百粒重是0.75 g,含有4个减效效应较大的位点等位变异。关联作图得到的信息可以弥补连锁定位信息的不足,尤其是全基因组位点上复等位变异的信息为育种提供了亲本选配和后代等位条带辅助选择的依据。     

籼稻稻米品质性状遗传特点新解析

本研究以丝苗型籼稻优质品种七丝占与抗稻瘟病品种外选35为亲本杂交,从F_2代开始采用单粒传法构建了含543个株系的重组近交系(RILs)群体,并分析了群体中各株系包括整精米率、垩白粒率、垩白大小、垩白度、透明度、直链淀粉含量和胶稠度共7个稻米品质性状的基因分布频率和性状相关性.根据实验数据分析结果,我们推测RILs群体中7个性状都符合2个基因控制的遗传模式,并存在4类遗传频率分布:(Ⅰ)两亲本间有极端差异的2个等位基因分离,其中一个亲本含2个增效等位基因,另1个亲本为2个减效等位基因的杂交类型,直链淀粉含量性状属于该分布类型;(Ⅱ)2个亲本各有1个增效等位基因,表现为2个中等值材料的杂交类犁,包括的性状类型为透明度和垩白大小;(Ⅲ)两个较低值亲本杂交类型,实际上2个亲本共同有1个减效等位基因,另有1个等位基因的差异,相应性状为垩白度和垩白粒率:(Ⅳ)2个较高值亲本杂交,2个亲本各有1个增效等位基因,另有1个等位基因的差异,包含性状为整精米率和胶稠度.各性状间相关系数分析表明,垩白粒率、垩白度、透明度和直链淀粉含量这4个性状存在2个等位基因的高度连锁(75%);垩白度与垩白粒率/垩白大小之间呈极显著正相关;直链淀粉含量与垩白粒率/垩白度之间呈极显著正相关;整精米率与垩白粒率/垩白度之间呈显著负相关;直链淀粉含量与胶稠度之间呈显著负相关;其它性状之间无显著相关性.     

利用陆海杂种BC1群体构建遗传连锁图谱并初步定位产量性状相关的QTL

摘要：本研究利用中棉所36和海1配制杂交组合,并用中棉所36为轮回亲本构建回交群体(BC1F1, BC2F1和 BC1S1)。用亲本和F1对新开发的2102对SSR引物进行多态性筛选,共筛选到317对含有海1显性带的引物,占筛选引物总数的15.08%;最终对其中的275对引物进行了BC1F1群体扩增,获得306个SSR标记差异位点。连锁分析表明（LOD=6.5）,有254个标记位点连锁,分布在42个连锁群中,覆盖2252.36cM,约占棉花基因组的50.05%;平均每个连锁群有6.08个标记,覆盖53.63 cM;标记间平均间距为8.87cM。利用BC1F1、BC2F1和BC1S1三个不同世代分离群体产量性状数据,共定位16个产量性状QTL,解释表型变异5.77%～19.86%。其中,衣分6个,铃重6个,籽指4个。有9个增效基因来自陆地棉亲本中棉所36,7个增效基因来自海岛棉亲本海1,说明了表型性状较差的品种同样可能含有可用于性状改良的增效基因。控制衣分的3个QTL可在不同的世代稳定检测到,效应稳定,增效基因均来自高值亲本陆地棉,为进一步分子标记辅助选择奠定了基础。     

利用陆海杂种BC1群体构建棉花遗传连锁图谱并初步定位产量性状相关的QTL

利用陆地棉推广品种中棉所36和海1配制杂交组合,并用中棉所36为轮回亲本构建回交群体(BC1F1,BC2F1和BC1S1).用亲本和F1对新开发的2102对SSR引物进行多态性筛选,共筛选到317对含有海1显性带的引物,占筛选引物总数的15.08%;最终对其中的275对引物进行了BC1F1群体扩增,获得306个SSR标记差异位点.连锁分析表明(LOD=6.5),有254个标记位点连锁,分布在42个连锁群中,覆盖2252.36 cM,约占棉花基因组的50.05%;平均每个连锁群有6.08个标记,覆盖53.63 cM;标记间平均间距为8.87 cM.利用BC1F1、BC2F1和BC1S1三个不同世代分离群体产量性状数据,共定位16个产量性状QTL,解释表型变异5.77%/～19.86%.其中,衣分6个,铃重6个,籽指4个.有9个增效基因来自陆地棉亲本中棉所36,7个增效基因来自海岛棉亲本海1,说明了表型性状较差的品种同样可能含有可用于性状改良的增效基因.控制衣分的3个QTL可在不同的世代稳定检测到,效应稳定,增效基因均来自高值亲本陆地棉,为进一步分子标记辅助选择奠定了基础.     

大豆育成品种农艺性状QTL与SSR标记的关联分析

利用85个SSR标记,对大豆育成品种群体(190份代表性材料)的基因组进行扫描,在检测群体结构基础上搜索连锁不平衡位点,并采用TASSEL软件的GLM方法对11个大豆农艺性状QTL进行关联分析。结果表明：(1) 在公共图谱上共线性或非共线性的SSR位点组合均广泛存在连锁不平衡(LD),但不平衡程度D′>0.5的组合数只占总位点组合的1.71%,共线位点D′值随遗传距离衰减较快;(2) SSR数据遗传结构分析表明,育成品种群体由7个亚群体组成,矫正后全群体共有45个位点累计136个位点(次)与11个大豆农艺性状QTL关联,其中22个位点(次)与家系连锁定位的QTL区间相重,有43个位点(次) 2年重复出现;(3) 一些标记同时与2个或多个性状关联,可能是性状相关或一因多效的遗传基础;(4) 育成品种群体关联位点与地方品种群体和野生群体只有少数相同,群体间育种性状的遗传结构有相当大差异;(5) 发掘出农艺性状优异等位变异及其载体品种,包括增效最大的产量等位变异Satt347-300 (+932 kg hm^-2,中豆26),生物量等位变异Satt365-294(+3 123 kg hm^-2,黄毛豆),蛋白质含量等位变异Be475343-198 (+0.41%,淮豆4号),脂肪含量等位变异Satt150-273 (+2.32%,科丰15)等。在此基础上作了设计育种的探讨。     

分子标记在油菜遗传多样性和杂种优势预测中的应用

<正>20世纪80年代以来,分子标记技术的发展为亲本的选配提供了新的技术平台,可从DNA水平了解亲本间的遗传差异。利用分子标记遗传距离来预测杂种优势的关键在于选择能表现表型多样性的标记类型和筛选与杂种优势性状相关的引物组合,这样才能保证得到的遗传差异是与杂种优势相关的遗传差异,从而保证对杂种优势预测的准确性。目前,RFLP、SSR、RAPD和AFLP等分子标记技术已广泛用于水稻、玉米、小麦、棉花和大豆等     

大豆杂种产量相关的位点及等位变异分析

选用来源于中国黄淮和美国的熟期组II~IV的8个大豆品种, 按Griffing方法II设计, 配成28个双列杂交组合, 包括8个亲本共计36份材料。选用300个SSR标记, 对8个大豆亲本进行全基因组扫描, 利用基于回归的单标记分析法, 对大豆杂种产量和分子标记进行相关性分析, 估计等位变异的效应和位点的基因型值, 剖析杂种组合的等位变异。结果表明, 300个SSR标记中有38个与杂种产量显著相关, 分布于17个连锁群上, 其中D1a和M等连锁群上较多, 有8个位于连锁定位的QTL区段内(±5 cM)。单个位点可分别解释杂种产量表型变异的11.95%~30.20%。杂种的位点构成中包括有增效显性杂合位点、增效加性纯合位点、减效加性纯合位点和减效显性杂合位点4部分, 其相对重要性依次递减。从38个显著相关的SSR标记位点中, 遴选出Satt449、Satt233和Satt631等9个优异标记基因位点, Satt449~A311、Satt233~A217和Satt631~A152等9个优异等位变异, 以及Satt449~A291/311、Satt233~A202/207和Satt631~A152/180等9个优异杂合基因型位点。这些结果为理解杂种优势的遗传构成和大豆杂种产量聚合育种提供了依据。     

南疆陆地棉杂种F2的遗传分析及遗传主效聚类

采用加性-显性及其与环境互作的遗传模型对298个陆地棉品种(系)及其884个F₂组合在新疆南疆阿拉尔垦区4个产量性状和5个纤维品质性状2年的资料进行遗传分析,并对亲本的加性效应和显性效应进行了聚类,以明确各类品种(系)的育种利用价值。结果表明,在南疆陆地棉“矮(0.8～1.0 m)、密(225,000～300,000株hm^-2)、早、膜”高密度种植模式下,298个亲本的加性效应被分为12类。第2类的23个品种(系)产量(除衣分外)和纤维品质性状的加性效应较高,可通过这类品种(系)间杂交较易获得产量性状和纤维品质性状兼优的后代。第8类品种(系)的纤维品质性状的加性效应较高,第4类品种(系)的产量性状加性效应较高,通过2类品种间杂交可以获得产量性状和纤维品质性状互补的后代。298个亲本的显性效应被分成了9类。第8类包括8个品种(系),其产量性状和纤维品质性状(除马克隆值外)的显性效应较高,可作为综合利用产量性状和纤维品质性状杂种优势兼优的一类亲本。产量性状的显性效应平均值较高的是第8类,第3类的纤维品质性状的显性效应较高。     

Identification and application of major quantitative trait loci for panicle length in rice (Oryza sativa) through single‐segment substitution lines

Panicle length (PL), an important yield‐related trait, strongly affects yield components, such as grain number, grain density and rice quality. More than 200 panicle length quantitative trait loci (PL QTLs) are identified, but only a small number are applied in rice breeding. In this study, we performed QTL analysis for PL using 42 single‐segment substitution lines (SSSLs) derived from nine donors in the genetic background of HJX74. Fourteen QTLs and five heterosis QTLs (HQTLs) for PL were recognised. Three QTLs and four HQTLs acted positively, and the other eleven QTLs and one HQTL acted negatively. By scanning the single heterozygous background region of the F₂ population with large‐genetic‐effect SSSLs, we mapped PL loci qPL6‐2 and qPL7‐1 to different locations on chromosomes 6 and 7, respectively, in three consecutive years of independent trials. The genetic effects of these QTLs were further assessed. qPL6‐2 demonstrated the most positive additive effect (QTL), whereas qPL7‐1 achieved the most positive dominant effect (HQTL) for PL. These results indicated that the pyramiding of PL QTLs might increase grain yield and facilitate the application of the beneficial allele in hybrid rice breeding.     

Tagging quantitative trait loci associated with grain yield and root morphological traits in rice (Oryza sativa L.) under contrasting moisture regimes

Plant breeding for drought-prone habitats envisages a favorable combination of grain yield and drought resistance. Though several components enhancing drought resistance have been identified in rice,their association with grain yield, under low-moisture stress, has been established in very few instances. We attempt to study the associations between rice grain yield and root system parameters both at phenotypic and genotypic levels. The doubled haploid population of IR64/Azucena was evaluated for root related traits at peak vegetative stage and grain yield related traits under both low-moisture stress and non stress conditions. ‘Mean environment’ was computed for yield related traits. Correlation and QTL mapping was attempted to find out the associations. The correlation between maximum root length and grain yield was positive under stress and negative in non stress. Genotypes with thicker and deeper roots, manifested higher biomass and grain yield under stress. Only one QTL found to increase days to flowering in non stress was also found to influence root volume and dry weight negatively under stress. The study suggests that loci enhancing grain yield and related traits were not pleiotropic with loci for desirable root morphological traits studied under low-moisture stress at vegetative stage, in the genetic material used in the study. It is thus possible to combine higher grain yield and desirable root morphological traits, favorably, to enhance productivity of rice under low-moisture stress. In rainfed ecologies, where deep roots contribute to enhanced drought resistance in rice, the results indicate the possibility of combining drought resistance with higher levels of grain yield. This revised version was published online in August 2006 with corrections to the Cover Date.     

Development and characterization of chromosome segment substitution lines derived from backcross between japonica donor rice cultivar Yukihikari and japonica recipient cultivar Kirara397

Grain yield-related traits and grain quality-related traits are important for rice cultivars. The quantitative trait loci (QTLs) involved in controlling the natural variation in these traits among closely related cultivars are still unclear. The present study describes the development of a novel chromosome segment substitution line (CSSL) population derived from a cross between the temperate japonica cultivars Yukihikari and Kirara397, which are grown in Hokkaido, the northernmost limit for rice cultivation. Days to heading, culm length, panicle length, panicle number, brown grain weight per plant, thousand brown grain weight, brown grain length, brown grain width, brown grain thickness, apparent amylose content, and protein content were evaluated. Panicle length, brown grain length and amylose content differed significantly in the parental cultivars. Thirty-five significant changes in the evaluated traits were identified in the CSSLs. A total of 28 QTLs were located on chromosomes 1, 2, 3, 4, 5, 6, 8, 9, 10, 11 and 12. These findings could be useful for breeding rice cultivars in the northernmost limit for rice cultivation.     

A QTL atlas for grain yield and its component traits in maize (Zea mays)

Grain yield and its component traits are essential targets in maize breeding. These traits are genetically complex and controlled by a large number of quantitative trait loci (QTL). The aim of this study was to compile reported QTL and major genes for grain yield and its component traits in a QTL atlas, as a valuable resource for the maize community. To this end, 1,177 QTL related to maize yield were collected from 56 studies published between 1992 and 2018. These QTL were projected to genetic map “IBM2 2008 Neighbors”, which led to the identification of 135 meta-QTL. Some genomic regions appear to be hotspots for yield-related meta-QTL, often affecting more than one of the investigated traits. Moreover, we catalogued 20 major maize loci associated with yield and identified 65 maize homologs of 21 rice yield-related genes. Interestingly, we found that a significant proportion of them are located in meta-QTL regions. Collectively, this study provides a reference for QTL fine-mapping and gene cloning, as well as for molecular marker-assisted breeding of yield-related traits in maize.     

Best linear unbiased prediction of triticale hybrid performance

Predicting single-cross performance is of special interest in hybrid breeding of triticale. We used molecular and phenotypic data of factorial triticale crosses and compared several approaches to predict their single-cross performance. Twenty-three inbred lines and their 76 incomplete factorial crosses were field evaluated for grain yield, plant height, and heading time at five locations in Central Europe. In addition, the parental lines were genotyped with 52 SSR markers. Plant height and heading time were predicted with high accuracy based on mid-parent performance. In contrast, prediction of hybrid performance based on mid-parent value was not accurate for grain yield. Using general combining ability effects led to an enhanced prediction accuracy of hybrid grain yield performance. This accuracy could be slightly improved using best linear unbiased prediction approaches. The prediction accuracy was considerably high even if the number of tested hybrids was small. Consequently, best linear unbiased prediction of hybrid performance is a promising tool for hybrid triticale breeding programs.     

Prediction of heterosis for grain yield in rice using 'key' informative EST-SSR markers

This study was undertaken to assess the comparative potential of 25 Expressed Sequence Tag derived simple sequence repeats (EST-SSRs) and 25 genomic SSRs in the prediction of grain yield heterosis using a set of nine cytoplasmic male sterile (CMS) lines and 32 restorer lines of rice. EST-SSRs and genomic SSRs exhibited an average Polymorphism Information Content value of 0.37 and 0.45, respectively. The coefficient of marker polymorphism among parental lines with respect to a set of hypervariable EST and genomic SSRs was correlated with standard heterosis for grain yield of six public bred rice hybrids. EST-SSRs gave a better correlation (r = 0.75) as compared with genomic SSRs (r = 0.09). When 10 'key' informative EST-SSR markers which showed a higher positive correlation with grain yield heterosis were validated in a new set of 14 experimental hybrids, the markers exhibited a higher correlation (r = 0.79), indicating the predictive value of these EST-SSRs. We recommend these 10 'key' informative EST-SSR markers for analysis of genetic diversity of parental lines and prediction of heterosis in hybrid rice breeding programmes.     

Prospects for hybrid breeding in winter triticale: II. Relationship between parental genetic distance and specific combining ability

Significant relative midparent heterosis (MPH%) for grain yield in triticale (×Triticosecale Wittm.) has generated interest in the development of hybrid cultivars. The objectives of this study were to (i) examine the association between parental genetic distance (GD) and specific combining ability (SCA), (ii) investigate the existence of genetically distant heterotic groups in elite germplasm, and (iii) draw conclusions for future hybrid breeding in winter triticale. Genetic distance between 61 lines was estimated, based on 93 polymorphic simple sequence repeat (SSR) marker loci and 10 AFLP (amplified fragment length polymorphism) primer‐enzyme combinations (PEC). Agronomic data of 206 F₁ crosses and their 61 parental lines grown in six German environments were published recently in a companion study. Correlations were made between SCA for grain yield, number of spikes/m², 1000‐kernel weight and number of kernels per spike with GD estimates of the 56 female and five male parents (testers). Principal co‐ordinate analyses (PCoA) based on SSR data revealed no distinct subgroups in the germplasm. Correlations between GD and SCA were low for all traits (|r| ≤ 0.31), which hampers the prediction of SCA from molecular data. A multi‐stage procedure is recommended for future hybrid breeding in triticale by applying a pragmatic approach for the grouping of germplasm following the early history of hybrid breeding of maize.     

Combining ability and heterosis under pest epidemics in a broad-based global wheat-breeding population

Wheat breeders rarely apply population improvement schemes or select parental sources according to combining ability and heterotic patterns. They rely on pedigree selection methods for breeding new cultivars. This experiment was undertaken to assess the advantages of using diallel crosses to define combining ability and understand heterosis in a broad‐based wheat‐breeding population across different environments affected by yellow rust. Sixty‐four genotypes derived from a full diallel mating scheme were assessed for grain yield in two contrasting growing seasons at two locations for two consecutive years. Parental genotypes showed significant combining ability for grain yield that was affected by yellow rust and genotype‐by‐environment (GE) interactions, both of which affected heterosis for grain yield. Significant GE interactions suggested that decentralized selection for specific environments could maximize the use of this wheat germplasm. Cultivar effects and specific heterosis were the most important factors influencing grain yield. Some crosses capitalized on additive genetic variation for grain yield. This research shows the power of available quantitative breeding tools to help breeders choose parental sources in a population improvement programme.     

应用导入系群体进行水稻产量相关性状的遗传剖析

以优质高产水稻品种丰矮占为轮回亲本, 以Khazar和IR64作供体亲本, 经连续回交分别构建了2套导入系(introgression lines)群体。对导入系后代分别在广州早造和晚造两种环境下进行重复产量鉴定。对两环境下产量及其组分性状的相关分析表明, 在广州早造和晚造环境下水稻产量构成因素存在很大差异。在早造, 每穗实粒数对产量供献最大, 而在晚造, 单株有效穗数对产量供献最大。应用SSR分子标记对这些导入系的供体片段进行全基因组扫描并应用单向方差分析(one-way ANOVA)剖析了导入系基因型与其产量及其组分的关系, 共检测到27个染色体区段与产量及组分性状相关, 包括10个产量QTL、9个单株穗数QTL、9个每穗实粒数QTL和14个千粒重QTL。大多数QTL只在一个环境条件下表达。在第3、7和9染色体上有3个QTL区域与产量及其两个组分有较大的效应, 值得关注。最终, 本研究在同步进行复杂农艺性状的改良和遗传剖析的研究上做出了有益的尝试。