Upland rice breeding in Brazil: a simultaneous genotypic evaluation of stability, adaptability and grain yield

A durum wheat recombinant inbred line population developed from PDW 233 × Bhalegaon 4 cross was analyzed in five environments to understand the genetic network responsible for test weight (TW), thousand kernel weight (TKW), grain yield (YLD), spike length (SL), spikelets per spike (SPS), kernels per spike (KER) and kernel weight per spike (KWS). Genotype, environment and their interactions were main sources of variance for all the traits. TW and TKW were influenced by 11 main effect QTL and 6 digenic epistatic interactions detected on chromosomes 2A, 2B, 4B and 7A. Grain yield was influenced by three epistatic interactions and five main effect QTL, of which two on chromosome 2A were most consistent. A major QTL for spike length was observed on chromosome 3B. QTL for spike characters were distributed over 9 chromosomes. All the traits showed significant influence of digenic epistasis (QQ) and, to a certain extent, QTL × environment interactions (QQE). Therefore, while breeding for complex traits like kernel characters and grain yield components, these interactions should also be considered important. The consistent QTL on chromosome 2A between the marker interval Xgwm71.2–Xubc835.4 with pleiotropic effect on TW and TKW, may be utilized in early generation selection to improve TW and TKW and thereby the milling potential of the durum wheat.     

小麦候选骨干亲本科农9204遗传构成及其传递率

科农9204是一个兼具高产和氮高效的候选小麦骨干亲本,其遗传背景复杂,携带冀麦38、小偃5号、绵阳75-18、小偃693和矮丰3号的遗传成分。利用221个PCR标记和89个DAr T标记,绘制了科农9204的全基因组基因型图谱。在2DL上,Xmag3596–Xmag4089区段与增加千粒重和籽粒含氮量的QTL紧密连锁;在4BL上,Xcnl10与增加穗粒数、降低株高和穗茎长的QTL紧密连锁;在6BS上,Xcnl113和Xwmc756均与降低株高、穗茎长和穗下节间长的QTL紧密连锁。这些标记在科农9204衍生后代的传递率均为100.0%。利用已报道的关联性标记检测科农9204基因型在衍生后代的传递情况,与增加穗粒数相关的1个优异等位基因位点在衍生后代中的传递率为71.6%;与增加千粒重相关的4个优异等位基因位点的传递率均为100.0%;与根部性状相关的4个基因位点中,3个传递率为100.0%。这些与重要农艺性状相关位点,科农9204基因型在其衍生后代中有很高的传递率,在很大程度上与其对应的优异的农艺性状密不可分。科农9204染色体区段上存在的重要QTL可能是其成为候选骨干亲本的遗传基础。     

不同生态环境下玉米产量性状QTL分析

以玉米（Zea mays L.）自交系黄早四和Mo17为亲本得到的191个F₂单株为作图群体,衍生的184个F_2∶3 家系作为性状评价群体,分析了单株穗数、穗行数、行粒数、百粒重和单株籽粒产量在北京和新疆2个生态环境下的表现和数量性状基因位点的定位结果。QTL检测结果表明,2个环境共检测出47个QTL,分布于除第10染色体以外的9条染色体,其中与单株穗数相关的QTL共10个,可解释的表型变异为5.3%~25.6%;与穗行数相关的QTL共13个,可解释的表型变异为4.5%~23.2%;与行粒数相关的QTL有9个,解释的表型变异为5.4%~13.7%;与百粒重相关的QTL达10个,可解释的表型变异为4.9%~13.3%;与单株籽粒产量相关的QTL有5个,可解释的表型变异为6.1%~35.8 %。大部分产量QTL只在单一环境下被检测到,说明产量相关QTL与环境之间存在明显的互作。表型相关显著的产量性状,它们的QTL容易在相同或相邻标记区间检测到。研究还发现了若干个QTL富集区域,可能是发掘通用QTL的候选位点。     

QTL for flag leaf size and their influence on yield-related traits in wheat

Flag leaf-related traits (FLRTs) are determinant traits affecting plant architecture and yield potential in wheat (Triticum aestivum L.). In this study, three related recombinant inbred line (RIL) populations with a common female parent were developed to identify quantitative trait loci (QTL) for flag leaf width (FLW), length (FLL), and area (FLA) in four environments. A total of 31 QTL were detected in four environments. Two QTL for FLL on chromosomes 3B and 4A (QFll-3B and QFll-4A) and one for FLW on chromosome 2A (QFlw-2A) were major stable QTL. Ten QTL clusters (C1–C10) simultaneously controlling FLRTs and yield-related traits (YRTs) were identified. To investigate the genetic relationship between FLRTs and YRTs, correlation analysis was conducted. FLRTs were found to be positively correlated with YRTs especially with kernel weight per spike and kernel number per spike in all the three RIL populations and negatively correlated with spike number per plant. Appropriate flag leaf size could benefit the formation of high yield potential. This study laid a genetic foundation for improving yield potential in wheat molecular breeding programs.     

Identification of QTLs for BYDV tolerance in bread wheat

We searched for QTLs involved in tolerance to barley yellow dwarf (BYD), a serious viral disease of small grain cereals in two wheat populations, Opata × Synthetic (ITMI)and Frontana × INIA66 (F × I), for which marker data had previously been generated. The populations were evaluated in replicated field trials under artificial inoculation with a BYDV-PAV-Mex isolate and under disease-free conditions. Disease symptoms (yellowing, dwarfism and biomass reduction) were visually recorded and agronomic traits (number of tillers,height, biomass, yield and thousand-kernel weight) were measured on five plants per plot. Phenotypic data on all evaluated traits showed normal distribution with high correlation between visual estimates and measured values. Heritabilities were mostly moderate to high in the 114 lines of the ITMI population, and from low to moderate in the 117 lines of the F × I population. QTL analyses were based on genetic maps containing 443 loci for the ITMI population and 317 loci for the F × I population. Using composite interval mapping, 22 QTLs in the ITMI population and seven in the F × I population were detected, explaining9.8–43.3% of total phenotypic variation (σ² _P)per agronomic trait in the first population, and 4.1–13.7% in the second. Individual QTLs explained less than 15.8%of σ² _P. In the F × I population a minor QTL explaining 7% of σ² _P for yellowing was detected on the short arm of 7D, linked to leaf tip necrosis, a morphological marker for linked genes Bdv1, Yr18 andLr34. A QTL consistently detected for several traits on 2D in the ITMI population and on the short arm of group 6 chromosome(6S) in F × I explained 10–15% of σ² _P. The large number of QTLs having mostly small effects and the continuous distribution of all evaluated traits confirmed the polygenic nature and complexity of BYD tolerance in wheat. This revised version was published online in August 2006 with corrections to the Cover Date.     

利用小麦关联RIL群体定位产量相关性状QTL

为定位控制小麦产量相关性状的QTL位点,获得与重要位点连锁的分子标记和染色体区段,以分别含有229和485个家系的关联重组自交系(RIL)群体WY和WJ为材料,在4个环境中,用完备区间作图法(ICIM)对产量相关性状进行了QTL定位分析。结果表明,产量相关性状QTL分布在小麦21条染色体上。在WY群体中检测到每穗小穗数、主茎穗粒数、单株穗数、千粒重和单株产量的QTL分别有9、9、4、7和5个,其中16个(55.2%)解释大于10%的表型变异;在WJ群体中检测到这5个性状的QTL分别有20、16、11、14和9个,其中只有3个(6.7%)在单个环境中解释超过10%的表型变异。在WY群体中有5个QTL在2个环境中被重复检测到;在WJ群体中,有11个QTL在2个或2个以上环境中被重复检测到。在2个群体中均检测到产量相关性状的QTL在染色体上形成了含有一因多效或紧密连锁QTL的染色体区段,并在2个群体检测到可能相同的9对QTL和2个染色体区段。     

利用种子性状QTL定位高油玉米淀粉含量QTL

以普通玉米自交系8984与高油玉米自交系GY220为亲本组配得到284个F2:3家系群体,利用185个SSR标记构建玉米遗传连锁图谱。通过包含母体效应的种子性状QTL作图方法对玉米籽粒淀粉含量进行QTL定位和效应分析,共检测到7个与淀粉含量相关的QTL,分别位于第5,8,10染色体上,除qSTA8-3的遗传作用方式表现为加性外,其余QTL作用方式为部分显性。单个QTL贡献率为5.87%～10.93%,累计贡献率为53.37%。所有QTL的增效基因均来自普通玉米亲本8984。淀粉含量QTL qSTA5-2贡献率较大,可以作为进一步精细定位的主要目标QTL。     

玉米子粒产量及其组成性状的QTL研究进展

为推进分子标记辅助选择在玉米育种中的应用,总结出近30年玉米子粒产量及其组成性状的QTL研究进展。表明子粒产量的QTL为5~9个,主要分布在第1、2、5、6、7、8、9染色体上,穗行数、行粒数和百粒重的QTL均为3~6个,主要分布在第1、2、3、4、5、6、7、8染色体上,这些QTL成簇分布在几条主要染色体上,形成QTL富集区域,它们能解释性状表型变异的25%左右;多数性状的QTL主要表现为加性、显性、部分显性或超显性效应,部分性状的QTL存在遗传×环境互作效应。预示子粒产量及其组成性状的QTL存在共同染色体载体,育种选择应在多环境、大样本下进行,在不同环境下均能稳定表达的QTL更适用于育种选择;单株穗数、植株性状和抗逆性的QTL研究有待加强。     

QTL detection of seven spike-related traits and their genetic correlations in wheat using two related RIL populations

Spike-related traits contribute greatly to grain yield in wheat. To localize wheat chromosomes for factors affecting the seven spike-related traits??i.e., the spike length (SL), the basal sterile spikelet number (BSSN), the top sterile spikelet number (TSSN), the sterile spikelet number in total (SSN), the spikelet number per spike (SPN), the fertile spikelet number (FSN) and the spike density (SD)??two F_8:9 recombinant inbred line (RIL) populations were generated. They were derived from crosses between Weimai 8 and Jimai 20 (WJ) and between Weimai 8 and Yannong 19 (WY), comprising 485 and 229 lines, respectively. Combining the two new linkage maps and the phenotypic data collected from the four environments, we conducted quantitative trait locus (QTL) detection for the seven spike-related traits and evaluated their genetic correlations. Up to 190 putative additive QTL for the seven spike-related traits were detected in WJ and WY, distributing across all the 21 wheat chromosomes. Of these, at least nine pairwise QTL were common to the two populations. In addition, 38 QTL showed significance in at least two of the four different environments, and 18 of these were major stable QTL. Thus, they will be of great value for marker assisted selection (MAS) in breeding programs. Though co-located QTL were universal, every trait owned its unique QTL and even two closely related traits were not excluded. The two related populations with a large/moderate population size made the results authentic and accurate. This study will enhance the understanding of the genetic basis of spike-related traits.     

QTLs for uppermost internode and spike length in two wheat RIL populations and their affect upon plant height at an individual QTL level

Spike length (SL) is one of the most important components of spike morphology, and the uppermost internode represents an ideal organ to study the transportation system. We performed conditional and unconditional quantitative trait locus (QTL) mapping in two unrelated recombinant inbred line populations to precisely detect QTLs for uppermost internode length (UIL) and SL, and to dissect the genetic relationship between these two factors with plant height (PH). Both of the populations were derived from crosses with synthetic wheat. Ten repetitive QTLs for UIL and six environment-independent QTLs for SL were identified in this study, and twelve of these were completely independent of PH. Conditional QTL mapping analysis indicated that SL was more independent to PH than UIL was. The results indicated that the conditional QTL mapping method could evaluate PH component effects on PH, and thus accelerate the selection of suitable loci that improve commercial wheat morphology yet avoid changes to PH.     

Genetic analysis of bread-making quality in wheat and spelt

Bread‐making quality in wheat and spelt reflects the combination of several, mostly quantitatively inherited parameters. The aim was to find molecular markers linked to quantitative trait loci (QTL) for quality parameters. Zeleny sedimentation values (Zel), protein (Prot), kernel hardness (KH) and 1000‐kernel weight (TKW) of 226 F₅ recombinant inbred lines (RILs) from a cross between wheat and spelt were assessed in different environments. The dough properties of 204 RILs were assessed with an alveograph. Based on a genetic map of 187 loci, nine QTL were found for Zel and Prot, explaining 47% and 51% of the phenotypic variance, respectively. Fifty‐four per cent of the variance was explained by 10 QTL for KH and eight for TKW. For the alveograph parameters 10 QTL were found for baking strength, nine for tenacity, seven for configuration ratio, and four for elasticity index and extensibility. The phenotypic variance explained ranged from 25% to 48%. The population mean of the dough parameters was shifted towards the spelt parent. It is concluded that non‐additive effects are crucial in the expression of high bread‐making quality of wheat. The consequences for wheat and spelt breeding programmes are discussed.     

Vernalization gene combination to maximize grain yield in bread wheat (Triticum aestivum L.) in diverse environments

The major vernalisation genes of VRN1 are well understood at the molecular level. However, their quantitative contributions to flowering time and grain yield related traits are not clear. In this study, we used a double haploid population (225 lines) of Westonia × Kauz in which the Vrn-A1a (Westonia), Vrn-B1a (Westonia) and Vrn-D1a (Kauz) were segregating, and a high resolution genetic map of 1,159 loci, to determine the quantitative contributions of Vrn-A1a, Vrn-B1a and Vrn-D1a for the days to anthesis and grain yield related traits in diverse environments. The major quantitative trait loci (QTL) of spikelet number per spike and days to anthesis were contributed by the winter alleles of VRN1. The QTL of the time of grain filling were contributed by the spring alleles of VRN1. The wild genotype (vrn-A1vrn-B1vrn-D1) showed the latest flowering, the highest spikelet number per spike, lowest peduncle proportion and thousand grain weight in three environmental analyses, and the largest spikelet number per spike, which resulted in high kernel number per spike (KN) and grain weight (GW) in well-watered environments. One QTL of KN was located on 5B, contributed by winter allele of vrn-B1 in three environmental analyses, and one GW QTL was detected on 5A, contributed by the spring allele of Vrn-A1a in a drought environment. The results indicated that the genotype Vrn-A1avrn-B1Vrn-D1a would shorten the time to anthesis and give high GW and KN in drought environments. The early anthesis associated phenotype, peduncle proportion would provide an indicator in breeding programs.     

QTL analysis of kernel shape and weight using recombinant inbred lines in wheat

Quantitative trait locus (QTL) analysis of kernel shape and weight in common wheat was conducted using a set of 131 recombinant inbred lines (RIL) derived from ‘Chuan 35050’ × ‘Shannong 483’. The RIL and their two parental genotypes were evaluated for kernel length (KL), kernel width (KW), thousand-kernel weight (TKW), and test weight (TW) in four different environments. Twenty QTL were located on 12 chromosomes, 1A, 1B, 1D, 2A, 2B, 3B, 4A, 4B, 5D, 6A, 6B, and 7B, with single QTL in different environments explaining 5.9–26.4% of the phenotypic variation. Six, three, four, and seven QTL were detected for KL, KW, TKW, and TW, respectively. The additive effects for 17 QTL were positive with Chuan 35050 increasing the QTL effects, whereas the remaining three QTL were negative with Shannong 483 increasing the effects. Eight QTL (40%) were detected in two or more environments. Two QTL clusters relating to KW, TKW, and TW were located on chromosomes 2A and 5D, and the co-located QTL on chromosome 6A involved a QTL for KW found in two environments and a QTL for TKW detected in four environments.     

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。     

Detection of quantitative trait loci (QTLs) for seedling traits and drought tolerance in wheat using three related recombinant inbred line (RIL) populations

In order to detect quantitative trait loci (QTLs) for drought tolerance in wheat during seed germination conditional and unconditional QTL analyses of eight seedling traits were conducted under two water regimes using three related F₉ recombinant inbred line populations with a common female parent. A total of 87 QTLs for the eight seedlings traits and 34 specific QTLs related to drought tolerance were detected. Seventy-one of these QTLs were major QTLs with contributions to phenotypic variance of >10 %. Of the 34 QTLs related to drought tolerance only eight were also detected by unconditional analysis of seedling traits under osmotic stress conditions indicating that most of the QTLs related to drought tolerance could not be detected by unconditional QTL analysis. Therefore, conditional QTL analysis of stress-tolerance traits such as drought tolerance was feasible and effective. Of 11 important QTL clusters located on chromosomes 1BL, 1D, 2A, 2B, 2D, 4A, 6B, and 7B, nine were detected in multiple populations and eight were detected by both unconditional and conditional analyses.     

利用非条件和条件QTL解析油菜产量相关性状的遗传关系

基于前期研究中构建的Sollux/Gaoyou DH群体在9个环境中的表型数据和新版遗传图谱,对油菜角果长度进行QTL定位,估测QTL的加性、上位性和环境互作效应。并通过条件QTL方法,解析角果长度与角果粒数和粒重之间的遗传关系,以期利用标记辅助,探讨通过选择角果长度基因型以增加角果粒数、提高千粒重,最终达到增加产量的可能性。结果共检测到在3个环境以上稳定表达的控制角果长度QTL 8个,加性效应值在0.09~0.26 cm之间,效应总和解释群体遗传总变异的60%。8对上位性QTL效应值在0.035~0.075 cm之间,效应总和为加性总效应的38%。QTL与环境互作效应只在少数位点和个别环境中显著。条件QTL研究表明,q SLA2、q SLC1-2和q SLC8-1位点,角果长度的变化对角果粒数影响较大;而通过选择q SLA7、q SLC1-2、q SLC8-1和q SLC8-2长角果标记基因型,可望同时提高角果粒数和千粒重。6个主效QTL 11个连锁标记基因型和表现型的关联分析,验证了条件QTL分析结果,表明通过对q SLA2、q SLA7、q SLC8-1和q SLC8-2位点6个连锁标记(ZAAS423、SUC1-3、ZAAS12a、ZAASA7-28、ZAAS433和ZAAS437)长角果基因型的聚合,可增长角果约2 cm,间接增加角果粒数2粒,同时提高千粒重0.4 g,从而可望实质性地提高油菜产量水平。     

小麦籽粒产量及穗部相关性状的QTL定位

由小麦品种花培3号和豫麦57杂交获得DH群体168个株系,种植于3个环境中,利用305个SSR标记对籽粒产量和穗部相关性状(穗长、穗粒数、总小穗数、可育小穗数、小穗着生密度、千粒重和粒径)进行了QTL定位。利用基于混合线性模型的QTLNetwork 2.0软件,共检测到27个加性效应和13对上位效应位点,其中 8个加性效应位点具有环境互作效应。相关性高的性状间有一些共同的QTL位点,表现出一因多效或紧密连锁效应。5D染色体区段Xwmc215–Xgdm63,检测到控制籽粒产量、穗粒数、总小穗数、可育小穗数和小穗着生密度5个性状的QTL位点,各位点的遗传贡献率较大且遗传效应方向相同,增效等位基因均来源于豫麦57,适用于分子标记辅助育种和聚合育种。控制千粒重与穗粒数的QTL位于染色体不同区段,有利于实现穗粒数与粒重的遗传重组。     

Genetic dissection of rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) tiller,plant height,and grain yield based on QTL mapping and metaanalysis

Tiller number per plant (TN) and plant height (PH) are important agronomic traits related to grain yield (GY) in rice (Oryza sativa L.). A total of 30 additive quantitative trait loci (A-QTL) and 9 significant additive × environment interaction QTLs (AE-QTL) were detected, while the phenotypic and QTL correlations confirmed the intrinsic relationship of the three traits. These QTLs were integrated with 986 QTLs from previous studies by metaanalysis. Consensus maps contained 7156 markers for a total map length of 1112.71 cM, onto which 863 QTLs were projected; 78 meta-QTLs (MQTLs) covering 11 of the 30 QTLs were detected from the cross between Dongnong422 and Kongyu131 in this study. A total of 705 predicted genes were distributed over the 21 MQTL intervals with physical length <0.3 Mb; 13 of the 21 MQTLs, and 34 candidate genes related to grain yield and plant development, were screened. Five major QTLs, viz. qGY6-2, qPH7-2, qPH6-3, qTN6-1, and qTN7-1, were not detected in the MQTL intervals and could be used as newly discovered QTLs. Candidate genes within these QTL intervals will play a meaningful role in molecular marker-assisted selection and map-based cloning of rice TN, PH, and GY.     

Genome-wide association study of differences in 14 agronomic traits under low- and high-density planting models based on the 660k SNP array for common wheat

One hundred and ninety-seven wheat accessions from Yellow and Huai Winter Wheat Region (YHW) were evaluated for differences of 14 agronomic traits under low- and high-density plantings. Compared with the high-density plantings, plant height, neck length, uppermost internode length, flag leaf angle and number of sterile spikelets under the low-density plantings reduced, while heading date, flowering date, flag leaf length and width, spike length, number of fertile spikelets, grain number per spike, thousand-kernel weight and grain weight per spike increased. A total of 1,118 markers were detected based on GWAS, and seven QTLs were confirmed. One QTL on chromosomes 5BL and two other QTLs on 5Dl were all tightly associated with flowering date difference. Bioinformatics analysis revealed that two haploblocks in 5Dl were involved, and the Vrn-D1 locus was located in this interval. A region on chromosome 5B at around 531.5 Mb was significantly associated with plant height difference. Two QTLs including AX-94840438 (7BL) and AX-94563647 (7DS) were responsible for neck length or uppermost internode length difference.     

Modelling nitrogen stress with probe genotypes to assess genetic parameters and genetic determinism of winter wheat tolerance to nitrogen constraint

Environmental and economical constraints in Europe will favour low nitrogen (N) input systems and wheat varieties adapted to moderate N deficiency. In this context, we studied the dynamics of genetic parameters according to N stress intensity and characterized the genetic determinants for plant tolerance to N deficiency. Thus, we combined N stress modelling with a genetic approach. Two hundred and twenty-two doubled haploid lines were experimented in the field for a range of nitrogen conditions. Those conditions were characterized by the Nitrogen Nutrition Index (NNI) of Récital. Grain Yield (GY) and Kernel Number (KN) were assessed. For GY and KN, and for each line, factorial regressions using NNI of Récital as environmental index were performed. In addition, we assessed the sensitivity to N stress (slopes of the regression) and the performances under low N conditions (predicted values for a NNI of 0.5). QTL detection was performed on these parameters as well as on KN and GY measured in each environment. G × N variance increased with N stress intensity whereas heritability and genetic variance decreased. 11 QTL regions were detected: 3 were N supply-specific QTL (on linkage groups 2A2, 3A and 4B) while 4 contained QTL detected under N⁺ and under N⁻ (2D1, 4B and 5A1). Out of these four, 2 coincided with QTL for factorial regression parameters (2D1 and 4B). Finally, 4 QTL were specific for factorial regression parameters (3B, 5A2 and 7B2). The role of genes commonly used in breeding programs (rht-B1 on 4B, and Ppd1 on 2D1) in plant adaptation to nitrogen constraint was highlighted. Future studies should focus on grain protein yield, another target for low-N breeding scheme.