Genetic diversity within spelta and macha wheats based on RAPD analysis

Genetic diversity in a crop species is basic to improvement of the species and can be estimated at the molecular level. The objective of this study was to estimate genetic diversity within and between spelta and macha wheats. Random amplified polymorphic DNA (RAPD) analysis was conducted on 69 spelta and 32 macha wheat accessions. The classification of spelta and macha accessions, based on Jaccard genetic similarity coefficients for RAPD markers, was consistent with their geographic origin. The results indicated that the germplasm of macha wheat was more diverse than that of spelta wheat. In the dendrogram of macha wheat, four spelta-like accessions grouped together, separate from the remaining macha accessions, suggesting that these accessions were misclassified. In addition, accessions with identical RAPD patterns were found, indicating that these accessions were probably duplicated. Thus RAPD analysis can be used to estimate genetic diversity and identify duplicate accessions in wheat germplasm collections. This revised version was published online in August 2006 with corrections to the Cover Date.     

Genetic diversity of wheat storage proteins and bread wheat quality

To understand the genetic and biochemical basis of the bread makingquality of wheat varieties, a large experiment was carried out with a set of162 hexaploid bread wheat varieties registered in the French or EuropeanWheat Catalogue. This material was used to analyse their allelic compositionat the twelve main storage protein loci. A large genetic and biochemicaldiversity of the gluten proteins was found. Several gliadin encoding lociexhibited the highest allelic diversity whereas the lowest diversity was foundfor Glu-A1 and Glu-D3 loci encoding some high molecularweight glutenin subunits (HMW-GS) and LMW-GS respectively. Thevarieties were grown in three experimental locations in France. Qualityevaluation was carried out from material harvested in each location usingseven technological tests: grain protein content (Prot), grain hardness(GH), Zeleny sedimentation test (Zel), Pelshenke test (Pel), water solublepentosans (relative viscosity: Vr ), mixograph test (giving 11 parameters)and the alveograph test (dough strength W, tenacity P , extensibility L,swelling G, ratio P/L and the elasticity index Ie). Genetic and locationeffects as well as broad-sense heritability of each of the 22 technologicalparameters were calculated. GH, corresponding to the major Ha gene, Pel,and MtxW (mixograph parameter) had the highest heritability coefficients,alveograph parameters like W, P, the relative viscosity Vr and severalmixograph parameters had medium heritability coefficients whereas Protand L had the lowest. Variance analysis (using GLM procedure) allowed theeffect of the allelic diversity of the storage proteins, on the geneticvariations of each quality parameters, to be estimated. Glu-1 and Glu-3 loci had significant additive effects in the genetic variations of manyparameters. Gliadin alleles encoded at Gli-1 and Gli-2 were alsofound to play significant effect on several quality parameters. The majorpart of the phenotypic variation of the different quality parameters like Zel,Pel, W or mixograph peak time MPT was explained with the GH and allelesencoded at Glu-1 and Glu-3. Allelic variants encoded at Glu3and Gli-2 had similar contribution to the phenotypic variations ofquality parameters and accounted for 4% up to 21% each.     

Patterns of RFLP-based genetic diversity in germplasm pools of common wheat with different geographical or breeding program origins

A set of 292 accessions of common wheat (Triticum aestivum L.) representing 21 germplasm pools based on geographical or breeding program origins was assayed for RFLP diversity. Thirty cDNA and genomic DNA probes and the HindIII restriction enzyme were employed for RFLP analysis. About 61% of all 233 scored bands were present in 75% or more of the accessions. All but one of the 30 probes revealed polymorphism, and the average number of distinct patterns per probe over all accessions was 9.5.Polymorphic Information Content (PIC) values within a pool varied from 0 to 0.9 and depended on the identities of both the germplasm pool and the probe. Rare banding patterns with a relative frequency of ≤0.2 within a pool were detected. These rare patterns were more likely to occur in pools exhibiting high levels of heterogeneity. The highest level of polymorphism was observed in the Turkish landraces from Southwest Asia. The Eastern U.S. soft red winter wheat germplasm pool was more genetically diverse than the other advanced germplasm pools, and nearly as diverse as the Turkish landrace pool. RFLP-based genetic relationships between germplasm pools generally tracked expectations based on common geographical origin, breeding history and/or shared parentages. The Chinese wheat landraces from Sichuan, Tibet, and Yunnan provinces were distinct from other pools. Similarity matrices for among-pool genetic distance estimates based on either band frequencies or banding pattern frequencies showed good correlation with matrices derived from Nei and Li's mean genetic similarity estimates (r=−0.82^** and r=−0.73^**, respectively. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic diversity evolution through participatory maize breeding in Portugal

Natural, and in particular, artificial (human) selection may pose a danger to the existing crop genetic diversity. Nevertheless, on-farm breeding systems seem to achieve phenotypic improvements even though preserving variability. Using SSR markers, we analysed several selection cycles, over a 20 years period, of a Portuguese on-farm participatory maize OPV-‘Pigarro’ breeding project. No significant differences in allelic richness (N_ar), observed heterozygosity (H_O), expected heterozygosity (or gene diversity; H_E) or inbreeding coefficient (f) were detected among the selection cycles. 58 out of 107 alleles were common to all the selection cycles studied. The analysis of molecular variance showed that the variation among selection cycles represented only 7% of the total molecular variation. However, the number of private alleles varied among the selection cycles, being the highest detected at the beginning of the selection project. These findings demonstrate that an allele flow took place during the on-farm selection process of ‘Pigarro’ but the level of genetic diversity was not significantly influenced. Since interesting phenotypic improvements were also achieved, on-farm breeding projects, like this one, should be valued as a way to preserve unique Portuguese maize landraces in risk of disappearing.     

新疆冬小麦品种农艺及产量性状遗传多样性分析

Grain yield is one of the most important goals in wheat breeding, and agronomic or yield-related traits can directly reflect the characteristics of varieties. In order to determine the evolution of genetic diversity in agronomic traits of Xinjiang winter wheat varieties and their adaptabilities to different ecological environments, 134 winter wheat landraces and 54 moderns bred varieties from Xinjiang were selected for agronomic trait investigation. They were planted in three different ecological environments (Urumqi and Yining in Xinjiang province, and Tai’an in Shandong province) for two consecutive growth seasons, and nine agronomic and yield-related traits were surveyed and analyzed. The estimated broad sense heritability of nine agronomic and yield traits was in descending order: plant height > grain width > grain length/width ratio > spike length > spikelet number > thousand- kernel weight > grain number per spike > grain length > fertile spikelet number. Correlation analyses of nine agronomic and yield traits showed that these traits were correlated with each other. It was found that the plant height, spike length and grain length/width ratio of landraces were higher than that in modern bred varieties, but the grain number per spike, thousand kernel weight, grain length and grain width in landraces were less than that in modern bred varieties. However, the correlation coefficient of these nine traits was higher in modern bred varieties than that in landraces. These variations reflected the evolution of Xinjiang winter wheat varieties in agronomic traits in recent years. This study may provide important information for breeders to select the breeding parents in different winter wheat regions.     

蚂蚱麦和小白麦衍生系的遗传多样性分析

陕西关中蚂蚱麦和山西平遥小白麦是我国北方小麦品种的原始骨干亲本,解析蚂蚱麦和小白麦及其衍生系的遗传多样性对于小麦品种改良具有重要的参考意义。本研究利用小麦660KSNP芯片对蚂蚱麦、小白麦及其衍生品种(系)进行全基因组扫描,分析其遗传多样性。结果表明,小麦3个基因组的多态性SNP标记数为BAD,第4同源群的多态性标记数最少, 149份供试材料基因多样性(H)范围为0.095～0.500,平均值为0.336;核苷酸多样性指数(π)范围为0.272～0.435,平均值为0.340;而遗传相似系数(GS)变幅为0.335～0.997,平均值达0.619,表明蚂蚱麦和小白麦衍生系的遗传多样性较低。聚类分析表明蚂蚱麦和小白麦紧密地聚在亚群I,其衍生品种(系)分为5个亚群,其中2000年以前以蚂蚱麦或小白麦的单一衍生系为主,分在亚群I、II、III, 2000年以后多数品种同时拥有蚂蚱麦和小白麦血缘,分在亚群IV、V,遗传多样性较高,且与大面积推广品种聚为一类。因此,应加强优异基因资源导入,拓宽小麦品种的遗传基础,最终提高育种水平。     

Normalization method for canopy temperature as an indirect indicator of yield potential in wheat breeding programs

Canopy temperature (CT) is often related to potential yield and is a possible yield indicator in breeding programs. However, it is difficult to evaluate genetic variations of CT accurately in large-scale investigations, such as breeding programs, because CT is strongly affected by environmental conditions. In this study, to precisely evaluate these genetic variations, we determined the environmental factors that affect CT measurement and proposed a convenient normalization method to minimize their influence. We measured the CT of CT-high or CT-low cultivars in the field under various conditions. We found that as the sun and shade levels were alternated, the CT changed within seconds; the position in the field also critically affected the CT. However, even under these conditions, the differences between cultivars became clearer if CT was normalized by neighboring lines. Additionally, we revealed that CT measurements between 12:00 and 15:00 maximized the difference between cultivars. Using our normalization technique under the favorable conditions specified can help breeders select high-yield lines using CT in breeding programs.     

Development of molecular markers linked to the wheat powdery mildew resistance gene Pm4b and marker validation for molecular breeding

Powdery mildew, caused by Blumeria graminis (DC.) E.O. Speer f. sp. tritici, is an important disease in wheat (Triticum aestivum L.). Bulk segregant analysis (BSA) was employed to identify SRAP (sequence‐related amplified polymorphism), sequence tagged site (STS) and simple sequence repeat (SSR) markers linked to the Pm4b gene, which confers good resistance to powdery mildew in wheat. Out of 240 SRAP primer combinations tested, primer combinations Me8/Em7 and Me12/Em7 yielded 220‐bp and 205‐bp band, respectively, each of them associated with Pm4b. STS‐₂₄₁ also linked to Pm4b with a genetic distance of 4.9 cM. Among the eight SSR markers located on wheat chromosome 2AL, Xgwm382 was found to be polymorphic and linked to Pm4b with a genetic distance of 11.8 cM. Further analysis was carried out using the four markers to investigate marker validation for marker‐assisted selection (MAS). The results showed that a combination of the linked markers STS_?241, Me8/Em7_?220 and Xgwm382 could be used for marker‐assisted selection of the resistance gene Pm4b in wheat breeding programmes.     

Bringing wild relatives back into the family: recovering genetic diversity in CIMMYT improved wheat germplasm

Summary The dangers of a narrow genetic base of the world's major domesticated food crops have become a great global concern in recent decades. The efforts of the International Maize and Wheat Improvement Center (CIMMYT) to breed common wheat cultivars for resource poor farmers in the developing world (known as the Green Revolution wheats) has met with notable success in terms of improved yield, yield stability, increased disease resistance and utilization efficiency of agricultural inputs. However, much of the success was bought at the cost of an overall reduction in genetic diversity in the species; average Modified Roger's distances (MRD) within groups of germplasm fell from 0.64 in the landraces to a low of 0.58 in the improved lines in the 1980s. Recent efforts by CIMMYT breeders to expand the genetic base of common wheat has included the use of landraces, materials from other breeding programs, and synthetic wheats derived from wild species in the pedigrees of new advanced materials. The result, measured using SSR molecular markers, is a highly significant increase in the latent genetic diversity of recently developed CIMMYT breeding lines and cultivars compared to the original Green Revolution wheats (average MRD of the latest materials (0.63) is not significantly different from that of the landraces, as tested using confidence intervals). At the same time, yield and resistance to biotic and abiotic stresses, and end-use quality continue to increase, indicating that the Green Revolution continues to this day.     

基于形态学性状和SSR标记的花生品种遗传多样性分析和特异性鉴定

以101份南方花生区试品种为材料,利用形态学性状和SSR标记进行品种遗传多样性分析和特异性鉴定。结果表明, 29个形态学性状中有7个无多样性,其余22个的多样性指数为0.23～0.77,平均为0.43。在相似系数为0.76处,将供试品种划分为七大类群,同一育种单位的品种倾向于聚在一起。用40个SSR标记共检测出167个等位基因,单个标记检测的等位基因数2～6个,平均为4.18个。标记的多态性信息量(PIC)差异较大,最大为0.79,最小为0.26,平均为0.55。在相似系数为0.70处,供试品种可被划分为六大类群,同一省份育成的品种多聚为一类。Mantel检验发现品种间的形态学性状和SSR标记的相似系数矩阵相关性弱(r=0.36),SSR标记无法取代形态学性状单独用于花生品种特异性鉴定,但两者相结合能有效提高花生品种特异性鉴定的准确性。     

Impact of plant genetic resources on wheat breeding

This article describes the impact of plant genetic resources on wheat breeding. It defines the important contribution of N.I. Vavilov Institute (St. Petersburg, Russia) to broadening the genetic diversity of new wheat cultivars. Special attention is given to conducting a comprehensive evaluation of intraspecific variability for valuable characters, including: 1) formation of special subcollections, consisting of accessions with useful characters and accessions representing intraspecies diversity for a given character; 2) revealing genetic differences among phenotypically superior accessions; 3) determining a genetic system of intraspecific variability for a given character; 4) formation of a genetic collection; 5) revealing and developing the donors of useful characters. An example using plant height shows that the proposed research approach adequately determines the genetic potential of species and reveals the most effective genes for practical uses. It is assumed that the main sources of genes for breeding Triticum aestivum L. in order of importance will remain: 1) intraspecific diversity of T. aestivum itself; 2) other Triticum species; 3) other genera of the Triticeae Dum. tribe (particularly Aegilops L.); 4) more remote genera of the Poaceae Barnh. botanical family. It is stressed that existing diversity of T. aestivum has been poorly investigated genetically and only partially used by breeders. Properly evaluated, it can provide multiple solutions for traditional and new problems of wheat improvement. This revised version was published online in August 2006 with corrections to the Cover Date.     

Genetic diversity in bread wheat, as revealed by coefficient of parentage and molecular markers, and its relationship to hybrid performance

Variable results have been obtained in different crop species using geneticsimilarity (GS) estimates based on molecular markers and coefficient ofparentage (COP) to predict heterosis.This study was designed: i) to assess the level of GS among 40 breadwheat (Triticum aestivum L.) cultivars selected in Central and SouthEurope; ii) to compare GS with COP; iii) to correlate the estimates ofparental diversity with the heterotic effects detected on 149 F₁hybrids obtained by crossing the 40 cultivars according to three matingdesigns.The parental cultivars and the F₁ hybrids were grown in severallocations at normal seed density. Significant heterotic effects were detectedfor grain yield and other traits including quality attributes. The parentalcultivars were assayed for DNA polymorphisms using two classes ofmarkers: 338 RFLP and 200 AFLP^® bands were scored. GS estimates werecomputed considering each molecular marker set separately (GS_RFLP,GS_AFLP) and together (GS_TOT). Ample differentiation amongthe parental cultivars was detected with the two marker sets. Although theaverage GS_TOT (0.43) was higher than COP (0.10), the twomeasurements were significantly correlated (r = 0.36, p < 0.01).Correlations between the different estimates of genetic diversity andF₁ performance or mid parent heterosis for grain yield and otherrelated traits were in general low although statistically significant.A more detailed analysis was conducted on 28 F₁ hybridsproduced in a half diallel cross of eight parental cultivars characterized byhigh heterotic effects for grain yield. The GS estimates based on RFLP,AFLP^® markers and also on RAPD were partitioned into general andspecific components. Correlations with general and specific combiningability effects for the measured traits were in several cases statisticallysignificant but too low to be predictive and therefore exploitable in practicalbreeding.     

Genetic diversity of high-molecular-weight glutenin subunit compositions in landraces of hexaploid wheat from Japan

The high-molecular-weight (HMW) glutenin subunit composition of seed storage protein of 174 Japanese hexaploid wheat (Triticum aestivum) landraces have been examined by using sodium dodecyl sulfate polyacrylamide gel electrophoresis system. Twenty four different, major glutenin HMW subunits were identified, and each of the landraces contained three to five subunits and 17 different glutenin subunit patterns were observed for 13 alleles in the landraces. On the basis of HMW glutenin subunits composition, Japanese landraces showed a specific allelic variation, close to Japanese commercial wheats in HMW glutenin subunits, different from those in alien hexaploid wheats. Further, it could be concluded that all common glutenin alleles can be found in the 174 landraces originated from Japan. The variation detected in the glutenin subunits is useful for variety identification, has a bearing on our understanding of hexaploid wheat genetic resource evolution in Japan, and raises questions concerning the nature of this genetic variation. This revised version was published online in July 2006 with corrections to the Cover Date.     

小麦矮秆突变体je0098的遗传分析与其矮秆基因定位

倒伏易引发小麦严重减产,发掘和利用优异矮秆基因是培育高产抗倒伏小麦新品种的关键。本研究以京411(WT)及其经EMS诱变获得的产量相关性状优良的矮秆突变体je0098为试验材料,对其株高进行遗传分析,结合外显子捕获测序和遗传连锁分析定位矮秆基因。3年田间株高数据统计分析表明,je0098与WT相比株高降低15cm,组织细胞学观察结果显示,je0098与WT相比节间细胞长度缩短18%,暗示je0098的矮化是由于节间细胞长度变短所致;赤霉素敏感性分析表明, je0098为赤霉素敏感型矮秆突变体。利用WT和je0098杂交构建的由344个单株组成的F2分离群体,结合F2:3家系表型数据,选取矮秆纯合和高秆单株构建混池,对两亲本和子代混池分别进行外显子捕获测序,在2D染色体上定位到一个具有降秆效应的数量性状位点(QTL)。结合全基因组重测序所得SNP位点,在2D染色体开发了6个KASP分子标记,对F2单株进行基因分型。利用QTL IciMapping作图软件构建遗传连锁图谱,结合3年田间表型数据,将矮秆基因定位在20.77～28.84 Mb区间内,遗传距离为11.48 cM。本研究结果为突变...     

Marker‐assisted backcross breeding for improvement of drought tolerance in bread wheat (Triticum aestivum L. em Thell)

Drought stress is presently a major productivity limiting factor in wheat. This study developed five wheat lines with inbuilt tolerance to drought stress using marker‐assisted backcross breeding (MABB) approach employing three linked quantitative trait loci (QTLs) in an initial population of 516 BC₁F₁ plants. The high‐yielding wheat cultivar ‘HD2733’ grown over last few years extensively in the eastern plains of India is largely sensitive to drought and is used as the recurrent parent. ‘HI1500’ released for water‐limiting conditions and carrying drought‐tolerant QTLs was used as donor parent. MABB lines were advanced using foreground and background selection, coupled with stringent phenotyping. We identified 29 lines that were homozygous for targeted QTLs in different combinations with background recovery range of 89.2%–95.4%. Further evaluation of selected lines for physiological traits and distinctness, uniformity and stability (DUS) characters under rainfed condition identified five potential varieties for national varietal evaluation programme in the zone. The report is first of its kind in implementing known QTLs for the development of drought‐tolerant wheat lines through MABB approach.     

新疆冬小麦地方品种与育成品种基于SNP芯片的遗传多样性分析

新疆是我国西北重要的小麦优势产区和消费区。解析新疆冬小麦地方品种与育成品种之间的遗传多样性和亲缘关系,对新疆冬小麦育种中杂交组合的合理选配以及后代选择具有重要的指导意义。本研究利用小麦55K SNP(single nucleotide polymorphism)芯片对134份新疆冬小麦地方品种及54份育成品种进行全基因组扫描,估算其品种间的遗传距离,揭示其遗传多样性。结果表明,所有SNP位点的多态性比率达到95.62%(50,743/53,063)。每条染色体分布1068～2616个多态性位点,多态性标记在基因组间分布呈现A>B>D。188个品种间的两两遗传距离在0.002～0.723之间,平均为0.378。其中134个地方品种两两之间的遗传距离在0.002～0.400之间,平均为0.070; 54个育成品种两两之间的遗传距离在0.004～0.337之间,平均为0.114; 134个地方品种与54个育成品种之间的遗传距离在0.605～0.723之间,平均为0.699。聚类结果显示可将所有材料分为10个不同类群。综合SNP和系谱分析,育成品种与地方品种之间的遗传差异最大,其次...     

基于SNP标记揭示我国小麦品种(系)的遗传多样性

为了解我国主要小麦品种(系)的遗传多样性,为亲本组配提供参考,利用90KSNP芯片技术对国内为主的240个小麦品种(系)进行全基因组扫描,分析其遗传多样性和遗传基础。结果表明,多态性SNP位点在B基因组最多, D基因组最最少,尤其4D上最少;在全基因组范围内PIC平均值为0.26。参试品种间平均遗传相似系数为0.656,变幅为0.133～0.998,且87.05%品种间遗传相似系数在0.60～0.78之间;国内西南麦区和长江中下游麦区小麦品种(系)间的平均相似系数较高,分别为0.718和0.712,国外品种(系)间的相似系数最低,为0.552。聚类分析将参试品种(系)划分为7个类群,大部分类群含有来自不同区域育成品种(系),主成分分析显示各区域育成的品种(系)相互交集,表明我国各省市间种质资源交流较为频繁,但部分单位育成的品种(系)遗传基础不够丰富,部分品种(系)间遗传相似性较高,在育种中亟待引入新的种质,拓宽遗传基础。     

Recurrent selection using male sterility and hydroponic tiller culture in pedigree breeding of wheat

A procedure for recurrent selection based on the male sterility gene, Ms3, was implemented. To facilitate the production of large numbers of hybrid progeny, a simple hydroponic system was developed in which male‐sterile tillers cut at the flowering stage can be pollinated and maintained for about 8 weeks‐long enough to produce a large quantity of viable hybrid seeds. The recurrent selection steps were integrated with a pedigree breeding programme employing different selection cycles for male and female plants. F₁ female plants are subjected to a single screening for seedling resistance. In addition to F₁ seedling screening, F₂‐F₄ male families are field‐selected for disease resistance, agrotype and quality in a pedigree programme before being used in crosses.     

Assessment of the spatial genotypic and phenotypic diversity present in the various winter wheat breeding programs in Southeast Europe

The genetic diversity present in the breeding programs of southeast Europe was assessed in a set of 114 winter wheat (Triticum aestivum L.) cultivars using AFLP and SSR markers. The average genetic diversity characterised with the Jaccard’s distance coefficient was 0.605 with an interval of 0.053 and 0.889. The wheat cultivars originating from the four countries differed from each other in their clustering patterns, including the numbers of clusters and the most prevalent cluster, which was breeding program-specific. Hungarian and Romanian cultivars showed closer relationships, and Serbian and Macedonian cultivars grouped together more frequently. The phenotypic variability of the same cultivars was assessed under diverse ecological conditions of the four growing sites, measuring the disease resistance against two foliar diseases, and several agronomic traits. Of the phenotypic traits, powdery mildew and leaf rust responses showed significant associations with genetic diversity, whereas heading date, plant height and yield components did not. Through parallel assessment of genotypic and phenotypic diversity it was possible to separate winter wheat cultivars with similar genotype but diverse phenotype from those with similar phenotype but diverse genotype. This information will allow breeders to make informed decisions in selecting parents for new crosses.     

Applications of pedigree-based genome mapping in wheat and barley breeding programs

The aim of the pedigree-based genome mapping project is to investigate and develop systems for implementing marker assisted selection to improve the efficiency of selection and increase the rate of genetic gain in breeding programs. Pedigree-based whole genome marker application provides a vehicle for incorporating marker technologies into applied breeding programs by bridging the gap between marker–trait association and marker implementation. We report on the development of protocols for implementation of pedigree-based whole genome marker analysis in breeding programs within the Australian northern winter cereals region. Examples of applications from the Queensland DPI&F wheat and barley breeding programs are provided, commenting on the use of microsatellites and other types of molecular markers for routine genomic analysis, the integration of genotypic, phenotypic and pedigree information for targeted wheat and barley lines, the genomic impacts of strong selection pressure in case study pedigrees, and directions for future pedigree-based marker development and analysis.