Genetic variability in melon based on microsatellite variation

A set of 18 simple‐sequence repeat (SSR or microsatellite) markers was used to study genetic diversity in a collection of 27 melon (Cucumis melo L.) accessions, representing a broad range of wild and cultivated melons. The materials studied were highly polymorphic for SSRs and a total of 114 alleles were detected (average of 6.3 alleles per locus). Cluster analysis suggests the division of these accessions into two major groups, largely corresponding to the division of C. melo in the two subspecies agrestis and melo. The assignment of the accession to the subspecies was generally in agreement with published reports, except for those corresponding to the ‘dudaim’ and ‘chito’ cultivar groups, which, according to the observed SSR variability, should be included in subspecies agrestis. Based on cluster analysis, five groups of accessions were defined. The two most divergent groups include mainly accessions from the Mediterranean which form one group, and accessions from China, Japan, Korea and India forming the other. Both groups shared a low level of intra‐accession variation compared with the other groups, which suggests an erosion of their genetic variability because of drift and/or inbreeding. The remaining accessions, mainly from Central Africa and India, were more variable and may be an important source of genetic variation for melon breeding.     

Potential loss of unique genetic diversity in tomato landraces by genetic colonization of modern cultivars at a non-center of origin

We report the genetic diversity of tomato landraces from Myanmar, with reference to worldwide tomato accessions. Ten simple sequence repeat markers were screened and used to create diversity profiles of tomato germplasm. A total of 133 alleles were amplified from the germplasm investigated; alleles specific to landraces from Myanmar were also observed. Higher genetic diversity for the Myanmar landraces highlighted the broad genetic base of tomato germplasm. Principal component analysis showed that most of the Myanmar landraces were divergent from other accessions. The different approaches used to analyse landrace diversity documented the broader genetic base of germplasm from Myanmar, which is a non‐center of origin for tomato. Genetic diversity in the landraces may be attributable to diverse production systems used by different ethnic groups in Myanmar, ranging from natural hydroponics in eastern areas, to slash‐and‐burn fields in mountain areas and shifting cultivation in many parts of the country. The availability of uniform and high‐yielding cultivars/hybrids threatens the valuable landraces in Myanmar. We emphasize the need to evaluate tomato germplasm from Myanmar for different traits and sustainable use with simultaneous conservation.     

RFLP diversity within and between major groups of barley in Europe

Restriction fragment length polymorphism (RFLP) diversity has been determined and analyzed as expressed by 33 single‐ or low‐copy clone/ enzyme combinations at 32 loci distributed over all chromosomes of the barley genome within a sample of 223 European barley accessions comprised of pure line (single‐head progenies) genotypes. The accessions have been selected to include landraces and widely grown cultivars derived from crossbreeding during the 20th century in North‐, West‐ and Central European countries. Genetic diversity obtained from 83 alleles across all accessions is characterized by the diversity index H = 0.385. The diversity indices determined for landraces and cultivars were almost equal, with the difference between spring (H = 0.260) and winter (H = 0.415) barley approaching statistical significance, while comparisons of other groupings only revealed statistically insignificant trends. A more detailed analysis based on differences in allele frequency distributions at each locus (clone/enzyme combinations resp.) revealed very clear differences related to the existence, continuity and dynamics of changes in group‐specific RFLP profiles. With the majority (69%) of RFLP alleles at 23 out of 32 loci on all barley chromosomes involved, contributions from chromosomes 1H, 3H, 4H and 5H seem to be of special importance. Differences in the overall average of abundance indicate higher levels of genetic diversity within both groups of winter barley compared with both groups of spring barley, from which the most frequent alleles at 15 (2‐rowed spring barley) and 17 (6‐rowed spring barley) RFLP loci approach fixation. The results of this study are discussed in relation to the history of barley cultivation and barley breeding in Europe, and possible explanations for group‐specific differences in the RFLP profiles of landraces and cultivars as well as for the high levels of (nearly) fixed alleles of both subsets of spring barley, and with respect to progress in barley breeding that it has been possible to obtain within the rather narrow RFLP profiles.     

Agronomic and genetic diversity in intermediate wheatgrass (Thinopyrum intermedium)

Intermediate wheatgrass [Thinopyrum intermedium (Host) Barkworth & D. R. Dewey] plant introductions (PI) have played a critical role in the development of improved intermediate wheatgrass cultivars. The objective of this study was to characterize a large number of intermediate wheatgrass populations over its native range for dry matter yield (DMY), crude protein (CP), in vitro true digestibility (IVTD), neutral detergent fibre (NDF), and rhizome development and genetic diversity and structure to identify superior populations and possible geographical regions in which to collect. Analysis of molecular variance using 643 AFLP bands partitioned 31% of the total genetic variation among these populations with 69% variance detected within populations. Bayesian cluster analysis identified two large groups designated as Asian and European under K = 2. In general, European accessions had greater DMY than did Asian accessions. Observed trends were towards greater CP values in populations with Asian ancestry. Selection index values above zero were observed in populations with European ancestry, and the exception was the late‐maturing (208 days to bloom) populations with Asian ancestry. Plant populations 383 551, 383 561, 401 161, 401 173, 440 021, 578 692 (cv. Tegmar) and 598 740 had rhizome scores greater than 7.0. Despite significant differences detected between populations (Φ_ST = 0.3136; P < 0.001), there was strong indication of admixed co‐ancestry or possible gene flow between K = 2–9 models.     

Genetic diversity and population structure of Indian melon (Cucumis melo L.) landraces with special reference to disease and insect resistance loci

This study was aimed to examine the genetic diversity and population structure of Indian melon landraces with special reference to disease and insect resistance loci. Thirty‐six simple sequence repeat (SSR) markers along with seven markers at disease and insect resistance loci were used for this purpose on a panel of 91 accessions available at Indian Institute of Horticultural Research, Bengaluru, India. Model‐based structure analysis revealed the presence of four groups that were consistent with the results of principal coordinate analysis (PCoA). The delineation of populations was mostly based on geography with improved varieties as a separate group. Ten accessions have been identified to possess beneficial alleles at all the selected disease resistance loci and shall be useful for incorporating multiple disease resistance after phenotypic validation. The results obtained in the current study demonstrate the importance of the Indian melon group as a valuable genetic reservoir and the need to plan strategies for its conservation and utilization in breeding programmes.     

糯玉米自交系SSR标记遗传多样性及群体遗传结构分析

为了解糯玉米种质的遗传基础,利用29对SSR标记对87份糯玉米自交系进行遗传多样性分析,共检测出180个等位变异,平均每个位点6个等位变异,多态性信息含量变幅为0.308～0.915,平均为0.572。材料间遗传相似系数为0.49～0.93,平均为0.66。通过聚类分析UPGMA (unweighted pair-group method with arithmetic means)方法在遗传相似系数0.64处将87份糯玉米自交系划分为4个类群,分别包含9、66、10和2份材料。此外,利用Structure群体遗传结构分析也将87份糯玉米自交系分为4个类群,分别包含24、25、19和19份材料;进一步分析表明,供试群体中大部分糯玉米自交系的遗传变异较单一。本研究为糯玉米新品种选育和遗传进化分析提供了种质基础和理论依据。     

Phenotypic expression of quantitative and qualitative components of partial resistance to powdery mildew (Sphaerotheca fuliginea race 1) in melon (Cucumis melo) germplasm

A study was conducted to investigate the expression of four components of partial resistance to Sphaerotheca fuliginea race 1 in selected melon (Cucumis melo L.) lines viz. infection frequency, latent period, spore production, and disease-severity score. Those components were evaluated at two developmental stages of the host: the cotyledon stage and the stage of the first two true leaves. Detached plant parts (disks of cotyledons and true leaves) were inoculated using a vacuum-operated settling tower. All four components showed significant variation among genotypes, and correlations between components at both developmental stages were large and significant. The line ‘CNPH 83–095’ (without any major resistance gene to powdery mildew) presented the highest level of partial resistance in both vegetative stages for almost all components evaluated. The lines ‘W-6’ (Pm1Pm1, Pm2Pm2), ‘Cinco’ (Pm1Pm1, Pm2Pm2), and CNPH ‘84–147’ (Pm1Pm1), even though carrying the major gene Pm1 for complete resistance to race 1 of the fungus, showed slight but significant differences for quantitative components of partial resistance at the cotyledonal stage. Different levels of partial resistance may be expressed, even in lines with a major race-specific resistance gene to powdery mildew, in specific developmental stages of the melon plants.     

Generation means analysis of plant architectural traits and fruit yield in melon

Unique architectural phenotypes have the potential for increasing yield in commercial melon (Cucumis melo L.). Therefore, a generation means analysis was conducted to investigate the inheritance of architectural traits (days to anthesis, primary branch number, fruit number and weight, and average weight per fruit). Progeny (F₁, F₂, BC₁P₁ and BC₁P₂) from a cross between US Department of Agriculture (USDA) line, USDA 846‐1 (P₁) and ‘TopMark’ (P₂) were evaluated at Arlington (AR) and Hancock (HCK), Wisconsin in 2001. Significant (P ≤ 0.05) environment effects and genotype × environment interactions (G × E) analyses necessitated analysis by location. Significant differences (P ≤ 0.05) among parents and generations were observed for all traits, and the two parental lines differed significantly for primary branch number, fruit number and average weight per fruit. Additive gene effects were most important in governing primary branch number and fruit number per plant, while dominance and epistatic genetic effects mainly controlled days to anthesis, fruit weight per plant and average weight per fruit. Narrow‐sense heritabilities were 0.62 (AR) for days to anthesis, 0.71 (AR) and 0.76 (HCK) for primary branch number, 0.68 (AR) and 0.70 (HCK) for fruit weight per plant, 0.33 (AR) and 0.45 (HCK) for fruit weight per plant, and 0.06 (AR) and 0.79 (HCK) for average weight per fruit. Estimations of the least number of effective factors for primary branch number were relatively consistent at both AR (approx. 4) and HCK (approx. 2). Results suggest that introgression of yield‐related genes from highly branched melon types (e.g. USDA 846‐1) into US Western Shipping germplasm may aid in the development of high‐yielding cultivars with concentrated fruit set suitable for machine and/or hand‐harvesting operations.     

Inheritance of resistance to races 1, 2 and 5 of powdery mildew in the melon TGR-1551

The inheritance of resistance to races 1, 2 and 5 of Podosphaera xanthii in the melon TGR-1551 was studied in a cross with the susceptible cultivar 'Bola de oro'. Under artificial inoculation conditions, four phenotypic classes were defined according to the level of fungal sporulation. The segregation ratios for resistance/susceptibility observed in the different populations and the results of the progeny test indicated that resistance to races 1, 2 and 5 of P. xanthii in TGR-1551 was governed by two independent genes, one dominant and one recessive, which means that the genetic control is a dominant–recessive epistasis. This is the first time that a recessive gene that confers resistance to more than one race of powdery mildew has been identified in melon. TGR-1551 could be considered a good genetic source for the development of powdery mildew resistant breeding lines.     

Allelic variation and genetic diversity of HMW glutenin subunits in Chinese wheat (Triticum aestivum L.) landraces and commercial cultivars

Wheat landraces have abundant genetic variation at the Glu-1 loci, which is desirable germplasms for genetic enhancement of modern wheat varieties, especially for quality improvement. In the current study, we analyzed the allelic variations of the Glu-1 loci of 597 landraces and 926 commercial wheat varieties from the four major wheat-growing regions in China using SDS-PAGE. As results, alleles Null, 7+8, and 2+12 were the dominant HMW-GSs in wheat landraces. Compared to landraces, the commercial varieties contain higher frequencies of high-quality alleles, including 1, 7+9, 14+15 and 5+10. The genetic diversity of the four commercial wheat populations (alleles per locus (A) = 7.33, percent polymorphic loci (P) = 1.00, effective number of alleles per locus (Ae) = 2.347 and expected heterozygosity (He) = 0.563) was significantly higher than that of the landraces population, with the highest genetic diversity found in the Southwestern Winter Wheat Region population. The genetic diversity of HMW-GS is mainly present within the landraces and commercial wheat populations instead of between populations. The landraces were rich in rare subunits or alleles may provide germplasm resources for improving the quality of modern wheat.     

基于SNP和InDel标记的巴西木薯遗传多样性与群体遗传结构分析

为了对巴西木薯种质资源进行遗传多样性、亲缘关系和群体遗传结构分析,本研究利用了7946个SNPs和1997个InDels分子标记,通过ADMIXTURE软件进行群体结构分析、GCTA软件进行主成分分析。结果显示,巴西木薯被划分为9个亚群。这与利用PHYLIP进行的聚类分析结果大概一致,其中亚群1、亚群2、亚群4、亚群6和亚群8能较好地分别聚在一起,而其他亚群中的样品大致能聚在一起,且样品间有一定的交叉。巴西木薯种质资源遗传多样性指数(0.274)高于中国、尼日利亚等,其中巴西木薯亚群5具有相对较高的遗传多样性水平(0.29)。巴西木薯各亚群的群体遗传分化程度较低(群体分化指数在0.03~0.15之间),但高于中国木薯种质资源的群体分化指数。各木薯材料间的遗传距离变幅为0.084~0.297,平均遗传距离为0.228。本研究结果可为后续关联分析发掘优良等位基因及引种提供依据。     

Genetic diversity of garlic (Allium sativum L.) germplasm from China by fluorescent‐based AFLP,SSR and InDel markers

Garlic (Allium sativum L.), an asexually propagated crop, is an important vegetable and medicinal plant. China is the biggest garlic producer in the world; however, the genetic background of garlic from China is not well understood. In this study, population structure and clustering analysis of garlic germplasm was performed using amplified fragment length polymorphism (AFLP), simple sequence repeat (SSR) and insertion–deletion (InDel) markers. Among 212 accessions of garlic, genetic diversity analysis identified 546 alleles amplified by AFLP, SSR and InDel primers, and 492 of these were polymorphic. All accessions were divided into five groups by structure analysis and neighbor‐joining clustering. Most traits, including allicin content, were only slightly affected by population structure, which indicated that this germplasm can be used as populations for association mapping. The results provide a molecular basis for understanding the genetic diversity of the garlic germplasm preserved in China.     

Genetic diversity in barley landraces from Syria and Jordan

Summary Single-head progenies derived from barley landraces collected along the Fertile Crescent in Syria and Jordan were evaluated for agronomic, morphological, and quality traits in a typical barley growing area in Northern Syria. A large diversity was observed both between and within collection sites, and in most cases the variation was useful for breeding purposes. Single plant progenies were identified with larger yields and more desirable expressions of agronomic characters than the original landraces. The utilization of this material in a breeding program for dry areas is discussed.     

Diversity among melon landraces (Cucumis melo L.) from Greece and their genetic relationships with other melon germplasm of diverse origins

Diversity among 17 melon landraces and inbred lines of Group Cantalupensis, Inodorus, and Flexuosus germplasm from Greece was assessed using 24 RAPD primers, 11 morphological traits of fruit, two yield-related characteristics, and resistance to powdery mildew. Accessions were genetically diverse and the greatest variation was detected in Group Flexuosus. Comparative analysis of Greek germplasm and an array of previously characterized reference accessions [RA; 68 from Africa (15), United States (U.S.; 5), Central Europe (14), Japan (19), and Spain (15)], spanning major market classes employing 19 RAPD primers (standard marker array), indicates that all but one of the accessions from Greece showed genetic affinities among themselves and with 23 RA of various origin (i.e., Japan, U.S., Central Europe, Spain and Israel) and market class. Accessions from Greece were, however, distinct from the African landraces and most Spanish melons. Greek accessions also showed little genetic affinity with the Casabas (Blanco and Crenshaw), Ogen, and U.S. Eastern Market accessions. Group Flexuosus and Inodorus accessions from Greece possessed genetic affinities with Western Asian (Group Conomon) and Mediterranean (Group Inodorus) market classes, respectively. The uniqueness of Greek melon landraces portends their potential usefulness for the enhancement of U.S., European, and Asian melon market classes. This revised version was published online in July 2006 with corrections to the Cover Date.     

基于SNP和InDel标记的巴西木薯遗传多样性与群体遗传结构分析

As a typical tropical crop, cassava (Manihot esculenta Crantz) has the characteristics of drought resistance, barren resistance, high biomass and so on. In addition to being used for food and forage, it can also be used for production, processing and starch extraction. Due to highly heterozygous cassava genome, breeding is more difficult. Enriching the genetic diversity of cassava germplasm, comprehensively evaluating its genetic background and traits, and discovering superior alleles that control excellent traits are of great significance for cassava breeding in the future. In order to analyze the genetic diversity, genetic relationship and population structure of cassava germplasm in Brazil, 7946 SNPs and 1997 InDels molecular markers were used. Population structure analysis was performed by ADMIXTURE software, and principal component analysis was performed by GCTA software. Brazilian cassava was divided into nine subgroups, and was roughly consistent with the results of cluster analysis using PHYLIP. Among them, subgroup 1, subgroup 2, subgroup 4, subgroup 6, and subgroup 8 could be clustered together respectively, while the samples of other subgroups could be roughly clustered, and there was a certain cross between the samples. The genetic diversity of cassava germplasm in Brazil (0.274) was higher than the genetic diversity level of cassava germplasm in China and Nigeria. Subgroup 5 of Brazil cassava had a relatively high genetic diversity (0.29). The genetic differentiation of subgroups was low (the genetic differentiation vary from 0.03 to 0.15), but higher than domestic cassava germplasm. The genetic distance between cassava accessions varied from 0.084 to 0.297, with the average of 0.228. The results of this study can provide a basis for subsequent association analysis to identify great alleles and introduction.     

Resistance to melon vine decline derived from Cucumis melo ssp. agrestis: genetic analysis of root structure and root response

Melon vine decline is a major soilborne disease that causes severe economic losses around the world. The fungal pathogens Monosporascus cannonballus Pollack et Uecker and Acremonium cucurbitacearum Alfaro‐García, W. Gams et J. García‐Jiménez have been reported as the main causal agents of this disease. A relatively high level of resistance has been reported in Cucumis melo L. ssp. agrestis (Naud.) Pangalo in the Asiatic accession Pat 81. Although specific resistance mechanisms controlling pathogen‐induced root lesions have been characterized in Pat 81, the development of a vigorous and branched root system can also appreciably increase its tolerance to vine collapse. The genetics of root traits related to root vigour and structure were studied in the progeny derived from a cross between Pat 81 and the highly susceptible cultivar ‘Piñonet’ market class ‘Piel de Sapo’(C. melo L. ssp. melo). The inheritance of specific resistance to soilborne fungi was also studied by analysing root response to inoculation employing naturally infested soil. Estimates of the broad‐(H) and narrow‐sense (h²) heritabilities indicated that the majority of the variation for lesion resistance in lateral and fine roots, in the root weight, root length, and the root surface area could be explained by additive effects, whereas dominance is important in plant biomass and resistance to lesions in hypocotyls. Selection for improved root systems conferring resistance and tolerance to vine decline was successfully conducted in BC₁ progeny derived from a Pat 81 בPiñonet’ mating. Moderate values of heritabilities (0.03–0.76) suggest that breeding strategies that combine family and individual selection could enhance genetic progress. As some of the traits analysed exhibited heterosis, breeding methods directed towards recovering hybrid vigour may increase gain from selection.     

Utility of AFLP markers for the assessment of genetic diversity within Brassica nigra germplasm

Genetic diversity of 18 Brassica nigra accessions was estimated using amplified fragment length polymorphism (AFLP) marker technology. Two B. rapa and two B. juncea accessions were selected as outliers in the study. Eight AFLP primer combinations generated a total of 426 bands, of which 79% were polymorphic. The UPGMA method was employed to construct a dendrogram based on the Jaccard's similarity coefficient. The accessions of B. rapa separated from those of B. nigra at a genetic similarity coefficient of 0.27 while those of B. juncea did so at 0.5. The genetic similarity coefficients within the B. nigra accessions ranged from 0.58 to 0.86. Based on these coefficients it was concluded that the B. nigra accessions show high levels of genetic variation. These results have significant implications in the crop improvement programmes for the agronomically important crop B. juncea, an amphidiploid of B. nigra and B. rapa. Two incorrectly labelled B. nigra accessions were also identified. These accessions were found to cluster with those of B. juncea accessions. This result demonstrates the great value of AFLP markers in the management of genebanks.     

Development of a core set of KASP markers for assaying genetic diversity in Brassica rapa subsp. chinensis Makino

Single‐nucleotide polymorphisms (SNPs) are rapid, economical and reliable genotyping tools. Non‐heading Chinese cabbage (Brassica rapa L. subsp. chinensis Makino) is now an economically important vegetable crop worldwide. In this study, 1,167 SNPs were evaluated for 7polymorphism among 70 representative non‐heading Chinese cabbage inbred lines using a Kompetitive Allele Specific PCR (KASP) genotyping assay. On the basis of identified polymorphisms and the results of a principal component analysis, we selected 50 core SNPs that were balanced sufficiently to provide adequate information for genetic identification. The core SNPs were used for construction of a neighbour‐joining dendrogram that separated the 70 inbred lines into four main groups and several subgroups corresponding to Caixin, Heiyebaicai, Huangxinwu, Naibaicai, Taitsai, Pak‐choi, and Wutatsai. This categorization was superior to that achieved using a dataset of 479 polymorphic SNPs. To confirm the utility of the core SNP markers in genetic identification, we tested their stability and resolution using 162 commercial hybrid cultivars. The SNPs, which represent a cost‐effective, accurate marker set for germplasm analysis and cultivar identification, are suitable for molecular marker‐assisted breeding in non‐heading Chinese cabbage.     

‘河套’蜜瓜果实内源激素含量变化以及ABA对果实成熟的影响

以‘河套’蜜瓜果实为试材,通过内源检测和外源温育方法,研究果实发育期间内源激素的动态变化以及脱落酸对果实成熟的影响。结果显示：果实发育前期生长素和玉米素含量较高;进入缓慢生长期后赤霉素含量逐渐升高;脱落酸含量则在果实成熟期间一直维持较高水平。进一步研究脱落酸对果实成熟期间糖分转化的影响,结果显示,脱落酸温育处理后果实圆片蔗糖合成酶活性大幅提高,转化酶活性被显著抑制,相应地果实圆片蔗糖含量增加,葡萄糖含量下降。综合分析认为,生长素、玉米素和赤霉素与果实发育前期细胞分裂、膨大有关;脱落酸对启动果实成熟发挥重要作用,通过调节蔗糖代谢相关酶活性来调节果实蔗糖积累,并促进果实向成熟品质转化是其作用机制之一。