SnToxA,SnTox1, and SnTox3 originated in Parastagonospora nodorum in the Fertile Crescent

The centre of origin of the globally distributed wheat pathogen Parastagonospora nodorum has remained uncertain because only a small number of isolates from the Fertile Crescent were included in earlier population genetic and phylogeographic studies. We isolated and genetically analysed 193 P. nodorum strains from three naturally infected wheat fields distributed across Iran using 11 neutral microsatellite loci. Compared to previous studies that included populations from North America, Europe, Africa, Australia, and China, the populations from Iran had the highest genetic diversity globally and also exhibited greater population structure over smaller spatial scales, patterns typically associated with the centre of origin of a species. Genes encoding the necrotrophic effectors SnToxA, SnTox1, and SnTox3 were found at a high frequency in the Iranian population. By sequencing 96 randomly chosen Iranian strains, we detected new alleles for all three effector genes. Analysis of allele diversity showed that all three effector genes had higher diversity in Iran than in any population included in previous studies, with Iran acting as a hub for the effector diversity that was found in other global populations. Taken together, these findings support the hypothesis that P. nodorum originated either within or nearby the Fertile Crescent with a genome that already encoded all three necrotrophic effectors during its emergence as a pathogen on wheat. Our findings also suggest that P. nodorum was the original source of the ToxA genes discovered in the wheat pathogens Phaeosphaeria avenaria f. sp. tritici 1, Pyrenophora tritici-repentis, and Bipolaris sorokiniana.     

Genetic diversity of potato landraces from northwestern Argentina assessed with simple sequence repeats (SSRs)

Andean potato varieties are cultivated in the northwest of Argentina and constitute the most important staple food for the local farmers. The genetic diversity of 155 accessions conserved at the Genebank of Balcarce (INTA) was tested using four microsatellites. Three commercial potato varieties of Tuberosum group and one accession of Curtilobum group were used as outgroups. The presence of bands was scored for each microsatellite and for each accession and the data were analysed by principal coordinate analysis. The polymorphism information content was obtained for each molecular marker from banding patterns. Analysis of molecular variance was carried out with a variable number of accessions for each landrace, from different departments and sites within departments. More than one genotype was detected in the majority of the potato landraces. Some accessions within each landrace did not differentiate. AMOVA revealed that most of the genetic variation occurred among sites within departments and among local varieties. These findings are discussed considering the agricultural practices carried out in the Andean farming system.     

Varietal discrimination and genetic relationships of Vitis vinifera L. cultivars from two major Controlled Appellation (DOC) regions in Portugal

Thirty-nine grapevine cultivars widely grown in Portugal, especially in Vinhos Verdes and Douro regions, and two well known international cultivars as standards, were genotyped at 12 microsatellite loci. The number of alleles per locus ranged from 6 to 12, and the number of allelic combinations per locus from 13 to 26. The total number of unique genotypes in the 12 analysed loci was 120, having most of the cultivars (38 out of 41) at least one unique genotype in any of the loci. The microsatellite profiles were adequate to discriminate 41 cultivars. The level of observed heterozygosity at each locus varied from 70.7% to 95.1%. VVMD28 has been revealed as one of the most informative markers. Several synonymies between Spanish and Portuguese cultivars were confirmed, and some homonymies are discussed. The genetic profiles of all 41 cultivars were searched for possible parent-offspring groups. The data obtained revealed the possible descendence of Touriga Franca from Touriga Nacional and Marufo.     

Origin and genetic diversity of Tunisian grapes as revealed by microsatellite markers

Ten SSR loci, previously developed for grapevine, were analyzed to evaluate the genetic variability, cultivar relatedness, and parentage in a collection of 61 autochthonous Vitis vinifera cultivars from Tunisia.The number of alleles per locus ranged from 6 to 11, while the number of genotype patterns varied between 10 and 21. The expected heterozygosity varied between 0.621 and 0.855 and the observed heterozygosity was higher than 0.9 at 4 loci (VVMD28, VVMD5, VVIP31 and VVS2) indicating that the SSRs were highly informative.Cluster analysis using unweighted pair group method with arithmetic averaging (UPGMA) suggested 14 groups among studied cultivars and 53 grapevine denominations out of 61 were unequivocally distinguished, with all accessions showing at least one-specific combination of alleles.On the other hand, in order to overcome the existing confusion in Tunisian grapevine nomenclature, of the analyzed homonymous pairs of cultivars, only ‘Balta 2’ and ‘Balta 3’ have shown identical allelic profiles, consistent with their being the same genotype. Hence, nomenclature distinction is meaningless and only one denomination should be retained.Due to the high overall power of exclusion (Q) (greater than 99.99%) and to the absence of null alleles, the set of microsatellite loci used is appropriate to determine parentage in Tunisian grapevines beyond any reasonable doubt. The analysis of fingerprints indicated that the Tunisian grape vines have evolved through out crossing between five possible parents: Balta 1, Beldi Baddar, Beldi Rafraf, Beldi Local Rafraf and Khedhiri 3.     

Isolation and characteristics of eight novel polymorphic microsatellite loci from the genome of garlic (Allium sativum L.)

Here we characterized eight novel polymorphic SSR markers, developed from an enriched genomic library of garlic (Allium sativum L.). These SSRs produced a total of 64 alleles across 90 garlic accessions, with an average of 8 alleles per locus. Values for observed (H_O) and expected (H_E) heterozygosity ranged from 0.16 to 0.77 (mean = 0.44) and from 0.22 to 0.86 (mean = 0.65), respectively. Six loci deviated significantly (P < 0.05) from Hardy–Weinberg equilibrium (HWE). The averages of gene diversity and PIC values were 0.65 and 0.62, respectively. The mean genetic similarity coefficient was 0.4380, indicating that among garlic accessions existed wide genetic variation. Based on 64 alleles obtained by 8 SSRs, a phenogram was constructed to understand the relationships among the 90 accessions. These newly developed SSRs should prove very useful tools for genotypes identification, assessment of genetic diversity and population structure in garlic.     

利用配合力和SSR标记对热带和温带玉米自交系进行杂种优势群划分

本研究用代表我国温带玉米主要杂种优势群的4个标准测验种（B73、丹340、Mo17和黄早四)和来自5个热带的玉米群体Suwan1、Pop21、Pop32、Pop28及Antigua种族的25个典型自交系,采用NC－Ⅱ设计得到100个杂交组合,将这些组合种植在云南省景洪、德宏、保山三种不同生态条件下进行观察鉴定,再根据产量进行配合力分析,并结合SSR分子标记进行杂种优势群划分。结果将供试自交系划分为4个类群,第一群包括丹340和黄早四,属国内玉米种质类群;第二类群包括Mo17和来自Antigua种质的M9,属Lancaster种质类群;第三类群包括B73,属Reid种质类群;第四大类群包括除M9以外的24个热带自交系,属于热带玉米种质。第四类群又可分为A和B两个杂种优势群,其中A群属于马齿型的Tuxpeno种质,可再分为亚群1和亚群2,其中亚群1包括除除M15以外的Pop21的4个自交系;亚群2包括M15和M17两个自交系;B群是硬粒型种质,可再分为4个亚群,其中亚群1属于Suwan1种质,包括自交系M1、M2、M3和M5;亚群2属于黄色硬粒型的Antigua种质,包括自交系M6、M7、M8、M10和来自Suwan1的M4;亚群3基本属于硬粒型的ETO种质,包括来自Pop32的M16、M18、M19和来自Pop28的M22、M24;亚种4基本属于Antigua种质,包括来自Pop32(ETO)的M20和来自Pop28的自交系M21、M23、M25。划分结果与系谱来源基本一致。     

利用SSR标记分析"川育12"和人工合成小麦"SYN780"的遗传差异

四川育成品种“川育12”和CIMMYT硬粒小麦-节节麦人工合成种“SYN780”都具有优质小麦基因,本试验利用小麦A、B和D基因组上的229对引物对“川育12”和“SYN780”进行了SSR分子标记比较分析。结果表明,229个SSR标记位点中有140个位点“川育12”和“SYN780”存在多态性差异,占位点数的61.1%。这140个差异位点在A、B和D3个基因组的分布频率(占该基因组被检测位点数)不一致,其中B基因组分布最多,D基因组分布最少,其顺序为B(64.2%)>A(63.5%)>D(54.9%)。     

玉米苗期耐碱性QTL定位分析

利用郑58/昌7-2构建的156个玉米F₂：3家系为作图群体,在100 mmol/L Na₂CO₃溶液的碱性胁迫下进行玉米苗期耐碱性鉴定,并利用SSR标记构建的分子遗传连锁图谱进行QTL分析。采用复合区间作图法共检测到4个与玉米苗期耐碱率相关的QTL,分布于第2、5、7条染色体上,单个QTL可解释的表型贡献率范围为1.1%～8.6%。所检测到的4个QTL的增益等位基因均来自于耐碱亲本郑58。     

Markers, old and new, for examining Phytophthora infestans diversity

Late blight, caused by Phytophthora infestans , is an ongoing threat to potato and tomato crop production worldwide and considerable fundamental and applied research is conducted with the long-term aim of improved disease control. Understanding the mechanisms, processes and rates of P. infestans evolution is an important factor in predicting the effectiveness and durability of new management practices. A range of phenotypic and genotypic tests has been applied to achieve this goal, but each has limitations and new methods are sought. Recent progress in P. infestans genomics is providing the raw data for such methods and new high-throughput codominant biomolecular markers are currently being developed that have tremendous potential in the study of P. infestans population biology, epidemiology, ecology, genetics and evolution. This paper reviews some key applications, recommends some changes in approach and reports on the status and potential of new and existing methods for probing P. infestans genetic diversity.     

Molecular characterization and genetic relationship among almond cultivars assessed by RAPD and SSR markers

RAPDs and SSRs were used to study the genetic diversity of Iranian almond cultivars and their relationship to important foreign cultivars and three related species. Eight unidentified almond Shahrodi cultivars and three wild almonds (Prunus communis, Prunus orientalis and Prunus scoparia) were also included. Of the primers tested, 42 (out of 80) RAPD and 18 (out of 26) SSR primers were selected for their reproducibility and high polymorphism. A total of 664 polymorphic RAPD bands were detected out of 729 bands. The number of presumed alleles revealed by the SSR analysis ranged from 3 to 10 alleles per locus with a mean value of 6.64 alleles per locus. Both techniques discriminated the genotypes very effectively, but only RAPDs were able to discriminate the cultivars Monagha and Sefied. Results demonstrated an extensive genetic variability within the tested cultivars as well as the value of SSR markers developed in peach for characterization of almond and related species of Prunus. Dice similarity coefficient was calculated for all pair wise comparisons and was used to construct a UPGMA dendrogram. For both markers a high similarity in dendrogram topologies was obtained although some differences were observed. All dendrograms, including that obtained by the combined use of both the marker data, depicted the phenetic relationships among the cultivars and species, depending upon their geographic region and/or pedigree information. Almond cultivars clustered with accession of P. communis showing their close relationship. P. orientalis and P. scoparia were clustered out of the rest of P. dulcis.