Molecular characterization and similarity relationships among sunflower (Helianthus annuus L.) inbred lines using some mapped simple sequence repeats

Information about the genetic diversity and relationships among breeding lines and varieties is not only useful for germplasm conservation and inbred line identification, but also for the selection of parental lines for quantitative trait loci (QTL) mapping as well as hybrid breeding in crops, including sunflower. In order to develop mapping populations, genetic distances among twenty eight sunflower genotypes were evaluated using simple sequence repeat (SSR) markers. One hundred and two markers were generated by 38 SSR loci and the mean for the number of allele per locus was 2.32. Polymorphism information content (PIC) values ranged from 0.09 (locus ha3555) to 0.62 (locus ORS598) with an average of 0.41. Jaccard's coefficient similarity matrix for the studied sunflower  genotypes varied from 0.25 to 0.9 indicating a broad genetic base. The maximum similarity (0.9) was observed between genotypes RT931 and ENSAT-R5, while the lowest similarity (0.25) was between genotypes LC1064C and LR64. Based on unweighted pair group method with arithmetic mean (UPGMA) clustering algorithm, the studied genotypes were clustered in four groups. However, some genotypes have the same specific characters that influence their clustering, and as a result, the results of the principal coordinate analysis (PCoA) largely corresponded to those obtained through cluster analysis.Key words: Cluster analysis, genetic diversity, principal coordinate analysis, sunflower, simple sequence repeat

Natural incidence of tomato viruses in the North of Iran

A survey was conducted in Qazvin province in the North of Iran, to determine the incidence of tomato viruses including: Tobacco mosaic virus (TMV), Tomato yellow leaf curl virus (TYLCV), Tomato chlorotic spot virus (TCSV), Tomato bushy stunt virus (TBSV), Tomato spotted wilt virus (TSWV), Tomato ring spot virus (ToRSV), Tomato aspermy virus (TAV), Potato virus Y (PVY), Beet curly top virus (BCTV), and Cucumber mosaic virus (CMV). A total of 742 tomato symptomatic samples were collected during the summer of 2007 in five regions of Qazvin province (Qazvin, Takestan, Boeen-Zahra, Alborz and Abiyek) and tested by enzyme-linked immunosorbent assay (ELISA). TSWV was detected in Alborz (4.4 %) and Abiyek (3.57%) regions but TMV and CMV were detected in all five regions. The greatest and least incidence of tomato viruses were recorded in Alborz (40.7 %) and Takestan (11.1 %), respectively. The presence of these viruses was also evaluated in the weed hosts as natural sources of plant viruses. The greatest and least incidence of tomato viruses in weed hosts were recorded in Boeen-Zahra (25.6 %) and Qazvin (12.8 %), respectively. TSWV was not detected in weeds. Transmission tests demonstrated that Thrips tabaci acts as TSWV carrier and Myzus persicae and Aphis gossypii were CMV carriers. Seed transmission tests were positive for TMV (13 tomato seedlings from 100 seedlings), but no TSWV transmission was observed through the seeds of infected tomato fruits

Identification of novel plant architecture mutants in barley

In grasses, biomass and grain production are affected by plant architecture traits such as tiller number, leaf size and orientation. Thus, knowledge regarding their genetic basis is a prerequisite for developing new improved varieties. Mutant screens represent a powerful approach to identify genetic factors underpinning these traits: the HorTILLUS population, obtained by mutagenesis of spring two-row cultivar Sebastian, is a valuable resource for this purpose in barley. In this study, 20 mutant families from the HorTILLUS population were selected and evaluated for tiller number, leaf angle and a range of other plant architecture and agronomic traits using an unreplicated field design with Sebastian as a check cultivar. Principal Component Analysis revealed strong relationships among number of tillers, upper canopy leaf angle, biomass and yield-related traits. Comparison to the Sebastian background revealed that most mutants significantly differed from the wild-type for multiple traits, including two mutants with more erect leaves and four mutants with increased tiller number in at least one phenological stage. Heatmap clustering identified two main groups: the first containing the two erect mutants and the second containing Sebastian and the high-tillering mutants. Among the high-tillering mutants, two showed significantly higher biomass and grain yield per plant compared to Sebastian. The selected mutants represent promising materials for the identification of genetic factors controlling tillering and leaf angle in barley

Development of IRAP- and REMAP-derived SCAR markers for marker-assisted selection of the strip rust resistance gene Yr15 derived from wild emmer wheat

Stripe rust (Pucinia striformis f.sp. tritici) is one of the most important fungal diseases of wheat, found on all continents and in over 60 countries. Wild emmer wheat, Triticum dicoccoides, which is the tetraploid progenitor of durum wheat, is a valuable source of novel stripe rust resistance genes for wheat breeding. T. dicoccoides G25 accession carries Yr15, a gene on chromosome arm 1BS. Yr15 confers resistance to all known stripe rust isolates; it is also effective in introgressed durum and bread wheat. Retrotransposons generate polymorphic insertions, which can be scored as Mendelian markers with techniques including REMAP and IRAP. Six REMAP and IRAP-derived SCAR markers were developed using 1256 F2 plants derived from crosses of the susceptible T. durum accession D447 with its resistant BC3F9 and BC3F10 (B9 and B10) near isogenic lines, which carried Yr15 introgressed from G25. The nearest markers segregated 0.1 cM proximally and 1.1 cM distally to Yr15. These markers were also mapped and validated at the same position in another independent 500 F2 plants derived from crosses of B9 and B10 with the susceptible cultivar Langdon. SCAR270 and SCAR790, surrounding Yr15 at an interval of 1.2 cM, were found to be reliable and robust co-dominant markers in a wide range of wheat lines and cultivars with and without Yr15. These markers are useful tags in marker-assisted wheat breeding programs aiming to incorporate Yr15 into elite wheat lines and cultivars for durable and broad-spectrum resistance against stripe rust.Peer reviewe

Assessment of genetic diversity in tomato landraces using ISSR markers

Tomato is one of the most economically important vegetable crops in many parts of the world. Turkey and Iran are the main producers of tomatoes in the world. The objective of this study was to assess the genetic variation of 93 tomato landraces from East Anatolian region of Turkey and North-West of Iran, along with three commercial cultivars using 14 ISSR primers. The percentage of polymorphic loci (PPL) for all primers was 100%. The mean of expected heterozygosity (He) for the primers varied from 0.153 (UBC808) to 0.30 (UBC848). The dendrogram placed the landraces and commercial cultivars into nine groups. The genotypes originating from the same region, often located in the same group or two adjacent groups. The highest likelihood of the data was obtained when population were located into 2 sub-populations (K = 2). These sub-populations had Fst value of 0.16 and 0.21

IRAP and REMAP-based assessment of genetic diversity in chickpea collection from Iran

Retrotransposons (RTN) make a significant contribution to the size, organization and genetic diversity of their host genomes. Several RTN families have been identified in chickpea (Cicer arietinum L.) and other closely related species. In the current research, integration activity and insertional polymorphism of the RTNs CARE1, Tms1Ret1, TPS and LORE were studied in 64 chickpea accessions collected in Iran using inter retrotransposon amplified polymorphism (IRAP) and retrotransposon-microsatellite amplified polymorphism (REMAP) techniques. Results indicated that all RTNs studied, are transpositionally active in chickpea genome and amplified scorable and polymorphic banding pattern. Among the RTN families used, the highest percentage of polymorphic loci (PPL) was produced by TPS family (81.82%). Totally, 129 loci were amplified using 18 IRAP and REMAP primers which 83 (64.34%) were polymorphic. The Dice genetic similarity coefficients among accessions ranged from 0.84 (accessions Tj48 and Ba4) to 0.98 (accessions Ka30 and Urm61), averaging 0.93. The parameters of expected heterozygosity (He), Shannon’s information index (I) and number of effective alleles (Ne) were the highest for Urmia accessions. Cluster analysis based on UPGMA algorithm and Dice similarity coefficient categorized the 64 accessions in 7 main groups. The mean Fst values of all groups except for groups IV and VII, were lower than 0.20, demonstrating no clear differentiation among the groups, no genetic structure of the studied chickpea collection and probably occurrences of gene flow among the origins. In conclusion, although RTN-based markers were able to differentiate the chickpea accessions but the measured relative genetic similarity among accessions were not correlated with geographical distances between places of their origins

Genetic Mapping of Quantitative Trait Loci for Yield-Affecting Traits in a Barley Doubled Haploid Population Derived from Clipper × Sahara 3771

Many traits play essential roles in determining crop yield. Wide variation for morphological traits exists in Hordeum vulgare L., but the genetic basis of this morphological variation is largely unknown. To understand genetic basis controlling morphological traits affecting yield, a barley doubled haploid population (146 individuals) derived from Clipper × Sahara 3771 was used to map chromosome regions underlying days to awn appearance, plant height, fertile spike number, flag leaf length, spike length, harvest index, seed number per plant, thousands kernel weight, and grain yield. Twenty-seven QTLs for nine traits were mapped to the barley genome that described 3–69% of phenotypic variations; and some genomic regions harbor a given QTL for more than one trait. Out of 27 QTLs identified, 19 QTLs were novel. Chromosomal regions on 1H, 2H, 4H, and 6H associated with seed grain yield, and chromosome regions on 2H and 6H had major effects on grain yield (GY). One major QTL for seed number per plant was flanked by marker VRS1-KSUF15 on chromosome 2H. This QTL was also associated with GY. Some loci controlling thousands kernel weight (TKW), fertile spike number (FSN), and GY were the same. The major grain yield QTL detected on linkage PSR167 co-localized with TAM10. Two major QTLs controlling TKW and FSN were also mapped at this locus. Eight QTLs on chromosomes 1H, 2H, 3H, 4H, 5H, 6H, and 7H consistently affected spike characteristics. One major QTL (ANIONT1A-TACMD) on 4H affected both spike length (SL) and spike number explained 9 and 5% of the variation of SL and FSN, respectively. In conclusion, this study could cast some light on the genetic basis of the studied pivotal traits. Moreover, fine mapping of the identified major effect markers may facilitate the application of molecular markers in barley breeding programs

Retrotransposon insertional polymorphism in sunflower (<i>Helianthus annuus</i> L.) lines revealed by IRAP and REMAP markers

<p>Retrotransposons are ubiquitous components of plants genomes, making them useful molecular markers for genetic diversity studies. We used inter-retrotransposon amplified polymorphism (IRAP) and retrotransposon-microsatellite amplified polymorphism (REMAP) markers to assess genetic diversity and survey activity of LTR retrotransposon elements in 106 sunflower (<i>Helianthus annuus</i> L.) genotypes from different research centers. We found 118 (out of 128) and 113 (out of 120) polymorphic loci using 14 IRAP and 14 REMAP primers, respectively. The Mantel test between IRAP and REMAP cophenetic matrices revealed low correlation (<i>r</i> = 0.55) between them. Dice similarities based on combined (IRAP + REMAP) data ranged from 0.34 to 0.93 among (“11 × 12” and “F1250/03”) and (“HA335B” and “TMB51”) genotypes, respectively. Classification of genotypes using the Dice similarity matrix derived from IRAP+REMAP data based on the un-weighted pair-group method using the arithmetic average algorithm resulted in nine distinct groups. The studied genotypes were divided into seven groups considering their origins (research centers). Classification of genotypes can be useful to assess the genetic variation and gene flow between and within research centers. Analysis of molecular variance based on IRAP+REMAP data revealed a higher level of genetic variation within (94%) than between (6%) research centers. A high amount of gene flow was detected among USDA, ASGROW, and ENSAT groups. Because environmental factors have no influence on molecular markers, the construction of heterotic groups based on retrotransposon markers will be useful for the selecting of parents with a high probability of producing superior hybrids.</p