Investigation of the genetic structure of some common bean (Phaseolus vulgaris L.) commercial varieties and genotypes used as a genitor with SSR and SNP markers

Common bean is a species belonging to the Phaseolus genus of the Leguminosae family. It has economic importance due to being rich in protein, vitamin A and C, and minerals. Being one of the most cultivated species of legumes, the determination of genetic diversity in bean genotypes or populations has an important role in terms of our genetic resources. The objective of this study was to evaluate the genetic structure of 94 genotypes which were cultivated in different parts of the world and our country with SSR and SNP markers. 10 SSR loci and 73 SNP primers were used for the determination of genetic structure in commercial cultivars and breeding lines. All of the SSR and SNP loci used in the study were found to be polymorphic. A total of 89 alleles were identified for 10 SSR loci. Mean number of alleles per locus (Na?=?8.9), effective allele number (Ne?=?3.731), Shannon information index (I?=?1.468), observed heterozygosity (Ho?=?0.023), and expected heterozygosity (He?=?0.654) were calculated based on SSR analysis. According to the results of Bayesian-based STRUCTURE analysis using SSR and SNP data, 94 bean genotypes were genetically divided into three main clusters. According to genetic distance based UPGMA dendrogram obtained from SNP analysis, 94 bean genotypes were divided into 2 main clusters corresponding Mesoamerican and Andean gene pools. The obtained results provide important information about the genetic structures of the studied bean cultivars and breeding lines. With the obtained results, it will be possible to develop breeding programs to develop new cultivars by using our gene resources.

     

Assessment of genetic diversity in Egyptian barley (<Emphasis Type="Italic">Hordeum vulgare</Emphasis> L.) genotypes using SSR and SNP markers

A barley core collection can be studied extensively and the derived information can be used to identify loci/genes for the genetic improvement of quantitative and qualitative traits. To assess genetic diversity, allelic variation and population structure of Egyptian barley, 134 barley genotypes collected from a different region along with 19 cultivated genotypes obtained from of the Egyptian Agricultural Research Center. All genotypes were analyzed with 261 polymorphic SSR and SNP alleles. The mean number of alleles per locus was 4 and PIC was 0.49, while the level of genetic diversity was 0.55 ranging from 0.03 to 0.82. The genotypes were assigned to three subpopulations that were consistent with their origins. The genetic variation within population was higher (51%) than among population at the molecular levels (F_ST =?0.491 when P?<?0.10). The level of polymorphic variation was highest in subpopulations-II, due to collected from different regions with different ear-types thus, expected to contain more diversity than local genotypes in subpopulations-I and subpopulations-III. The structured study found that the 153 barley genotypes are in harmony with clustering approaches using the SSR and SNP genotypic data in a neighbor-joining tree and principal components analysis, which identified three subpopulations. These results demonstrated genetic diversity among the Egyptian barley genotypes can be applied to suggest approaches, such as association analysis, classical mapping population development, and parental line selection in breeding programs. Therefore, it is necessary to use the exotic genotypes as the genetic resources for developing new barley cultivars in Egypt.     

Genetic Diversity of Asian Cotton (Gossypium arboreum L.) in China Evaluated by Microsatellite Analysis

Asian cotton (Gossypium arboreum L.) was once widely cultivated in China. It has also been a valuable source of genetic variation in modern cotton improvement. In this study, the genetic diversity of selected G. arboreum accessions collected from different regions of China was evaluated by microsatellite (simple sequence repeats, SSRs) analysis. Of the 358 microsatellite markers analyzed, 74 primer pairs detected 165 polymorphic DNA fragments among 39 G. arboreum accessions examined. Twelve accessions could be fingerprinted with one or more SSR markers. With the exception of two accessions, DaZiJie and DaZiMian, genetic similarity coefficients among all accessions ranged from 0.58 to 0.87 suggesting high level of genetic variation in the G. arboreum collections. The UPGMA dendrogram constructed from genetic similarity coefficients revealed positive correlation between cluster groupings and geographic distances. In addition, comparison of the microsatellite amplification profiles of the diploid G. arboreum and tetraploid Gossypium hirsutum L. found that size distribution of amplified products in G. arboreum was dispersive and that of G. hirsutum was relatively concentrated. The information on the genetic diversity and SSR fingerprinting from this study is useful for developing mapping populations for constructing diploid cotton genetic linkage map and tagging economically important traits.Diqiu Liu, Xiaoping Guo: These two authors contributed equally to this work.     

Genetic variation among populations of wild safflower, <Emphasis Type="Italic">Carthamus oxyacanthus</Emphasis> analyzed by agro-morphological traits and ISSR markers

Wild species of safflower, Carthamus oxyacanthus Bieb., is highly crossable with cultivated species, C. tinctorius L. and could be directly exploited in broadening safflower gene pool and improving the crop for biotic and abiotic stress environments. In this study, genetic diversity among accessions of C. oxyacanthus and their relationships with cultivated safflower were evaluated using agro-morphological traits and polymorphic inter-simple sequence repeats (ISSR) markers. Significant variation was observed among accessions particularly for seeds per capitulum, seed yield per plant, harvest index and capitula per plant. Cluster analysis based on agro-morphological traits classified the wild accessions in two groups according to their geographical regions, and separated them from the cultivated genotypes. ISSR marker also revealed a high genetic variation among the accessions, and cluster analysis based on this marker divided genotypes into four groups, with cultivated ones in a separate clade. Genetic variation observed among the wild safflower germplasm at the DNA level was higher than the agro-morphological traits, indicating that ISSR is an effective marker system for detecting diversity among safflower genotypes and their genetic relationships. Accessions of C. oxyacanthus with high genetic relationship to cultivated species could be used for interspecific hybridization in breeding programs of safflower.     

Simple sequence repeats marker polymorphism in emmer wheat (<Emphasis Type="Italic">Triticum dicoccon</Emphasis> Schrank): Analysis of genetic diversity and differentiation

Genetic diversity was investigated in 73 accessions of emmer wheat (Triticum dicoccon Schrank) from 11 geographical regions using a set of 29 simple-sequence repeat (SSR or microsatellite) markers, representing at least two markers for each chromosome. The SSR primers amplified a total of 357 different alleles with an average of 12.31 alleles per locus. The number of fragments detected by each primer ranged between 6 (Xgwm1066) and 21 (Xgwm268). Null alleles were detected in nine of the 29 primers used. A high level of gene diversity index was observed. Across the 29 primers, gene diversity ranged from 0.60 (Xgwm46) to 0.94 (Xgwm655), with a mean of 0.82. There was a highly significant correlation (r=0.882; p<0.01) between gene diversity index and the number of loci, showing the number of loci per se is a strong indicator of diversity. Analysis of genetic diversity within and among eleven geographical regions revealed most of the genetic diversity of the total sample resided within regions. The coefficient of gene differentiation (Gst = 0.27) showed that the genetic variation within and among the 11 geographical regions was 73 and 27%, respectively. High value of mean number of alleles per locus was found in Iran (4.86) followed by Morocco (4.10) and Armenia (4.03). On the contrary, lower mean number of alleles per locus was detected in Yemen (2.83). The average gene diversity index across regions ranged from 0.52 (Slovakia) to 0.67 (Morocco) with an average of 0.60. Multivariate techniques of principal component analysis and clustering were employed to examine genetic relationship among the 73 emmer wheat accessions vis-à-vis geographical regions of collections. The genetic distance coefficients for all possible 55 pairs of regional comparisons ranged from 0.63 (between Iran and Armenia, Georgia and Azerbaijan, Georgia and Slovakia) to 0.97 (between Morocco and Yemen, Spain and Georgia, and Turkey and Iran) with a mean of 0.82. From the PCA results, a two dimensional plot of PC1 versus PC2 was constructed. The scatter plot of the first two principal components which explained altogether 27% of the total variation depicted the presence of a clear pattern of geographical differentiation except in few cases like accessions from Caucasian region. Similar pattern of genetic relationships among accessions was observed in cluster analysis. The study provided genetic information of emmer wheat in relation to geographical regions of origin. The information could be utilized in crop improvement, germplasm conservation programs, and in further investigation.     

Genetic diversity analysis of common bean (Phaseolus vulgaris L.) genotypes for resistance to Mexican bean weevil (Zabrotes subfasciatus), using single nucleotide polymorphism and phenotypic markers

ABSTRACT

The objective of this study was to examine the genetic diversity present among 297 common bean genotypes using 2554 SNPs and 12 insects and seed-related traits. The phenotyping was done under laboratory condition while the genotyping was conducted by using the Illumina SNP BeadChip. High phenotypic diversity among traits were recorded, ranging from 0.87 to 0.96, with a mean of 0.92. Principal component and discriminant analyses identi?ed four PCs and three discriminant functions, which explained 82% and 100% of the total phenotypic variations among genotypes, respectively. Polymorphic Information Content ranged from 0.21 to 0.38, with a mean of 0.34. The mean gene diversity among genotypes ranged from 0.24 to 0.50, with a mean of 0.44. Genetic distance ranged from 0.19 to 0.82, with a mean of 0.62, while the phenotypic distance ranged from 0.00 to 1.00, with a mean of 0.64 were observed aamong genotypes. The analysis of molecular variance revealed highly signi?cant differences (p<0.001) among and within individuals and among populations. Both the SNP and the phenotypic markers grouped the 297 genotypes into two major distinct clusters and three sub-clusters. This information is useful for identi?cation and development of common bean germplasm with economically valuable traits and the conservation and utilization of genotypes.     

Worldwide genotyping of castor bean germplasm (<Emphasis Type="Italic">Ricinus communis</Emphasis> L.) using AFLPs and SSRs

Worldwide genetic diversity in 200 individuals comprising 41 castor bean accessions was assessed using amplified fragment polymorphisms (AFLPs) and simple sequence repeats (SSRs). We found that, despite surveying five continents and 35 countries, genetic diversity in castor bean germplasm is relatively low (overall H _e = 0.126 for AFLPs and 0.188 for SSRs) compared to estimates of genetic diversity in other plant species. Our data also show no geographic structuring of genotypes across continents or countries within continents. An assessment of the congruence between AFLP and SSRs indicates a low correlation (R ² = 0.19) between the two data sets, but each marker class nonetheless shows similar patterns of low-genetic diversity and a lack of geographic structure. Our data do suggest that SSRs yield a higher percentage of polymorphic loci, higher heterozyosity and a greater range of genetic distances, and are therefore more informative than are AFLPs on a locus-by-locus basis. Based on comparisons with numerous other plant species, we suggest that the lower genetic variation in this worldwide collection may be due to one or more factors including: sampling strategies that have not captured the full extent of genetic variation in the species; artifactual variation due to long-term germplasm storage and seed regeneration; or intense selection followed by domestic cultivation of a limited number of castor bean genotypes, which are widely propagated for their horticultural and agro-economic value.     

Geographical Patterns of Variation in Bari Faba Bean Germplasm Collection

A large collection of great interest and usefulness for faba bean breeding has been assembled at the Bari Germplasm Institute. Our objective was to describe the phenotypic diversity of a large sample (1565 entries from 39 countries) of this collection. Entries were characterized for 10 discontinuous traits to determine variation within and among geographical regions. Phenotypic variation was found within all regions for most traits. The Shannon-Weaver diversity index varied widely across regions, but was relatively even for most traits scored. Canonical discriminant analysis and clustering of the canonical means conducted separately for each botanical type, revealed useful phenotypic groupings of origin for future faba bean germplasm management. Based on the diversity and number of entries, East Europe, South-East Asia and North America seem under represented in the collection while South America is not represented at all. Information presented in this study could be used to devise a core collection, which would contain much of the diversity found in the Bari collection.     

Genetic diversity in cultivated yam bean (<Emphasis Type="Italic">Pachyrhizus</Emphasis> spp.) evaluated through multivariate analysis of morphological and agronomic traits

Yam bean [Pachyrhizus DC.] is a legume genus of the subtribe Glycininae with three root crop species [P. erosus (L.) Urban, P. tuberosus (Lam.) Spreng., and P. ahipa (Wedd.) Parodi]. Two of the four cultivar groups found in P. tuberosus were studied: the roots of ‘Ashipa’ cultivars with low root dry matter (DM) content similar to P. erosus and P. ahipa are traditionally consumed raw as fruits, whereas ‘Chuin’ cultivars with high root DM content are cooked and consumed like manioc roots. Interspecific hybrids between yam bean species are generally completely fertile. This study examines the genetic diversity of the three crop species, their potentials for breeding and the identification of useful traits to differentiate among yam bean genotypes and accessions. In total, 34 entries (genotypes and accessions) were grown during 2000?2001 at two locations in Benin, West Africa, and 75 morphological and agronomical traits, encompassing 50 quantitative and 25 qualitative characters were measured. Diversity between entries was analyzed using principal component analysis, cluster analysis, multivariate analysis of variance and discriminant function analysis. Furthermore, phenotypic variation within and among species was investigated. Intra- and interspecific phenotypic diversity was quantified using the Shannon–Weaver diversity index. A character discard was tested by variance component estimations and multiple regression analysis. Quantitative trait variation ranged from 0.81 (for total harvest index) to 49.35% (for no. of storage roots per plant). Interspecific phenotypic variation was higher than intraspecific for quantitative traits in contrast to qualitative characters. Phenotypic variation was higher in overall for quantitative than qualitative traits. In general, intraspecific phenotypic variation ranged from 0.00 to 82.61%, and from 0.00 to 80.03% for quantitative and qualitative traits, respectively. Interspecific phenotypic variation ranged from 0.00 to 95.02%, and 0.00?81.58% for the two trait types, respectively. The Shannon–Weaver diversity index (H′) was in general high and over 0.80 for most of the trait. Diversity within P. tuberosus was higher than within P. erosus and P. ahipa. Across the 50 quantitative and 25 qualitative traits, the Shannon–Weaver diversity index of intra- and interspecific variation was around 0.83 and 0.51, respectively and was lower for qualitative than for quantitative traits. Monomorphism was observed in eight qualitative traits and one quantitative character. The first, second and third principal components explained, respectively, 39.1, 21.3 and 8.3% of the total variation in all traits. Pachyrhizus erosus, P. ahipa, and P. tuberosus (‘Chuin’ and ‘Ashipa’) were clearly separated from each other by these analyses. Multivariate analysis of variance indicates significant differences between Pachyrhizus species for all individual or grouped traits. Discriminant function analysis revealed that the first two discriminant functions were almost significant. Biases due to unbalanced sample size used per species were small. Within each species a similar amount of diversity was observed and was determinable to 70% by only ten traits. We conclude that the cultivated yam bean species represent distinct genepools and each exhibits similarly large amounts of genetic diversity.     

Evaluation of <Emphasis Type="Italic">Phaseolus acutifolius</Emphasis> A. Gray plant introductions under high temperatures in a controlled environment

Heat susceptibility is a cause of yield loss in common bean (Phaseolus vulgaris L.) in temperate and tropical lowland growing regions. Interspecific hybridization with related species that include tepary bean (Phaseolus acutifolius A. Gray) can potentially be used to transfer heat tolerance traits to common bean. This study evaluated 25 tepary bean plant introductions (PIs) following exposure to high-temperature (35 °C day/32 °C night) and control temperature (27 °C day/24 °C night) during reproductive development. These 25 PIs were selected for high yield potential in a 14 h photoperiod greenhouse environment. High temperature when compared to non-stress treatment resulted in a mean reduction in seed yield of 88.8% among tepary beans and caused 100% yield loss in common beans. Twelve P. acutifolius PIs exhibited negligible yield under heat-stress when compared to control treatment. Although yields of these accessions were low under very high-temperature conditions, PI 200902, PI 312637, PI 440785, PI 440788, and PI 440789 exhibited the highest yield component stability under the high temperature treatment.     

Leaf gas exchange and water-use efficiency of dry-land wheat genotypes under water stressed and non-stressed conditions

The objective of this study was to determine drought tolerance characteristics of dryland wheat genotypes based on leaf gas exchange and water-use efficiency in order to identify promising genotypes for drought tolerance breeding. Physiological responses of ten genetically diverse wheat genotypes were studied under non-stressed (NS) and water stressed (WS) conditions using a 2?×?10 factorial experiment replicated 3 times. A highly significant water condition?×?genotype interaction (P?<?0.001) was observed for photosynthetic rate (A), ratio of photosynthetic rate and internal CO₂ concentration (A/C_i), ratio of internal and atmospheric CO₂ (C_i/C_a), intrinsic (WUE_i) and instantaneous (WUE_inst) water-use efficiencies suggesting genotypic variability among wheat genotypes under both test conditions. Principal component analysis (PCA) identified three principal components (PC’s) under both test conditions accounting for 84% and 89% of total variation, respectively. Bi-plot analysis identified G339 and G344 as drought tolerant genotypes with higher values of A, T, gs, A/C_i, WUE_i and WUE_inst under WS condition. The current study detected significant genetic variation for drought tolerance among the tested wheat genotypes using physiological parameters. Genotypes G339 and G344 were identified to be drought tolerant with efficient A, T, gs, A/Ci and water-use under water stressed condition.     

Genetic relationship among selected heat and drought tolerant bread wheat genotypes using SSR markers,agronomic traits and grain protein content

ABSTRACT

Assessing the genetic variation and relationships present in crop germplasm is a pre-requisite for parental selection and breeding. The objective of this study was to determine the genetic relationships present among selected heat and drought tolerant wheat genotypes using simple sequence repeat (SSR) markers, agronomic traits and grain quality parameters to select desirable parents for breeding. Twenty-four agronomically selected wheat genotypes sourced from the International Maize and Wheat Improvement Centre (CIMMYT)’s heat and drought tolerance nursery and four local check varieties were genotyped using 12 selected polymorphic SSR markers. The test genotypes were phenotyped using yield and yield-component traits, and grain protein content (GPC) under non-stressed (NS) and drought-stressed (DS) conditions. Expected heterozygosity mean value of 0.58 indicated moderate genetic diversity for breeding. The studied wheat genotypes were delineated into six genetic groups using cluster analysis. Significant genotypic differences were observed for agronomic traits and GPC under NS and DS conditions. Genetically unrelated breeding parents including LM02, LM13, LM23, LM41, LM44, LM71, LM73 and LM75 were selected for population development and breeding for enhanced grain yield and protein content under heat and drought-stressed environments.     

Using SSR markers to determine the population genetic structure of wild apricot (<Emphasis Type="Italic">Prunus armeniaca</Emphasis> L.) in the Ily Valley of West China

Genetic structure of three wild populations (Xinyuan, Gongliu and Daxigou) of apricot in the Ily Valley, Xinjiang Uygur Autonomous Region of China, was investigated with microsatellite (simple sequence repeat, SSR) markers. The higher polymorphism and greater transportability of these markers between Prunus species proved SSR markers were much efficient for conducting genetic diversity studies in wild apricot. Nei's gene diversity (He) and Shannon's index of diversity (I) were 0.287 and 0.458, respectively. This indicated that the wild apricot in the Ily Valley still maintained a relatively high level of diversity. The Gst of 0.137 and Fst of 0.164 revealed that genetic variation mainly resided among individuals within populations (83.6–86.3%). Population differentiation could also be found according to the distribution of SSR alleles between the populations. Mantel test showed the genetic distance between populations was significantly correlated to the geographical distance. The modest amount of gene flow (2.684) would reduce the disjunction between wild apricots. The long-distance dispersal of pollen by insects was probably the main way of gene flow between populations. Based on the study of population genetic structure, an effective conservation strategy of the species was discussed.     

Comparison of morphological traits and molecular markers to analyse diversity and structure of alfalfa (<Emphasis Type="Italic">Medicago sativa</Emphasis> L.) cultivars

Diversity and structure of populations may differ substantially between morphological traits and molecular markers. Explanations of such discrepancies are crucial for further progress in breeding as well as for the maintenance of genetic resources. Our objective was to compare indices of among-cultivars differentiation for morphological traits (Q_ST) and molecular markers (F_ST) in alfalfa (Medicago sativa), a legume forage species. Ten cultivars representing the Northern and Southern types commonly grown in Europe were investigated. For each cultivar, 40 genotypes were analysed with 16 SSR markers and four morphological traits measured in two locations and several cuts. Q_ST values were in general high (0.02–0.39) compared to the differentiation observed with molecular markers (F_ST = 0.01), especially for growth habit, indicating that morphological traits were more efficient to structure the diversity than molecular markers. For morphological traits, a clear separation of Northern and Southern cultivars was observed, whereas for molecular markers, no clear structure was detected. Nevertheless, the grazing type cultivar Luzelle was separated from the rest of the cultivars for both morphological traits and molecular markers. Although pairwise differences between cultivars were significant for both morphological traits and molecular markers, the main part of the variation was found within cultivars. This large within-cultivar variation may be explained, besides the outcrossing reproductive mode and autotetraploid genetics, by the recent history of M. sativa domestication in Europe and the frequent seed exchanges. Selection for morphological traits (Q_ST > F_ST) was achieved without modification of within-cultivar neutral diversity.     

Genetic Diversity Among Traditional Ethiopian Highland Maize Accessions Assessed by Simple Sequence Repeat (SSR) Markers

Over the past three centuries, maize has become adapted to complex environmental conditions in the highlands of Ethiopia. We analyzed 62 traditional Ethiopian highland maize accessions, using 20 simple sequence repeat (SSR) markers and 15 morphological traits, to assess genetic diversity and relationships among these accessions and to assess the level of correlation between phenotypic and genetic distances. The accessions varied significantly for all of the measured morphological traits. The average number of alleles per locus was 4.9. Pair-wise genetic dissimilarity coefficients ranged from 0.27 to 0.63 with a mean of 0.49. Ward minimum variance cluster analysis showed that accessions collected from the Northern agroecology were distinct from the Western and Southern agroecologies. However, there was no differentiation between the Western and Southern accessions. This suggested gene flow between these regions. The relationship between morphological and SSR-based distances was significant and positive (r = 0.43, p = 0.001). The high genetic diversity observed among these set of accessions, suggests ample opportunity for the development of improved varieties for different agroecologies of Ethiopia. From conservation perspective, sampling many accessions from all agroecologies would be an effective way of capturing genetic variation for future collections and conservation.     

Salinity effect on root and shoot characteristics of common and tepary beans evaluated under hydroponic solution and sand culture

The effects of increased salinity [NaCl + CaCl₂] on seedling of three tepary and four common bean cultivars/lines, of known resistance and susceptibility at germination stage, grown for thirty‐eight‐days in salinized hydroponic and sand cultures were assessed at electrical conductivity (EC) of 1.89 (control), 4.00, 8.00, and 12.00 dS/m of half strength Hoagland solution inside a glasshouse at 30/25±2°C day/night temperature. The hydroponic culture screening method was more severe than the sand culture method. Common bean cultivars/lines expressed genetic variability to salinity stress at thirty‐eight‐days old seedlings. ‘Badrieh’ was tolerant to salinity as the tolerant tepary bean T#l line under sand culture. However, this was not evident under hydroponic culture. T#l showed salinity injury symptoms at EC = 4 dS/m, while ‘Badrieh’ showed’ no salinity injury symptoms at EC = 4 dS/m. These results indicate that the mechanisms involved for tolerating salinity in the tepary could be different from that involved in common beans. Inverse and significant correlations between salinity injury symptoms and several root and shoot characters were evident from the data, indicating that variation in whole‐plant foliar injury symptoms to salinity would thus seem to provide the best means of initial selection of salinity tolerant genotypes by plant breeders.     

Characterization of a flint maize (Zea mays var. indurata) Italian landrace, II. Genetic diversity and relatedness assessed by SSR and Inter-SSR molecular markers

A comparative characterization of 10 field populations of the maize (Zea mays var. indurata) landrace Nostrano di Storo was carried out using different types of PCR-based markers. The inbred line B73 and three synthetics (VA143, VA154 and VA157) selected from as many landraces were also used. Genetic diversity and relatedness were evaluated over 84 SSR and 53 I-SSR marker alleles using a total of 253 individual DNAs. Up to 23 alleles per SSR locus were scored while the average effective number of alleles per population was 6.99. Nei's total genetic diversity as assessed with SSR markers was H_T = 0.851 while the average diversity within populations was H_S = 0.795. The overall Wright's fixation index F_ST was as low as 0.066. Thus, more than 93% of the total variation was within population. Unique alleles over all SSR loci were found for six populations. An average of 17.7 marker alleles per I-SSR primer were scored with an effective number of marker alleles per locus of 1.34. The Shannon's diversity information index over all populations and I-SSR loci was 0.332, varying from 0.286 to 0.391. The extent of differentiation between populations was as low as G_ST = 0.091. Dice's genetic similarity matrices were estimated for both SSR and I-SSR markers. The mean genetic similarity coefficients within and between populations were respectively 0.269 and 0.217, for SSR markers, and 0.591 and 0.564, for I-SSR markers. UPGMA dendrograms displayed all field populations but one clustered into a distinct group, in which the synthetic VA154, selected from the Marano Vicentino landrace, was also included. One field population and the other two synthetics were clustered separately as well B73. The matrix correlation assayed by the Mantel's correspondence test was as high as 0.908. Findings suggest that, although a high variability can be found among plants, most plant genotypes belong to the same landrace called Nostrano di Storo. Although gene flow from commercial hybrids might have occurred, the large number of polymorphisms and the presence of both unique alleles and alleles unshared with B73 and synthetics are the main factors underlying the value of this flint maize landrace as a source of genetic variation and peculiar germplasm traits. Because of its exclusive utilization for human consumption, such a molecular marker characterization will be a key step for obtaining the IGP mark and so promote the in situ conservation and protection of the landrace Nostrano di Storo.     

Genetic variation of Ethiopian and Eritrean sorghum (Sorghum bicolor (L.) Moench) germplasm assessed by random amplified polymorphic DNA (RAPD)

The extent and patterns of distribution of genetic variation among 80 sorghum (Sorghum bicolor (L.) Moench) germplasm accessions from Ethiopia and Eritrea were investigated using RAPD with 20 oligonucleotide primers. The primers generated a total of 147 polymorphic bands across the 80 accessions with a mean of 7.35 bands per primer. Estimation of the extent of variation by the Shannon-Weaver diversity index revealed an intermediate level of overall variation (H = 53), although the levels varied among regions of origin of the accessions. Partitioning of the total variation revealed considerable variation (77%) within the region of origin of the accessions and the remainder (23%) among regions of origin. Similarly, a large portion (94%) of the total variation was found within the adaptation zones compared to among the adaptation zones (6%). The results suggest a weak differentiation of the sorghum material both on regional and agro-ecological bases, which could be ascribed to the high rate of outcrossing in cultivated sorghum and its free natural hybridization with its wild and weedy relatives, as well as to seed movement by humans. The average genetic dissimilarity was found to be 36% among the 80 accessions and 13% among the 15 regions of origin. Cluster analysis failed to group accessions of the same region or the same adaptation zone, which further confirmed the weak differentiation of the material studied. The clustering pattern of the regions of origin was broadly concordant with previous clustering patterns obtained using morphological characters, in which regions with broad agro-climatic conditions were grouped together.     

Genetic characterization of the orphan crop tef [Eragrostis tef (Zucc.) Trotter] accessions using simple sequence repeat markers

Tef is the most important and well adapted cereal crop in Ethiopia and grows better than other cereals both in biotic and abiotic stress conditions. In this study 93 tef accessions representative of various agro-ecologies of Ethiopia along with four improved varieties, one local check and six wild relatives were studied. The materials were genotyped with 12 simple sequence repeat markers (SSRs) to investigate the extent and structure of the genetic diversity of tef. A total of 152 alleles were detected indicating high polymorphism in the studied accessions. The number of alleles per polymorphic loci ranged from seven for CNLT 538 to 29 for CNLT150 with an average of 12.67. High average polymorphic information content (0.82) and average expected heterozygosity (0.86) also signifies the suitability and efficiency of SSR markers to discriminate among tef genotypes. Cluster, principal coordinate and structure analyses grouped the 98 tef genotypes and six wild relatives into four distinct classes. The groupings showed no special pattern despite the different regions of origins for the accessions; however, the five wild relatives were grouped together. The analysis of molecular variance and fixation index showed low genetic differentiation and high gene flow between regions revealing that much of the variability was attributed to within populations variation. Generally, the present study showed that there is high genetic variability with unstructured genetic pattern among the studied tef genotypes which implies the vitality of conserved tef germplasms at Ethiopian Biodiversity Institute and the impact of the seed exchange system on tef breeding activities in Ethiopia.

     

Wild melon diversity in India (Punjab State)

We present here the first comprehensive genetic characterization of wild melon accessions from northern India. The genetic diversity among 43 wild melon accessions collected from the six agro-ecological regions of the Punjab State of India was assessed by measuring variation at 16 Simple Sequence Repeat (SSR) loci, morphological traits of plant habit and fruit morphological traits, two yield-associated traits, root nematode resistance and biochemical composition (ascorbic acid, carotenoids, titrable acidity). Variation among accessions was observed in plant habit and fruit traits and wild melon germplasm with high acidity and elevated carotenoid content and possessing resistance to Meloidogyne incognita was identified in the collection. A high level of genetic variability in wild melon germplasm was suggested by SSR analysis. Comparative analysis using SSRs of the genetic variability between wild melons from the north and other melons from the south and east regions of India and also reference accessions of cultivated melon from Spain, Japan, Korea, Maldives, Iraq and Israel, showed regional differentiation among Indian melon accessions and that Indian germplasm was not closely related to melon accessions from other parts of the world. A highly drought tolerant accession belonging to var. agrestis Naud. was also identified.