Evaluation of genetic diversity in a Camelina sativa (L.) Crantz collection using microsatellite markers and biochemical traits

A genomic DNA library enriched with GA/TC repeats from Camelina sativa variety Calena has been analysed. After sequencing of about 200 randomly selected clones, approximately 60 % of them showed to contain simple or compound microsatellites with a high number of repeats. Among all microsatellite markers analysed 15 primer pairs amplified polymorphic fragments. Forty C. sativa accessions of different origin were genotyped with 15 microsatellite markers that generated 134 alleles with an average of 8.93 alleles per locus. The observed heterozygosity (Ho) among the accessions ranged from 0.0 to 0.15 with an average of 0.0370, whereas the average of expected heterozygosity (He) among accessions was 0.2769. The analysis of the average total heterozygosity (H_T = 0.651), the intrapopulation genetic diversity (H_S = 0.260), the interpopulation genetic diversity (D_ST = 0.391) and the coefficient of genetic differentiation among populations (G_ST = 0.574) demonstrated that 57.4 % of the genetic diversity is among the accessions, while 42.6 % resides within them. Phylogenetic tree of the 40 C. sativa accessions was constructed based on Nei’s genetic distance. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram shows, except for CAM108 and CAM170, a clear discrimination among C. sativa accessions grouping them in five subgroups. ANOVA analysis indicates significant differences in some biochemical and agronomic parameters among the C. sativa accessions grouped according to Nei’s genetic distance. The result of the Tukey HSD test demonstrated that the A4 subgroup showed a significant higher TWS and linoleic acid (LA) content, while the subgroup A1 showed a significant higher linolenic and lower LA content compared to the remaining groups.     

Genetic diversity in sorghum [<Emphasis Type="Italic">Sorghum bicolor</Emphasis> (L.) Moench] germplasm from Southern Africa as revealed by microsatellite markers and agro-morphological traits

Cultivated sorghum [Sorghum bicolor (L.) Moench] is an important food security crop in the semi-arid regions of the world including Asia and Africa. Its genetic diversity is contained mostly in traditional varieties and modern cultivars used by farmers. In this study, agro-morphological traits and molecular markers were used to assess genetic diversity in 22 accessions of cultivated sorghum from five countries (Botswana, Namibia, Swaziland, Zambia and Zimbabwe) in the Southern African Development Community (SADC) region. The study revealed a significant variation among 22 accessions in both qualitative and quantitative morphological traits, indicating the accessions’ promising potential as breeding material. For molecular analysis, 11 microsatellite primer-pairs were used, and generated a total of 70 alleles across 20 accessions. Analysis of molecular variance revealed a high level of genetic variation; 67 % among the accessions and 10 % among the five countries. The patterns of genetic diversity and the relationships observed in this study should provide insights for genetic resource conservation and utilization of sorghum germplasm in the SADC region.     

Genetic diversity of anchote (Coccinia abyssinica (Lam.) Cogn.) from Ethiopia as revealed by ISSR markers

Anchote (Coccinia abyssinica) is plant endemic in Ethiopia with a high calcium content grown for its edible tuberous roots. In spite of its importance as food security crop, there is no information available on molecular genetic diversity of this crop. Therefore, the aim of this study was to assess genetic diversity within and among 12 populations of anchote using ISSR markers. Using nine ISSR primers, a total of 87 scorable bands was generated of which 74 were polymorphic. Within population diversity based on polymorphic bands ranged from 13.8 to 43.53 % with a mean of 33.05 %, Nei’s genetic diversity of 0.04–0.156 with a mean of 0.12, Shannon information index of 0.07–0.23 with a mean of 0.175 and analysis of molecular variation (AMOVA) of 51.4 % were detected. With all diversity parameters, the highest diversity was obtained from Gimbi, Bedele and Ale populations, whilst the lowest was from Manna. AMOVA showed a 48.56 % between populations variability and significantly lower than that of within population variation. Population differentiation with F_ST was 48.56 %. From Jaccard’s pairwise similarity coefficient, Decha and Nedjo were most related populations exhibiting 0.76 similarity and Manna and Nedjo were the most distantly related populations with similarity of 0.52. The only pentanucliotide primer used in the study, Primer 880 (GGAGA)3, showed a unique band in some individuals that appeared to be associated with morphological quantitative traits (lowest seed number, high protein content, largest fruit size and smallest vine length). Illubabor and Gimbi populations exhibited highest genetic diversity so that the populations should be considered as the primary sites in designing conservation areas for this crop.     

Morphological and genetic diversity of shea tree (<Emphasis Type="Italic">Vitellaria paradoxa</Emphasis>) in the savannah regions of Ghana

Vitellaria paradoxa C. F. Gaertn., commonly known as shea tree or Vitellaria, is ranked the most important tree species of the savannah regions in the most African countries due to its ecological and economic importance for livelihoods and national economies. However, the savannah regions are the most vulnerable areas to the global climate change. Moreover, the Vitellaria populations on farmlands are threatened by the dominance of old trees with low or lack of regeneration. In this study both morphological and genetic diversity were assessed using several phenotypic traits and 10 microsatellite markers, respectively, to assess the impact of land use and agro-ecozone types on Vitellaria in Ghana. The land use types were forests and farmlands, and the agro-ecozone types included the Transitional, Guinea, and Sudan savannah zones. The mean values of morphological traits, such as diameter at breast height (DBH) and canopy diameter (CD), were statistically different between forest (DBH = 22.20, CD = 5.37) and farmland (DBH = 39.85 CD = 7.49) populations (P < 0.00001). The Sudan savannah zone with mean petiole length of 4.96 cm showed significant difference from the other zones, likely as a result of adaptation to drier climate conditions. Genetic data analysis was based on 10 microsatellite markers and revealed high genetic diversity of Vitellaria in Ghana: mean expected heterozygosity, H _e was 0.667, and allelic richness, measured as number of effective alleles A _e , was 4.066. Both farmlands and forests were very diverse indicating lack of negative influence of farmer’s selection on genetic diversity. Fixation index was positive for all populations (mean F _IS = 0.136) with farmlands recording relatively higher values than forests in all ecological zone types studied, probably indicating less gene flow in the farmlands. Moderate differentiation (F′ _ST = 0.113) was comparable to other similar tree species. Both land use and ecological zone types influenced genetic differentiation of Vitellaria at varying levels. The species was spatially structured across three ecozones and following climatic gradient. The forest reserves are used in situ conservation for Vitellaria in Ghana. High diversity observed in the most arid zones provides opportunity to find and use appropriate plant materials for breeding climate change resilient trees.     

Genetic diversity analysis in Phaseolus vulgaris L. using morphological traits

Common bean (Phaseolus vulgaris) is an important export crop in Kyrgyzstan since the end of the twentieth century. Genetic diversity analysis of common bean populations is useful for breeding programs, as it helps to select genetic material to be used for further crossing. Twenty-seven common bean accessions were analyzed using 13 qualitative morphological traits. In some cases, obtained morphological data were combined with previously published results based on microsatellite markers. The similarity matrices generated from the molecular and morphological data were significantly correlated (r = 0.49, P < 0.01). Cluster analyses based on Dice’s similarity coefficient were constructed based on morphological data and the combined data set of morphology and microsatellite, and both grouped the 27 accessions according to their origin: 15 belonged to the Andean and 12 to the Mesoamerican gene pool. On average, the Andean accessions were less diverse than the Mesoamerican accessions. The average diversity based on the Shannon diversity index for the 13 qualitative morphological traits was 0.05. Overall, this study revealed that qualitative morphological markers are efficient in assigning modern cultivars to their gene pools of origin.     

Genetic relationships among improved varieties of rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) in Indonesia over the last 60 years as revealed by morphological traits and DNA markers

Morphological traits and two kinds of molecular markers were employed to study the genetic relationships among improved rice (Oryza sativa ) varieties of Indonesia since 1943. Dendrograms based on morphological traits and both molecular markers (simple sequence repeats, SSR and single nucleotide polymorphism, SNP) agreed in separating the varieties into two primary groups. Based on the morphological traits, a larger group (>60 %) contains varieties with smaller sizes compared with those in the smaller group (<40 %). SSR and SNP markers revealed that most of the varieties belonged to indica (88; 89 %) and japonica (9; 8 %) subspecies, and 3 % of varieties were not involved in two subspecies. The molecular markers revealed that the genetic diversity (H) stagnated between stage II (1967–1985) and stage III (1986–2003). However, during stage I (1943–1966), H was higher than in the other stages as revealed by SNP markers, while H in stage I was lower than in the other stages as revealed by SSR markers. In this study, the two molecular data sets were positively correlated and positive correlations between the phenotypic and molecular data depended on the kind of molecular marker: SNP had higher Mantel r values than SSRs. Besides, SSR markers seem to be appropriate for pedigree studies, while SNP markers could be used to reveal genomic relationships. These findings were attributable to the different properties of these two different markers. These results suggested that the diversity and differentiation of both the phenotypic and molecular marker variations were probably resulted from the crossing and selection in rice breeding in Indonesia. We suggest that Indonesia needs another strategy to improve new varieties to avoid a reduction in genetic diversity and similarity.     

Population differentiation and genetic variation inform translocation decisions for Liatris scariosa var. novae-angliae, a rare New England grassland perennial

Augmentation of small rare species populations is sometimes suggested on genetic grounds. However, outbreeding depression via dilution of local adaptation or break-up of genomic coadaptation may occur. These effects depend on the causes of population divergence. Here, we compare genetic measures of population divergence in Liatris scariosa var. novae-angliae, a rare New England perennial. We measured G_ST, neutral marker subdivision, and Q_ST, quantitative subdivision of propagule and juvenile plant traits. G_ST was relatively high. Q_ST for leaf shape exceeded G_ST, indicating local adaptation, while Q_ST for other traits fell within or below the G_ST range. Local adaptation appears low for juvenile traits, although the high G_ST cautions against translocation because of potential coadaptation. If translocation is still required, however, donor populations should contain high quantitative genetic diversity. We assess population size and allozyme diversity as predictors of quantitative genetic variation, but find these poor proxies for direct measurement.     

Zinc accumulation in lettuce cultivars grown with organic or chemical based nutritional regimes

This study determined the potential to increase Zn density of lettuce (Lactuca sativa L.) through cultivar selection and nutrient management. Organic fertilizer and Hoagland and Arnon no.1 solution factored with three zinc (Zn) levels provided as zinc sulfate (ZnSO₄) were the fertilizer regimes in a greenhouse experiment. Modern cultivars had a 32% higher fresh head weight than heritage cultivars, but each accumulated the same Zn concentration (65 mg kg^?1 dry wt). Butterhead phenotypes had a 38% lower yield than loose-leaf and had the highest Zn concentration (78 mg kg^?1 dry wt) followed by romaine (66 mg kg^?1 dry wt) and loose-leaf (53 mg kg^?1 dry wt). Concentration of Zn did not differ between fertility regimes, being about 66 mg kg^?1 dry wt with each regime. Differences in Zn concentrations were significant among individual cultivars with ranges from 42 mg g^?1 dry wt to 91 mg kg^?1 dry wt. ‘Tom Thumb’, ‘Adriana’, ‘Claremont’, and ‘Focea’ were the top in cultivar ranking, with mean Zn concentration of 63 mg kg^?1 dry wt. The results signify that selection of cultivars may be utilized to increase Zn accumulation in lettuce but that nutritional regimes had little effect on accumulation.     

Genetic variability of wild apricot (Prunus armeniaca L.) populations in the Ili Valley as revealed by ISSR markers

The genetic variability of 14 wild Prunus armeniaca populations was investigated using morphological analysis and inter-simple sequence repeat markers. 10 morphological characters revealed a high level variation, especially Fruit number, Fruit weight, Seed weight and Tree height. Totally, 15 selected primers generated 155 loci, with an average of 10.3 bands per primer. Nei’s gene diversity (H _e ) and Shannon’s index of diversity (I) were fairly high at the species level (H _e  = 0.2741, I = 0.4220). High molecular and morphological variability indicated that wild apricots in the Ili Valley still maintained a relatively high level of diversity. The G _ST of 0.2275 revealed a low level of genetic differentiation among populations, and genetic variation mainly resided within populations (81.51 %), which was identified with the moderate gene flow value (N _m  = 1.6974). The relatively high intraspecific genetic diversity and low inter-population genetic differentiation was largely attributed to long-distance dispersal of pollen, continuous distribution of populations and the self-incompatible breeding system.     

Characterization of Italian chickpea (Cicer arietinum L.) germplasm by multidisciplinary approach

Characterization of 15 chickpea (Cicer arietinum L.) accessions (6 cultivars, 3 selected lines and 6 landraces) was performed using morphological, agronomic, and technological traits, together with biochemical (seed storage proteins) and molecular markers. Field trials, performed in two different geographical areas of Southern Italy, one in a plain area near Tyrrhenian sea and one in an hilly internal area, revealed a high influence of field location on yield. A wide variation was also registered for technological traits and molecular markers. Microsatellite (SSR) markers grouped chickpea accessions in different clusters, providing useful information on genetic variation and relationships among them, with polymorphic fragments useful to discriminate among all accessions. On the contrary, seed storage protein pattern showed scarce variation resulting very similar among all the accessions considered.     

Genetic diversity among Polish landraces of common oat (Avena sativa L.)

All over the world about 220,000 accessions of the genus Avena is preserved in gene banks. Polish oats collection, in the National Centre for Plant Genetic Resources, consists of about 2,500 accessions. More than 80 % of them belong to the species Avena sativa. Only 136 accessions have the landrace or traditional cultivar status and 91 of them were collected in Poland. The main objective of this study was to estimate genetic diversity of a set of 67 Polish landraces using inter simple sequence repeat (ISSR) markers. We also tried to determine whether genetic diversity depended on the region and altitude of collection site and if there was a relationship between DNA polymorphism and some morphological traits. The accessions were collected between years 1973 and 1999 from areas of Northern, Southern and Eastern Poland. The obtained results indicated a relatively low diversity (0.09–0.37) of the common oat landraces. Analysis of molecular variation (AMOVA) showed that there were no significant differences within designated geographic regions. It indicated that at the same time the altitude of collection site had significant effect on the genetic differentiation of the accessions. AMOVA also showed the presence of variance between groups formed on the basis of the colour of lemma. White lemma accessions were also characterized by highest genetic distinctiveness. Considering the evident impact of local climatic conditions on the genetic distinctiveness of Polish landraces utility of them in the Polish breeding programs should be considered.     

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.     

Effect of salt stress on Growth and Ion accumulation of alfalfa (Medicago sativa L.) cultivars

Alfalfa (Medicago sativa L.) yield and nutrient contents may be affected under salinity condition. Thus, this experiment was conducted to determine the effect of three salinity levels (60, 120, and 180 mM NaCl) on shoot and root dry weights, and mineral contents of three alfalfa cultivars. With the increasing salinity levels sodium (Na) and magnesium (Mg) contents increased; but potassium (K), nitrogen (N), phosphorous (P), calcium (Ca), zinc (Zn), and copper (Cu) contents and root and leaf weights decreased; however, changes in these traits depended on cultivar and salinity level. However, Rehnani, a tolerant cultivar, had the lowest Na and Mg contents and the highest K, N, P, Ca, Zn, and Cu contents and dry weights under all of the salinity levels. Moreover, leaf dry weight and leaf P content had the highest correlation with salt tolerance suggesting that these traits may be used as a marker for selecting salts that are tolerant among genotypes in alfalfa.     

Genetic structure and differentiation among grapevines (<Emphasis Type="Italic">Vitis vinifera</Emphasis>) accessions from Maghreb region

Three gene pools representative of Vitis vinifera L. subsp. vinifera (=subsp. sativa Beger) growing in the Maghreb regions (North Africa) from Tunisia (44), Algeria (31) and Morocco (18) and 16 wild grape accessions (Vitis vinifera L. subsp. sylvestris (Gmelin) Beger) from Tunisia were analysed for genetic diversity and differentiation at twenty nuclear microsatellites markers distributed throughout the 19 grape chromosomes. 203 alleles with a mean number of 10.15 alleles per locus were observed in a total of 109 accessions. Genetic diversities were high in all populations with values ranging from 0.6775 (Moroccan cultivars) to 0.7254 (Tunisian cultivars). F _st pairwise values between cultivated grapevine populations were low but found to be significantly different from zero. High F _st pairwise values were shown between wild and cultivated compartments. Two parent offspring relationships, two synonyms and two clones of the same cultivar were detected. The rate of gene flow caused by vegetative dissemination of cultivated grapevine plants was not sufficient to genetically homogenise the pools of cultivars grown in different regions. The Neighbour Joining cluster analysis showed a clear separation according to geographical origins for the cultivated grapevines gene pools and revealed a high dissimilarity between cultivated and wild grapevine. However, three cultivars (Plant d’Ouchtata 1, Plant de Tabarka 3 and Plant d’Ouchtata 3) are very close to wild accessions and may result from a hybridisation between cultivated and wild accessions. The high level of differentiation between cultivated and wild accessions indicates that the cultivated accessions do not derive directly from local wild populations but could mostly correspond to imported materials introduced from others regions during historical times or derived from crossing between them.     

Single-locus EST-SSR markers for characterization of population genetic diversity and structure across ploidy levels in switchgrass (<Emphasis Type="Italic">Panicum virgatum</Emphasis> L.)

Polyploidy, ploidal variation between populations, and aneuploidy within some populations complicate population genetic analyses in switchgrass. We report 21 genic-simple sequence repeat marker loci with single-locus disomic segregation in tetraploids and apparently tetrasomic inheritance in octoploids, thus allowing population genetic analyses across ploidy levels. Based on 472 individuals sampled over four tetraploid and eight octoploid cultivars, six to 55 alleles were detected per locus with an average of 24.1. Genetic diversity was greater in octoploids than tetraploids, as expected from polysomic inheritance. One tetraploid cultivar displayed comparable diversity to the least diverse octoploid cultivars, suggesting breeding history or population history in the native stands of origin may have also affected within-cultivar diversity. Amplicon number at each locus and population relationships suggest autopolyploid origin of octoploids within upland tetraploids with significant cultivar differentiation. However, model-based Bayesian clustering of individuals indicated that closely related octoploid cultivars are difficult to identify, possibly due to slowed differentiation by polysomic inheritance. The analysis of the sampling effect indicated addition of loci is more effective for cultivar identification than more individuals sampled per cultivar. Discriminating power of loci tended to correlate with their variability. The eight loci with greatest discriminatory power within tetraploids were equally successful as 20 loci at identifying the four tetraploid cultivars. The set of markers reported in this study are useful for characterization of switchgrass germplasm and identifying population structure for association studies.     

Responses of Tomato Cultivars to Water-Deficit Conditions (Case Study: Moghan Plain,Iran)

A field experiment was arranged in split plot based on randomized complete block design in three replications at Moghan plain, Iran, during the years 2014–2016. Treatments included four irrigation levels, 100%, 80%, 60%, and 40% of water requirements for the main plot, and tomato cultivars included for a subplot. Results indicated that deficit irrigation resulted in a decrease in yield and yield components, morphological characteristics and water use efficiency (WUE), and volumetric soil moisture in different layers of soil, while resulting in an increase in qualitative characteristics. Reductions of tomato fruit yield and other studied traits were different in the first and second agronomic years. But in general, comparison of means showed that, based on the normal irrigation, optimal growth and plant growth were observed for 08 cultivar. Moreover, under deficit irrigation conditions, Superbita cultivar exhibited higher yield and WUE compared to 08 and Matin cultivars.

Abbreviations: WUE = Water use efficiency; IWUE = Irrigation water use efficiency; K = Kelvin; IR = Irrigation water; Cul = Cultivar; ETo = Reference evapotranspiration; Etc = Evapotranspiration; Kc = Crop coefficient; Kp = Pan coefficient; cm = Centimeter; gr = Gram; t = Tone; ha = Hectare; ? = Volumetric water content; kg = kilogram.     

Presence of phylogeographic structure among wild diploid alfalfa accessions (Medicago sativa L. subsp. microcarpa Urb.) with evidence of the center of origin

The genetic structure of wild germplasm on a macrogeographic scale has implications for collection and conservation of wild genetic resources of economically important plants. Cultivated alfalfa is derived from a taxonomic group called the Medicago sativa–falcata complex, which includes a number of morphologically and genetically differentiated diploid and tetraploid subspecies representing the primary gene pool for alfalfa improvement. Although the origin of the taxa included in M. sativa–falcata complex has been described broadly, the center of diversity for each taxon is not clear. In this study, 60 individual genotypes from 16 accessions of the diploid taxon M. sativa subsp. microcarpa Urb. [M. sativa subsp. caerulea (Less. ex Ledeb.) Schmalh.] were obtained from the two proposed centers of diversity, Caucasia and Central Asia, and were genotyped with 89 simple sequence repeat markers. Phylogenetic reconstructions together with population genetics statistics (heterozygosity, allelic diversity, and F_ST) were used to describe the pattern of present genetic diversity, to deduce biogeographic history, and to infer the center of diversity. Our results revealed that the Central Asian accessions were distinct from the Caucasian accessions, and that overall accessions, genetic distance was positively correlated with geographical distance, indicating a spatial genetic structure. The accessions from the Caucasian region had higher mean F_ST values, higher allele diversity and higher heterozygosity, suggesting that the Caucasian region is the likely center of diversity for M. sativa subsp. microcarpa [M. sativa subsp. caerulea] and the accessions recolonized Central Asia from Caucasia after the glacial retreat.     

Quantitative Caloric Energy Distribution and Variations in Two Rice Varieties Related to Different Nitrogen Application Levels in Paddy Field

Abstract

A field experiment was conducted in Hangzhou, Zhejiang Province, P.R. of China in 1999 to investigate the quantitative caloric energy characteristics of two rice cultivars (Oryza sativa L.), early crop rice Jia yu 948 and late crop rice Jia yu 93390 were grown in different nitrogen levels and climate conditions. The two cultivars were grown with 0, 80, 120, 160, and 200 kg ha^?1 of nitrogen fertilizer and in ample water and farming management activities. Analysis of caloric energy showed that significant differences occurred among treatments and plant organs in both rice cultivars. However, no significant differences occurred among same organs under different nitrogen treatments in both cultivars except for the panicles. The mean caloric energy of both cultivars increased with nitrogen fertilizer application. However, no optimal level of nitrogen fertilizer treatment with caloric energy was established, as there was still an increase in caloric energy even at 200 kg N ha^?1 fertilizer treatment. Cultivar Jia yu 948 had a higher mean caloric energy of 4172 cal g^?1 compared to 4117 cal g^?1 of cultivar Jia yu 93390. There were significant differences in caloric energy among the plant organs. The ascending order of energy distribution was as follows; root, stem, husk, leaf, grains, and panicles. Of great interest is the relatively high amount of energy invested in the husks. This amount was similar to that of the leaf. There was a linear relationship between caloric energy and nitrogen application levels. The basic rice caloric values are 4058 cal g^?1, an increase in 1 kg N ha^?1 of nitrogen (pure) resulted in an increase of 0.41 cal g^?1 and 0.29 cal g^?1 of dry weight in the cultivar Jia yu 948 and cultivar Jia yu 93390 respectively. Thus Jia yu 948 had a better utilization efficiency of nitrogen nutrient than Jia yu 93390 considering the caloric value increase.