Genetic diversity in wild species of passion fruit (Passiflora trintae) based on molecular markers

In spite of the importance of and the considerable variability observed in Passiflora (Passifloraceae), little is known about the genetic diversity of most of the species of this genus. We evaluated the genetic diversity by RAPD markers in 18 genotypes of Passiflora trintae. The 15 primers generated 112 markers, 84% of which were polymorphic. The genetic distance estimated by the complement of the Dice index (average dissimilarity = 0.30) and genotype grouping based on the UPGMA algorithm showed low variability among genotypes. More attention should be given to the study and conservation of the biodiversity of this economically important genus.     

Genetic variability in wild genotypes of Passiflora cincinnata based on RAPD markers

The genetic diversity and characteristics of commercial interest of Passiflora species make it useful to characterize wild germplasm, because of their potential use for fruit, ornamental and medicinal purposes. We evaluated genetic diversity, using RAPD markers, of 32 genotypes of Passiflora cincinnata collected from the wild in the region of Vitória da Conquista, Bahia, Brazil. Thirteen primers generated 95 polymorphic markers and only one monomorphic marker. The mean genetic distance between the genotypes estimated by the complement of the Dice index was 0.51 (ranging from 0.20-0.85), and genotype grouping based on the UPGMA algorithm showed wide variability among the genotypes. This type of information contributes to identification and conservation of the biodiversity of this species and for the identification of pairs of divergent individuals for maximum exploitation of existing variability.     

Assessment of genetic diversity within and among germplasm accessions in cultivated sorghum using microsatellite markers

Microsatellite markers are increasingly being used in crop plants to discriminate among genotypes and as tools in marker-assisted selection. Here we evaluated the use of microsatellite markers to quantify the genetic diversity within as well as among accessions sampled from the world germplasm collection of sorghum. Considerable variation was found at the five microsatellite loci analysed, with an average number of alleles per locus equal to 2.4 within accessions and 19.2 in the overall sample of 25 accessions. The collection of sorghum appeared highly structured genetically with about 70% of the total genetic diversity occurring among accessions. However, differentiation among morphologically defined races of sorghum, or among geographic origins, accounted for less than 15% of the total genetic diversity. Our results are in global agreement with those obtained previously with allozyme markers. We were also able to show that microsatellite data are useful in identifying individual accessions with a high relative contribution to the overall allelic diversity of the collection. Received: 10 August 1999 / Accepted: 27 August 1999     

Diversification of indigenous gene- pool by using exotic germplasm in lentil (Lens culinaris Medikus subsp. culinaris)

Genetic diversity was studied among 21 accessions of lentil using SSR markers and morphological traits in order to assess the diversification of Indian gene-pool of lentil through introgression of exotic genes and introduction of germplasm. Among these , 16 genotypes either had ‘Precoz’ gene, an Argentine line in their pedigree or genes from introduced lines from ICARDA. Sixty five SSR markers and eight phenotypic traits were used to analyse the level of genetic diversity in these genotypes. Forty three SSR markers (66 %) were polymorphic and generated a total of 177 alleles with an average of 4.1 alleles per SSR marker. Alleles per marker ranged from 2 to 6. The polymorphic information content ranged 0.33 to 0.80 with an average of 0.57, suggesting that SSR markers are highly polymorphic among the studied genotypes. Genetic dissimilarity based a dendrogram grouped these accessions into two main clusters (cluster I and cluster II) and it ranged 33 % to 71 %, suggesting high level of genetic diversity among the genotypes. First three components of PCA based morphological traits explained higher variance (95.6 %) compared to PCA components based on SSR markers (42.7 %) of total genetic variance. Thus, more diversity was observed for morphological traits and genotypes in each cluster and sub-cluster showed a range of variability for seed size, earliness, pods/plant and plant height. Molecular and phenotypic diversity analysis thus suggested that use of germplasm of exotic lines have diversified the genetic base of lentil germplasm in India. This diversified gene-pool will be very useful in the development of improved varieties of lentil in order to address the effect of climate change, to adapt in new cropping systems niches such as mixed cropping, relay cropping, etc. and to meet consumers’ preference.     

Molecular characterization and genetic diversity analysis of soybean (Glycine max (L.) Merr.) germplasm accessions in India

Molecular characterization and genetic diversity among 82 soybean accessions was carried out by using 44 simple sequence repeat (SSR) markers. Of the 44 SSR markers used, 40 markers were found polymorphic among 82 soybean accessions. These 40 polymorphic markers produced a total of 119 alleles, of which five were unique alleles and four alleles were rare. The allele number for each SSR locus varied between two to four with an average of 2.97 alleles per marker. Polymorphic information content values of SSRs ranged from 0.101 to 0.742 with an average of 0.477. Jaccard’s similarity coefficient was employed to study the molecular diversity of 82 soybean accessions. The pairwise genetic similarity among 82 soybean accessions varied from 0.28 to 0.90. The dendrogram constructed based on genetic similarities among 82 soybean accessions identified three major clusters. The majority of genotypes including four improved cultivars were grouped in a single subcluster IIIa of cluster III, indicating high genetic resemblance among soybean germplasm collection in India.

Electronic supplementary material

The online version of this article (doi:10.1007/s12298-014-0266-y) contains supplementary material, which is available to authorized users.     

Evaluation of SSR Markers for the Assessment of Genetic Diversity and Fingerprinting of Gossypium hirsutum Accessions

A total 177 simple sequence repeat (SSR) markers were screened using a set of 47 Upland cotton genotypes comprising 14 commercial varieties, 14 germplasm accessions and 19 advanced breeding lines to identify informative markers for genetic diversity assessment and fingerprinting in G. hirsutum. Only 21% (381177) of SSR markers tested showed polymorphism with a mean of 2.18 alleles per locus and with average polymorphism information content (PIC) of 0.32. The SSR markers revealed a Jaccard’ similarity coefficient ranging between 0.43 and 0.89, with an average of 0.67 among accessions. Cluster analysis using unweighted pair group method with arithmetic averages (UPGMA) and principal component analysis (PCA) indicated that majority of the genotypes were very closely related. All the 47 genotypes showed heterorygosity for at least one of the SSR loci. We discovered 19 rare and 6 unique alleles among the tested genotypes of cotton. Fingerprint based on all the 38 loci revealed a probability of identical match by chance of 3.98x10. A set of ten SSR markers was identified which could distinguish all the 47 genotypes with a moderate probability of identical match by chance (X?_D ⁿ = 0.01).     

Molecular analysis of introgressive breeding in coffee (Coffea arabica L.)

Nineteen arabica coffee introgression lines (BC₁F₄) and two accessions derived from a spontaneous interspecific cross (i.e. Timor Hybrid) between Coffea arabica (2n=4x=44) and C. canephora (2n=2x=22) were analysed for the introgression of C. canephora genetic material. The Timor Hybrid-derived genotypes were evaluated by AFLP, using 42 different primer combinations, and compared to 23 accessions of C. arabica and 8 accessions of C. canephora. A total of 1062 polymorphic fragments were scored among the 52 accessions analysed. One hundred and seventy-eight markers consisting of 109 additional bands (i.e. introgressed markers) and 69 missing bands distinguished the group composed of the Timor Hybrid-derived genotypes from the accessions of C. arabica. AFLP therefore seemed to be an extremely efficient technique for DNA marker generation in coffee as well as for the detection of introgression in C. arabica. The genetic diversity observed in the Timor Hybrid-derived genotypes appeared to be approximately double that in C. arabica. Although representing only a small proportion of the genetic diversity available in C. canephora, the Timor Hybrid obviously constitutes a considerable source of genetic diversity for arabica breeding. Analysis of genetic relationships among the Timor Hybrid-derived genotypes suggested that introgression was not restricted to chromosome substitution but also involved chromosome recombinations. Furthermore, the Timor Hybrid-derived genotypes varied considerably in the number of AFLP markers attributable to introgression. In this way, the introgressed markers identified in the analysed arabica coffee introgressed genotypes were estimated to represent from 9% to 29% of the C. canephora genome. Nevertheless, the amount of alien genetic material in the introgression arabica lines remains substantial and should justify the development of adapted breeding strategies. Received: 2 February 1999 / Accepted: 12 May 1999     

Genetic characterization of an elite coffee germplasm assessed by gSSR and EST-SSR markers

Coffee is one of the main agrifood commodities traded worldwide. In 2009, coffee accounted for 6.1% of the value of Brazilian agricultural production, generating a revenue of US$6 billion. Despite the importance of coffee production in Brazil, it is supported by a narrow genetic base, with few accessions. Molecular differentiation and diversity of a coffee breeding program were assessed with gSSR and EST-SSR markers. The study comprised 24 coffee accessions according to their genetic origin: arabica accessions (six traditional genotypes of C. arabica), resistant arabica (six leaf rust-resistant C. arabica genotypes with introgression of Híbrido de Timor), robusta (five C. canephora genotypes), Híbrido de Timor (three C. arabica x C. canephora), triploids (three C. arabica x C. racemosa), and racemosa (one C. racemosa). Allele and polymorphism analysis, AMOVA, the Student t-test, Jaccard's dissimilarity coefficient, cluster analysis, correlation of genetic distances, and discriminant analysis, were performed. EST-SSR markers gave 25 exclusive alleles per genetic group, while gSSR showed 47, which will be useful for differentiating accessions and for fingerprinting varieties. The gSSR markers detected a higher percentage of polymorphism among (35% higher on average) and within (42.9% higher on average) the genetic groups, compared to EST-SSR markers. The highest percentage of polymorphism within the genetic groups was found with gSSR markers for robusta (89.2%) and for resistant arabica (39.5%). It was possible to differentiate all genotypes including the arabica-related accessions. Nevertheless, combined use of gSSR and EST-SSR markers is recommended for coffee molecular characterization, because EST-SSRs can provide complementary information.     

普通小麦Genomic-SSR和EST-SSR分子标记遗传差异及其与系谱遗传距离的比较研究

采用Genomic-SSR和EST—SSR标记技术,对来自我国北方冬麦区的18份普通小麦品种(系)的遗传多样性进行了探讨,并与系谱遗传距离进行了比较分析。研究发现,平均每个Genomic—SSR检测到的等位基因数为3．34个,明显高于EST-SSR的2．31个。遗传距离(GD)计算结果显示,18个小麦基因型之间的EST—SSR平均遗传距离较小,仅为0．3996,低于Genomic—SSR的GD平均值0．5458。尽管EST-SSR揭示出的多态性明显低于Genomic-SSR,但系谱分析和聚类结果均表明,与Genomic—SSR相比,EST—SSR标记能更准确地反映出不同小麦基因型之间的遗传和亲缘关系。据此可以认为,EST—SSR是评价小麦遗传多样性的一种理想标记形式。研究还证实,一个骨干亲本与由其衍生出来的品种(系)之间的遗传差异一般较小,并对拓宽普通小麦遗传基础的策略和方法进行了讨论。     

Joint analysis of phenotypic and molecular diversity provides new insights on the genetic variability of the Brazilian physic nut germplasm bank

The genetic variability of the Brazilian physic nut (Jatropha curcas) germplasm bank (117 accessions) was assessed using a combination of phenotypic and molecular data. The joint dissimilarity matrix showed moderate correlation with the original matrices of phenotypic and molecular data. However, the correlation between the phenotypic dissimilarity matrix and the genotypic dissimilarity matrix was low. This finding indicated that molecular markers (RAPD and SSR) did not adequately sample the genomic regions that were relevant for phenotypic differentiation of the accessions. The dissimilarity values of the joint dissimilarity matrix were used to measure phenotypic + molecular diversity. This diversity varied from 0 to 1.29 among the 117 accessions, with an average dissimilarity among genotypes of 0.51. Joint analysis of phenotypic and molecular diversity indicated that the genetic diversity of the physic nut germplasm was 156% and 64% higher than the diversity estimated from phenotypic and molecular data, respectively. These results show that Jatropha genetic variability in Brazil is not as limited as previously thought.     

Molecular characterization of the wild relatives of wheat using CAAT-box derived polymorphism

A molecular assessment of genetic diversity was performed on a set of 228 selected accessions belonging to the different Aegilops and Triticum species using CAAT-box derived polymorphism (CBDP) markers. Fifteen CBDP primers generated 141 polymorphic fragments with an average of 9.40 per primer. The average of polymorphic information content and resolving power revealed a high efficiency of CBDP markers in analyzing genetic diversity among different wheat genotypes. The diversity indexes including polymorphic loci percent, number of observed and effective alleles, Shannon’s index and gene diversity among different populations were 76.24%, 1.67, 1.49, 0.42 and 0.28, respectively. These essentially coincided with the analysis of molecular variance results, indicating that 86, 68, and 59.46% of genetic variation were found within two Aegilops and Triticum genera and their populations, respectively. Genetic relationships inferred from cluster analysis was matched with STRUCTURE analysis, disclosing the accessions were grouped based on their genomic constitution. Furthermore, these results were confirmed by principal coordinate analysis (PCoA). Taken together, our results suggest that CBDP markers will be useful for genetic diversity assessment in the domesticated and wild relatives of wheat.     

Evaluation of genetic diversity in jackfruit (Artocarpus heterophyllus Lam.) based on amplified fragment length polymorphism markers

Artocarpus heterophyllus Lam., commonly called jackfruit, is a medium-sized evergreen tree that bears high yields of the largest known edible fruit. Yet, it has been little explored commercially due to wide variation in fruit quality. The genetic diversity and genetic relatedness of 50 jackfruit accessions were studied using amplified fragment length polymorphism markers. Of 16 primer pairs evaluated, eight were selected for screening of genotypes based on the number and quality of polymorphic fragments produced. These primer combinations produced 5976 bands, 1267 (22%) of which were polymorphic. Among the jackfruit accessions, the similarity coefficient ranged from 0.137 to 0.978; the accessions also shared a large number of monomorphic fragments (78%). Cluster analysis and principal component analysis grouped all jackfruit genotypes into three major clusters. Cluster I included the genotypes grown in a jackfruit region of Karnataka, called Tamaka, with very dry conditions; cluster II contained the genotypes collected from locations having medium to heavy rainfall in Karnataka; cluster III grouped the genotypes in distant locations with different environmental conditions. Strong coincidence of these amplified fragment length polymorphism-based groupings with geographical localities as well as morphological characters was observed. We found moderate genetic diversity in these jackfruit accessions. This information should be useful for tree breeding programs, as part of our effort to popularize jackfruit as a commercial crop.     

Assessment of genomic imprinting of SLC38A4, NNAT, NAP1L5, and H19 in cattle

Background

Sesame is an important oil crop in tropical and subtropical areas. Despite its nutritional value and historic and cultural importance, the research on sesame has been scarce, particularly as far as its genetic diversity is concerned. The aims of the present study were to clarify genetic relationships among 32 sesame accessions from the Venezuelan Germplasm Collection, which represents genotypes from five diversity centres (India, Africa, China-Korea-Japan, Central Asia and Western Asia), and to determine the association between geographical origin and genetic diversity using amplified fragment length polymorphism (AFLP).

Results

Large genetic variability was found within the germplasm collection. A total of 457 AFLP markers were recorded, 93 % of them being polymorphic. The Jaccard similarity coefficient ranged from 0.38 to 0.85 between pairs of accessions. The UPGMA dendrogram grouped 25 of 32 accessions in two robust clusters, but it has not revealed any association between genotype and geographical origin. Indian, African and Chinese-Korean-Japanese accessions were distributed throughout the dendrogram. A similar pattern was obtained using principal coordinates analysis. Genetic diversity studies considering five groups of accessions according to the geographic origin detected that only 20 % of the total diversity was due to diversity among groups using Nei's coefficient of population differentiation. Similarly, only 5% of the total diversity was attributed to differences among groups by the analysis of molecular variance (AMOVA). This small but significant difference was explained by the fact that the Central Asia group had a lower genetic variation than the other diversity centres studied.

Conclusion

We found that our sesame collection was genetically very variable and did not show an association between geographical origin and AFLP patterns. This result suggests that there was considerable gene flow among diversity centres. Future germplasm collection strategies should focus on sampling a large number of plants. Covering many diversity centres is less important because each centre represents a major part of the total diversity in sesame, Central Asia centre being the only exception. The same recommendation holds for the choice of parents for segregant populations used in breeding projects. The traditional assumption that selecting genotypes of different geographical origin will maximize the diversity available to a breeding project does not hold in sesame.     

Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated peanut (<Emphasis Type="Italic">Arachis</Emphasis><Emphasis Type="Italic">hypogaea</Emphasis> L.) genotypes

Cultivated peanut possesses an extremely narrow genetic basis. Polymorphism is considerably difficult to identify with the use of conventional biochemical and molecular tools. For the purpose of obtaining considerable DNA polymorphisms and fingerprinting cultivated peanut genotypes in a convenient manner, start codon targeted polymorphism technique was used to study genetic diversity and relatedness among 20 accessions of four major botanical varieties of peanut. Of 36 primers screened, 18 primers could produce unambiguous and reproducible bands. All 18 primers generated a total of 157 fragments, with a mean of 8.72 ranging from 4 to 17 per primer. Of 157 bands, 60 (38.22%) were polymorphic. One to seven polymorphic bands were amplified per primer, with 3.33 polymorphic bands on average. Polymorphism per primer ranged from 14.29 to 66.67%, with an average of 36.76%. The results revealed that not all accessions of the same variety were grouped together and high genetic similarity was detected among the tested genotypes based on cluster analysis and genetic distance analysis, respectively. Further, accession-specific markers were observed in several accessions. All these results demonstrated the following: (1) start codon targeted polymorphism technique can be utilized to identify DNA polymorphisms and fingerprint cultivars in domesticated peanut, and (2) it possesses considerable potential for studying genetic diversity and relationships among peanut accessions.     

Using microsatellites,isozymes and AFLPs to evaluate genetic diversity and redundancy in the cassava core collection and to assess the usefulness of DNA-based markers to maintain germplasm collections

The cassava core collection was selected to represent, with minimum repetitiveness, the potential genetic diversity of the crop. The core (630 accessions) was chosen from the base collection (over 5500 accessions) on the basis of diversity of origin (country and geographic), morphology, isozyme patterns and specific agronomic criteria. To asses the genetic diversity of the core, 521 accessions were typed with four microsatellite loci. Allele diversity and frequency, and size variance of dinucleotide repeats (Rst statistic) were estimated. Microsatellite allele numbers and frequencies varied among countries: Colombia and Brazil had the largest number of different alleles across all loci. Mexico also had a high number, ranking fifth after Peru, Costa Rica and Venezuela (which tied). Unique alleles were present in accessions from Brazil, Colombia, Guatemala, Venezuela and Paraguay. A small number (1.34%) of potential duplicates were identified through isozyme and AFLP profiles. Thus, the present results indicated that traditional markers have been highly effective at selecting unique genotypes for the core. Future selections of cassava germplasm sets can be aided by DNA-based markers to ensure genetically representative, non-redundant samples. This revised version was published online in June 2006 with corrections to the Cover Date.     

Nucleotide-binding site (NBS) profiling of genetic diversity in durum wheat.

Molecular markers are effective tools to investigate genetic diversity for resistance to pathogens. NBS (nucleotide-binding site) profiling is a PCR (polymerase chain reaction)-based approach to studying genetic variability that specifically targets chromosome regions containing R-genes and R-gene analogues. We used NBS profiling to measure genetic diversity among 58 accessions of durum wheat. Mean polymorphism rates detected using MseI and AluI as restriction enzymes were 34% and 22%, respectively. Mean number of polymorphisms per enzyme-primer combination was equal to 23.8 +/- 5.9, ranging from 13 to 31 polymorphic bands. In total, 96 markers over 190 indicated a good capacity to discriminate between accessions (the polymorphic index content ranging from 0.30 to 0.50). The results obtained with NBS profiling were compared with simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) data of the same set of accessions. The genetic distances computed with 190 NBS profiling markers were in close agreement with those obtained with AFLP and SSR markers (r = 0.73 and 0.76, respectively). Our results indicate that NBS profiling provides an effective means to investigate genetic diversity in durum wheat.     

Genetic characterization of Iranian safflower (Carthamus tinctorius) using inter simple sequence repeats (ISSR) markers

Safflower (Carthamus tinctorious L.) is valued as a source of high quality vegetable oil. 20 ISSR primers were used to assess the genetic diversity of 18 accessions of safflower collected from different geographical regions of Iran. The ISSR primers combinations revealed 57.6 % polymorphism, among 338 genetic loci amplified from the accessions. The sum of effective number of alleles and observed number of alleles were 29.76 and 36.77, respectively. To understand genetic relationships among these cultivars, Jacquards’ similarity coefficient and UPGMA clustering algorithm were applied to the ISSR marker data set. ISSR markers grouped accessions into two main clusters and four sub clusters. Also, the principal coordinate analysis (PCoA) supported the cluster analysis results. The results showed these genotypes have high genetic diversity, and can be used for alternative safflower breeding program.     

Assessment of genetic variation and differentiation of hop genotypes by microsatellite and AFLP markers.

Microsatellites have many desirable marker properties and have been increasingly used in crop plants in genetic diversity studies. Here we report on the characterisation of microsatellite markers and on their use for the determination of genetic identities and the assessment of genetic variability among accessions from a germplasm collection of hop. Thirty-two polymorphic alleles were found in the 55 diploid genotypes, with an average number of eight alleles (3.4 effective alleles) for four microsatellite loci. Calculated polymorphic information content values classified three loci as informative markers and two loci as suitable for mapping. The average observed heterozygosity was 0.7 and the common probability of identical genotypes was 3.271 x 10(-4). An additional locus, amplified by one primer pair, was confirmed by segregation analysis of two crosses. The locus discovered was heterozygous, with a null allele in the segregating population. The same range of alleles was detected in nine triploid and five tetraploid hop genotypes. Cultivar heterozygosity varied among all 69 accessions, with only one cultivar being homozygous at four loci. Microsatellite allele polymorphisms distinguished 81% of all genotypes; the same allelic profile was found mainly in clonally selected cultivars. Cultivar-specific alleles were found in some genotypes, as well as a specific distribution of alleles in geographically distinct hop germplasms. The genetic relationship among 41 hop accessions was compared on the basis of microsatellite and AFLP polymorphisms. Genetic similarity dendrograms showed low correlation between the two marker systems. The microsatellite dendrogram grouped genetically related accessions reasonably well, while the AFLP dendrogram showed good clustering of closely related accessions and, additionally, separated two geographically distinct hop germplasms. The results of microsatellite and AFLP analysis are discussed from the point of view of the applicability of the two marker systems for different aspects of germplasm evaluation.     

Influence of number and map distribution of AFLP markers on similarity estimates in carrot

When genetic diversity among organisms was measured with molecular markers, the question of genome coverage was currently stressed out. In order to check if well-distributed, mapped AFLP markers were more efficient in assessing varietal identification of carrot accessions than randomly chosen markers, nine closely related genotypes were analysed. A software was developed to realise 1,000 random choices of 20 to 70 mapped or unmapped markers, offering numerous genome coverages. We statistically showed that taking into account marker position does not provide a better estimation of genetic distances. Moreover, in the case of carrot, we concluded that 60 AFLP markers offer the best compromise between the level of precision and minimal expense.