Islands and streams: clusters and gene flow in wild barley populations from the Levant

The domestication of plants frequently results in a high level of genetic differentiation between domesticated plants and their wild progenitors. This process is counteracted by gene flow between wild and domesticated plants because they are usually able to inter‐mate and to exchange genes. We investigated the extent of gene flow between wild barley Hordeum spontaneum and cultivated barley Hordeum vulgare, and its effect on population structure in wild barley by analysing a collection of 896 wild barley accessions (Barley1K) from Israel and all available Israeli H. vulgare accessions from the Israeli gene bank. We compared the performance of simple sequence repeats (SSR) and single nucleotide polymorphisms (SNP) marker data genotyped over a core collection in estimating population parameters. Estimates of gene flow rates with SSR markers indicated a high level of introgression from cultivated barley into wild barley. After removing accessions from the wild barley sample that were recently admixed with cultivated barley, the inference of population structure improved significantly. Both SSR and SNP markers showed that the genetic population structure of wild barley in Israel corresponds to the three major ecogeographic regions: the coast, the Mediterranean north and the deserts in the Jordan valley and the South. Gene flow rates were estimated to be higher from north to south than in the opposite direction. As has been observed in other crop species, there is a significant exchange of alleles between the wild species and domesticated varieties that needs to be accounted for in the population genetic analysis of domestication.     

A comparison of genetic variation among wild and cultivated Morus Species (Moraceae: Morus) as revealed by ISSR and SSR markers

In this study, inter-simple sequence repeats (ISSR) ans simple sequence repeat (SSR) markers were used to investigate genetic diversity of 27 mulberry accessions including 19 cultivated accessions (six M. multicaulis, three M. alba, two M. atropurpurea, two M. bombycis, one M. australis, two M. rotundiloba, one M. alba var. pendula, one M. alba var. macrophylla, and one M. alba var. venose) and 8 wild accessions (two M. cathayana, two M. laevigata, two M. wittiorum, one M. nigra and one M. mongolica). ISSRs and SSRs were compared in terms of their informativeness and efficiency in a study of genetic diversity and relationships among 27 mulberry genotypes. SSRs presented a higher level of polymorphism and greater information content. All index values of genetic diversity both markers analyzed using Popgene 32 software indicated that within wild species had higher genetic diversity than within cultivated species. Cultivation may caused the lose of genetic diversity of mulberry compared with wild species revealed by ISSR and SSR markers. The mean genetic similarity coefficients among all mulberry genotypes ascribed by ISSR and SSR matrices were 0.7677 and 0.6131, respectively. For all markers a high similarity in dendrogram topologies was obtained although some differences were observed. Cluster analysis of ISSR and SSR using UPGMA method revealed that the wild species are genetically distant from the domesticated species studied here. The correlation coefficients of similarity were statistically significant for both marker systems used. Principal coordinates analysis (PCA) for ISSR and SSR data also supports their UPGMA clustering. These results have an important implication for mulberry germplasm characterization, improvement, molecular systematics and conservation.     

RAPD and ISSR fingerprints as useful genetic markers for analysis of genetic diversity, varietal identification, and phylogenetic relationships in peanut (Arachis hypogaea) cultivars and wild species.

Abstract: Twenty-one random and 29 SSR primers were used to assess genetic variation and interrelationships among subspecies and botanical varieties of cultivated peanut, Arachis hypogaea (2n = 4x = 40), and phylogenetic relationships among cultivated peanut and wild species of the genus Arachis. In contrast with the previous generalization that peanut accessions lack genetic variation, both random and SSR primers revealed 42.7 and 54.4% polymorphism, respectively, among 220 and 124 genetic loci amplified from 13 accessions. Moreover, the dendrograms based on RAPD, ISSR, and RAPD + ISSR data precisely organized the five botanical varieties of the two subspecies into five clusters. One SSR primer was identified that could distinguish all the accessions analysed within a variety. Although the polymorphic index content varied from 0.1 to 0.5 for both ISSR and RAPD markers, primer index values were substantially higher for RAPD primers (0.35-4.65) than for SSR primers (0.35-1.73). It was possible to identify accessions, particularly those of divergent origins, by RAPD and (or) ISSR fingerprints. Based on these results, marker-based genetic improvement in A. hypogaea appears possible. None of the 486 RAPD and 330 ISSR amplification products were found to be commonly shared among 13 species of section Arachis and one species each of sections Heteranthae, Rhizomatosae, and Procumbentes. Dendrograms constructed from RAPD, ISSR, and RAPD + ISSR data showed overall similar topologies. They could be resolved into four groups corresponding to the species grouped in four taxonomic sections. The present results strongly support the view that Arachis monticola (2n = 4x = 40) and A. hypogaea are very closely related, and indicate that A. villosa and A. ipaensis are the diploid wild progenitors of these tetraploid species.     

Genetic Diversity and Identity of Chinese Loquat Cultivars/Accessions (<Emphasis Type="Italic">Eriobotrya japonica</Emphasis>) Using Apple SSR Markers

Loquat (Eriobotrya japonica) is an underutilized fruit crop that originated in China and for which only a small number of molecular markers are available. This number can be increased by identifying apple SSRs that are transferable to loquat cultivars/accessions to provide new insight into the level of genetic diversity within loquat and synteny with apple. We evaluated 71 apple SSR markers distributed across 17 linkage groups, and identified 39 SSRs transferable to loquat. Testing 54 loquat accessions, from Japan, Spain, four provinces in China, and two wild species gave a total of 155 different alleles with a mean value of 3.38 per locus. The mean effective number of alleles was 2.21, and the mean observed heterozygosity was 0.47. These values indicate a high degree of genetic diversity in the set of Chinese loquat accessions analyzed. Unweighted pair-group method analysis based on simple matching coefficent clustered the accessions into two groups, cultivated and wild loquat. The cultivated loquat can be subdivided into three subgroups which generally reflect their geographic origin in China. The Spanish cultivars clustered with those of the Jiangsu and Zhejiang provinces. A core set of five SSR markers could distinguish most accessions.     

Genetic diversity of Triticum turgidum L. based on microsatellite markers

Using microsatellite (SSR) markers, the genetic diversity and genetic relationships among 48 Triticum turgidum L. accessions, including 30 Triticum turgidum L. ssp. turgidum, 7 Triticum turgidum L. ssp. durum, 4 Triticum turgidum L. ssp. carthlicum, 3 Triticum turgidum L. ssp. paleocolchicum, 2 Triticum turgidum L. ssp. turanicum, and 2 Triticum turgidum L. ssp. polonicum accessions, were investigated. A total of 97 alleles were detected at 16 SSR loci. At each locus, the number of alleles ranged from two to fourteen, with an average of 6.1. The genetic similarity (GS) value ranged from 0.20 to 0.92, with the mean of 0.59. In cluster analysis, it was found the 48 Triticum turgidum L. accessions could be distinguished easily by SSR markers, whereas the six subspecies taxonomic entities of T. turgidum L. could not differentiate with each other, indicating that the morphological differences present among the six subspecies could not be reflected by the SSR markers. These results suggested that SSR markers had superiority in detecting the genetic diversity of T. turgidum L., while they were not good for studies of the phylogenic relationships among the subspecies of T. turgidum L. The text was submitted by the authors in English.     

Genetic differentiation of wild and cultivated Lens based on molecular markers

Genetic diversity among 83 lentil genotypes including 23 wild types, 19 indigenous varieties, 5 exotic lines and 36 advanced breeding lines was studied using molecular markers. A total of 112 amplicons were produced using 15 RAPD and 8 SSR markers. Dendrogram based on Jaccard similarity coefficient and UPGMA analysis revealed two major clusters and one minor cluster. Cluster I comprised 21 wild accessions of L. orientalis and 1 L. ervoides subspecies. Nineteen Indian varieties grouped together in subcluster IIA indicating their narrow genetic base. Subcluster IIB consisted of 41 genotypes including 5 exotic and 36 advanced breeding lines mainly derived from exotic genotypes. The narrow genetic base of released cultivars and germplasm lines emphasized the need for broadening of genetic base of breeding material using exotic collections and wild species to ascertain genetic improvement upon existing cultivars.     

Microsatellite variation in <Emphasis Type="Italic">Avena sterilis</Emphasis> oat germplasm

The Avena sterilis L. collection in the Plant Gene Resources of Canada (PGRC) consists of 11,235 accessions originating from 27 countries and is an invaluable source of genetic variation for genetic improvement of oats, but it has been inadequately characterized, particularly using molecular techniques. More than 35 accessions have been identified with genes for resistance to oat crown and stem rusts, but little is known about their comparative genetic diversity. This study attempted to characterize a structured sample of 369 accessions representing 26 countries and two specific groups with Puccinia coronata avenae (Pc) and Puccinia graminis avenae (Pg) resistance genes using microsatellite (SSR) markers. Screening of 230 SSR primer pairs developed from other major crop species yielded 26 informative primer pairs for this characterization. These 26 primer pairs were applied to screen all the samples and 125 detected alleles were scored for each accession. Analyses of the SSR data showed the effectiveness of the stratified sampling applied in capturing country-wise SSR variation. The frequencies of polymorphic alleles ranged from 0.01 to 0.99 and averaged 0.28. More than 90% of the SSR variation resided within accessions of a country. Accessions from Greece, Liberia, and Italy were genetically most diverse, while accessions from Egypt, Georgia, Ethiopia, Gibraltar, and Kenya were most distinct. Seven major clusters were identified, each consisting of accessions from multiple countries and specific groups, and these clusters were not well congruent with geographic origins. Accessions with Pc and Pg genes had similar levels of SSR variation, did not appear to cluster together, and were not associated with the other representative accessions. These SSR patterns are significant for understanding the progenitor species of cultivated oat, managing A. sterilis germplasm, and exploring new sources of genes for oat improvement.     

Assessment of genetic diversity and relationship among a collection of US sweet sorghum germplasm by SSR markers

Sweet sorghum (Sorghum bicolor L.) is a type of cultivated sorghums and has been recognized widely as potential alternative source of bio-fuel because of its high fermentable sugar content in the stalk. A substantial variation of sugar content and related traits is known to exist in US sweet sorghum. The objectives of the study were to assess the genetic diversity and relationship among the US sweet sorghum cultivars and lines using SSR markers and to examine the genetic variability within sweet sorghum accessions for sugar content. Sixty-eight sweet sorghum and four grain sorghum cultivars and lines were genotyped with 41 SSR markers that generated 132 alleles with an average of 3.22 alleles per locus. Polymorphism information content (PIC) value, a measure of gene diversity, was 0.40 with a range of 0.03–0.87. The genetic similarity co-efficient was estimated based on the segregation of the 132 SSR alleles. Clustering analysis based on the genetic similarity (GS) grouped the 72 sorghum accessions into 10 distinct clusters. Grouping based on clustering analysis was in good agreement with available pedigree and genetic background information. The study has revealed the genetic relationship of cultivars with unknown parentage to those with known parentage. A number of diverse pairs of sweet sorghum accessions were identified which were polymorphic at many SSR loci and significantly different for sugar content as well. Information generated from this study can be used to select parents for hybrid development to maximize the sugar content and total biomass, and development of segregating populations to map genes controlling sugar content in sweet sorghum.     

Characterization and utilization of microsatellites in the <Emphasis Type="Italic">Coffea canephora</Emphasis> genome to assess genetic association between wild species in Kenya and cultivated coffee

Coffee is an important beverage crop in the world and has a significant contribution to Kenya’s economy. Here, we analyzed the genome-wide distribution of microsatellites in the Coffea canephora genome. A total of 159,041 SSRs were identified, with an overall density of 308 SSRs per Mb. Tetra-nucleotide repeats are the most abundant, accounting for 32 % of the total SSRs. AT-rich motifs are dominant across all SSR repeat units, while GC-rich motifs were generally rare. A set of 100 SSRs was selected to amplify 96 coffee accessions, including 10 wild accessions collected from Mt. Marsabit (Kenya). Of these SSRs, 33 % generated clear polymorphic bands among all tested accessions, with an average of 3.9 alleles per SSR locus. Wild coffee species from Mt. Marsabit showed a close genetic similarity with cultivated accessions in Kenya, suggesting that the wild species in Mt. Marsabit played an important role in the domestication of cultivated coffee in Kenya. Significantly low pairwise genetic divergence was observed between cultivated and wild accessions in Kenya, suggesting a relatively narrow level of genetic basis among coffee germplasm in Kenya. In addition, cultivated and wild coffee accessions in Kenya show a great divergence from those in other countries. Our results not only provide molecular tools for genetic studies in coffee but are also helpful for conservation and coffee breeding programs in Kenya.     

Genetic diversity of cultivated and wild-type peanuts evaluated with M13-tailed SSR markers and sequencing

Thirty-one genomic SSR markers with a M13 tail attached were used to assess the genetic diversity of the peanut mini core collection. The M13-tailed method was effective in discriminating almost all the cultivated and wild accessions. A total of 477 alleles were detected with an average of 15.4 alleles per locus. The mean polymorphic information content (PIC) score was 0.687. The cultivated peanut (Arachis hypogaea L.) mini core produced a total of 312 alleles with an average of 10.1 alleles per locus. A neighbour-joining tree was constructed to determine the interspecific and intraspecific relationships in this data set. Almost all the peanut accessions in this data set classified into subspecies and botanical varieties such as subsp. hypogaea var. hypogaea, subsp. fastigiata var. fastigiata, and subsp. fastigiata var. vulgaris clustered with other accessions with the same classification, which lends further support to their current taxonomy. Alleles were sequenced from one of the SSR markers used in this study, which demonstrated that the repeat motif is conserved when transferring the marker across species borders. This study allowed the examination of the diversity and phylogenetic relationships in the peanut mini core which has not been previously reported.     

Genetic variation and covariation in a population of tetraploid Dactylis L. accessions

Summary Efficient utilization of divergent germ plasm sources in breeding cultivated Dactylis glomerata L. ssp. glomerata Domin depends on knowledge of quantitative variation within and among accessions. This study was undertaken to quantify variation and covariation for forage yield, maturity, disease reaction, and ground cover within a population of tetraploid Dactylis accessions. Variation was observed among families within the population for each variable. Most genetic variation (73%–93% of the family sums of squares) was within country sources or within accessions. Thus, country boundaries, which are traditionally important factors used in defining limits of plant exploration expeditions, have limited expected use in targeting future exploration for specific sources of high yield, disease resistance, or ground cover. Maturity was the exception to this; late-maturing accessions were identified as originating exclusively from the USSR. Some relationships among traits, such as that for yield and disease reaction, differed for accessions and cultivars. Several accessions and families within accessions were identified to have performance superior to most or all cultivars included in this study. Existing germ plasm from several countries was identified to have potential in breeding orchardgrass, while that from other countries appeared to have little or no potential in supplying germ plasm for hay production in humid-temperate environments.     

Genetic Diversity in Lens Species Revealed by EST and Genomic Simple Sequence Repeat Analysis

Low productivity of pilosae type lentils grown in South Asia is attributed to narrow genetic base of the released cultivars which results in susceptibility to biotic and abiotic stresses. For enhancement of productivity and production, broadening of genetic base is essentially required. The genetic base of released cultivars can be broadened by using diverse types including bold seeded and early maturing lentils from Mediterranean region and related wild species. Genetic diversity in eighty six accessions of three species of genus Lens was assessed based on twelve genomic and thirty one EST-SSR markers. The evaluated set of genotypes included diverse lentil varieties and advanced breeding lines from Indian programme, two early maturing ICARDA lines and five related wild subspecies/species endemic to the Mediterranean region. Genomic SSRs exhibited higher polymorphism in comparison to EST SSRs. GLLC 598 produced 5 alleles with highest gene diversity value of 0.80. Among the studied subspecies/species 43 SSRs detected maximum number of alleles in L. orientalis. Based on Nei’s genetic distance cultivated lentil L. culinaris subsp. culinaris was found to be close to its wild progenitor L. culinaris subsp. orientalis. The Prichard’s structure of 86 genotypes distinguished different subspecies/species. Higher variability was recorded among individuals within population than among populations.     

Features of SNP and SSR diversity in a set of ICARDA barley germplasm collection

Detection and utilization of genetic variation available in the germplasm collection for crop improvement have been the prime activities of breeders. Here a set of ICARDA barley germplasm collection comprising of 185 cultivated (Hordeum vulgare L.) and 38 wild (H. spontaneum L.) genotypes originated from 30 countries of four continents was genotyped with 68 single nucleotide polymorphism (SNP) and 45 microsatellite or simple sequence repeat (SSR) markers derived from genes (expressed sequence tags, ESTs). As two SNP markers provided 2 and 3 datapoints, a total of 71 SNPs were surveyed that yielded a total of 143 alleles. The number of SSR alleles per locus ranged from 3 to 22 with an average of 7.9 per marker. Average PIC (polymorphism information content) value for SSR and SNP markers were recorded as 0.63 and 0.38, respectively. Heterogeneity was recorded at both SNP and SSR loci in an average of 5.72 and 12.42% accessions, respectively. Genetic similarity matrices for SSR and SNP allelic data were highly correlated (r = 0.75, P < 0.005) and therefore allelic data for both markers were combined and analyzed for understanding the genetic relationships among the germplasm surveyed. Majority of clusters/subclusters were found to contain genotypes from the same geographic origins. While comparing the genetic diversity, the accessions coming from Middle East Asia and North East Asia showed more diversity as compared to that of other geographic regions. Majority of countries representing Africa, Middle East Asia, North East Asia and Arabian Peninsula included the genotypes that contained rare alleles. As expected, spontaneum accessions, as compared to vulgare accessions, showed a higher number of total alleles, higher number of alleles per locus, higher effective number of alleles and higher allelic richness and a higher number of rare alleles were observed. In summary, the examined ICARDA germplasm set showed ample natural genetic variation that can be harnessed for future breeding of barley as climate change and sustainability have become important throughout all growing areas of the world, drought/heat tolerance being the most important ones.     

Genetic variation and comparison of orchardgrass (Dactylis glomerata L.) cultivars and wild accessions as revealed by SSR markers

Orchardgrass is a highly variable, perennial forage grass that is cultivated throughout temperate and subtropical regions of the world. Despite its economic importance, the genetic relationship and distance among and within cultivars are largely unknown but would be of great interest for breeding programs. We investigated the molecular variation and structure of cultivar populations, compared the level of genetic diversity among cultivars (Baoxing, Anba, Bote, and Kaimo), subspecies (Dactylis glomerata ssp Woronowii) and advanced breeding line (YA02-116) to determine whether there is still sufficient genetic diversity within presently used cultivars for future breeding progress in China. Twenty individuals were analyzed from each of six accessions using SSR markers; 114 easily scored bands were generated from 15 SSR primer pairs, with an average of 7.6 alleles per locus. The polymorphic rate was 100% among the 120 individuals, reflecting a high degree of genetic diversity. Among the six accessions, the highest genetic diversity was observed in Kaimo (H = 0.2518; I = 0.3916; P = 87.3%) and 02-116 had a lower level of genetic diversity (H = 0.1806; I = 0.2788; P = 58.73%) compared with other cultivars tested. An of molecular variance revealed a much larger genetic variation within accessions (65%) than between them (35%). This observation suggests that these cultivars have potential for providing rich genetic resource for further breeding program. Furthermore, the study also indicated that Chinese orchardgrass breeding has involved strong selection for adaptation to forage production, which may result in restricted genetic base of orchardgrass cultivar.     

A comparative study of genetic relationships among the AA-genome<Emphasis Type="Italic"> Oryza</Emphasis> species using RAPD and SSR markers

In order to estimate genetic relationships of the AA-genome Oryza species, RAPD and SSR analyses were performed with 45 accessions, including 13 cultivated varieties (eight Oryza sativa and five Oryza glaberrima) and 32 wild accessions (nine Oryza rufipogon, seven Oryza nivara, three Oryza glumaepatula, four Oryza longistaminata, six Oryza barthii, and three Oryza meridionalis). A total of 181 clear and repeatable bands were amplified from 27 selected RAPD primers, and 101 alleles were detected from 29 SSR primer pairs. The dendrogram constructed using UPGMA from a genetic-similarity matrix based on the RAPD data supported the clustering of distinct five groups with a few exceptions: O. rufipogon/O. nivara/O. meridionalis, O. barthii/O. glaberrima, O. glumaepatula, O. sativa and O. longistaminata. The dendrogram based on the SSR analysis showed a more-complicated genetic variation pattern, but the O. longistaminata and O. barthii/O. glaberrima accessions were consistently separated from all other accessions, indicating significant differentiation of the African AA-genome Oryza species. For accessions in the O. rufipogon/O. nivara/O. sativa complex, it is apparent that geographical isolation has played an important role in differentiation of the Asian AA-genome Oryza taxa. It is also demonstrated from this study that both RAPD and SSR analyses are powerful methods for detecting polymorphisms among the different AA-genome Oryza accessions. However, the RAPD analysis provides a more-informative result in terms of the overall genetic relationships at the species level compared to the SSR analysis. The SSR analysis effectively reveals diminutive variation among accessions or individuals within the same species, given approximately the same number of primers or primer-pairs used in the studies.Communicated by Q. Zhang     

Genetic diversity assessment in greek Medicago truncatula genotypes using microsatellite markers

In this study we examined the genetic diversity and geographic scale of genotype distribution within the model legume species Medicago truncatula widely distributed in pasture and marginal agricultural lands in Greece and other Mediterranean countries. Thirty one Medicago truncatula and Medicago littorialis accessions were chosen on the basis of their geographical distributions and studied using 9 polymorphic simple sequence repeats (SSR) markers. The number of alleles per locus varied between 3 and 7. A total of 42 alleles were detected with a mean value of 4.66 alleles per locus. Geographic origin was not related with genotypic similarity among accessions. However, there were instances of close genetic relatedness between accessions from neighboring locations in a geographic compartment. In conclusion, the presented data revealed extensive M. truncatula genotype dispersal in Greece pointing to the significance of preserving local genetic resources in their natural environment.     

The pattern of genetic diversity of Guinea-race Sorghum bicolor (L.) Moench landraces as revealed with SSR markers

The Guinea-race of sorghum [Sorghum bicolor (L.) Moench] is a predominantly inbreeding, diploid cereal crop. It originated from West Africa and appears to have spread throughout Africa and South Asia, where it is now the dominant sorghum race, via ancient trade routes. To elucidate the genetic diversity and differentiation among Guinea-race sorghum landraces, we selected 100 accessions from the ICRISAT sorghum Guinea-race Core Collection and genotyped these using 21 simple sequence repeat (SSR) markers. The 21 SSR markers revealed a total of 123 alleles with an average Dice similarity coefficient of 0.37 across 4,950 pairs of accessions, with nearly 50% of the alleles being rare among the accessions analysed. Stratification of the accessions into 11 countries and five eco-regional groups confirmed earlier reports on the spread of Guinea-race sorghum across Africa and South Asia: most of the variation was found among the accessions from semi-arid and Sahelian Africa and the least among accessions from South Asia. In addition, accessions from South Asia most closely resembled those from southern and eastern Africa, supporting earlier suggestions that sorghum germplasm might have reached South Asia via ancient trade routes along the Arabian Sea coasts of eastern Africa, Arabia and South Asia. Stratification of the accessions according to their Snowden classification indicated clear genetic variation between margeritiferum, conspicuum and Roxburghii accessions, whereas the gambicum and guineënse accessions were genetically similar. The implications of these findings for sorghum Guinea-race plant breeding activities are discussed.     

Genetic diversity and differentiation of lotus (Nelumbo nucifera) accessions assessed by simple sequence repeats

Nelumbo nucifera (lotus) is a perennial aquatic crop of substantial economical and ecological importance. Currently, the evaluation of the genetic variation of lotus germplasm accessions using codominant simple sequence repeat (SSR) markers is significant, and it is essential for understanding the population structure of N. nucifera. Here we report the genetic diversity and differentiation of 92 N. nucifera accessions (82 cultivated varieties and 10 wild lotus) using 50 polymorphic SSR markers. A total of 195 alleles were detected, with an average of 3.9 alleles/locus. The mean polymorphic information content (PIC) and the mean expected heterozygosity were 0.43 and 0.50, respectively. The genetic relationships among accessions were estimated using an unweighted pair‐group method with arithmetic average (UPGMA) cluster and principal coordinate analysis (PCA). Both methods revealed that the lotus accessions from China and those from its adjacent Asian countries formed a single cluster, respectively. The cultivated varieties were correlated with their major characteristics in cultivation (the seed, rhizome and flower type) rather than their geographic distribution. On the basis of the Bayesian model‐based analyses, two genetically distinct groups (the seed lotus group and the rhizome lotus group) were generated, with a strong differentiation between them (F_ST = 0.57). The seed lotus group exhibited higher genetic diversity than did the rhizome lotus group. The results herein indicated that the current levels of genetic diversity and differentiation between the lotuses have been greatly influenced by artificial selection.     

Assessing genetic diversity in <Emphasis Type="Italic">Gossypium arboreum</Emphasis> L. cultivars using genomic and EST-derived microsatellites

The cultivated diploid, Gossypium arboreum L., (A genome) is an invaluable genetic resource for improving modern tetraploid cotton (G. hirsutum L. and G. barbadense L.) cultivars. The objective of this research is to select a set of informative and robust microsatellites for studying genetic relationships among accessions of geographically diverse G. arboreum cultivars. From more than 1,500 previously developed simple sequence repeat (SSR) markers, 115 genomic (BNL) and EST-derived (MUCS and MUSS) markers were used to evaluate the allelic diversity of a core panel of G. arboreum accessions. These SSR data enabled advanced genome analyses. A set of 25 SSRs were selected based both upon their high level of informativeness (PIC ≥ 0.50) and the production of clear PCR bands on agarose gels. Subsequently, 96 accessions representing a wide spectrum of diversity of G. arboreum cultivars were analyzed with these markers. The 25 SSR loci revealed 75 allelic variants (polymorphisms) ranging from 2 to 4 alleles per locus. The Neighborjoining (NJ) method, based on genetic dissimilarities, revealed that cultivars from geographically adjacent countries tend to cluster together. Outcomes of this research should be useful in decreasing redundancy of effort and in constructing a core collection of G. arboreum, important for efficient use of this genetic resource in cotton breeding.     

Microsatellite markers help to assess genetic diversity among Opuntia ficus indica cultivated genotypes and their relation with related species

Opuntia spp. belong to the Cactaceae family and are native to Central America. The most economically important species is O. ficus indica, cultivated both for fruits and cladodes. The genus includes other important edible species (from diploid to octoploid) that occur worldwide as either wild or cultivated species in many arid or semiarid areas (e.g., the Mediterranean region). Several accessions are cultivated in different growing regions, but little is known about their ancestries and levels of genetic diversity. The aim of this study was to investigate the level of intraspecific genetic diversity among O. ficus indica cultivated varieties and some related species. Specifically, six highly polymorphic simple sequence repeats (SSR) and two expressed sequence tag (EST)-SSR loci were investigated in 62 wild and cultivated genotypes belonging to 16 Opuntia species. The clusters identified by the distance and model-based analyses clearly separated the wild opuntias from the cultivated ones. However, the O. ficus indica accessions did not cluster separately from other arborescent cactus pear species, such as O. amyclaea, O. megacantha, O. streptacantha, O. fusicaulis, and O. albicarpa, indicating that their current taxonomical classifications do not fit with their genetic variability. In general, the genotypes cultivated in Mexico showed high levels of diversity, whereas most of the spineless accessions collected in other countries had a very narrow genetic base. This study increases our knowledge of the variability among some of the most diffused Opuntia cultivated accessions. This study also points to the inconsistencies of previous taxonomical genotype assignments that were based solely on morphological characteristics.