Phylogeny and origin of pearl millet (Pennisetum glaucum [L.] R. Br) as revealed by microsatellite loci

During the last 12,000 years, different cultures around the world have domesticated cereal crops. Several studies investigated the evolutionary history and domestication of cereals such as wheat in the Middle East, rice in Asia or maize in America. The domestication process in Africa has led to the emergence of important cereal crops like pearl millet in Sahelian Africa. In this study, we used 27 microsatellite loci to analyze 84 wild accessions and 355 cultivated accessions originating from the whole pearl millet distribution area in Africa and Asia. We found significantly higher diversity in the wild pearl millet group. The cultivated pearl millet sample possessed 81% of the alleles and 83% of the genetic diversity of the wild pearl millet sample. Using Bayesian approaches, we identified intermediate genotypes between the cultivated and wild groups. We then analyzed the phylogenetic relationship among accessions not showing introgression and found that a monophyletic origin of cultivated pearl millet in West Africa is the most likely scenario supported by our data set.     

Restriction fragment variation in the nuclear and chloroplast genomes of cultivated and wild Sorghum bicolor

Summary Fifty-six accessions of cultivated and wild sorghum were surveyed for genetic diversity using 50 low-copy-number nuclear DNA sequence probes to detect restriction fragment length polymorphisms (RFLPs). These probes revealed greater genetic diversity in wild sorghum than in cultivated sorghum, including a larger number of alleles per locus and a greater portion of polymorphic loci in wild sorghum. In comparison to previously published isozyme analyses of the same accessions, RFLP analysis reveals a greater number of alleles per locus. Furthermore, many RFLP alleles have frequencies between 0.25–0.75, while the vast majority of isozyme alleles are either rare (< 0.25) or near fixation (> 0.75). Correlations between genetic and geographic distances among the accessions were stronger when calculated with RFLP than with isozyme data. Systematic relationships revealed by nuclear and chloroplast restriction site analysis indicate that cultivated sorghum is derived from the wild ssp. arundinaceum. The portion of the wild gene pool most genetically similar to the cultivars is from central-northeastern Africa. Previous published data also suggested that this is most likely the principal area of domestication of sorghum. Introgression between wild and cultivated sorghum was inferred from disconcordant relationships shown by nuclear and chloroplast DNA markers. Introgression apparently occurs infrequently enough that the crop and its wild relatives maintain distinct genetic constitutions.     

Massive Sorghum Collection Genotyped with SSR Markers to Enhance Use of Global Genetic Resources

Large ex situ collections require approaches for sampling manageable amounts of germplasm for in-depth characterization and use. We present here a large diversity survey in sorghum with 3367 accessions and 41 reference nuclear SSR markers. Of 19 alleles on average per locus, the largest numbers of alleles were concentrated in central and eastern Africa. Cultivated sorghum appeared structured according to geographic regions and race within region. A total of 13 groups of variable size were distinguished. The peripheral groups in western Africa, southern Africa and eastern Asia were the most homogeneous and clearly differentiated. Except for Kafir, there was little correspondence between races and marker-based groups. Bicolor, Caudatum, Durra and Guinea types were each dispersed in three groups or more. Races should therefore better be referred to as morphotypes. Wild and weedy accessions were very diverse and scattered among cultivated samples, reinforcing the idea that large gene-flow exists between the different compartments. Our study provides an entry to global sorghum germplasm collections. Our reference marker kit can serve to aggregate additional studies and enhance international collaboration. We propose a core reference set in order to facilitate integrated phenotyping experiments towards refined functional understanding of sorghum diversity.     

Genetic variation in the endangered wild apple (Malus sylvestris (L.) Mill.) in Belgium as revealed by amplified fragment length polymorphism and microsatellite markers

The genetic variation within and between wild apple samples (Malus sylvestris) and cultivated apple trees was investigated with amplified fragment length polymorphisms (AFLP) and microsatellite markers to develop a conservation genetics programme for the endangered wild apple in Belgium. In total, 76 putative wild apples (originating from Belgium and Germany), six presumed hybrids and 39 cultivars were typed at 12 simple sequence repeats (SSR) and 139 amplified fragment length polymorphism (AFLP) loci. Principal co-ordinate analysis and a model-based clustering method classified the apples into three major gene pools: wild Malus sylvestris genotypes, edible cultivars and ornamental cultivars. All presumed hybrids and two individuals (one Belgian, one German) sampled as M. sylvestris were assigned completely to the edible cultivar gene pool, revealing that cultivated genotypes are present in the wild. However, gene flow between wild and cultivated gene pools is shown to be almost absent, with only three genotypes that showed evidence of admixture between the wild and edible cultivar gene pools. Wild apples sampled in Belgium and Germany constitute gene pools that are clearly differentiated from cultivars and although some geographical pattern of genetic differentiation among wild apple populations exists, most variation is concentrated within samples. Concordant conclusions were obtained from AFLP and SSR markers, which showed highly significant correlations in both among-genotypes and among-samples genetic distances.     

Genetic diversity and structure of the zombi pea (<Emphasis Type="Italic">Vigna vexillata</Emphasis> (L.) A. Rich) gene pool based on SSR marker analysis

Zombi pea (Vigna vexillata (L.) A. Rich) is an underutilized legume species and a useful gene source for resistance to biotic and abiotic stresses, although there is little understanding on its genetic diversity and structure. In this study, 422 (408 wild and 14 cultivated) accessions of zombi pea from diverse origins (201 from Africa, 126 from America, 85 from Australia, 5 from Asia and 5 from unknown origin) were analyzed with 20 simple sequence repeat (SSR) markers to determine its genetic diversity and genetic structure. The SSR markers detected 273 alleles in total with a mean of 13.6 alleles per locus. Polymorphism information content values of the markers varied from 0.58 to 0.90 with an average of 0.76. Overall gene diversity was 0.715. Gene diversity and average allelic richness was highest in Africa (0.749 and 8.08, respectively) and lowest in America (0.435 and 4.10, respectively). Nei’s genetic distance analysis revealed that the highest distance was between wild Australia and cultivated Africa (0.559), followed by wild West Africa and wild Australia (0.415). STRUCTURE, neighbor-joining (NJ), and principal coordinate analyses consistently showed that these zombi pea accessions were clustered into three major groups, viz. America, Africa and Asia, and Australia. NJ tree also suggested that American and Australian accessions are originated from East African zombi peas, and that the cultivated accessions from Africa and Asia were genetically distinct, while those from America were clustered with some cultivated accessions from Africa. These results suggest that Africa is the center of origin and diversity of zombi pea, and that domestication of this pea took place more than once in different regions.     

RFLP-based assay of Sorghum bicolor (L.) Moench genetic diversity

Sixty-two single-copy sorghum DNA clones were used to compare restriction fragment patterns of 53 sorghum accessions from Africa, Asia and the United States. Included were accessions from five morphological races of the cultivated subspecies bicolor, and four races of the wild subspecies verticilliflorum. From two to twelve alleles were detected with each probe. There was greater nuclear diversity in the wild subspecies (255 alleles in ten accessions) than in the domestic accessions (236 alleles in 37 accessions). Overall, 204 of the 340 alleles (60%) that were detected occurred in both subspecies. Phylogenetic analysis using parsimony separated the subspecies into separate clusters, with one group of intermediate accessions. Though exceptions were common, especially for the race bicolor, accessions classified as the same morphological race tended to group together on the basis of RFLP similarities. Selection for traits such as forage quality may have led to accessions genetically more similar to other races being classified as bicolors, which have a loose, small-grained panicle similar to wild races. Population statistics, calculated using four nuclear and four cytoplasmic probes that detect two alleles each, revealed a low but significant amount of heterozygosity, and showed little differentiation in alleles in the wild and cultivated subspecies. Outcrossing with foreign pollen appears to have been more important than migration via seed dispersal as a mechanism for gene flow between the wild and domestic accessions included in this study.     

Assessment of genetic diversity in the sorghum reference set using EST-SSR markers

Selection and use of genetically diverse genotypes are key factors in any crop breeding program to develop cultivars with a broad genetic base. Molecular markers play a major role in selecting diverse genotypes. In the present study, a reference set representing a wide range of sorghum genetic diversity was screened with 40 EST-SSR markers to validate both the use of these markers for genetic structure analyses and the population structure of this set. Grouping of accessions is identical in distance-based and model-based clustering methods. Genotypes were grouped primarily based on race within the geographic origins. Accessions derived from the African continent contributed 88.6 % of alleles confirming the African origin of sorghum. In total, 360 alleles were detected in the reference set with an average of 9 alleles per marker. The average PIC value was 0.5230 with a range of 0.1379–0.9483. Sub-race, guinea margaritiferum (Gma) from West Africa formed a separate cluster in close proximity to wild accessions suggesting that the Gma group represents an independent domestication event. Guineas from India and Western Africa formed two distinct clusters. Accessions belongs to the kafir race formed the most homogeneous group as observed in earlier studies. This analysis suggests that the EST-SSR markers used in the present study have greater discriminating power than the genomic SSRs. Genetic variance within the subpopulations was very high (71.7 %) suggesting that the germplasm lines included in the set are more diverse. Thus, this reference set representing the global germplasm is an ideal material for the breeding community, serving as a community resource for trait-specific allele mining as well as genome-wide association mapping.     

Genetic structure and relationships within and between cultivated and wild sorghum (<Emphasis Type="Italic">Sorghum bicolor</Emphasis> (L.) Moench) in Kenya as revealed by microsatellite markers

Understanding the extent and partitioning of diversity within and among crop landraces and their wild/weedy relatives constitutes the first step in conserving and unlocking their genetic potential. This study aimed to characterize the genetic structure and relationships within and between cultivated and wild sorghum at country scale in Kenya, and to elucidate some of the underlying evolutionary mechanisms. We analyzed at total of 439 individuals comprising 329 cultivated and 110 wild sorghums using 24 microsatellite markers. We observed a total of 295 alleles across all loci and individuals, with 257 different alleles being detected in the cultivated sorghum gene pool and 238 alleles in the wild sorghum gene pool. We found that the wild sorghum gene pool harbored significantly more genetic diversity than its domesticated counterpart, a reflection that domestication of sorghum was accompanied by a genetic bottleneck. Overall, our study found close genetic proximity between cultivated sorghum and its wild progenitor, with the extent of crop-wild divergence varying among cultivation regions. The observed genetic proximity may have arisen primarily due to historical and/or contemporary gene flow between the two congeners, with differences in farmers’ practices explaining inter-regional gene flow differences. This suggests that deployment of transgenic sorghum in Kenya may lead to escape of transgenes into wild-weedy sorghum relatives. In both cultivated and wild sorghum, genetic diversity was found to be structured more along geographical level than agro-climatic level. This indicated that gene flow and genetic drift contributed to shaping the contemporary genetic structure in the two congeners. Spatial autocorrelation analysis revealed a strong spatial genetic structure in both cultivated and wild sorghums at the country scale, which could be explained by medium- to long-distance seed movement.     

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.     

Simple sequence repeat diversity in diploid and tetraploid Coffea species.

Thirty-four fluorescently labeled microsatellite markers were used to assess genetic diversity in a set of 30 Coffea accessions from the CENICAFE germplasm bank in Colombia. The plant material included one sample per accession of seven East African accessions representing five diploid species and 23 wild and cultivated tetraploid accessions of Coffea arabica from Africa, Indonesia, and South America. More allelic diversity was detected among the five diploid species than among the 23 tetraploid genotypes. The diploid species averaged 3.6 alleles/locus and had an average polymorphism information content (PIC) value of 0.6, whereas the wild tetraploids averaged 2.5 alleles/locus and had an average PIC value of 0.3 and the cultivated tetraploids (C. arabica cultivars) averaged 1.9 alleles/locus and had an average PIC value of 0.22. Fifty-five percent of the alleles found in the wild tetraploids were not shared with cultivated C. arabica genotypes, supporting the idea that the wild tetraploid ancestors from Ethiopia could be used productively as a source of novel genetic variation to expand the gene pool of elite C. arabica germplasm.     

Local scale patterns of gene flow and genetic diversity in a crop–wild–weedy complex of sorghum (Sorghum bicolor (L.) Moench) under traditional agricultural field conditions in Kenya

Little information is available on the extent and patterns of gene flow and genetic diversity between cultivated sorghum and its wild related taxa under local agricultural conditions in Africa. As well as expanding knowledge on the evolutionary and domestication processes for sorghum, such information also has importance in biosafety, conservation and breeding programmes. Here, we examined the magnitude and dynamics of crop–wild gene flow and genetic variability in a crop–wild–weedy complex of sorghum under traditional farming in Meru South district, Kenya. We genotyped 110 cultivated sorghum, and 373 wild sorghum individuals using a panel of ten polymorphic microsatellite loci. We combined traditional measures of genetic diversity and differentiation with admixture analysis, population assignment, and analyses of spatial genetic structure to assess the extent and patterns of gene flow and diversity between cultivated and wild sorghum. Our results indicate that gene flow is asymmetric with higher rates from crop to wild forms than vice versa. Surprisingly, our data suggests that the two congeners have retained substantial genetic distinctness in the face of gene flow. Nevertheless, we found no significant differences in genetic diversity measures between them. Our study also did not find evidence of isolation by distance in cultivated or wild sorghum, which suggests that gene dispersal in the two conspecifics is not limited by geographic distance. Overall our study highlights likely escape and dispersal of transgenes within the sorghum crop–wild–weedy complex if genetically engineered varieties were to be introduced in Africa’s traditional farming systems.     

Isolation and characterization of microsatellite loci in Bemisia tabaci

Bemisia tabaci (Hemiptera: Aleyrodidae) is a haplo‐diploid species with a global distribution demonstrating strong geographical structure with eight recognizable genetic groups. Fifteen microsatellite loci (335 alleles, 6–44 alleles per locus) were derived from four of the eight groups and were then screened across 33 populations. These loci clearly differentiate the populations. The microsatellites amplified best in individuals from genetic groups rep‐resenting the Mediterranean, Middle East, Asia (three groups) and Australasia/Oceania and amplified less well with populations from sub‐Saharan Africa and the New World. This differential amplification pattern is a direct result of the relatedness to the microsatellite source material.     

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.     

Allozyme Variation in Turkmenian Populations of Wild Barley, Hordeum spontaneum Koch.

The extent and structure of genetic variation in 720 individualsrepresenting 36 populations of wild barley, Hordeum spontaneum,from Central Asia (Turkmenistan) were determined using starchgel electrophoresis of eight water soluble leaf proteins encodedby 13 loci. The populations were grouped into seven ecogeographicregions. The study found: (a) a similar amount of within populationgenetic diversity (H_e = 0.106), but lower total genetic diversity(H_T = 0.166) to that reported for Middle East populations ofH. spontaneum; (b) of the total genetic diversity, 61% was attributableto variation within populations, 27% between populations ofa region, and 12% among regions; (c) of the 42 alleles found,11 were ubiquitous, 22 were widespread and common, three localand common and seven local and rare; (d) there was a poor correlationbetween population genetic and geographic distances; and (e)the frequencies of only a few alleles correlated significantlywith climatic or geographic parameters. The extent and structureof genetic variation of Turkmenian populations, which representthe Central Asian part of the species' range, were significantlydifferent in some important aspects from Middle Eastern andeastern Mediterranean populations. The mosaic pattern of geneticvariation found in wild barley in the Middle East is less pronouncedin populations from Central Asia where there is less geneticdifferentiation among populations and regions, and more ubiquitousor common and fewer localized alleles. Copyright 2001 Annalsof Botany Company Allozyme, Central Asia, genetic diversity, Hordeum spontaneum, wild barley     

Genetic diversity, structure, gene flow and evolutionary relationships within the Sorghum bicolor wild�Cweedy�Ccrop complex in a western African region

Gene flow between domesticated plants and their wild relatives is one of the major evolutionary processes acting to shape their structure of genetic diversity. Earlier literature, in the 1970s, reported on the interfertility and the sympatry of wild, weedy and cultivated sorghum belonging to the species Sorghum bicolor in most regions of sub-Saharan Africa. However, only a few recent surveys have addressed the geographical and ecological distribution of sorghum wild relatives and their genetic structure. These features are poorly documented, especially in western Africa, a centre of diversity for this crop. We report here on an exhaustive in situ collection of wild, weedy and cultivated sorghum assembled in Mali and in Guinea. The extent and pattern of genetic diversity were assessed with 15 SSRs within the cultivated pool (455 accessions), the wild pool (91 wild and weedy forms) and between them. F (ST) and R (ST) statistics, distance-based trees, Bayesian clustering methods, as well as isolation by distance models, were used to infer evolutionary relationships within the wild-weedy-crop complex. Firstly, our analyses highlighted a strong racial structure of genetic diversity within cultivated sorghum (F (ST) = 0.40). Secondly, clustering analyses highlighted the introgressed nature of most of the wild and weedy sorghum and grouped them into two eco-geographical groups. Such closeness between wild and crop sorghum could be the result of both sorghum's domestication history and preferential post-domestication crop-to-wild gene flow enhanced by farmers' practices. Finally, isolation by distance analyses showed strong spatial genetic structure within each pool, due to spatially limited dispersal, and suggested consequent gene flow between the wild and the crop pools, also supported by R (ST) analyses. Our findings thus revealed important features for the collection, conservation and biosafety of domesticated and wild sorghum in their centre of diversity.     

High level of genetic diversity among spelt germplasm revealed by microsatellite markers.

The genetic diversity of spelt (Triticum aestivum (L.) Thell. subsp. spelta (L.) Thell.) cultivated presently is very narrow. Although the germplasm collections of spelt are extensive, the related genetic knowledge is often lacking and makes their use for genetic improvement difficult. The genetic diversity and structure of the spelt gene pool held in gene banks was determined using 19 simple sequence repeat (SSR) markers applied to 170 spelt accessions collected from 27 countries and 4 continents. The genetic distances (1 - proportion of shared alleles) were calculated and an unweighted pair-group method with arithmetic averaging (UPGMA)-based dendrogram was generated. The genetic diversity was high: 259 alleles were found and the mean interaccession genetic distance was 0.782 +/- 0.141. The dendrogram demonstrated the much higher genetic diversity of spelt held in germplasm collections than in the currently used genotypes. Accessions with the same geographical origin often tended to cluster together. Those from the Middle East were isolated first. All but one of the Spanish accessions were found in a unique subcluster. Most accessions from eastern Europe clustered together, while those from northwestern Europe were divided into two subclusters. The accessions from Africa and North America were not separated from the European ones. This analysis demonstrates the extent of genetic diversity of spelts held in germplasm collections and should help to widen the genetic basis of cultivated spelt in future breeding programs.     

普遍野生稻和亚洲栽培稻遗传多样性的研究

用 ４４个 ＲＦＬＰ标记对来自中国、印度、泰国等亚洲 １０个国家的普通野生稻（简称普野,下同）和来自多个国家的７５个栽培稻品种,从多态位点的比率、等位基因数、基因型数、平均杂合度及平均基因多样性等多个方面,比较了不同国家和不同地区的普通野生稻、栽培稻籼粳亚种及栽培稻与普野之间遗传多样性的差异。结果表明：中国普野的遗传多样性最大;其次是印度普野;南亚普野的平均基因多样性大于东南亚普野,而多态位点的比率、等位基因数及基因型数等却低于东南亚普野;栽培稻的遗传多样性明显小于普通野生稻。在所检测的４４个位点中,栽培稻的多态位点数仅为野生稻的３／４,等位基因数约为野生稻的６０％,基因型种类约为野生稻的１／２。栽培稻中籼稻的遗传多样性高于粳稻。在平均每个位点的实际杂合度上,以中国普野杂合度最高,普通野生稻是栽培稻的２倍。说明从野生稻演化成栽培稻的过程中,经过自然选择和人工选择,杂合度降低,等位基因减少,基因多样性下降。     

Diversity and selection in sorghum: simultaneous analyses using simple sequence repeats

Although molecular markers and DNA sequence data are now available for many crop species, our ability to identify genetic variation associated with functional or adaptive diversity is still limited. In this study, our aim was to quantify and characterize diversity in a panel of cultivated and wild sorghums (Sorghum bicolor), establish genetic relationships, and, simultaneously, identify selection signals that might be associated with sorghum domestication. We assayed 98 simple sequence repeat (SSR) loci distributed throughout the genome in a panel of 104 accessions comprising 73 landraces (i.e., cultivated lines) and 31 wild sorghums. Evaluation of SSR polymorphisms indicated that landraces retained 86% of the diversity observed in the wild sorghums. The landraces and wilds were moderately differentiated (F st=0.13), but there was little evidence of population differentiation among racial groups of cultivated sorghums (F st=0.06). Neighbor-joining analysis showed that wild sorghums generally formed a distinct group, and about half the landraces tended to cluster by race. Overall, bootstrap support was low, indicating a history of gene flow among the various cultivated types or recent common ancestry. Statistical methods (Ewens-Watterson test for allele excess, lnRH, and F st) for identifying genomic regions with patterns of variation consistent with selection gave significant results for 11 loci (approx. 15% of the SSRs used in the final analysis). Interestingly, seven of these loci mapped in or near genomic regions associated with domestication-related QTLs (i.e., shattering, seed weight, and rhizomatousness). We anticipate that such population genetics-based statistical approaches will be useful for re-evaluating extant SSR data for mining interesting genomic regions from germplasm collections.Electronic Supplementary Material Supplementary material is available for this article at     

Detection of major loci associated with the variation of 18 important agronomic traits between Solanum pimpinellifolium and cultivated tomatoes

Wild species can be used to improve various agronomic traits in cultivars; however, a limited understanding of the genetic basis underlying the morphological differences between wild and cultivated species hinders the integration of beneficial traits from wild species. In the present study, we generated and sequenced recombinant inbred lines (RILs, 201 F₁₀ lines) derived from a cross between Solanum pimpinellifolium and Solanum lycopersicum tomatoes. Based on a high‐resolution recombination bin map to uncover major loci determining the phenotypic variance between wild and cultivated tomatoes, 104 significantly associated loci were identified for 18 agronomic traits. On average, these loci explained ~39% of the phenotypic variance of the RILs. We further generated near‐isogenic lines (NILs) for four identified loci, and the lines exhibited significant differences for the associated traits. We found that two loci could improve the flower number and inflorescence architecture in the cultivar following introgression of the wild‐species alleles. These findings allowed us to construct a trait–locus network to help explain the correlations among different traits based on the pleiotropic or linked loci. Our results provide insights into the morphological changes between wild and cultivated tomatoes, and will help to identify key genes governing important agronomic traits for the molecular selection of elite tomato varieties.     

Assessment of molecular diversity and evolutionary relationship of kenaf (Hibiscus cannabinus L.), roselle (H. sabdariffa L.) and their wild relatives

Kenaf (Hibiscus cannabinus L.) and roselle (H. sabdariffa L.) are valuable fibre crop species with diverse end use. Phylogenetic relationship of 73 accessions of kenaf, roselle and their wild relatives from 15 countries was assessed using 44 inter-simple sequence repeat (ISSR) and jute (Corchorus olitorius L.) specific simple sequence repeats (SSR) markers. A total of 113 alleles were identified of which 61.95 % were polymorphic. Jute specific SSR markers exhibited high polymorphism and resolving power in kenaf, although ISSR markers exhibited higher resolving power than SSR markers. Number of polymorphic alleles varied from 1 to 5 for ISSR and 1 to 6 for SSR markers. Cultivated species exhibited higher allele polymorphism (57 %) than the wild species (35 %), but the improved cultivars exhibited lower genetic diversity compared to germplasm accessions. Accessions with common genetic lineage and geographical distribution clustered together. Indian kenaf varieties were distinct from cultivars bred in other countries and shared more genetic homology with African accessions. High genetic diversity was observed in the Indian (J = 0.35–0.74) and exotic kenaf germplasm collections (J = 0.38–0.79), suggesting kenaf might have been introduced in India from Africa through Central Asia during early domestication. Genetic similarity-based cluster analysis was in close accordance with taxonomic classification of Hibiscus.