Genetic diversity and population structure of popcorn germplasm resources using genome-wide SNPs through genotyping-by-sequencing

Genetic Resources and Crop Evolution - Popcorn is a kind of snack food and has a breeding history of nearly 40 years in China, however, there are relatively few studies on its genetic...     

Genetic diversity,population structure and differentiation of rice species from Niger and their potential for rice genetic resources conservation and enhancement

Rice genetic resources conservation and evaluation is crucial to ensure germplasm sources for further crop breeding. We conducted a wide collection of Oryza species in Niger and characterize its diversity with microsatellites (or simple sequence repeats, SSR). The aims of this research were to get a better understanding of the extent of genetic diversity, its structure and partition within rice eco-geographical zones of Niger. There were 264 accessions found in farmers’ and other fields: 173 O. sativa (Asia’s rice), 65 O. glaberrima (Africa’s rice), 25 O. barthii, and 1 O. longistaminata (weedy perennial rice), which were genotyped with 18 SSR. A total of 178 alleles were detected, with a mean of 9.89 alleles per locus. The polymorphism information content was 0.65 and heterozygosity was estimated as 0.14. Two main well-differentiate genotypic groups, which correspond to Asian and African rice species, were identified. The SSR set divided the Asia’s rice group (solely indica) into irrigated and floating rice, with rainfed lowland rice in between. The African rice species group was composed of O. glaberrima, O. longistaminata and O. barthii accessions, but without any clear genetic differentiation among them likely due admixtures within the samples of O. barthii. Five accessions that could be natural interspecific hybrids were too admixed for assigning them to any of the two well-differentiated groups. The partitioning of the overall diversity showed that maximum variation was within genotypic groups and subgroups or cropping ecologies, rather than between eco-geographical zones. The eco-geographical distribution of the diversity suggests germplasm exchange in Niger. Next-steps for conserving rice and crop wild relatives in Niger could be taken using the findings of this research.     

Microsatellite based analysis of the genetic structure and diversity of Capsicum chinense in the Neotropics

Capsicum chinense Jacq., one of the five domesticated species of pepper grown in the New World, is a major contributor to both local and international markets and the economy of the Caribbean islands. The planning and implementation of germplasm conservation and breeding programs for the sustainable use of C. chinense genetic resources are hampered by the poor understanding of the genetic structure and diversity of C. chinense in the region. In the present study, the genetic structure, diversity and relatedness of C. chinense germplasm collections within the Caribbean basin and South America were assessed using nuclear microsatellite markers. C. chinense accessions (102) representing seven geographical regions were genotyped using nine polymorphic nuclear microsatellite markers along with 16 accessions representing four other species of Capsicum. The results revealed that the highest genetic diversity (He = 0.58) was found in the Amazon region supporting the postulated center of diversity of C. chinense as the Amazon basin. The cluster analysis resulted in two distinct genetic clusters corresponding to Upper Amazon and Lower Amazon regions, suggesting two independent domestication events or two putative centers of diversity in these regions respectively. The cluster analysis further revealed that populations in Central America and the Caribbean may have been primarily derived from progenitors from Upper Amazon region and later diverged through geographical isolation. Conservation and germplasm collection programs should therefore target these genetically distinct clusters and satellite populations, towards supporting breeding programs to harness heterosis.     

Genetic diversity and population structure of diverse Iranian Nepeta L. taxa

Genetic Resources and Crop Evolution - In the present study, we utilized ISSR molecular markers to investigate infraspecific and infrageneric genetic variations in 34 populations from 25 Nepeta L....     

Taxonomy and genetic diversity of domesticated Capsicum species in the Andean region

The Capsicum genus is native to tropical America and consists of 27 species, five of which are used as fresh vegetables and spices: Capsicum annuum L., Capsicum chinense Jacq., Capsicum frutescens L., Capsicum baccatum L. and Capsicum pubescens R. et P. The study of the relationships among species of cultivate Capsicum species will be useful for breeding new cultivars or hybrids. This study is focused on the genetic diversity and relationships of these species that were collected in the Andean region. Ten microsatellites and four AFLP combinations were used to characterize 260 Capsicum accessions. The AFLP tree turned out to be informative regarding relationships among species. The data clearly showed the close relationships between C. chinense and C. frutescens. Moreover, C. cardenasii and C. eximium were indistinguishable as a single, morphologically variable species. Our data showed C. baccatum and C. praetermissum to be distinct species that form a compact group. In the present work, AFLP fingerprinting indicated that C. chacoense was placed in the C. baccatum complex and showed C. tovarii as a separate species. In addition, SSR data indicated that there is intraspecific differentiation in the species C. chinense, C. baccatum and C. pubescens, as the PCoA-based clustering showed a clear geographic division related to country. Even though Bolivia is considered to be the nuclear area for these species, we have found similar variability in Ecuador and Peru for several Capsicum species.     

Chinese Cornus officinalis: genetic resources, genetic diversity and core collection

Cornus officinalis is plant species that is widely used in traditional Chinese medicine. To help the efficient utilization and conservation of this species, the genetic diversity of 73 germplasm resources collected from Zhejiang, Henan and Shaanxi provinces in China were used in a primary core collection. The germplasm resources were classified nine types and the analysis of morphological traits and chemical components showed wide variations among the germplasm types. The primary core collection of C. officinalis was evaluated by using 18 inter-simple sequence repeat (ISSR) markers and a mini core collection was developed based on three strategies on construction of a core germplasm resources. The ISSR results showed that a total of 233 alleles were identified in these 73 accessions, the genetic diversity (P?=?91.02%, H?=?0.293, I?=?0.446) revealed with an average of 2 alleles per locus. The genetic diversity index analysis suggested that there is a great richness and uniqueness of genetic variation in this primary core collection. Cluster analysis by UPGMA and STRUCTURE placed the 73-germplasm resources into four linkage clusters. Almost all samples from one sampling location were clustered together. Compared to the RS and SW strategy, the LDSS strategy proved to be more representative in the core collection of C. officinalis. Finally, a mini core collections by LDSS, composed of 18 accessions (24.66% of the primary core collection), let more than 94.85% of polymorphic loci remained, 97.55% of the observed number of alleles and 99.28% of the effective number of alleles of the mini core collection, respectively. The Nei’s gene diversity and Shannon’s Information index of core collection were 0.294 and 0.443, respectively. Taken all together, the results indicated that mini core collections constructed by the LDSS strategy represented their primary core collections and provided a rational framework for intensive surveys of natural variation in C. officinalis genetic resources.     

Genetic diversity and population structure in medicinal plant Melissa officinalis L. (Lamiaceae)

Genetic Resources and Crop Evolution - Melissa officinalis is an important medicinal plant and is extensively used by locals. This species is growing in different regions of Iran and forms several...     

Genetic diversity,population structure and genetic relationships in apricot (Prunus armeniaca L.) germplasm of Jammu and Kashmir,India using ISSR markers

Genetic Resources and Crop Evolution - The collection and characterization of apricot germplasm is an important step for its utilization, conservation, and breeding programs. In the present study,...     

Genetic diversity, conservation, and utilization of Theobroma cacao L.: genetic resources in the Dominican Republic

Cacao (Theobroma cacao L.) is a significant agricultural commodity in the Dominican Republic, which ranks 11th in the world for cacao exports. To estimate genetic diversity, determine genetic identity, and identify any labeling errors, 14 SSR markers were employed to fingerprint 955 trees among cacao germplasm accessions and local farmer selections (LFS). Comparisons of homonymous plants across plots revealed a significant misidentification rate estimated to be 40.9 % for germplasm accessions and 17.4 % for LFS. The 14 SSRs amplified a total of 117 alleles with a mean allelic richness of 8.36 alleles per locus and average polymorphism information content (PIC) value of 0.67 for the germplasm collection. Similar levels of variation were detected among the LFS where a total of 113 alleles were amplified with a mean of 8.07 alleles per locus and PIC of 0.57. The observed heterozygosity (H_obs) was 0.67 for the germplasm collection and 0.60 for LFS. Based on population structure analysis 43.9 % of the germplasm accessions and 72.1 % of the LFS are predominantly of the Amelonado ancestry. Among these Amelonado, 51.7 % for the germplasm collection and 50.6 % for LFS corresponded to Trinitario hybrid lineage. Criollo ancestry was found in 7.6 and 9.5 % of the germplasm accessions and LFS, respectively. The Contamana, Nacional, and Iquitos backgrounds were also observed in both populations, but the Curaray background was only detected in the germplasm accessions. No Purús or Guiana ancestry was found in either of the populations. Overall, significant genetic diversity, which could be exploited in the Dominican Republic breeding and selection programs, was identified among the germplasm accessions and LFS.     

Genetic structure and diversity of India hybrid tea

The most important evolutionary event in the success of commercial tea cultivation outside China in ~30 countries came about by the origin of India hybrid tea in India, derived from the extensive spontaneous hybridization that took place between the Assam type tea growing in the forest regions of Assam, North-East India and China type tea introduced from China in ~1875 to many regions of North-East India. The release of an enormous pool of vigorous and highly variable plants of India hybrid tea in North-East India was a significant step forward for the origin and evolution of tea as a highly successful crop plant. The 1,644 accessions and clones of India hybrid tea, representatives of known 15 morphotypes, were screened by 412 AFLP markers amplified by 7 AFLP primer pair combinations. All the 412 genetic loci were polymorphic across the 1,644 accessions and clones. The analysis was done with distance (PCoA and NJ) methods, and the STRUCTURE (Bayesian) model. Both PCoA and NJ analysis clustered 1,644 tea accessions and clones into six major groups with one group in each, constituted mostly by China hybrid, Assam China hybrid and Assam hybrid morphotypes, of distinct genetic identity. No group was exclusive for any particular morphotype. The accessions and clones belonging to morphotypes, Assam type, Assam hybrid, China hybrid and China Cambod were distributed in all the groups. It is the Assam type/Assam hybrid morphotypes which exhibit much broader genetic variability than in China type/China hybrid/Cambod type/Cambod hybrid morphotypes. The STRUCTURE analysis inferred 16 populations (K = 16), for which the greatest values of probability were obtained. Nine of the 16 clusters were constituted by the tea accessions and clones of ‘pure’ ancestry. The remaining clusters were of ‘mixed’ ancestry. This analysis provides evidence that the accessions and clones of the same morphotype are not always of same genetic ancestry structure. The tea accessions and clones obtained from outside North-East India shared the same groups (distance method) and clusters (STRUCTURE model) which were constituted by North-East India accessions. The present study also demonstrates very narrow genetic diversity in the commercial tea clones vis-à-vis the profound genetic diversity existing in the tea accessions. These clones were distributed in hardly two of the six groups in NJ tree. The identified 105 core accessions and clones, capturing 98% diversity, have their origin from almost all groups/subgroups of NJ tree.     

Revealing genetic diversity and population structure in Pistachio (Pistacia vera L.) by SSR markers

Genetic Resources and Crop Evolution - Pistachio (Pistacia vera L.) is the only cultivated species in Pistacia genus and it is one of the most important species of hard-shelled fruits. Pistachio...     

Genetic diversity and population structure in Jatropha (Jatropha curcas L.) based on molecular markers

Genetic Resources and Crop Evolution - Jatropha (Jatropha curcas L.) is an oleaginous potential, howetever, some studies report that there is low genetic diversity in Brazilian genotypes....     

From genetic diversity and structure to conservation: Genetic signature of recent population declines in three mouse lemur species (Microcebus spp.)

The exceptional biodiversity of Madagascar is threatened by anthropogenic landscape changes that took place during the 2000 years of human colonization. This study focuses on the influence of geographic distance and forest fragmentation on genetic diversity and population differentiation of three rare, nocturnal, arboreal lemur species in northwestern Madagascar. Historic declines in population sizes as a consequence of forest fragmentation are quantified and dated. Eighteen sites were visited, and a total of 205 Microcebus ravelobensis, 45 M. bongolavensis and 78 M. danfossi were genotyped with eight microsatellite loci. Genetic differentiation among the sites, as measured by F_ST, ranged from 0.01 to 0.19. These values were significant in almost all cases and indicated genetic structure in the samples. Isolation-by-distance was detected in one species and a STRUCTURE analysis indicated that fragmentation further promoted genetic differentiation. Bayesian methods revealed that populations from all three species underwent a major demographic collapse of around two orders of magnitude. This decrease probably began after the arrival of humans, most likely within the last 500 years. This result suggests that anthropogenic changes may have been limited during the first 1500 years of human colonization in all three ranges. Two of the study species (M. danfossi, M. bongolavensis) lack effectively protected areas in their ranges. Consequently, quick conservation actions are now needed in order to secure the remaining genetic diversity of these species.     

Genetic diversity and local population structure of fragmented populations of Trillium camschatcense (Trilliaceae)

Trillium camschatcense, a long-lived common woodland herb, has been experiencing intensive habitat fragmentation over the last century in eastern Hokkaido, Japan. We examined the genetic diversity and population genetic structure of 12 fragmented populations with different population sizes using allozyme electrophoresis. The percentage of polymorphic loci and mean number of alleles per locus were positively related to population size, probably due to the stochastic loss of rare alleles (frequency of q<0.1) in small populations. Populations with 350 flowering plants or fewer had lost almost all of their rare alleles. While the heterozygosity and inbreeding coefficient were not related to population size, some small populations showed relatively high inbreeding coefficients. In spite of the low genetic differentiation among overall populations (F_ST=0.130), local population structuring was recognized between the two geographically discontinuous population groups. Within groups, sufficient historical gene flow was inferred, whereas a low dispersal ability of this species and geographical separation could produce apparent differentiation between groups.     

Genetic diversity and population structure of Chinese Cherry revealed by chloroplast DNA trnQ-rps16 intergenic spacers variation

Chinese Cherry, generally referring to Prunus pseudocerasus Lindl. species, is one of the most economically important domestic fruit tree in China. To effectively preserve and sustainably utilize this species, a study in genetic diversity and population structure was carried out by the sequence variation of chloroplast DNA trnQ-rps16 intergenic spacers. Polymorphism was calculated among the 200 individuals from 7 local and 10 wild populations across its geographical range in China. The results showed that (1) Total genetic variation in species level was poor (h = 0.478, π = 0.0018). But in the wild populations, it was much higher than that in the local populations (h = 0.565, π = 0.0021 vs. h = 0.152, π = 0.0006). (2) Low levels of genetic differentiation (F_SC = 0.19595, P = 0.000), genetic distance (0.00000–0.00297), as well as pairwise Fst value among populations were detected. These results, combined with the insignificant gene genealogy pattern and neutrality tests indicate that Chinese Cherry has relatively low levels of genetic diversity and insignificant population structure. Coancestry might be a combined effect of the reduction in effective population size with the recent demographic bottlenecks and mating systems. The pronounced seed dispersal abilities and relatively high rates of gene exchange are supported by the limited genetic differentiation among populations.     

Insights from putatively neutral EST-SSR markers on the population genetic structure and genetic diversity of the Qinghai-Tibetan Plateau endemic Medicago archiducis-nicolai Sirjaev

Medicago archiducis-nicolai Sirjaev and M. ruthenica (L.) Ledebour are two phylogenetically closely related species in the section Platycarpae within Medicago. M. archiducis-nicolai is endemic to the Qinghai–Tibetan Plateau (QTP), shows more tolerance to abiotic stress than M. ruthenica, which inhabits relatively temperate areas, and has the potential to be domesticated and used as a legume forage germplasm in alpine meadows. Here, we analyzed the population genetic structure and genetic diversity of these species using 20 putatively neutral EST-SSR markers. Twenty-four wild populations, including 21 M. archiducis-nicolai and 3 M. ruthenica, were divided into two clusters that were consistent with current taxonomy. The 21 M. archiducis-nicolai populations were clustered into two geographically related groups. Positive relationships between population genetic distance and geographical factors, including geographical distance and altitudinal difference, revealed that the genetic differentiation of M. archiducis-nicolai populations was driven by both geographical distance and the complex topography of the QTP. Medicago archiducis-nocilai, a narrow-range endemic on the QTP, had lower genetic diversity than the more widespread M. ruthenica. Medicago archiducis-nicolai populations from the central platform of the QTP had relatively high genetic diversity, whereas those occupying the east platform and edge of the QTP showed variable levels of genetic diversity, implying the presence of refugia on the central platform. These results have implications for the genetic resource management and exploitation of M. archiducis-nicolai and provide novel insights into the mechanisms underlying the adaptation of this species to the harsh environment of the QTP.

     

Genetic diversity and population structure of cultivated Dendrobium nobile Lindl. in southwest of China based on genotyping-by-sequencing

Genetic Resources and Crop Evolution - Dendrobium nobile Lindl. is one of the most important Orchid plants worldwide. The genotype-by-sequencing (GBS) method has now been widely used to access...     

Genetic structure of the Japanese soybean population

The genetic structure of the Japanese soybean population was evaluated based on the variation at 16 isozyme and seed protein loci for 781 landraces and pure line selections. A relatively high diversity was found in the Japanese population, compared with 158 Korean accessions and 94 Chinese accessions that were tested for comparison. The average gene diversity in the Japanese population was 0.248, being comparable to the estimate obtained for the Chinese population (0.249) but higher than that for the Korean population (0.209). There were a number of alleles that differentiated the Japanese population from either of the Korean or Chinese populations or both. The presence of the alleles which are characteristic of the Japanese population suggests that the Japanese population is not solely a part of the population of China, which is considered as the place of origin of soybean. Only 11% of the total variation was attributable to the differences among seven regional groups, which occurred mainly between Hokkaido or Okinawa and the other regions. A test of two-locus associations revealed that the variation was itself highly structured despite the high level of variation at each of the polymorphic loci. In addition, Aco1, Aco4, Dia1, Enp and Idh1 varied with maturity or seed size. The Japanese soybean population may consist of different cultivar groups that had been established independently as the result of adaptation to different environmental conditions and/or diversification of food culture. The origins of the cultivar groups are discussed.