Genetic diversity in kiwifruit polyploid complexes: insights into cultivar evaluation,conservation, and utilization

Understanding the extent and partitioning of crop genetic diversity is necessary for conserving and utilizing their genetic potentials for breeding. In the present study, fluorescence-labeled amplified fragment length polymorphism markers were used to characterize the genetic diversity and relationships of 79 cultivars and also of 122 F1 hybrids which resulted from six kiwifruit interploid crosses. A high level of mean genetic diversity was detected (Hj > 0.22) for all cultivars investigated, without significant differences among diploids (2x), tetraploids (4x), and hexaploids (6x). This suggested that no significant genetic erosion occurred in these cultivars, which were directly selected from natural resources or created from crosses. The Unweighted Pair Group Method with Arithmetic Mean analysis of the genetic dissimilarity between cultivars showed three main groups mostly based on their three ploidy levels. Among these, the red-fleshed cultivars which were originally derived from ‘Hongyang’ clustered into one subgroup of group I, suggesting their unique genetic background despite they were marked as different cultivars used in the current kiwifruit industry. By analyzing the genetic variation of hybrids with variable ploidy levels, our genetic analyses further revealed that interploid crosses can increase the genetic diversity of F1 offsprings, especially from the parental combinations of 6x–2x and 6x–4x, in which both parents showed significant differences in morphology and genetic backgrounds. Based on these findings, strategies were proposed for the conservation and utilization of the current kiwifruit genetic resources for future breeding programs.     

Are plant populations in expanding ranges made up of escaped cultivars? The case of Ilex aquifolium in Denmark

Rapid range expansions are becoming more prevalent, especially as climate continues to change. The escape of ornamental plants within their native range represents a significant, but often overlooked component of this process. Few studies have focused on the role of ornamental plants in range expansions using molecular markers to identify the possibility of mixed native and cultivar populations. The purpose of the present study was to determine the genetic variation of a native woody plant with ornamental conspecifics at the edge of its distribution. We selected Ilex aquifolium L. (English holly) which grows naturally in Denmark but is spreading eastward in Scandinavia, possibly due to a combination of climate change and introduction of more frost-tolerant cultivars. We sampled 187 individuals from older and recently established populations, and cultivated I. aquifolium throughout Denmark, and compared them using nuclear SSR and AFLP. The overall results showed no structure or clustering of plants from the historical or the expanding range, or of wild or cultivated plants. The only clusters found were for a group of cultivated hybrid I. aquifolium. The samples represented four genetic groupings, indicating either hybridization between cultivated and wild I. aquifolium or replacement of the latter by cultivars. Thus, ornamental genotypes of I. aquifolium contribute to the northeastern range expansion of the species and eventual invasiveness within its native range.     

Whole-genome sequencing of a Plasmodium vivax isolate from the China-Myanmar border area

Currently, there is a trend of an increasing number of Plasmodium vivaxmalaria cases in China that are imported across its Southeast Asia border, especially in the China-Myanmar border area (CMB). To date, little is known about the genetic diversity of P. vivax in this region. In this paper, we report the first genome sequencing of a P. vivaxisolate (CMB-1) from a vivax malaria patient in CMB. The sequencing data were aligned onto 96.43% of the P. vivax Salvador I reference strain (Sal I) genome with 7.84-fold coverage as well as onto 98.32% of 14 Sal I chromosomes. Using the de novo assembly approach, we generated 8,541 scaffolds and assembled a total of 27.1 Mb of sequence into CMB-1 scaffolds. Furthermore, we identified all 295 known virgenes, which is the largest subtelomeric multigene family in malaria parasites. These results provide an important foundation for further research onP. vivax population genetics.     

Genetic homogeneity between populations of cotton bollworm from Xinjiang,China

We studied the population structure of cotton bollworm (CBW), Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae), in Xinjiang, the largest cotton-growing region in China, using a fragment of cytochrome c oxidase subunit I (COI) gene. Alignments of all 192 COI sequences revealed 28 haplotypes including 23 in southern Xinjiang, 5 in eastern Xinjiang and 13 in northern Xinjiang. Negative and significant values of neutrality tests for the Tajima's D and Fu's FS parameters, combined with the high values of haplotype diversity (H_d), low values of nucleotide diversity (π) and a high number of low frequency haplotypes indicated a recent demographic expansion of Xinjiang CBW populations. Analysis of molecular variation (AMOVA) indicated low and non-significant genetic structure, regardless of geographical scale or crop, with most of genetic variation occurring within local CBW populations. Pairwise F_ST analyses also indicated low genetic differentiation. This demographic event and high gene flow could be responsible for the low genetic structure currently found. CBW populations in Xinjiang need to be considered as one panmictic unit in its management, especially for the design of refuges to delay the development of resistance by this migratory pest to transgenic Bt (Bacillus thuringiensis) cotton.     

Physical and Genetic Map of the Pasteurella multocida A:1 Chromosome

A physical and genetic map of the Pasteurella multocida A:1 genome was generated by using the restriction enzymes ApaI, CeuI, and NotI. The positions of 23 restriction sites and 32 genes, including 5 rrn operons, were localized on the 2.35-Mbp single circular chromosome. This report presents the first genetic and physical map for this genus.     

Genetic diversity and phylogenetic relations of salmon trematode Nanophyetus japonensis

Nanophyetiasis is the severe zoonotic disease caused by parasitic worms from the genus Nanophyetus. Humans and carnivorous animals become infected when they ingest raw fish containing metacercariae, especially Pacific salmonids. Nanophyetiasis is detected in limited geographical areas which include the coastal regions of the North Pacific: the United States of America, Russian Federation and Japan. Despite the epidemiological significance, Nanophyetus species have not been well studied genetically. In this research, we for the first time explored genetic diversity of Nanophyetus japonensis from Japan in comparison with those of related species, N. salmincola from North America and N. schikhobalowi from the Russian Far East, based on sequence variation in the nuclear ribosomal gene family (18S, ITS1–5.8S–ITS2 and 28S) and mitochondrial nad1 gene, encoding subunit I of the respiratory chain NADH dehydrogenase. The results confirmed the independent species status for the compared flukes, demonstrated a greater genetic similarity of Asian species between themselves than each of them with the North American one, suggesting that N. japonensis and N. schikhobalowi are close sister species, and also revealed discrepancy between the levels of morphological and genetic differentiation.     

Characterization of 11 novel polymorphic microsatellite loci in the threatened Korean loach,Iksookimia koreensis,isolated using a next-generation sequencing method

To investigate the genetic diversity and population structure of Iksookimia koreensis, we characterized 11 novel polymorphic microsatellite markers developed using next-generation sequencing. The number of alleles per locus ranged from 4 to 10 (average = 6.26). Observed and expected heterozygosities ranged from 0.333 to 0.866 and from 0.375 to 0.866, respectively. No loci showed significant deviation from Hardy–Weinberg equilibrium (HWE). These loci were also used successfully to study the genetic diversity of a closely related species, Iksookimia longicorpa. Four of the 11 loci amplified in the two species showed different allele frequency and distribution, indicating deep genetic divergence between I. koreensis and I. longicorpa. The newly developed microsatellite markers reported here will provide a useful tool for examining gene flow, population genetic structure, and genetic diversity of these species.     

Pathogenetic mechanisms in hereditary dysfunctions of complex I of the respiratory chain in neurological diseases

This paper covers genetic and biochemical aspects of mitochondrial bioenergetics dysfunction in hereditary neurological disorders associated with complex I defects. Three types of hereditary complex I dysfunction are dealt with: (i) homozygous mutations in the nuclear genes NDUFS1 and NDUFS4 of complex I, associated with mitochondrial encephalopathy; (ii) a recessive hereditary epileptic neurological disorder associated with enhanced proteolytic degradation of complex I; (iii) homoplasmic mutations in the ND5 and ND6 mitochondrial genes of the complex, cohexistent with mutation in the nuclear PINK1 gene in familial Parkinsonism. The genetic and biochemical data examined highlight different mechanisms by which mitochondrial bioenergetics is altered in these hereditary defects of complex I. This knowledge, besides clarifying molecular aspects of the pathogenesis of hereditary diseases, can also provide hints for understanding the involvement of complex I in sporadic neurological disorders and aging, as well as for developing therapeutical strategies.     

The balance of weak and strong interactions in genetic networks

Genetic interactions are being quantitatively characterized in a comprehensive way in several model organisms. These data are then globally represented in terms of genetic networks. How are interaction strengths distributed in these networks? And what type of functional organization of the underlying genomic systems is revealed by such distribution patterns? Here, I found that weak interactions are important for the structure of genetic buffering between signaling pathways in Caenorhabditis elegans, and that the strength of the association between two genes correlates with the number of common interactors they exhibit. I also determined that this network includes genetic cascades balancing weak and strong links, and that its hubs act as particularly strong genetic modifiers; both patterns also identified in Saccharomyces cerevisae networks. In yeast, I further showed a relation, although weak, between interaction strengths and some phenotypic/evolutionary features of the corresponding target genes. Overall, this work demonstrates a non-random organization of interaction strengths in genetic networks, a feature common to other complex networks, and that could reflect in this context how genetic variation is eventually influencing the phenotype.     

A genetic toolbox for metabolic engineering of Issatchenkia orientalis

The nonconventional yeast Issatchenkia orientalis can grow under highly acidic conditions and has been explored for production of various organic acids. However, its broader application is hampered by the lack of efficient genetic tools to enable sophisticated metabolic manipulations. We recently constructed an episomal plasmid based on the autonomously replicating sequence (ARS) from Saccharomyces cerevisiae (ScARS) in I. orientalis and developed a CRISPR/Cas9 system for multiplexed gene deletions. Here we report three additional genetic tools including: (1) identification of a 0.8 kb centromere-like (CEN-L) sequence from the I. orientalis genome by using bioinformatics and functional screening; (2) discovery and characterization of a set of constitutive promoters and terminators under different culture conditions by using RNA-Seq analysis and a fluorescent reporter; and (3) development of a rapid and efficient in vivo DNA assembly method in I. orientalis, which exhibited ~100% fidelity when assembling a 7 kb-plasmid from seven DNA fragments ranging from 0.7 kb to 1.7 kb. As proof of concept, we used these genetic tools to rapidly construct a functional xylose utilization pathway in I. orientalis.     

Variation in the ratio of physical to genetic distance in intervals adjacent to theMla locus on barley chromosome 1H

Variants of the pulsed-field gel electrophoresis technique were used in conjunction with two-dimensional DNA gel electrophoresis (2-DDGE) to determine the ratio of physical to genetic distance in two genetically defined intervals on barley chromosome 1H.2-DDGE analysis demonstrated that two loci that define a 0.3 cM interval, as determined by hybridization with BCD249, reside on a single 450-kbMluI fragment. This result indicates a maximum ratio of physical to genetic distance in this interval of 1500 kb/cM as compared to 3.7–4.2 Mb/cM for the barley genome as a whole. High molecular weight (HMW) DNA restricted withNotI and probed sequentially with MWG068 and BCD249 yield diffuse bands at approximately 2.8 Mb and 3.0 Mb in the C.I. 16151 and C.I. 16155 parental lines, respectively. These results suggest the maximum ratio of physical to genetic distance in the interval defined by these probes is 7.8 Mb/cM. unique HMW DNA restriction fragment length polymorphisms (RFLP) were attributed to the presence of recombination breakpoints. Data from the recombination breakpoint analysis were used to estimate a ratio of physical to genetic distance of 2.5 Mb/cM in theXbcd249.2-Xmwg068 interval and 0.465 Mb/cM in theXbcd249.1-Xbcd249.2 interval. Both physical linkage and recombination breakpoint analysis indicate theXbcd249.1-Xbcd249.2 interval is approximately five-fold smaller, physically, than theXbcd249.2-Xmwg068 interval.     

Evaluating hybridization as a potential facilitator of successful cogongrass (Imperata cylindrica) invasion in Florida,USA

Interspecific hybridization is cited as one potential mechanism for increased invasiveness, particularly among some grass species. In the southeastern United States, the successful invasion of cogongrass (Imperata cylindrica) has sometimes been attributed to hybridization with the previously naturalized Imperata brasiliensis. This research aimed to determine whether genetic signals are consistent with these two species having experienced interspecific hybridization in Florida (USA), where it has been proposed that such an event facilitated cogongrass invasion across the region. Individuals of invasive I. cylindrica populations (n = 66) were sampled broadly from the state, and I. brasiliensis (n = 63) individuals were sampled from expertly identified and vouchered populations in Miami-Dade County. Genetic analysis utilized amplified fragment length polymorphisms in sampled individuals, and failed to detect significant genetic differentiation between the two species. Analysis of molecular variance partitioned the majority of detected variation within populations (86 %), while only 8 % was significantly partitioned between I. cylindrica and I. brasiliensis (F_ST = 0.135, P < 0.001). Both STRUCTURE analysis and principal coordinates analysis strongly indicated the presence of a single genetic group across the sampled populations. Hybrid analysis furthermore failed to support interspecific hybridization. Florida populations thus are suggested to share genetic parent material(s) and/or have experienced substantial admixture across the state. Therefore, this study suggests Imperata populations in South Florida that are currently considered to be I. brasiliensis are not genetically distinct from I. cylindrica, and regional cogongrass invasion likely was not facilitated by previously postulated interspecific hybridization.     

Comparison of three QTL detection models on biochemical,sensory, and yield characters in Coffea canephora

Coffea canephora is subject to enormous competitive challenges from other crops, especially for farmer sustainability and consumer requirements. Coffee breeding programs have to focus on specific traits linked to these two key targets, such as quality character, largely depending on the bean’s biochemical composition and field yield. Two segregating populations A and B, from crosses between a hybrid (Congolese?×?Guinean) FRT58 parental clone and a Congolese FRT51 genotype and between two Congolese parents FRT67 and FRT51, respectively, were used to characterize the quantitative trait loci (QTL) involved in agronomic and biochemical traits. A consensus genetic map was established using 249 SSRs covering 1,201 cM. Three QTL detection models per population with MapQTL (model I) and MCQTL (model II) followed by a connected population approach with MCQTL (model III) were compared based on their efficiency, precision for QTL detection, and their genetic effect assessment (additive, dominance, and parental-favorable allele). The analysis detected a total of 143 QTLs, 60 of which were shared between the three models; 28 found with two models; and two, 13, and 40 specific from models I, II, and III, respectively. The last model III based on connected populations is much more efficient in detecting QTLs with low variance explained and led to the genetic characterization of favorable allele. Thanks to this comparison of three QTL detection models on our quantitative genetic study, we will give a new insight for coffee breeding programs dedicated to managing complex agronomic or qualitative traits.     

Genetic Diversity of Daphnia pulex in the Middle and Lower Reaches of the Yangtze River

Increased human activities and environmental changes may lead to genetic diversity variations of Cladocerans in water. Daphnia pulex are distributed throughout the world and often regarded as a model organism. The 16S rDNA, cytochrome c oxidase subunit I (COI), and 18S genes were used as molecular marks. The genetic diversity and phylogeny of D. pulex obtained from 10 water bodies in the middle and lower reaches of the Yangtze River were studied. For 16S rDNA, COI gene, and 18S gene, the A+T content (65.4%, 58.4%, and 54.6%) was significantly higher than the G+C content (34.6%, 41.6% and 45.4%). This result was consistent with higher A and T contents among invertebrates. Based on the genetic distances of 16S rDNA and COI genes, the genetic differences of D. pulex from 10 water bodies located in the middle and lower reaches of the Yangtze River in China was minimal (0%–0.8% for 16S rDNA and 0%–1.5% for COI gene). However, D. pulex evolved into two branches in the phylogenetic trees, which coincided with its geographical distribution. Compared with D. pulex from other countries, the average genetic distance of D. pulex obtained from 10 water bodies in the middle and lower reaches of the Yangtze River reached 9.1%–10.5%, thereby indicating that D. pulex may have evolved into different subspecies.     

Intra-specific variability in the thirteen known populations of the fairy shrimp Chirocephalus ruffoi (Crustacea: Anostraca): resting egg morphometrics and mitochondrial DNA reveal decoupled patterns of deep divergence

Chirocephalus ruffoi is a fairy shrimp endemic to the Italian peninsula, where it is known only from thirteen high mountain locations. Twelve of these are in the Northern Apennines while the thirteenth is about 700 km away in the Calabrian Apennines (Southern Italy). We quantified degree of genetic divergence within the species by sequencing a fragment of the mitochondrial DNA encoding for Cytochrome Oxidase I. We then combined genetic data with the re-analysis of two different datasets on the morphometrics of the resting eggs (cysts) produced by the species as an adaptation to survive seasonal droughts. Genetic data revealed profound divergence; we identified four clusters of haplotypes within the species phylogeography, three in the Northern Apennines and one in the Calabrian Apennines with most of the genetic variation (≈70%) being apportioned among haplogroups. We found high variability in cyst morphometrics, especially in cyst size and height of the spines ornamenting the surface. Genetic and morphometric data are decoupled suggesting that cyst morphology is either under selection or a plastic trait. We, therefore, caution against using cyst morphology for taxonomic purposes in anostracans.     

Genetic variability of myostatin and prolactin genes in popular goat breeds in Egypt

The genetic polymorphisms of two functional genes named: myostatin (MSTN) and prolactin (PRL) were investigated in three goat breeds (Barki, Damascus and Zaraibi) using Sanger nucleotide sequence and restriction fragment length polymorphism (RFLP) methods, in order to differentiate between these breeds. Nucleotide sequencing of 337 bp MSTN gene detected five SNPs in Barki breed, two SNPs in Damascus breed, while the Zaraibi breed did not show any SNPs. Moreover, MSTN-HaeIII/PCR-RFLP gave a single Genotype BB was found in all the studied breeds. Meanwhile, Nucleotide sequencing of 196 bp PRL gene showed two SNPs in Damascus breed, one SNPs in Zaraibi breed, while the Barki breed did not show any SNPs. Moreover, PRL-Eco24I/PCR-RFLP showed three genotypes (AA, AB and BB). The genotype AB showed the maximum frequency in all the studied breeds (0.75, 0.85, and 0.90 for Damascus, Barki and Zaraibi breeds, respectively). Observed heterozygosity (Ho) value was higher than expected heterozygosity (He) value all studied breeds. In addition, the values of both Ho and He were the highest in Zaraibi breed (0.90 and 0.51 respectively). Chi-square (χ²) value revealed a significant variation Hardy-Weinberg equilibrium (P < .05) in the three studied breeds. It is the highest in Zaraibi goats and lowest in Damascus breed. The results demonstrated that the PRL-Eco24I/PCR-RFLP polymorphism may be utilized as effective marker for genetic differentiation between goat breeds, but MSTN-HaeIII/PCR-RFLP revealed no polymorphism or variation, thus it is not recommended in the selection program. Moreover, these results open up interesting prospects for future selection programs, especially marker assisted selection. In addition, the results established that PCR-RFLP method is a suitable tool for calculating genetic variability.     

Analysis of genetic diversity among indigenous landraces from sesame (Sesamum indicum L.) core collection in China as revealed by SRAP and SSR markers

The molecular genetic diversity of 404 indigenous landraces from sesame core collection in China were evaluated by 11 SRAP and 3 SSR markers, 175 fragments were generated, of which 126 were polymorphic with an average polymorphism rate of 72%. Jaccard’s genetic similarity coefficients (GS=0.7130), Nei’s gene diversity (h=0.2418) and Shannon’s Information index (I=0.3847) were calculated, a dendrogram of the 404 landraces was made, landraces from various zones were distributed throughout the dendrogram, accessions from different agro-ecological zones were indistinguishable by cluster analysis, geographical separation did not generally result in greater genetic distance, a similar pattern was obtained using principal coordinates (PCO) analysis. As to seven agro-ecological zones, the maximum Nei’s gene diversity (h = 0.2613) and Shannon index (I = 0.3980) values in zone VII indicated that they were genetically more diverse than those in other zones, while the least genetically diverse region was zone III (h = 0.1772, I = 0.2858). Nei’s genetic identity and genetic distance among landraces from seven agro-ecological zones were also analyzed, the genetic relationship of seven zones was inferred using the UPGMA method. This study demonstrated that SRAP and SSR markers were appropriate for evaluation of sesame genetic diversities. There existed extensive genetic diverse among indigenous landraces and the abundance of genetic diversity of landraces in different agro-ecological zones was various. Understanding of these characteristics of indigenous landraces in China can provide theoretical foundation for further collection, effective protection and reasonable utilization of these sesame landraces in breeding.     

AFLP analysis of genetic diversity within and between Arabidopsis thaliana ecotypes

The degree of genetic diversity within and between 21 Arabidopsis thaliana (L.) Heynh ecotypes was estimated by AFLP analysis. Within seven of the 21 ecotypes, a low but significant level of polymorphism was detected, and for five of these ecotypes two or three distinct subgroups could be distinguished. As these ecotypes represent natural populations, this intra-ecotypic diversity reflects natural genetic variation and diversification within the ecotypes. The source of this diversity remains unclear but is intriguing in view of the predominantly self-fertilizing nature of Arabidopsis. Interrelationships between the different ecotypes were estimated after AFLP fingerprinting using two enzyme combinations (EcoRI/MseI and SacI/MseI) and a number of selective primer pairs. SacI recognition sites are less evenly distributed in the genome than EcoRI sites, and occur more frequently in coding sequences. In most cases, AFLP data from only one enzyme combination are used for genetic diversity analysis. Our results show that the use of two enzyme combinations can result in significantly different classifications of the ecotypes both in cluster and ordination analysis. This difference most probably reflects differences in the genomic distribution of the AFLP fragments generated, depending on the enzymes and selective primers used. For closely related varieties, as in the case of Arabidopsis ecotypes, this can preclude reliable classification.     

Discordant patterns of morphological and genetic divergence in the closely related species Schizanthus hookeri and S.?grahamii (Solanaceae)

In this study I have examined the patterns of morphological and genetic differentiation between two species of the Andean genus Schizanthus that differ in their pollination and mating systems. Schizanthus hookeri has a bee pollination syndrome and is strongly dependent on pollinators for seed set. In contrast, S.?grahamii has a hummingbird pollination syndrome and exhibits late autonomous selfing. Southern populations of the latter species have red flowers (reddish morph), while northern populations have yellow (yellowish morph) or pink flowers (pinkish morph). I used two noncoding chloroplast DNA (cpDNA) regions to investigate the genetic affinities between S.?hookeri and the three morphs of S.?grahamii. I also performed intra- and interspecific crosses to assess whether gene flow between species was possible. Phylogenetic analyses supported the existence of two differentiated clades that did not match currently accepted taxonomic classification. Accordingly, genetic distance did not correlate significantly with morphological distance. No fruits were produced from interspecific crosses, and there were no individuals with intermediate morphology that could indicate current and frequent hybridization events between species.?I propose that the discordance between cpDNA data and conventional taxonomy could be explained by parallel evolution, or alternatively, by a very sporadic hybridization.