Diploid Species Research Articles

Molecular characterization and phylogenetic analysis of novel Wx genes from Psathyrostachys juncea and Eremopyrum bonaepartis

The ratio of amylose/amylopectin can greatly influence the end-use quality of wheat products, and amylose synthesis only needs the granule-bound starch synthase I that is encoded by the Waxy (Wx) gene. Hence, the Wx allele variability is a vital determinant of amylose synthesis. In this study, four novel Wx genes were isolated from two diploid Triticeae species. Their sequence variations were analyzed, which showed that the polymorphism among the Wx-F1 alleles was low; only seven single nucleotide polymorphisms (SNPs) and one amino acid (AA) residue change (Arg541 ? Cys) were detected in the exon regions, and this change in Wx-F1b was predicted to have deleterious effects on protein function. The two Wx-Ns1 alleles in this study were different from two published alleles obtained using three overlapping primer sets. The polymorphism among the four Wx-Ns1 alleles was high, and 37 SNPs and ten AA residue changes were found, while all of those substitutions were neutral. However, one substitution (Leu237 ? Pro) between Wx-H1 and Wx-Ns1 was predicted that would probably affect the protein function. Divergence time analysis showed that Wx-Ns1a diverged from Wx-Ns1b about 1.06 MYAs. Phylogenetic analysis indicated that Wx-F1 were more closely related to Wx-O1 from Henrardia persica, Wx-R1 from Secale cereale ssp. cereale, and Wx-Xe1 from Eremopyrum triticeum, while Wx-Ns1 were more closely related to Wx-H1 from Hordeum vulgare ssp. vulgare and Wx-Hch1 from Hordeum chilense. These genes may be important candidates for wheat quality improvement.

Tools for Drawing Informative Idiograms.

Each species has a typical karyotype, which represents the phenotypic appearance of the somatic chromosomes including number, size, and morphology. An idiogram is a diagrammatic representation of the chromosomes showing their relative size, homologous groups, and different cytogenetic landmarks. Chromosomal analysis of cytological preparations is an essential component of many investigations, which involves the calculation of karyotypic parameters and the generation of idiograms. Although various tools are available for karyotype analysis, here we demonstrate karyotype analysis using our recently developed tool named KaryoMeasure. KaryoMeasure is a semi-automated free and user-friendly karyotype analysis software that facilitates data collection from different digital images of metaphase chromosome spreads and calculates a wide variety of chromosomal and karyotypic parameters along with the related standard errors. KaryoMeasure draws idiograms of both diploid and allopolyploid species into a vector-based SVG or PDF image file.

Inferring the Demographic History and Inheritance Mode of Tetraploid Species Using ABC.

Genomic patterns of diversity and divergence are impacted by certain life history traits, reproductive systems, and demographic history. The latter is characterized by fluctuations in population sizes over time, as well as by temporal patterns of introgression. For a given organism, identifying a demographic history that deviates from the standard neutral model allows a better understanding of its evolution but also helps to reduce the risk of false positives when screening for molecular targets of natural selection. Tetraploid organisms and beyond have demographic histories that are complicated by the mode of polyploidization, the mode of inheritance, and different scenarios of gene flow between sub-genomes and diploid parental species. Here we provide guidelines for experimenters wishing to address these issues through a flexible statistical framework: approximate Bayesian computation (ABC). The emphasis is on the general philosophy of the approach to encourage future users to exploit the enormous flexibility of ABC beyond the limitations imposed by generalist data analysis pipelines.

Evolution of a hybrid zone of two willow species (Salix L.) in the European Alps analyzed by RAD-seq and morphometrics.

Natural hybridization of plants can result in many outcomes with several evolutionary consequences, such as hybrid speciation and introgression. Natural hybrid zones can arise in mountain systems as a result of fluctuating climate during the exchange of glacial and interglacial periods, where species retract and expand their territories, resulting in secondary contacts. Willows are a large genus of woody plants with an immense capability of interspecific crossing. In this study, the sympatric area of two diploid sister species, S.foetida and S.waldsteiniana in the eastern European Alps, was investigated to study the genomic structure of populations within and outside their contact zone and to analyze congruence of morphological phenotypes with genetic data. Eleven populations of the two species were sampled across the Alps and examined using phylogenetic network and population genetic structure analyses of RAD Seq data and morphometric analyses of leaves. The results showed that a homoploid hybrid zone between the two species was established within their sympatric area. Patterns of genetic admixture in homoploid hybrids indicated introgression with asymmetric backcrossing to not only one of the parental species but also one hybrid population forming a separate lineage. The lack of F1 hybrids indicated a long-term persistence of the hybrid populations. Insignificant isolation by distance suggests that gene flow can act over large geographical scales. Morphometric characteristics of hybrids supported the molecular data and clearly separated populations of the parental species, but showed intermediacy in the hybrid zone populations with a bias toward S.waldsteiniana. The homoploid hybrid zone might have been established via secondary contact hybridization, and its establishment was fostered by the low genetic divergence of parental species and a lack of strong intrinsic crossing barriers. Incomplete ecological separation and the ability of long-distance dispersal of willows could have contributed to the spatial expansion of the hybrid zone.

Genome-wide family prediction unveils molecular mechanisms underlying the regulation of agronomic traits in Urochloa ruziziensis.

Tropical forage grasses, particularly those belonging to the Urochloa genus, play a crucial role in cattle production and serve as the main food source for animals in tropical and subtropical regions. The majority of these species are apomictic and tetraploid, highlighting the significance of U. ruziziensis, a sexual diploid species that can be tetraploidized for use in interspecific crosses with apomictic species. As a means to support breeding programs, our study investigates the feasibility of genome-wide family prediction in U. ruziziensis families to predict agronomic traits. Fifty half-sibling families were assessed for green matter yield, dry matter yield, regrowth capacity, leaf dry matter, and stem dry matter across different clippings established in contrasting seasons with varying available water capacity. Genotyping was performed using a genotyping-by-sequencing approach based on DNA samples from family pools. In addition to conventional genomic prediction methods, machine learning and feature selection algorithms were employed to reduce the necessary number of markers for prediction and enhance predictive accuracy across phenotypes. To explore the regulation of agronomic traits, our study evaluated the significance of selected markers for prediction using a tree-based approach, potentially linking these regions to quantitative trait loci (QTLs). In a multiomic approach, genes from the species transcriptome were mapped and correlated to those markers. A gene coexpression network was modeled with gene expression estimates from a diverse set of U. ruziziensis genotypes, enabling a comprehensive investigation of molecular mechanisms associated with these regions. The heritabilities of the evaluated traits ranged from 0.44 to 0.92. A total of 28,106 filtered SNPs were used to predict phenotypic measurements, achieving a mean predictive ability of 0.762. By employing feature selection techniques, we could reduce the dimensionality of SNP datasets, revealing potential genotype-phenotype associations. The functional annotation of genes near these markers revealed associations with auxin transport and biosynthesis of lignin, flavonol, and folic acid. Further exploration with the gene coexpression network uncovered associations with DNA metabolism, stress response, and circadian rhythm. These genes and regions represent important targets for expanding our understanding of the metabolic regulation of agronomic traits and offer valuable insights applicable to species breeding. Our work represents an innovative contribution to molecular breeding techniques for tropical forages, presenting a viable marker-assisted breeding approach and identifying target regions for future molecular studies on these agronomic traits.

The allopolyploid origin of <i>Euphorbia stevenii</i> and <i>E. boöphthona</i> (Euphorbiaceae)

To elucidate the ancestry of the allopolyploids <i>E. stevenii</i> and <i>E. boöphthona</i>, I examined eleven isozyme loci and 24 morphological characters from 28 populations representing five related <i>Euphorbia</i> species from Australia. According to an analysis of genetic and morphological data, three diploid species differentiated recently, but two independent polyploid species are estimated to have differentiated a relatively long time ago. Fixed heterozygosity for most isozymes in <i>E. stevenii</i> and <i>E. boöphthona</i> strongly suggests that these two species are allopolyploids rather than autopolyploids. The isozyme profiles of <i>E. stevenii</i> indicate that it is an allopolyploid that evolved from interspecific hybridization between the diploid <i>E. tannensis</i> and unidentified or extinct tetraploid species. In addition, isozyme patterns strongly suggest that <i>E. stevenii</i> was one of the ancestors of <i>E. boöphthona</i>. However, <i>E. boöphthona</i> showed a large number of fixed alleles that were not detected in any other Australian <i>Eremophyton</i> species. The most likely hypothesis for the origin of <i>E. boöphthona</i> is that it was formed by hybridization and chromosomal doubling between an extinct diploid species and the hexaploid <i>E. stevenii</i>.

Physiological Response of Selected Rice Accessions to Salinity and In Silico Analysis of DREB1A Gene Among Diploid Oryza Species

The responses of selected rice accessions to variant salt concentrations and in-silico analysis of DREB1A gene among diploid Oryza species were evaluated. Ten (10) rice accessions were selected based on their popularity in farmer's fields. Seedlings of each variety (one per pot) were watered with variant salt concentrations of 0mM, 100mM and 200mM for 21 days. The morpho-physiological characters (plant height, number of tillers, root length and dry weight) were evaluated using a standard evaluation system for rice. The reference sequences of OsDREB1A and AtDREB1A were used as queries to search against the 10 diploid Oryza species in the BLASTN of the PlantEnsembl database to reveal DREB1A orthologs. The retrieved DREB1A orthologs were used to compute the physicochemical properties of their proteins, gene motifs, intron-exon architecture and phylogenetic relationship. The studied accessions showed significant differences (p<0.05) in morpho-physiological responses to salinity. The accessions Zaqama, Yar-Garnaki, Yar-Yuti, Samira and Chana-Beru performed better under salt stress and there was no significant difference (p>0.05) between the control and salt-treated groups. Additionally, the in-silico analysis of DREB1A gene identified 10 orthologs with conserved single transcript, AP2 domain and unstable protein (characteristics of TFs) across the 10 diploid Oryza species. Phylogenetic analysis revealed 3 clusters of African rice and its progenitor, Asian rice and their relatives and O. brachyantha/O. punctata complex, similar to the evolution of rice species. Conclusively, salt stress affects rice in a concentration-dependent manner and DREB1A gene is a conserved plant transcription factor (TF) across diploid Oryza species.

Conserved and divergent evolution of the bZIP transcription factor in five diploid Gossypium species.

495 bZIP members with 12 subfamilies were identified in the five diploid cottons. Segmental duplication events in cotton ancestor might have led to primary expansion of the cotton bZIP members. The basic leucine zipper (bZIP) transcription factor is one of the largest and most diverse families in plants. The evolutionary history of the bZIP family is still unclear in cotton. In this study, a total of 495 bZIP members were identified in five diploid Gossypium species, including 100 members in Gossypium arboreum, 104 members in Gossypium herbaceum, 95 members in Gossypium raimondii, 96 members in Gossypium longicalyx, and 100 members in Gossypium turneri. The bZIP members could be divided into 12 subfamilies with biased gene proportions, gene structures, conserved motifs, expansion rates, gene loss rates, and cis-regulatory elements. A total of 239 duplication events were identified in the five Gossypium species, and mainly occurred in their common ancestor. Furthermore, some GabZIPs and GhebZIPs could be regarded as important candidates in cotton breeding. The bZIP members had a conserved and divergent evolution in the five diploid Gossypium species. The current study laid an important foundation on the evolutionary history of the bZIP family in cotton.

Population genomics and subgenome evolution of the allotetraploid frog Xenopus laevis in southern Africa

Allotetraploid genomes have two distinct genomic components called subgenomes that are derived from separate diploid ancestral species. Many genomic characteristics such as gene function, expression, recombination, and transposable element mobility may differ significantly between subgenomes. To explore the possibility that subgenome population structure and gene flow may differ as well, we examined genetic variation in an allotetraploid frog-the African clawed frog (Xenopus laevis)-over the dynamic and varied habitat of its native range in southern Africa. Using reduced representation genome sequences from 91 samples from 12 localities, we found no strong evidence that population structure and gene flow differed substantially by subgenome. We then compared patterns of population structure in the nuclear genome to the mitochondrial genome using Sanger sequences from 455 samples from 183 localities. Our results provide further resolution to the geographic distribution of mitochondrial and nuclear diversity in this species and illustrate that population structure in both genomes corresponds roughly with variation in seasonal rainfall and with the topography of southern Africa.

Inter-Specific Hybridization in Cotton (Gossypium hirsutum) for Crop Improvement

Interspecific hybridization has contributed significantly to land diversity, species evolution, and crops’ domestication, including upland cotton, the cultivated form of Gossypium hirsutum. Being the world’s most important fiber crop species, Gossypium hirsutum belongs to the allotetraploid Gossypium consisting of six additional tetraploid species. The lint fiber evolved once in diploid parent A-genome species in the Gossypium’s history and passed on during hybridization of the A-genome with the D-genome and was maintained in subsequent evolution. The domestication history of G. hirsutum involved the collection and use of lint fibers by indigenous people for the purpose of making strings and other textile products; hence, spinnable lint fibers were likely to have evolved under domestication. Crossing with G. barbadense has resulted in the development of multiple genetic lines in contemporary upland cotton. However, in later-generation hybrids between G. hirsutum and other polyploid species, reproductive barriers such as reduced fertility, segregation distortion, and hybrid breakdown are frequently observed, complicating the task of introgressing new, stably inherited allelic variation from inter-specific hybridization. Recent efforts in molecular genetics research have provided insights into the location and effects of QTLs from wild species that are associated with traits important to cotton production. These and future research efforts will undoubtedly provide the tools that can be utilized by plant breeders to access novel genes from wild and domesticated allotetraploid Gossypium for upland cotton improvement.

Sequencing of Camelina neglecta, a diploid progenitor of the hexaploid oilseed Camelina sativa.

Camelina neglecta is a diploid species from the genus Camelina, which includes the versatile oilseed Camelina sativa. These species are closely related to Arabidopsis thaliana and the economically important Brassica crop species, making this genus a useful platform to dissect traits of agronomic importance while providing a tool to study the evolution of polyploids. A highly contiguous chromosome-level genome sequence of C.neglecta with an N50 size of 29.1Mb was generated utilizing Pacific Biosciences (PacBio, Menlo Park, CA) long-read sequencing followed by chromosome conformation phasing. Comparison of the genome with that of C.sativa shows remarkable coincidence with subgenome 1 of the hexaploid, with only one major chromosomal rearrangement separating the two. Synonymous substitution rate analysis of the predicted 34 061 genes suggested subgenome 1 of C.sativa directly descended from C.neglecta around 1.2mya. Higher functional divergence of genes in the hexaploid as evidenced by the greater number of unique orthogroups, and differential composition of resistant gene analogs, might suggest an immediate adaptation strategy after genome merger. The absence of genome bias in gene fractionation among the subgenomes of C.sativa in comparison with C.neglecta, and the complete lack of fractionation of meiosis-specific genes attests to the neopolyploid status of C.sativa. The assembled genome will provide a tool to further study genome evolution processes in the Camelina genus and potentially allow for the identification and exploitation of novel variation for Camelina crop improvement.

Evaluation of In Vitro Morphogenic Response of Triticum urartu, a Donor of Au Genome of Modern Wheat

Triticum urartu Thum. ex Gandil. is a wild diploid wheat species (2n = 2x = 14) that is an Au genome donor of modern polyploid cultivars of durum and bread wheat. In the last decade, this relict species has attracted breeders as donors of various agronomically important characteristics to broaden the genetic diversity of cultivated wheat. In addition, T. urartu can be considered as a model species for studying the evolution, biology and genomics of wheat without the cross-influence of homologous sub-genomes. Various genetic engineering technologies, including transgenesis and genome editing, may be applied to facilitate the functional characterization of genes located in A chromosomes. Such biotechnological techniques are still required for the efficient tissue culture systems to allow easy plant regeneration. The objective of our study was to assess the abilities of in vitro plant regeneration from zygotic immature embryo-derived tissues of spring and winter types of T. urartu. Three synthetic auxins, 2,4-D, Dicamba and Picloram, at four concentrations were studied to stimulate morphogenic responses in spring T. urartu. The induction medium supplemented with 4 mg·L−1 Dicamba stimulated the highest frequency of regenerable callus production (65.8%), promoting the generation of 5.7 plants. Although the presence of 2 mg·L−1 2,4-D was less effective in stimulating regenerable callus formation (53.2%) than Dicamba, it allowed the regeneration of more plants from one regenerable callus (9.3 plants). These two treatments also successfully initiated morphogenesis in winter assertions; however, their regenerative capacity was generally lower. The frequency of regenerable callus production was accession-dependent and fluctuated within 31.3 to 49.2%, with a formation of an average 2.2–5.8 plants per callus. The relatively simple and fast regeneration system described in this study could be further used as the basis for regenerating transgenic plants of T. urartu.

Dual Domestication, Diversity, and Differential Introgression in Old World Cotton Diploids.

Domestication in the cotton genus is remarkable in that it has occurred independently four different times at two different ploidy levels. Relatively little is known about genome evolution and domestication in the cultivated diploid species Gossypium herbaceum and Gossypium arboreum, due to the absence of wild representatives for the latter species, their ancient domestication, and their joint history of human-mediated dispersal and interspecific gene flow. Using in-depth resequencing of a broad sampling from both species, we provide support for their independent domestication, as opposed to a progenitor-derivative relationship, showing that diversity (mean π = 6 × 10-3) within species is similar, and that divergence between species is modest (FST = 0.413). Individual accessions were homozygous for ancestral single-nucleotide polymorphisms at over half of variable sites, while fixed, derived sites were at modest frequencies. Notably, two chromosomes with a paucity of fixed, derived sites (i.e., chromosomes 7 and 10) were also strongly implicated as having experienced high levels of introgression. Collectively, these data demonstrate variable permeability to introgression among chromosomes, which we propose is due to divergent selection under domestication and/or the phenomenon of F2 breakdown in interspecific crosses. Our analyses provide insight into the evolutionary forces that shape diversity and divergence in the diploid cultivated species and establish a foundation for understanding the contribution of introgression and/or strong parallel selection to the extensive morphological similarities shared between species.

Nonsymbiotic legumes are more invasive, but only if polyploid.

Both mutualism and polyploidy are thought to influence invasion success in plants, but few studies have tested their joint effects. Mutualism can limit range expansion when plants cannot find a compatible partner in a novel habitat, or facilitate range expansion when mutualism increases a plant's niche breadth. Polyploids are also expected to have greater niche breadth because of greater self-compatibility and phenotypic plasticity, increasing invasion success. For 847 legume species, we compiled data from published sources to estimate ploidy, symbiotic status with rhizobia, specificity on rhizobia, and the number of introduced ranges. We found that diploid species have had limited spread around the globe regardless of whether they are symbiotic or how many rhizobia partners they can host. Polyploids, by contrast, have been successfully introduced to many new ranges, but interactions with rhizobia constrain their range expansion. In a hidden state model of trait evolution, we also found evidence of a high rate of re-diploidization in symbiotic legume lineages, suggesting that symbiosis and ploidy may interact at macroevolutionary scales. Overall, our results suggest that symbiosis with rhizobia limits range expansion when legumes are polyploid but not diploid.

The Gossypium herbaceum L. Wagad genome as a resource for understanding cotton domestication.

Gossypium herbaceum is a species of cotton native to Africa and Asia that is one of the 2 domesticated diploids. Together with its sister-species G. arboreum, these A-genome taxa represent models of the extinct A-genome donor of modern polyploid cotton, which provide about 95% of cotton grown worldwide. As part of a larger effort to characterize variation and improve resources among diverse diploid and polyploid cotton genomes, we sequenced and assembled the genome of G. herbaceum cultivar (cv.) Wagad, representing the first domesticated accession for this species. This chromosome-level genome was generated using a combination of PacBio long-read technology, HiC, and Bionano optical mapping and compared to existing genome sequences in cotton. We compare the genome of this cultivar to the existing genome of wild G. herbaceum subspecies africanum to elucidate changes in the G. herbaceum genome concomitant with domestication and extend these analyses to gene expression using available RNA-seq. Our results demonstrate the utility of the G. herbaceum cv. Wagad genome in understanding domestication in the diploid species, which could inform modern breeding programs.

Comparative phylogenomic analysis of 5’cis-regulatory elements (CREs) of miR160 gene family in diploid and allopolyploid cotton (Gossypium)

Cotton fiber development is a complex process regulated by numerous microRNAs (miRNAs), including miR160 that regulates auxin signaling in a grwoing cell. However, the evolution of cis-regulatory elements (CREs) in the 5’upstream regulatory regions of miR160 genes during cotton allopolyploidy is least known. Therefore, 1.5 kb upstream DNA sequences (−1 to −1500 bp) of miR160 genes from progenitor diploid A2 (G. arboreum), D5 (G. raimondii) and descendant allopolyploid AD1 (G. hirsutum) and AD2 (G. barbadense) cotton species were analyzed to visualize the evolutionary patterns preserved within the promoter regions of these homologous sequences. Several light-responsive, developmental-responsive, organ-specific, stress-responsive (biotic and abiotic), and hormone-responsive CREs were identified with diverse frequencies and wide distribution patterns. The structural alterations in the promoter regions were more prominent than the evolutionary changes acquired by miR160 genes, suggesting that miR160 gene sequences have been conserved throughout evolution, and the observed expression variations across cotton species are primarily due to the structural differences of their regulatory regions. The abiotic stress-responsive and hormone-responsive CREs exhibited prominent clustering at both proximal and distal ends, displaying varying frequencies. Thus, the origin of these CREs can be attributed to the genomic hybridization of diploid species that had led to the allopolyploid formation, or to the natural speciation/diversification of an allopolyploid event. Also, there is a high correlation between CREs-binding transcription factors and miR160 gene expression, suggesting a regulatory mechanism for spatiotemporal expression profiles of miR160 genes during cotton fiber development.

Agrobacterium-mediated transformation of Nicotiana glauca and Nicotiana sylvestris.

Agrobacterium-mediated transformation is the most popular approach for obtaining transgenic plants nowadays. There are plenty of protocols developed for different plant species. These protocols usually include the medium composition, the technology for preparing plant explants and cultivation conditions, as well as the choice of agrobacteria strains. Nicotiana tabacum, or cultivated tobacco, was one of the f irst successfully transformed plant species. Nicotiana tabacum is a model object in plant genetics, particularly due to its ability for transformation and regeneration. N. tabacum is a naturally transgenic plant since its genome contains a cellular T-DNA acquired from Agrobacteria. The signif icance of cT-DNA for plants has not yet been established. Some assume that cT-DNA can increase the ability of plants to regenerate due to some of the genes they contain. For example, rolC has been shown to affect the hormonal balance of plants, but the molecular mechanisms underlying this have yet to be found. RolC is also somehow involved in the secondary metabolism of plants. Like N. tabacum, Nicotiana glauca produces a wide range of secondary metabolites and contains an intact rolC gene in its genome. At the same time, unlike N. tabacum, N. glauca is a diploid species, which makes it more suitable for genetic engineering approaches. Nicotiana sylvestris is one of the ancestral species of N. tabacum and does not contain cT-DNA. The aim of this work was to develop a protocol for transformation and regeneration of N. glauca and N. sylvestris. We managed to find an optimum ratio of auxins and cytokinins that promotes both active callus formation and organogenesis in N. glauca and N. sylvestris leaf explants. The developed technique will be useful both for fundamental research that includes the N. glauca and N. sylvestris species, and for practical application in the pharmaceutical industry and biosynthesis.

Bioactive Compounds from Eruca sativa Seeds

Eruca sativa Miller (Brassicaceae) is an insect-pollinated diploid annual species which grows spontaneously in the entire Mediterranean basin from semi-arid to arid-hot conditions and is cultivated in Northern America, Europe, and Asia as either salad or oilseed crop. Here, some essential background was provided on this versatile crop, summarizing the present status of Eruca sativa research focusing on the wealth of bioactive ingredients in its seeds, which may find exploitation in agriculture, in the food industries and as nutraceuticals for their antioxidant and anti-inflammatory properties. Fatty acids of Eruca sativa seed oil, gums, glucosinolates and soluble and insoluble phenol and flavonoid fractions in the defatted press cake are the main bioactive compounds considered to date by the scientific literature and that deserve attention for their physical and biological activities.

Pseudorogneria libanotica Intraspecific Genetic Polymorphism Revealed by Fluorescence In Situ Hybridization with Newly Identified Tandem Repeats and Wheat Single-Copy Gene Probes.

The genus Pseudoroegneria (Nevski) Löve (Triticeae, Poaceae) with its genome abbreviated 'St' accounts for more than 60% of perennial Triticeae species. The diploid species Psudoroegneria libanotica (2n = 14) contains the most ancient St genome. Therefore, investigating its chromosomes could provide some fundamental information required for subsequent studies of St genome evolution. Here, 24 wheat cDNA probes covering seven chromosome groups were mapped in P. libanotica to distinguish homoelogous chromosomes, and newly identified tandem repeats were performed to differentiate seven chromosome pairs. Using these probes, we investigated intraspecific population chromosomal polymorphism of P. libanotica. We found that (i) a duplicated fragment of the 5St long arm was inserted into the short arm of 2St; (ii) asymmetrical fluorescence in situ hybridization (FISH) hybridization signals among 2St, 5St, and 7St homologous chromosome pairs; and (iii) intraspecific population of polymorphism in P. libanotica. These observations established the integrated molecular karyotype of P. libanotica. Moreover, we suggested heterozygosity due to outcrossing habit and adaptation to the local climate of P. libanotica. Specifically, the generated STlib_96 and STlib_98 repeats showed no cross-hybridization signals with wheat chromosomes, suggesting that they are valuable for identifying alien chromosomes or introgressed fragments of wild relatives in wheat.

QTL analysis for low temperature tolerance of wild potato species Solanum commersonii in natural field trials

Potato cultivars (Solanum tuberosum L.) are delicate to cold and frost. Low temperatures have a negative impact on potato growth, development and yield. However, genetic detection of frost tolerance loci is currently lacking. Here, we report a BC1 population that was constructed by crossing the diploid cold-resistant wild species S. commersonii with the diploid cold-sensitive wild species S. verrucosum. The frost tolerance of the resulting offspring was determined through four years of natural field frost experiments. Together with bulked segregant analysis (BSA) technology and traditional quantitative trait locus (QTL) mapping, four highly related QTLs were detected on Chr02 and Chr11. Furthermore, we constructed a partial genetic linkage map of Chr02, and two QTLs (QTL1 and QTL2) were detected on Chr02. Four genes located in candidate intervals have been reported to be associated with tolerance to abiotic stress and were significantly differentially expressed among the resistant and sensitive. Taken together, our results also suggest that the frost resistance of plants under variable low-temperature conditions is controlled by different loci.