Diploid Populations Research Articles

QTL mapping in outbred tetraploid (and diploid) diallel populations.

Over the last decade, multiparental populations have become a mainstay of genetics research in diploid species. Our goal was to extend this paradigm to autotetraploids by developing software for quantitative trait locus (QTL) mapping in connected F1 populations derived from a set of shared parents. For QTL discovery, phenotypes are regressed on the dosage of parental haplotypes to estimate additive effects. Statistical properties of the model were explored by simulating half-diallel diploid and tetraploid populations with different population sizes and numbers of parents. Across scenarios, the number of progeny per parental haplotype (pph) largely determined the statistical power for QTL detection and accuracy of the estimated haplotype effects. Multiallelic QTL with heritability 0.2 were detected with 90% probability at 25 pph and genome-wide significance level 0.05, and the additive haplotype effects were estimated with over 90% accuracy. Following QTL discovery, the software enables a comparison of models with multiple QTL and nonadditive effects. To illustrate, we analyzed potato tuber shape in a half-diallel population with three tetraploid parents. A well-known QTL on chromosome 10 was detected, for which the inclusion of digenic dominance lowered the Deviance Information Criterion (DIC) by 17 points compared to the additive model. The final model also contained a minor QTL on chromosome 1, but higher-order dominance and epistatic effects were excluded based on the DIC. In terms of practical impacts, the software is already being used to select offspring based on the effect and dosage of particular haplotypes in breeding programs.

Overdominant Mutations Restrict Adaptive Loss of Heterozygosity at Linked Loci.

Loss of heterozygosity is a common mode of adaptation in asexual diploid populations. Because mitotic recombination frequently extends the full length of a chromosome arm, the selective benefit of loss of heterozygosity may be constrained by linked heterozygous mutations. In a previous laboratory evolution experiment with diploid yeast, we frequently observed homozygous mutations in the WHI2 gene on the right arm of Chromosome XV. However, when heterozygous mutations arose in the STE4 gene, another common target on Chromosome XV, loss of heterozygosity at WHI2 was not observed. Here, we show that mutations at WHI2 are partially dominant and that mutations at STE4 are overdominant. We test whether beneficial heterozygous mutations at these two loci interfere with one another by measuring loss of heterozygosity at WHI2 over 1,000 generations for ∼300 populations that differed initially only at STE4 and WHI2. We show that the presence of an overdominant mutation in STE4 reduces, but does not eliminate, loss of heterozygosity at WHI2. By sequencing 40 evolved clones, we show that populations with linked overdominant and partially dominant mutations show less parallelism at the gene level, more varied evolutionary outcomes, and increased rates of aneuploidy. Our results show that the degree of dominance and the phasing of heterozygous beneficial mutations can constrain loss of heterozygosity along a chromosome arm, and that conflicts between partially dominant and overdominant mutations can affect evolutionary outcomes.

Detecting Selection on Segregating Gene Duplicates in a Population.

Gene duplication is a fundamental process that has the potential to drive phenotypic differences between populations and species. While evolutionarily neutral changes have the potential to affect phenotypes, detecting selection acting on gene duplicates can uncover cases of adaptive diversification. Existing methods to detect selection on duplicates work mostly inter-specifically and are based upon selection on coding sequence changes, here we present a method to detect selection directly on a copy number variant segregating in a population. The method relies upon expected relationships between allele (new duplication) age and frequency in the population dependent upon the effective population size. Using both a haploid and a diploid population with a Moran Model under several population sizes, the neutral baseline for copy number variants is established. The ability of the method to reject neutrality for duplicates with known age (measured in pairwise dS value) and frequency in the population is established through mathematical analysis and through simulations. Power is particularly good in the diploid case and with larger effective population sizes, as expected. With extension of this method to larger population sizes, this is a tool to analyze selection on copy number variants in any natural or experimentally evolving population. We have made an R package available at https://github.com/peterbchi/CNVSelectR/ which implements the method introduced here.

Combining conventional QTL analysis and whole-exome capture-based bulk-segregant analysis provides new genetic insights into tuber sprout elongation and dormancy release in a diploid potato population

Tuber dormancy and sprouting are commercially important potato traits as long-term tuber storage is necessary to ensure year-round availability. Premature dormancy release and sprout growth in tubers during storage can result in a significant deterioration in product quality. In addition, the main chemical sprout suppressant chlorpropham has been withdrawn in Europe, necessitating alternative approaches for controlling sprouting. Breeding potato cultivars with longer dormancy and slower sprout growth is a desirable goal, although this must be tempered by the needs of the seed potato industry, where dormancy break and sprout vigour are required for rapid emergence. We have performed a detailed genetic analysis of tuber sprout growth using a diploid potato population derived from two highly heterozygous parents. A dual approach employing conventional QTL analysis allied to a combined bulk-segregant analysis (BSA) using a novel potato whole-exome capture (WEC) platform was evaluated. Tubers were assessed for sprout growth in storage at six time-points over two consecutive growing seasons. Genetic analysis revealed the presence of main QTL on five chromosomes, several of which were consistent across two growing seasons. In addition, phenotypic bulks displaying extreme sprout growth phenotypes were subjected to WEC sequencing for performing BSA. The combined BSA and WEC approach corroborated QTL locations and served to narrow the associated genomic regions, while also identifying new QTL for further investigation. Overall, our findings reveal a very complex genetic architecture for tuber sprouting and sprout growth, which has implications both for potato and other root, bulb and tuber crops where long-term storage is essential.

Induction of Autotetraploidy and its effects on morphophysiological traits in some annual and perennial medics

In order to study of the effects of polyploidy on morph-physiological traits in some annual and perennial medics, five annual and three perennial diploid medics were subjected to different concentrations of colchicine solution (0.1%, 0.5%, 1% and 2%) in mitosis stage. The induced tetraploids were identified by counting stomata guard cells chloroplasts. The highest survival rate and tetraploidy induction with average values of 80.2% and 74.3% were obtained using 0.1% colchicine concentration. All of the 21 entries (5 annual diploids and their induced tetraploids as M. lupulina, M. radiata, M. rijidula, M. truncatula, M. turbinata, and 3 populations of perennial diploid of M. sativa ssp. Caerulea (Karaj1, Karaj2 and Tehran) and their induced tetraploids and 5 commercial tetraploid alfalfa cultivars (Bami, Hamadani, Baghdadi, Ghareyongeh and Renger) grown in pots in a glasshouse experiment using completely randomized design with five replications in 2018 in Ahvaz, Iran. Data were collected for leaf length, leaf width, shoot and root length, seedling weight, shoot weight, root weight, branch number, leaf area index (LAI) and water use efficiency (WUE). Result of mean comparisons between three groups (2x, induced 4x and controls 4x), showed that both groups of induced and natural tetraploids had significantly higher mean values for all the traits except leaf length, shoot length and root length than that for diploids. For the latter traits there were no significant differences between 2x and induced 4x. On the overall, the induced 4x had 60%, 62%, 68%, 65%, 22%, 109% and 47% higher mean values than their parental 2x for seedling weight, shoot weight, root weight, LAI, WUE and branch number, respectively. It was concluded that increasing ploidy level provides plant breeders with a promising tool in the breeding improve new varieties suited for future climate scenarios.

Increased ploidy of Butomus umbellatus in introduced populations is not associated with higher phenotypic plasticity to N and P.

Separate introductions or post-introduction evolution may lead to multiple invader genotypes or cytotypes that differ in growth rates, biomass or chemical profile responses (phenotype) to a range of environments. If the invader has high trait plasticity to a range of resource levels, then sediment N or P enrichment may enhance invasiveness. However, the ways in which ploidy, plasticity, and available N or P interact are unknown for most species despite the potential to explain spread and impacts by invaders with multiple introduced lineages. We conducted a common garden experiment with four triploid and six diploid populations of Butomus umbellatus, collected from across its invasive range in the USA. Plants were grown under different N or P nutrient levels (4, 40, 200, 400 mg L-1 N; 0.4, 4, 40 mg L-1 P) and we measured reaction norms for biomass, clonal reproduction and tissue chemistry. Contrary to our expectation, triploid B. umbellatus plants were less plastic to variation in N or P than diploid B. umbellatus in most measured traits. Diploid plants produced 172 % more reproductive biomass and 57 % more total biomass across levels of N, and 158 % more reproductive biomass and 33 % more total biomass across P than triploid plants. Triploid plants had lower shoot:root ratios and produced 30 % and 150 % more root biomass than diploid plants in response to increases in N and P, respectively. Tissue chemistry differed between cytotypes but plasticity was similar; N was 8 % higher and C:N ratio was 30 % lower in triploid than diploid plants across levels of N and plant parts, and N was 22 % higher and C:N ratio 27 % lower across levels of P and plant parts. Our results highlight differences in nutrient response between cytotypes of a widespread invader, and we call for additional field studies to better understand the interaction of nutrients and ploidy during invasion.

Distant hybridization and gynogenesis between Nile tilapia Oreochromis niloticus and Jaguar cichlid Parachromis managuensis

To investigate the distant hybridization and gynogenesis between Nile tilapia Oreochromis niloticus and Jaguar cichlid Parachromis managuensis, reciprocal crossing was first performed between the two species. No offspring, however, were viable when there were these hybridizations. Gynogenesis was induced in O. niloticus and P. managuensis using ultraviolet (UV)-irradiated spermatozoa from P. managuensis and O. niloticus, respectively. The morphology during embryonic development indicated gynogenetic offspring of both O. niloticus and the P. managuensis were normal and deformed, and the results from flow cytometric analysis indicated normal fry were diploid and deformed fry were haploid. Gynogenetic O. niloticus and P. managuensis had the same DNA content and chromosome number as their species of origin, indicating that gynogenetic individuals were produced in both species. The presence of only females for both gynogenetic P. managuensis and O. niloticus was indicative of an XX genotype in the female P. managuensis and O. niloticus. Results from studies on genetic diversity indicated the average heterozygosity of the gynogenetic diploid population of O. niloticus were less than that of the cultured population, but the genetic homozygosity of the gynogenetic diploid population of O. niloticus was greater than that of the cultured population after one generation of gynogenesis, which achieved the goal of rapidly establishing genetic homozygosity.

Euphrasia ultima, a new locally endemic diploid species from the Ortler/Ortles range (Italy), is a close relative of widespread allotetraploid E. minima

The goal of this study was to tackle two questions related to the systematics of small-flowering Euphrasia species from the Eastern Alps. Our first aim was to test the hypothesis of a wider distribution of diploid E. inopinata, considered endemic to the uppermost Ötztal valley in Austria based on ploidy screening of ca. 70 populations along a latitudinal transect. We failed to find new populations of E. inopinata but during the sampling campaign, a diploid population was detected in the eastern Ortler/Ortles mountain range (Italy), which could neither be assigned to E. inopinata nor to E. minima. Thus, our second aim was to clarify, based on a comprehensive sampling of individuals and the use of Amplified Fragment Length Polymorphisms (AFLPs) and/or morphometric data, if this diploid population is morphologically and genetically consistently divergent from both, tetraploid widespread E. minima and E. inopinata. As this was confirmed, we established the relationships of the new entity based on Internal Transcribed Spacer sequences, which uncovered a close relationship with E. minima and describe it here as a new diploid species, E. ultima, which, based on current knowledge, is locally endemic even if a bigger distribution area appears likely.

Abstract 2199: Identifying genomic heterogeneity at single-cell resolution in endometrial cancer

Abstract Introduction: Endometrial cancer accounts for ~76,000 deaths amongst women worldwide. In the United States, it is estimated 65,620 new cases and 12,590 deaths occurring in 2020, being the fourth most common gynecologic malignancy in the country. It has been reported that specific molecular characteristics in tissues are associated with poorer prognosis. Publicly available data generated from bulk molecular profiling of tumors has provided a molecular taxonomy of endometrial cancers with common alterations occurring in a number of known oncogenic pathways. However, little is known about the degree of heterogeneity in endometrial cancer. Thus, we have set out to utilize single cell technologies to assess tumor heterogeneity in endometrial cancers. Methods: Our preliminary study includes serous and mixed lineage endometrial tumors from five (3 African Americans, 1 Hispanic/Latino, 1 Caucasian) cases. In addition to bulk whole exome sequencing, we utilized single cell whole genome sequencing to assess global copy number heterogeneity. OCT-embedded frozen tumor sections were dissociated to collect nuclei, which were subjected to single nuclei sequencing using the 10x ChromiumTM single cell copy number variation (scCNV) assay targeting 500 cells per sample. Single cell libraries were quality assessed and sequenced using the Illumina NovaSeq6000 system. Data were processed using the 10X Genomics CellRanger pipeline for assessment of copy number heterogeneity. Results: We generated scCNV data on a total of 1,546 cells across five tumors. Hierarchical clustering and visual inspection of scCNV data reveals obvious somatic copy number tumor cell heterogeneity in all samples, including single and mixed histology tumors. Heterogeneity was mostly distinguished by whole chromosome or chromosome arm level gains or losses. Clonal focal amplifications were detected at 5p, 8p, 8q, and 17q encompassing known oncogenes. As we are able to identify clustered diploid populations of normal cells, we are using these data to perform segregation analysis for CGH analysis and the identification of somatic mutations in clonal populations of cells. These data are being compared to bulk exome sequencing data to determine the power of scCNV for detecting clonal populations of tumor cells. Conclusions: This project used high resolution single cell sequencing in five endometrial cancers with varying histologies. scCNV analysis provided clear evidence of heterogeneity in all tumors that were assessed in our study. This single cell whole genome data is being further analyzed for the presence of focal events, breakpoints and mutations that further stratify clonal tumor cell components in these cases. We plan to further expand this cohort to establish additional evidence for heterogeneity in endometrial cancer. Citation Format: Enrique I. Velazquez Villarreal, Lee D. Gibbs, Dana Mahinbakht, Diane M. Da Silva, Lynda D. Roman, David W. Craig, John D. Carpten. Identifying genomic heterogeneity at single-cell resolution in endometrial cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2199.

High-Density Linkage Map Construction and QTL Identification in a Diploid Blueberry Mapping Population.

Genotyping by sequencing approaches have been widely applied in major crops and are now being used in horticultural crops like berries and fruit trees. As the original and largest producer of cultivated blueberry, the United States maintains the most diverse blueberry germplasm resources comprised of many species of different ploidy levels. We previously constructed an interspecific mapping population of diploid blueberry by crossing the parent F1#10 (Vaccinium darrowii Fla4B × diploid V. corymbosum W85–20) with the parent W85–23 (diploid V. corymbosum). Employing the Capture-Seq technology developed by RAPiD Genomics, with an emphasis on probes designed in predicted gene regions, 117 F1 progeny, the two parents, and two grandparents of this population were sequenced, yielding 131.7 Gbp clean sequenced reads. A total of 160,535 single nucleotide polymorphisms (SNPs), referenced to 4,522 blueberry genome sequence scaffolds, were identified and subjected to a parent-dependent sliding window approach to further genotype the population. Recombination breakpoints were determined and marker bins were deduced to construct a high density linkage map. Twelve blueberry linkage groups (LGs) consisting of 17,486 SNP markers were obtained, spanning a total genetic distance of 1,539.4 cM. Among 18 horticultural traits phenotyped in this population, quantitative trait loci (QTLs) that were significant over at least 2 years were identified for chilling requirement, cold hardiness, and fruit quality traits of color, scar size, and firmness. Interestingly, in 1 year, a QTL associated with timing of early bloom, full bloom, petal fall, and early green fruit was identified in the same region harboring the major QTL for chilling requirement. In summary, we report here the first high density bin map of a diploid blueberry mapping population and the identification of several horticulturally important QTLs.

Ecotypic differentiation of a circumpolar Arctic-alpine species at mid-latitudes: variations in the ploidy level and reproductive system of Vaccinium vitis-idaea.

Although plant species originated from Arctic regions commonly grow in alpine habitats at mid-latitudes, some populations of these species exist also in some specific habitats below the treeline. Local populations at lower elevations may have different origins, ploidy levels, mating systems and/or morphological traits from alpine populations, but comparative studies between alpine and low-elevation populations are scarce. We aimed to reveal the ecological and genetic differentiations between higher and lower populations of Vaccinium vitis-idaea in Hokkaido, northern Japan by comparing 22 populations growing in diverse environments. We analysed the ploidy level of individual populations using flow cytometry. Genetic differentiation among populations, and genetic diversity within populations were calculated using microsatellite markers. Fruit and seed production were recorded under natural conditions, and a pollination experiment was conducted to reveal the variations in mating system across populations. Furthermore, we compared shoot growth and leaf characteristics among populations. Most of the low-elevation populations were tetraploid, whereas all but one of the alpine populations were diploid. Tetraploid populations were clearly differentiated from diploid populations. Some tetraploid populations formed huge clonal patches but genetic diversity was higher in tetraploids than in diploids. Alpine diploids were self-incompatible and produced more seeds per fruit than tetraploid populations. In contrast, tetraploids showed high self-compatibility. Leaf size and foliar production were greater in tetraploid populations. Our results indicate that the genetic compositions of low-elevation tetraploid populations are different from those of alpine diploid populations. Most populations at lower elevations contained unique ecotypes suited to persistence in isolated situations. Local, low-elevation populations of typical alpine species maintain ecologically and genetically specific characteristics and could be valuable in terms of evolutionary and conservation biology. The present study demonstrates the biological importance of small and isolated populations at the edges of species distribution.

Influence of Butomus umbellatus L. lineage and age on leaf chemistry and performance of a generalist caterpillar

Invasive plants may display age or genotype-specific defenses against herbivory. Thus, the importance of herbivory for preventing or mitigating plant invasions may depend on genetics and age-structure of invader populations. We used an excised-leaf experiment to test whether constitutive herbivore defenses in Butomus umbellatus L. (flowering rush) plants decline with age between colonizing (1st year) and established (2nd year) plants and whether the decline was parallel between introduced diploid and triploid genotypes. Leaves from colonizing and established plants were fed to the generalist herbivore fall armyworm (FAW; Spodoptera frugiperda) and then short-term FAW development was measured. Additionally, leaf dry matter content (DMC), % carbon (%C), % nitrogen (%N), carbon:nitrogen (C:N) ratio, and total leaf phenolics were determined for leaves from a subset of test plants. FAW fed leaves from diploid plants grew 27 % less than those fed leaves from triploid plants but were only 1 % smaller when fed leaves from second-year versus first-year plants of either cytotype. DMC of diploid leaves was 11 % greater overall (11 % DMC) but the difference in cytotypes depended on age (1 % difference in colonizing plants vs. 21 % difference in established plants). In general, diploid plants were characterized by 29 % higher total phenolics, 17 % less leaf nitrogen, and 21 % higher C:N ratio, regardless of age. Measured traits were, on average, 27 % more variable for diploid than triploid plants, possibly a reflection of increased genetic diversity of diploid flowering rush populations used in the study. These results demonstrate that diploid B. umbellatus plants are, overall, better defended against generalist herbivory than triploid plants. Differences in herbivore performance on B. umbellatus lineages, and to a lesser extent plants of varying ages, may therefore contribute to spatial or temporal heterogeneity in the dominance of genotypes in areas where they grow together.

A unified haplotype-based method for accurate and comprehensive variant calling.

Almost all haplotype-based variant callers were designed specifically for detecting common germline variation in diploid populations, and give suboptimal results in other scenarios. Here we present Octopus, a variant caller that uses a polymorphic Bayesian genotyping model capable of modeling sequencing data from a range of experimental designs within a unified haplotype-aware framework. Octopus combines sequencing reads and prior information to phase-called genotypes of arbitrary ploidy, including those with somatic mutations. We show that Octopus accurately calls germline variants in individuals, including single nucleotide variants, indels and small complex replacements such as microinversions. Using a synthetic tumor data set derived from clean sequencing data from a sample with known germline haplotypes and observed mutations in a large cohort of tumor samples, we show that Octopus is more sensitive to low-frequency somatic variation, yet calls considerably fewer false positives than other methods. Octopus also outputs realigned evidence BAM files to aid validation and interpretation.

Variance and limiting distribution of coalescence times in a diploid model of a consanguineous population

Recent modeling studies interested in runs of homozygosity (ROH) and identity by descent (IBD) have sought to connect these properties of genomic sharing to pairwise coalescence times. Here, we examine a variety of features of pairwise coalescence times in models that consider consanguinity. In particular, we extend a recent diploid analysis of mean coalescence times for lineage pairs within and between individuals in a consanguineous population to derive the variance of coalescence times, studying its dependence on the frequency of consanguinity and the kinship coefficient of consanguineous relationships. We also introduce a separation-of-time-scales approach that treats consanguinity models analogously to mathematically similar phenomena such as partial selfing, using this approach to obtain coalescence-time distributions. This approach shows that the consanguinity model behaves similarly to a standard coalescent, scaling population size by a factor 1−3c, where c represents the kinship coefficient of a randomly chosen mating pair. It provides the explanation for an earlier result describing mean coalescence time in the consanguinity model in terms of c. The results extend the potential to make predictions about ROH and IBD in relation to demographic parameters of diploid populations.

Graph-structured populations and the Hill-Robertson effect.

The Hill–Robertson effect describes how, in a finite panmictic diploid population, selection at one diallelic locus reduces the fixation probability of a selectively favoured allele at a second, linked diallelic locus. Here we investigate the influence of population structure on the Hill–Robertson effect in a population of size N. We model population structure as a network by assuming that individuals occupy nodes on a graph connected by edges that link members who can reproduce with each other. Three regular networks (fully connected, ring and torus), two forms of scale-free network and a star are examined. We find that (i) the effect of population structure on the probability of fixation of the favourable allele is invariant for regular structures, but on some scale-free networks and a star, this probability is greatly reduced; (ii) compared to a panmictic population, the mean time to fixation of the favoured allele is much greater on a ring, torus and linear scale-free network, but much less on power-2 scale-free and star networks; (iii) the likelihood with which each of the four possible haplotypes eventually fix is similar across regular networks, but scale-free populations and the star are consistently less likely and much faster to fix the optimal haplotype; (iv) increasing recombination increases the likelihood of fixing the favoured haplotype across all structures, whereas the time to fixation of that haplotype usually increased, and (v) star-like structures were overwhelmingly likely to fix the least fit haplotype and did so significantly more rapidly than other populations. Last, we find that small (N < 64) panmictic populations do not exhibit the scaling property expected from Hill & Robertson (1966 Genet. Res. 8, 269–294. (doi:10.1017/S0016672300010156)).

In-vitro cytotoxicity in relation to chemotypic diversity in diploid and tetraploid populations of Gentiana kurroo Royle

Ethnopharmacological relevanceGentiana kurroo is a multipurpose critically endangered medicinal herb prescribed as medicine in Ayurveda in India and exhibits various pharmacological properties including anti-cancer activity. The species is rich repository of pharmacologically active secondary metabolites together with secoiridoidal glycosides. Aim of the studyThe study aimed to investigate the chemical diversity in different populations/cytotypes prevailing in G. kurroo to identify elite genetic stocks in terms of optimum accumulation/biosynthesis of desired metabolites and having higher in-vitro cytotoxicity potential in relation to chemotypic diversity. Material and methodsThe wild plants of the species were collected from different ranges of altitudes from the Kashmir Himalayas. For cytological evaluation, the standard meiotic analysis was performed. The standard LC-MS/MS technique was employed for phytochemical analysis based on different marker compounds viz. sweroside, swertiamarin, and gentiopicroside. Different tissues such as root-stock, aerial parts, and flowers were used for chemo-profiling. Further, the methanolic extracts of diploid and tetraploid cytotypes were assessed for cytotoxic activity by using MTT assay against four different human cancer cell lines. ResultsThe quantification of major bioactive compounds based on tissue- and location-specific comparison, as well as in-vitro cytotoxic potential among extant cytotypes, was evaluated. The comprehensive cytomorphological studies of the populations from NW Himalayas revealed the occurrence of different chromosomal races viz. n = 13, 26. The tetraploid cytotype was hitherto unreported. The tissue-specific chemo-profiling revealed relative dominance of different phytoconstituents in root-stock. There was a noticeable increase in the quantity of the analyzed compounds in relation to increasing ploidy status along the increasing altitudes. The MTT assay of methanolic extracts of diploid and tetraploid cytotypes displayed significant cytotoxicity potential in tetraploids. The root-stock extracts of tetraploids were highly active extracts with IC50 value ranges from 5.65 to 8.53 μg/mL against HCT-116 colon cancer. ConclusionThe chemical evaluation of major bioactive compounds in diverse cytotypes from different plant parts along different altitudes presented an appreciable variability in sweroside, swertiamarin, and gentiopicroside contents. Additionally, the concentrations of these phytoconstituents varied for cytotoxicity potential among different screened cytotypes. This quantitative difference of active bio-constituents was in correspondence with the growth inhibition percentage of different tested cancer cell lines. Thus, the present investigation strongly alludes towards a prognostic approach for the identification of elite cytotypes/chemotypes with significant pharmacological potential.

Strategies to Produce Grapefruit-Like Citrus Varieties With a Low Furanocoumarin Content and Distinctive Flavonoid Profiles.

Pummelos and hybrids, such as grapefruits, have high furanocoumarin and low flavonoid contents. Furanocoumarins interact negatively with certain drugs, while flavonoids are antioxidant compounds with health benefits. To obtain new grapefruit-like varieties with low furanocoumarin and high flavonoid contents, diploid and triploid hybrid populations from crosses between diploid and tetraploid “Clemenules” clementine and diploid “Pink” pummelo were recovered and analyzed. With regard to furanocoumarins, triploids produce less bergapten, bergamottin and 6,7-DHB than diploids. Regarding flavonoids, triploids yielded more eriocitrin, narirutin, hesperidin and neohesperidin than diploids, whereas no differences were observed in neoeriocitrin and naringin. These results indicate that, the strategy to recover triploid hybrids by 4x × 2x crosses is more appropriate than the recovery of diploid hybrids by 2x × 2x crosses for obtaining grapefruit-like varieties of citrus with lower furanocoumarin and higher flavonoid contents.

Assessing the Contribution of Sli to Self-Compatibility in North American Diploid Potato Germplasm Using KASP™ Markers

Diploid hybrid potato variety development requires the introduction of reliably transmitted self-compatibility (SC) to largely self-incompatible elite diploid germplasm. The diploid Solanum chacoense clone M6 has been widely used to introgress SC into North American potato diploid breeding programs. We determined that M6 is homozygous for six DNA Kompetitive Allele Specific PCR (KASP)™ markers spanning a 224 kb region, linked to Sli in Dutch germplasm. Self-compatible Sli alleles were identified in dihaploids of the cultivars ‘Atlantic’ and ‘Superior’ and breeding clone NY148. This finding demonstrates the potential of Sli genotyping to select S. tuberosum dihaploids that will contribute to SC. We appraised the transmission of Sli in a diploid recurrent selection population and in a diploid backcross population, each designed to introgress SC while improving agronomic traits. The frequency of the homozygous self-compatible Sli genotype at the six marker loci increased over the course of four cycles of recurrent selection. The homozygous Sli self-compatible genotype at any one of five marker loci within an 80.8 kb region on chromosome 12 (58,960,090-59,040,898 bp) perfectly predicted a SC phenotype in the recurrent selection population. The heterozygous Sli genotype was found in self-compatible and self-incompatible individuals. The discrepancy between phenotype and marker genotype can be attributed in part to the difficulty of accurately phenotyping SC. We also identified self-compatible individuals with the homozygous self-incompatible Sli genotype at all tested loci. The presence of the homozygous self-incompatible Sli haplotype in self-compatible clones 1S1 and DMRH-89 and a self-compatible individual from the S. chacoense PI 133664 further suggests that other genetic components contribute to SC. This work illustrates the ability of Sli markers to predict SC in some germplasm, but it also underscores the need to identify other genomic regions critical to SC and the role of the environment in expression of genes involved in the SC reaction.

Evolutionary history and genetic connectivity across highly fragmented populations of an endangered daisy

Conservation management can be aided by knowledge of genetic diversity and evolutionary history, so that ecological and evolutionary processes can be preserved. The Button Wrinklewort daisy (Rutidosis leptorrhynchoides) was a common component of grassy ecosystems in south-eastern Australia. It is now endangered due to extensive habitat loss and the impacts of livestock grazing, and is currently restricted to a few small populations in two regions >500 km apart, one in Victoria, the other in the Australian Capital Territory and nearby New South Wales (ACT/NSW). Using a genome-wide SNP dataset, we assessed patterns of genetic structure and genetic differentiation of 12 natural diploid populations. We estimated intrapopulation genetic diversity to scope sources for genetic management. Bayesian clustering and principal coordinate analyses showed strong population genetic differentiation between the two regions, and substantial substructure within ACT/NSW. A coalescent tree-building approach implemented in SNAPP indicated evolutionary divergence between the two distant regions. Among the populations screened, the last two known remaining Victorian populations had the highest genetic diversity, despite having among the lowest recent census sizes. A maximum likelihood population tree method implemented in TreeMix suggested little or no recent gene flow except potentially between very close neighbours. Populations that were more genetically distinctive had lower genetic diversity, suggesting that drift in isolation is likely driving population differentiation though loss of diversity, hence re-establishing gene flow among them is desirable. These results provide background knowledge for evidence-based conservation and support genetic rescue within and between regions to elevate genetic diversity and alleviate inbreeding.

Assessment of Lolium perenne tetraploid clones produced from a diverse diploid breeding population

Assessment of Lolium perenne tetraploid clones produced from a diverse diploid breeding population