High Levels Of Heterozygosity Research Articles

Genetic Characteristics of the Even Breed of Deer in Yakutia

Microsatellite markers Rt6, BMS1788, Rt 30, Rt1, Rt9, FCB193, Rt7, BMS745, C 143, Rt24, OheQ, C217, C32, NVHRT16, T40, C276 were used to study the genetic profile of the Even breed of deer cultivated in Yakutia. It was found that microsatellite markers in Even deer have a wide range of alleles. The total number of identified alleles reached 120 and varied depending on the locus from 3 (C32; C143) to 14 (BMS2088). The Chukchi deer breed is characterized by a high level of heterozygosity of microsatellite loci, the observed level of heterozygosity on average for all studied loci is 0.702. On average, 7.5 alleles (Na) were detected per locus, and the average number of effective alleles (Ne) was 3.9. The fixation index indicator has an average negative value of -0.024.

Genetic structure of rainbow trout Oncorhynchus mykiss (Salmoniformes, Salmonidae) from aquaculture by DNA-markers

The rational use of valuable fish species from aquaculture is difficult to implement without knowledge of the state of the genetic structure of local stocks. Different types of DNA markers can be used to achieve the goals of selection and breeding work. The genetic structure of a local stock of rainbow trout (Oncorhynchus mykiss Walbaum, 1792) (Salmoniformes, Salmonidae) farmed in Ukraine was studied using DNA-markers: microsatellite (SSR-markers – simple-sequence repeats-markers) and intermicrosatellite (ISSR – inter-simple sequence repeat). Five fragments of trinucleotide microsatellite motifs with a single anchor nucleotide at the 3'-end were used as a primer for analysis by the ISSR-PCR method. Totally, 85 amplicons were obtained across the five loci, of which 92.9% were polymorphic. The total number of alleles ranged from 10 (marker (ACC)₆G) to 23 (marker (AGC)₆G). The following monomorphic amplicons were determined for the studied local stock of rainbow trout: according to marker (CTC)₆C – 770 and 520 bp bands, for the marker (GAG)₆C – 345, 295 and 260 bp, and for the marker (AGC)₆C – 350 bp. The average number of polymorphic bands per locus was 15.8. The selected ISSR primers had a level of polymorphic information content above the average. The most effective markers for molecular-genetic analysis of rainbow trout were (AGC)₆G and (AGC)₆C according to the percentage of polymorphic bands, marker index, effective multiplex ratio and resolving power. The selected ISSR loci allow the genetic structure of the studied local stock to be characterized using the total and the effective number of alleles per locus (Na and Ne were 1.9 and 1.4, respectively), the Shannon index (average value I was 0.4) and the unbiased expected heterozygosity (mean uHe = 0.3). Microsatellite-based analysis showed features of the genetic structure of the local stock of rainbow trout at six microsatellite loci (OMM 1032, OMM 1077, OMM 1088, Str 15, Str 60, Str 73). Allelic diversity was established and alleles with the highest frequency and most typical for the given stock were identified. The Shannon index and unbiased expected heterozygosity were determined using SSR-markers and were 1.42 and 0.79, respectively. This depicts the complexity of the population structure, a high level of genetic diversity and indicates a high level of heterozygosity of local stock. The “gene pool profile” established as a result of ISSR-PCR in the future will help to differentiate local stocks of rainbow trout in aquaculture of Ukraine. Microsatellite markers provide the ability to determine individual features of genetic variation of local populations and to conduct the management of genetic resources on fish farms.

Optimum mating designs for exploiting dominance in genomic selection schemes for aquaculture species

BackgroundIn commercial fish, dominance effects could be exploited by predicting production abilities of the offspring that would be generated by different mating pairs and choosing those pairs that maximise the average offspring phenotype. Consequently, matings would be performed to reduce inbreeding depression. This can be achieved by applying mate selection (MS) that combines selection and mating decisions in a single step. An alternative strategy to MS would be to apply minimum coancestry mating (MCM) after selection based on estimated breeding values. The objective of this study was to evaluate, by computer simulations, the potential benefits that can be obtained by implementing MS or MCM based on genomic data for exploiting dominance effects when creating commercial fish populations that are derived from a breeding nucleus.MethodsThe selected trait was determined by a variable number of loci with additive and dominance effects. The population consisted of 50 full-sib families with 30 offspring each. Males and females with the highest estimated genomic breeding values were selected in the nucleus and paired using the MCM strategy. Both MCM and MS were used to create the commercial population.ResultsFor a moderate number of SNPs, equal or even higher mean phenotypic values are obtained by selecting on genomic breeding values and then applying MCM than by using MS when the trait exhibited substantial inbreeding depression. This could be because MCM leads to high levels of heterozygosity across the whole genome, even for loci affecting the trait that are in linkage equilibrium with the SNPs. In contrast, MS specifically promotes heterozygosity for SNPs for which a dominance effect has been detected.ConclusionsIn most scenarios, for the management of aquaculture breeding programs it seems advisable to follow the MCM strategy when creating the commercial population, especially for traits with large inbreeding depression. Moreover, MCM has the appealing property of reducing inbreeding levels, with a corresponding reduction in inbreeding depression for traits beyond those included in the selection objective.

Comparative study on growth performance and morphological characteristics of the meio- and mito-gynogenesis olive flounder (Paralichthys olivaceus)

Chromosome manipulation, such as gynogenetic induction, is an effective method in fish to quickly obtain high inbreeding coefficient which is useful for genetic breeding. Based on different induction protocols, there are two kinds of gynogenesis, meio-gynogenesis (MEG) and mito-gynogenesis (MIG), which retain high level of heterozygosity or theoretically homozygous. Until now, little is known about the growth and morphological differences between these two gynogenesis. The present study analyzed the growth and morphological characteristics of the MEG and MIG stocks in the olive flounder Paralichthys olivaceus, an important maricultured fish. The results showed that the growth trends of both the MEG and MIG stocks at 3, 6, 9, 12, 18, and 24 months post hatching (mph) were similar to the control stock, and the inflection point of growth curve was at 12 mph. They all presented fast growth from 12 to 18 mph (P < 0.05). Overall, the MEG fish showed a similar growth with the control diploids, while the MIG fish had a better growth performance to some extent although their growth was quite different. The difference of the specific growth rate in body weight (SGRw) among different stocks indicated their allometric growth. In terms of the morphological characteristics, different stocks showed different shapes. Compared with the control stock, the body shape of the MEG stock is thinner and longer, while that of the MIG stock is mellower. The frame data indicated that the cumulative contributive proportions of two main principal components extracted with principal component analysis were 79.75% and 78.88% in the MIG and MEG stocks at 12 mph, respectively. And the shape dispersion of the MIG stock was higher. Based on correlation and regression analyses of the morphological parameters and body weight, the morphological data were also shown to be correlated with the weight gain, and the key characteristic values related to the body weight among the flounder stocks concentrated mainly along the direction of head-tail axis. The results revealed that both the MEG and MIG ones have normal or even some advantages on their growth characteristics, which could be used for the flounder breeding.

Discovery of Genomic Characteristics and Selection Signatures in Southern Chinese Local Cattle.

Chinese local cattle with a high level of genetic diversity mainly originate from two subspecies; the cattle in northern China are primarily Bos Taurus, and the cattle in southern China are primarily Bos indicus. Cattle from southern China are characterized by a specific phenotype and adapted to the local environment. This study explored the genetic diversity, degree of admixture, and selection signature in eight local cattle breeds in southern China. The lowest level of heterozygosity was found in Hainan and Nandan cattle from Hainan and Guangxi province, respectively, whereas the highest level of heterozygosity was detected in Zhaotong cattle from Yunnan province. A neighbor-joining phylogenetic tree analysis clearly separated Lufeng cattle from other breeds, whereas Leiqiong and Hainan cattle have some crossover. Based on linkage disequilibrium-filtered single nucleotide polymorphisms (SNPs), the admixture analysis revealed two clusters corresponding to the taurine and indicine cattle lineages, and the local cattle breeds from southern China showed a certain degree of admixture. When K = 4 and 9, we found a slight separation among Leiqiong, Lufeng, and Hainan cattle. Meanwhile, we performed a selection signature analysis in Hainan, Leiqiong, and Lufeng cattle distributed in the extreme south of China, using the integrated haplotype score (iHS), Rsb statistic, and BayeScan software. Using the iHS approach, we identified 251, 270, and 256 candidate regions in Lufeng, Leiqiong, and Hainan cattle, respectively. Moreover, we identified 184, 174, and 146 candidate regions in pairwise comparisons of Leiqiong vs. Lufeng, Leiqiong vs. Hainan, and Hainan vs. Lufeng cattle using the Rsb approach. In addition, we identified 76 loci with a total of 48 genes under selection, based on the FST approach. Several candidate genes under selection were found to be related to meat quality, immunity, and adaptation to the local environment in southern China. Our results provide significant information about the genetic differences among the cattle breeds from southern China and the possible cause of difference in breed-specific characteristics. Selection signature analysis identified a few candidate SNPs and genes related to certain important traits of these cattle. In general, our results provide valuable insights into the genetic basis of specific traits under selection in certain local cattle breeds.

Quick and efficient approach to develop genomic resources in orphan species: Application in Lavandula angustifolia.

Next-Generation Sequencing (NGS) technologies, by reducing the cost and increasing the throughput of sequencing, have opened doors to generate genomic data in a range of previously poorly studied species. In this study, we propose a method for the rapid development of a large-scale molecular resources for orphan species. We studied as an example the true lavender (Lavandula angustifolia Mill.), a perennial sub-shrub plant native from the Mediterranean region and whose essential oil have numerous applications in cosmetics, pharmaceuticals, and alternative medicines. The heterozygous clone “Maillette” was used as a reference for DNA and RNA sequencing. We first built a reference Unigene, compound of coding sequences, thanks to de novo RNA-seq assembly. Then, we reconstructed the complete genes sequences (with introns and exons) using an Unigene-guided DNA-seq assembly approach. This aimed to maximize the possibilities of finding polymorphism between genetically close individuals despite the lack of a reference genome. Finally, we used these resources for SNP mining within a collection of 16 commercial lavender clones and tested the SNP within the scope of a genetic distance analysis. We obtained a cleaned reference of 8, 030 functionally in silico annotated genes. We found 359K polymorphic sites and observed a high SNP frequency (mean of 1 SNP per 90 bp) and a high level of heterozygosity (more than 60% of heterozygous SNP per genotype). On overall, we found similar genetic distances between pairs of clones, which is probably related to the out-crossing nature of the species and the restricted area of cultivation. The proposed method is transferable to other orphan species, requires little bioinformatics resources and can be realized within a year. This is also the first reported large-scale SNP development on Lavandula angustifolia. All the genomics resources developed herein are publicly available and provide a rich pool of molecular resources to explore and exploit lavender genetic diversity in breeding programs.

The budding yeast life cycle: More complex than anticipated?

The budding yeast, Saccharomyces cerevisiae, has served as a model for nearly a century to understand the principles of the eukaryotic life cycle. The canonical life cycle of S. cerevisiae comprises a regular alternation between haploid and diploid phases. Haploid gametes generated by sporulation are expected to quickly restore the diploid phase mainly through inbreeding via intratetrad mating or haploselfing, thereby promoting genome homozygotization. However, recent large population genomics data unveiled that heterozygosity and polyploidy are unexpectedly common. This raises the interesting paradox of a haplo-diplobiontic species being well-adapted to inbreeding and able to maintain high levels of heterozygosity and polyploidy, thereby suggesting an unanticipated complexity of the yeast life cycle. Here, we propose that unprogrammed mating type switching, heterothallism, reduced spore formation and viability, cell-cell fusion and dioecy could play key and uncharted contributions to generate and maintain heterozygosity through polyploidization.

Draft Genome of the Common Snapping Turtle, Chelydra serpentina, a Model for Phenotypic Plasticity in Reptiles.

Turtles are iconic reptiles that inhabit a range of ecosystems from oceans to deserts and climates from the tropics to northern temperate regions. Yet, we have little understanding of the genetic adaptations that allow turtles to survive and reproduce in such diverse environments. Common snapping turtles, Chelydra serpentina, are an ideal model species for studying adaptation to climate because they are widely distributed from tropical to northern temperate zones in North America. They are also easy to maintain and breed in captivity and produce large clutch sizes, which makes them amenable to quantitative genetic and molecular genetic studies of traits like temperature-dependent sex determination. We therefore established a captive breeding colony and sequenced DNA from one female using both short and long reads. After trimming and filtering, we had 209.51Gb of Illumina reads, 25.72Gb of PacBio reads, and 21.72 Gb of Nanopore reads. The assembled genome was 2.258 Gb in size and had 13,224 scaffolds with an N50 of 5.59Mb. The longest scaffold was 27.24Mb. BUSCO analysis revealed 97.4% of core vertebrate genes in the genome. We identified 3.27 million SNPs in the reference turtle, which indicates a relatively high level of individual heterozygosity. We assembled the transcriptome using RNA-Seq data and used gene prediction software to produce 22,812 models of protein coding genes. The quality and contiguity of the snapping turtle genome is similar to or better than most published reptile genomes. The genome and genetic variants identified here provide a foundation for future studies of adaptation to climate.

The way of value of Correlation of genomic DNA microsatellite loci and live weight of Chukchi reindeer

The article presents the genetic characteristic of the Chukchi reindeer breed. The object of the study was of the Chukchi reindeer. In recent years, the number of reindeer of the Chukchi breed has declined sharply. Reduced reindeer numbers could lead to biodiversity loss. The Chukchi breed of deer has good meat qualities, has high germination viability and is adapted in adverse tundra conditions of Yakutia. Herding of the Chukchi breed of deer in Yakutia are engaged only in the Nizhnekolymsky district. There are four generic communities and the largest of which is the agricultural production cooperative of nomadic tribal community «Turvaurgin», which was chosen to assess the genetic processes of breed using microsatellite markers: Rt6, BMS1788, Rt 30, Rt1, Rt9, FCB193, Rt7, BMS745, C 143, Rt24, OheQ, C217, C32, NVHRT16, T40, C276. It was found that microsatellite markers have a wide range of alleles and generally have a high informative value for identifying of genetic differences between animals and groups of animal. The number of identified alleles is one of the indicators of the genetic diversity of the population. The total number of detected alleles was 127. The Chukchi breed of deer is characterized by a high level of heterozygosity, and the random crossing system prevails over inbreeding in the population. On average, there were 7.9 alleles (Na) per locus, and the mean number of effective alleles (Ne) was 4.1. The index of fixation averaged 0.001. The polymorphism index (PIC) ranged from 0.217 to 0.946, with an average of 0.695.

Interspecific introgression and natural selection in the evolution of Japanese apricot (Prunus mume).

Domestication and population differentiation in crops involve considerable phenotypic changes. The logs of these evolutionary paths, including natural/artificial selection, can be found in the genomes of the current populations. However, these profiles have been little studied in tree crops, which have specific characters, such as long generation time and clonal propagation, maintaining high levels of heterozygosity. We conducted exon-targeted resequencing of 129 genomes in the genus Prunus, mainly Japanese apricot (Prunus mume), and apricot (Prunus armeniaca), plum (Prunus salicina), and peach (Prunus persica). Based on their genome-wide single-nucleotide polymorphisms merged with published resequencing data of 79 Chinese P. mume cultivars, we inferred complete and ongoing population differentiation in P. mume. Sliding window characterization of the indexes for genetic differentiation identified interspecific fragment introgressions between P. mume and related species (plum and apricot). These regions often exhibited strong selective sweeps formed in the paths of establishment or formation of substructures of P. mume, suggesting that P. mume has frequently imported advantageous genes from other species in the subgenus Prunus as adaptive evolution. These findings shed light on the complicated nature of adaptive evolution in a tree crop that has undergone interspecific exchange of genome fragments with natural/artificial selections.

The Genetic Diversity of Cranberry Crop Wild Relatives, Vaccinium macrocarpon Aiton and V. oxycoccos L., in the US, with Special Emphasis on National Forests.

Knowledge of the genetic diversity in populations of crop wild relatives (CWR) can inform effective strategies for their conservation and facilitate utilization to solve agricultural challenges. Two crop wild relatives of the cultivated cranberry are widely distributed in the US. We studied 21 populations of Vaccinium macrocarpon Aiton and 24 populations of Vaccinium oxycoccos L. across much of their native ranges in the US using 32 simple sequence repeat (SSR) markers. We observed high levels of heterozygosity for both species across populations with private alleles ranging from 0 to 26. For V. macrocarpon, we found a total of 613 alleles and high levels of heterozygosity (HO = 0.99, HT = 0.75). We also observed high numbers of alleles (881) and levels of heterozygosity (HO = 0.71, HT = 0.80) in V. oxycoccos (4x). Our genetic analyses confirmed the field identification of a native population of V. macrocarpon on the Okanogan-Wenatchee National Forest in the state of Washington, far outside the previously reported range for the species. Our results will help to inform efforts of the United States Department of Agriculture Agricultural Research Service (USDA-ARS) and the United States Forest Service (USFS) to conserve the most diverse and unique wild cranberry populations through ex situ preservation of germplasm and in situ conservation in designated sites on National Forests.

An improved draft genome sequence of hybrid Populus alba × Populus glandulosa

Populus alba × P. glandulosa clone 84 K, derived from South Korea, is widely cultivated in China and used as a model in the molecular research of woody plants because of high gene transformation efficiency. Here, we combined 63-fold coverage Illumina short reads and 126-fold coverage PacBio long reads to assemble the genome. Due to the high heterozygosity level at 2.1% estimated by k-mer analysis, we exploited TrioCanu for genome assembly. The PacBio clean subreads of P. alba × P. glandulosa were separated into two parts according to the similarities, compared with the parental genomes of P. alba and P. glandulosa. The two parts of the subreads were assembled to two sets of subgenomes comprising subgenome A (405.31 Mb, from P. alba) and subgenome G (376.05 Mb, from P. glandulosa) with the contig N50 size of 5.43 Mb and 2.15 Mb, respectively. A high-quality P. alba × P. glandulosa genome assembly was obtained. The genome size was 781.36 Mb with the contig N50 size of 3.66 Mb and the longest contig was 19.47 Mb. In addition, a total of 176.95 Mb (43.7%), 152.37 Mb (40.5%) of repetitive elements were identified and a total of 38,701 and 38,449 protein-coding genes were predicted in subgenomes A and G, respectively. For functional annotation, 96.98% of subgenome A and 96.96% of subgenome G genes were annotated with public databases. This de novo assembled genome will facilitate systematic and comprehensive study, such as multi-omics analysis, in the model tree P. alba × P. glandulosa.

The Genetic Structure of Nilaparvata lugens (Stal.) in Java Populations

The brown planthopper Nilaparvata lugens (Stal.) causes hopperburn in the rice field. The wing macropterous adults of this insect have capability for long distance flight. We aimed to analyze the genetic structure of six N. lugens populations in Java inferred from the combined COI-COII mitochondrial and ten loci of microsatellites markers. This study found low levels of nucleotides and high levels of haplotype diversity of the planthopper. The demographic test might indicate the genetic bottleneck history of N. lugens population in Java. The genetic diversity analyzed by using microsatellite markers also showed high levels of heterozygosity (Ho&gt;He) that indicated an isolated-breaking effect in the six populations in Java. Moreover, we found a homogenous genetic structure of N. lugens based on pairwise fixation indices (Fst) analyzes that appears to be maintained by high levels of gene flow and showed no correlation between genetic and geographical distance. Importantly, these studies also support accurate information of widely distributed and genetically intermixed among N. lugens across Asia populations. Thus, our results support the theory of long-distance migration among N. lugenspopulations. The genetic structure information of N. lugens in Java could support regional management, such as the new controlling strategies based on forecasting systems.

Genomic Features of Parthenogenetic Animals.

Evolution without sex is predicted to impact genomes in numerous ways. Case studies of individual parthenogenetic animals have reported peculiar genomic features that were suggested to be caused by their mode of reproduction, including high heterozygosity, a high abundance of horizontally acquired genes, a low transposable element load, or the presence of palindromes. We systematically characterized these genomic features in published genomes of 26 parthenogenetic animals representing at least 18 independent transitions to asexuality. Surprisingly, not a single feature was systematically replicated across a majority of these transitions, suggesting that previously reported patterns were lineage-specific rather than illustrating the general consequences of parthenogenesis. We found that only parthenogens of hybrid origin were characterized by high heterozygosity levels. Parthenogens that were not of hybrid origin appeared to be largely homozygous, independent of the cellular mechanism underlying parthenogenesis. Overall, despite the importance of recombination rate variation for the evolution of sexual animal genomes, the genome-wide absence of recombination does not appear to have had the dramatic effects which are expected from classical theoretical models. The reasons for this are probably a combination of lineage-specific patterns, the impact of the origin of parthenogenesis, and a survivorship bias of parthenogenetic lineages.

Microsatellite Diversity and Phylogenetic Relationships among East Eurasian Bos taurus Breeds with an Emphasis on Rare and Ancient Local Cattle.

Simple SummaryUsing microsatellite data, we analyzed various cattle breeds of European and Asian origins from different geo-climatic zones to study their genetic diversity, genetic distances, population structure, and other characteristics. The main focus was on the analysis of ancient and rare native breeds, which either have been unexplored or have received very little attention: the Altai, Ukrainian Grey, Tagil, and Buryat cattle breeds. Our findings provide important information on the population origin and diversity of the breeds, which can be useful for breeding and conservation purposes.We report the genetic analysis of 18 population samples of animals, which were taken from cattle (Bos taurus) breeds of European and Asian origins. The main strength of our study is the use of rare and ancient native cattle breeds: the Altai, Ukrainian Grey, Tagil, and Buryat ones. The cattle samples studied have different production purposes, belong to various eco-geographic regions, and consequently have distinct farming conditions. In order to clarify the genetic diversity, phylogenetic relationships and historical origin of the studied breeds, we carried out an analysis of the genetic variation of 14 high-variability microsatellite loci at 1168 genotyped animals. High levels of heterozygosity and allelic richness were identified in four of the ancient local breeds, namely the Kalmyk, Tagil, Kyrgyz native, and Buryat breeds. The greatest phylogenetic distances from a common ancestor were observed for the Yakut and Ukrainian Grey breeds, while the Tagil breed showed the smallest difference. By using clustering approaches, we found that the Altai cattle is genetically close to the Kyrgyz one. Moreover, both the Altai and Kyrgyz breeds exposed genetic divergences from other representatives of the Turano-Mongolian type and genetic relationships with the Brown Swiss and Kostroma breeds. This phenomenon can be explained by the extensive use of the Brown Swiss and Kostroma breeds in the breeding and improvement processes for the Kyrgyz breeds, which have been involved in the process of keeping the Altai cattle. Our results can be valuable for conservation and management purposes.

The Cypriot Indigenous Grapevine Germplasm Is a Multi-Clonal Varietal Mixture.

Cypriot vineyards are considered as one among the earliest niches of viticulture and a pivotal hub for the domestication and dissemination of grapevine. The millennial presence of Vitis spp. in this Eastern Mediterranean island has given rise to a plethora of biotypes that have not been adequately characterized, despite their unique attributes and stress tolerance. This ancient germplasm also has an additional value since it survived the phylloxera outbreak; hence, it possesses a large amount of genetic diversity that has been unnoticed. In order to provide useful insights to the lineage of Cypriot vineyards, a two-year-spanning collection of centennial grapevine cultivars mostly regarded to belong to four indigenous variety clusters (“Mavro”, “Xynisteri”, “Maratheftiko”, and “Veriko”) was initiated. There were 164 accessions across the broader Commandaria wine zone sampled and characterized using a universal microsatellite primer set. Genetic analysis indicated that considered indigenous Cypriot germplasm has a polyclonal structure with a high level of heterozygosity. Moreover, several lineages or unexplored varieties may exist, since a larger than considered number of discrete genotypes was discovered. Furthermore, it was established that grapevine lineages in Cyprus were shaped across eras via clonal, as well as, sexual propagation. The special attributes of the Cypriot landscape are discussed.

Genomic regions of Solanum tuberosum L. associated with the tuber eye depth.

Potato (Solanum tuberosum L.) is one of the most important food crops in the world. The genome of this potato species is autotetraploid and has a high level of heterozygosity, also this potato species is a cross-pollinated plant. These characteristics complicate the genetic analysis and breeding process. The tuber’s eye depth is an important trait that affects the suitability of potato varieties for processing. Potato breeding for this trait is based on phenotypic assessment. Identification of the loci that control tuber eye depth would allow diagnostic markers for the marker-assisted selection to be created. The aim of this study is to search for loci associated with the eye depth by analyzing Solanum tuberosum varieties from the GenAgro collection of the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, genotyped using the Illumina 22K SNP potato array DNA chip. The 24 significant markers associated with the “eye depth” trait were identified using 15,214 SNP markers genotyped with the Illumina 22K SNP potato array chip and the general linear model (GLM) taking into account the population structure. Data obtained showed the presence of SNPs in four genomic regions: on chromosome 4 (1 marker in the 3.92 Mb area), 5 (1 marker in the 4.67 Mb area) and 10 (1 marker in the 4.87 Mb area and 21 markers in the region between 48.1–48.9 Mb). The results of localization in the region 48.1–48.9 Mb of chromosome 10 correspond to previously published studies, the remaining three regions were detected for the first time. DNA sections containing SNPs linked to the tuber’s eye depth were studied in the SolTub_3.0 potato genome assembly (https://plants.ensembl.org/). KASP markers were developed based on the data obtained. It will be possible to screen the breeding material and to breed the varieties more effectively using current markers associated with a shallow tuber’s eye depth.

Regional sequence expansion or collapse in heterozygous genome assemblies.

High levels of heterozygosity present a unique genome assembly challenge and can adversely impact downstream analyses, yet is common in sequencing datasets obtained from non-model organisms. Here we show that by re-assembling a heterozygous dataset with variant parameters and different assembly algorithms, we are able to generate assemblies whose protein annotations are statistically enriched for specific gene ontology categories. While total assembly length was not significantly affected by assembly methodologies tested, the assemblies generated varied widely in fragmentation level and we show local assembly collapse or expansion underlying the enrichment or depletion of specific protein functional groups. We show that these statistically significant deviations in gene ontology groups can occur in seemingly high-quality assemblies, and result from difficult-to-detect local sequence expansion or contractions. Given the unpredictable interplay between assembly algorithm, parameter, and biological sequence data heterozygosity, we highlight the need for better measures of assembly quality than N50 value, including methods for assessing local expansion and collapse.

Genetic Diversity in Invasive Populations of Argentine Stem Weevil Associated with Adaptation to Biocontrol.

Modified, agricultural landscapes are susceptible to damage by insect pests. Biological control of pests is typically successful once a control agent has established, but this depends on the agent’s capacity to co-evolve with the host. Theoretical studies have shown that different levels of genetic variation between the host and the control agent will lead to rapid evolution of resistance in the host. Although this has been reported in one instance, the underlying genetics have not been studied. To address this, we measured the genetic variation in New Zealand populations of the pasture pest, Argentine stem weevil (Listronotus bonariensis), which is controlled with declining effectiveness by a parasitoid wasp, Microctonus hyperodae. We constructed a draft reference genome of the weevil, collected samples from a geographical survey of 10 sites around New Zealand, and genotyped them using a modified genotyping-by-sequencing approach. New Zealand populations of Argentine stem weevil have high levels of heterozygosity and low population structure, consistent with a large effective population size and frequent gene flow. This implies that Argentine stem weevils were able to evolve more rapidly than their biocontrol agent, which reproduces asexually. These findings show that monitoring genetic diversity in biocontrol agents and their targets is critical for long-term success of biological control.

Preferential Disomic Segregation and C. micrantha/C. medica Interspecific Recombination in Tetraploid 'Giant Key' Lime; Outlook for Triploid Lime Breeding.

The triploid ‘Tahiti’ lime (C. x latifolia (Yu. Tanaka) Tanaka) naturally originated from a merger between a haploid ovule of lemon (C. x limon (L.) Burm) and a diploid pollen from a ‘Mexican’ lime (C. x aurantiifolia (Christm.) Swing). The very limited natural inter-varietal diversity and gametic sterility of C. latifolia requires a phylogenomic based reconstruction breeding strategy to insure its diversification. We developed a strategy based on interploid hybridization between diploid lemon and the doubled diploid ‘Giant Key’ lime. This lime is a doubled diploid of ‘Mexican’ lime, itself a natural interspecific F1 hybrid between C. medica L. and C. micrantha Wester. For an optimized breeding program, we analyzed the meiotic behavior of the allotetraploid lime, the genetic structure of its diploid gametes, the interspecific recombination between C. medica and C. micrantha, and constructed its genetic map. A population of 272 triploid hybrids was generated using ‘Giant Key’ lime as pollinator. One hundred fifty-eight SNPs diagnostic of C. micrantha, regularly distributed throughout the citrus genome were successfully developed and applied. The genetic structure of the diploid gametes was examined based on C. micrantha doses along the genome. The diploid gametes transmitted in average 91.17% of the parental interspecific C. medica/C. micrantha heterozygosity. Three chromosomes (2, 8, and 9) showed disomic segregation with high preferential pairing values, while the remaining chromosomes showed an intermediate inheritance with a preferential disomic trend. A total of 131 SNPs were assigned to nine linkage groups to construct the genetic map. It spanned 272.8 cM with a low average recombination rate (0.99 cM Mb-1) and high synteny and colinearity with the reference clementine genome. Our results confirmed that an efficient reconstruction breeding strategy for ‘Tahiti’ lime is possible, based on interploid hybridization using a doubled diploid of C. aurantiifolia. The tetraploid parent should be selected for favorable agronomic traits and its genetic value should be efficiently inherited by the progeny thanks to transmission of the high level of parental heterozygosity. However, it would require developing numerous progeny to overcome the linkage drag caused by the limited interspecific recombination associated with the predominant disomic inheritance.