Recurrent Rearrangement during Adaptive Evolution in an Interspecific Yeast Hybrid Suggests a Model for Rapid Introgression

Genome rearrangements are associated with eukaryotic evolutionary processes ranging from tumorigenesis to speciation. Rearrangements are especially common following interspecific hybridization, and some of these could be expected to have strong selective value. To test this expectation we created de novo interspecific yeast hybrids between two diverged but largely syntenic Saccharomyces species, S. cerevisiae and S. uvarum, then experimentally evolved them under continuous ammonium limitation. We discovered that a characteristic interspecific genome rearrangement arose multiple times in independently evolved populations. We uncovered nine different breakpoints, all occurring in a narrow ∼1-kb region of chromosome 14, and all producing an “interspecific fusion junction” within the MEP2 gene coding sequence, such that the 5′ portion derives from S. cerevisiae and the 3′ portion derives from S. uvarum. In most cases the rearrangements altered both chromosomes, resulting in what can be considered to be an introgression of a several-kb region of S. uvarum into an otherwise intact S. cerevisiae chromosome 14, while the homeologous S. uvarum chromosome 14 experienced an interspecific reciprocal translocation at the same breakpoint within MEP2, yielding a chimaeric chromosome; these events result in the presence in the cell of two MEP2 fusion genes having identical breakpoints. Given that MEP2 encodes for a high-affinity ammonium permease, that MEP2 fusion genes arise repeatedly under ammonium-limitation, and that three independent evolved isolates carrying MEP2 fusion genes are each more fit than their common ancestor, the novel MEP2 fusion genes are very likely adaptive under ammonium limitation. Our results suggest that, when homoploid hybrids form, the admixture of two genomes enables swift and otherwise unavailable evolutionary innovations. Furthermore, the architecture of the MEP2 rearrangement suggests a model for rapid introgression, a phenomenon seen in numerous eukaryotic phyla, that does not require repeated backcrossing to one of the parental species.     

杨树杂种无性系生长与光合生理遗传变异研究

以美洲黑杨与大青杨的27个杂种无性系1年生盆栽扦插苗为材料,以美洲黑杨无性系I-69为对照,对其生长性状、扦插成活率以及主要光合生理指标进行遗传变异分析,并利用分析结果对杂种无性系进行初步选择.结果表明:(1)27个杂种无性系间苗期生长性状及光合生理等12个性状指标差异极显著,无性系重复力均在0.7以上,最高达0.987,均受强遗传控制.(2)结合生长性状分析不同无性系的净光合速率,发现具有较高净光合速率的无性系,同样具有较大生长量和较高成活率.(3)经主成分分析和聚类分析,初选出7个生长快、成活率较高、光合作用能力较强的无性系(编号依次为135、141、153、155、165、177和193),7个无性系苗高超对照10%~33%,地径超对照11%~24%,成活率超对照30%~48%,净光合速率超对照7%~29%,且干形优美,适应性强,可作为进一步选育的材料.     

Rin4 Causes Hybrid Necrosis and Race-Specific Resistance in an Interspecific Lettuce Hybrid

Some inter- and intraspecific crosses may result in reduced viability or sterility in the offspring, often due to genetic incompatibilities resulting from interactions between two or more loci. Hybrid necrosis is a postzygotic genetic incompatibility that is phenotypically manifested as necrotic lesions on the plant. We observed hybrid necrosis in interspecific lettuce (Lactuca sativa and Lactuca saligna) hybrids that correlated with resistance to downy mildew. Segregation analysis revealed a specific allelic combination at two interacting loci to be responsible. The allelic interaction had two consequences: (1) a quantitative temperature-dependent autoimmunity reaction leading to necrotic lesions, lethality, and quantitative resistance to an otherwise virulent race of Bremia lactucae; and (2) a qualitative temperature-independent race-specific resistance to an avirulent race of B. lactucae. We demonstrated by transient expression and silencing experiments that one of the two interacting genes was Rin4. In Arabidopsis thaliana, RIN4 is known to interact with multiple R gene products, and their interactions result in hypersensitive resistance to Pseudomonas syringae. Site-directed mutation studies on the necrosis-eliciting allele of Rin4 in lettuce showed that three residues were critical for hybrid necrosis.     

Interspecific Introgression in Cetaceans: DNA Markers Reveal Post-F1 Status of a Pilot Whale

Visual species identification of cetacean strandings is difficult, especially when dead specimens are degraded and/or species are morphologically similar. The two recognised pilot whale species (Globicephala melas and Globicephala macrorhynchus) are sympatric in the North Atlantic Ocean. These species are very similar in external appearance and their morphometric characteristics partially overlap; thus visual identification is not always reliable. Genetic species identification ensures correct identification of specimens. Here we have employed one mitochondrial (D-Loop region) and eight nuclear loci (microsatellites) as genetic markers to identify six stranded pilot whales found in Galicia (Northwest Spain), one of them of ambiguous phenotype. DNA analyses yielded positive amplification of all loci and enabled species identification. Nuclear microsatellite DNA genotypes revealed mixed ancestry for one individual, identified as a post-F1 interspecific hybrid employing two different Bayesian methods. From the mitochondrial sequence the maternal species was Globicephala melas. This is the first hybrid documented between Globicephala melas and G. macrorhynchus, and the first post-F1 hybrid genetically identified between cetaceans, revealing interspecific genetic introgression in marine mammals. We propose to add nuclear loci to genetic databases for cetacean species identification in order to detect hybrid individuals.     

皮下盘菌属种内及种间遗传多样性的ISSR分子标记

对皮下盘菌属（Hypoderma）4种23个菌株进行了ISSR分析。结果表明,被试材料ISSR标记多态性好,8个引物共扩增出131个条带,其中126条（占9618％）具有多态性。经欧氏最短距离中的类平均法聚类,得到各菌株之间的ISSR标记的遗传相似性系数（GS）变异范围为0．30—0．82,23个菌株可聚为6类。通过ISSR分析结果与表型性状的比较和分析,明确了悬钩子皮下盘菌种内遗传差异体现在子囊果大小、形状及埋生深度、唇特征、侧丝顶端形状、子囊和子囊孢子形状及大小,以及寄主、着生部位和分布区域方面;皮下盘菌属的种间差异主要表现在子囊果、唇、侧丝、子囊及分生孢子器等部分形态学特征、寄主及着生部位方面。     

番茄属种间杂种离体培养F1植株的细胞学分析

本文报道了栽培番茄（Lycopersico esculentum)“北京早红”等5个品种分别与野生型秘鲁番茄（L.peruvianum)PI128657中8号株系杂交,离体胚培养,得F1杂种植株,对花粉母细胞在减数分裂中染色体行为和终变期二价体交叉点的频率,以及亲和性程度等进行了.结果表明,6个亲本植株花粉母细胞减数分裂染色体的行为是正常的,中期I为12个二价体。其中环状二价体占多数,棒状二价体数较少,中期I没有单价体,后期I和II均正常,四分体阶段无微出现,但各亲本在终变期和中期I的环状二价体和棒状二价体的数有一定的差异,这可能与不同亲本基因型的亲和性程度和在遗传学上的不协调有关。5个组合的大多数F1杂种花粉母细胞减数分裂中染色体行为基本正常,12个二价体占多数,但染色体配对不稳定,有较多的单价体,染色单体桥。四分体阶段有微核,此外,在5个组合的F1杂种植株中,均出现双二倍体花粉母细胞,这些双二倍体花粉母细胞的染色体,在减数分裂中,也均,出现落后染色体和染色单体桥,以及较多的多价体,四分体阶段有微和不同类型的四分孢子群。     

QTL Mapping of Downy Mildew Resistance in an Introgression Line Derived from Interspecific Hybridization Between Cucumber and Cucumis hystrix

Downy mildew (DM), caused by Pseudoperonospora cubensis (Berk. & M.A. Curtis) Rostovzev, is a worldwide major disease of cucumbers (Cucumis sativus L.). By screening 10 introgression lines (ILs) derived from interspecific hybridization between cucumber and the wild Cucumis, C. hystrix, through a whole plant assay, one introgression line (IL52) was identified with high DM‐resistance. IL52 was further used as a resistant parent to make an F₂ population with ‘changchunmici’ (susceptible parent). The F₂ population (300 plants) was investigated for DM‐yellowing, DM‐necrosis and DM‐resistance in the adult stage. A genetic map spanning 642.5 cM with 104 markers was constructed and used for QTL analysis from the population. Three QTL regions were identified on chromosome 5 and chromosome 6. By interval mapping analysis, two QTLs for DM‐resistance were determined on chromosome 5 (DM_5.1 and DM_5.2), which explained 17.9% and 14.2% of the variation, respectively. QTLs for DM‐yellowing were in the same regions as DM‐resistance. For DM‐necrosis, by interval mapping analysis, one QTL was determined on chromosome 5 (Necr_5.1) that explained 18.3% of the variation and one on chromosome 6 (Necr_6.1) that explained 13.9% of the variation. Our results indicated that the identification of molecular markers linked to the QTLs could be further applied for marker‐assisted selection (MAS) of downy mildew resistance in cucumber.     

Fitness of Crop-Wild Hybrid Sunflower under Competitive Conditions: Implications for Crop-to-Wild Introgression

Understanding the likelihood and extent of introgression of novel alleles in hybrid zones requires comparison of lifetime fitness of parents and hybrid progeny. However, fitness differences among cross types can vary depending on biotic conditions, thereby influencing introgression patterns. Based on past work, we predicted that increased competition would enhance introgression between cultivated and wild sunflower (Helianthus annuus) by reducing fitness advantages of wild plants. To test this prediction, we established a factorial field experiment in Kansas, USA where we monitored the fitness of four cross types (Wild, F₁, F₂, and BC_w hybrids) under different levels of interspecific and intraspecific competition. Intraspecific manipulations consisted both of density of competitors and of frequency of crop-wild hybrids. We recorded emergence of overwintered seeds, survival to reproduction, and numbers of seeds produced per reproductive plant. We also calculated two compound fitness measures: seeds produced per emerged seedling and seeds produced per planted seed. Cross type and intraspecific competition affected emergence and survival to reproduction, respectively. Further, cross type interacted with competitive treatments to influence all other fitness traits. More intense competition treatments, especially related to density of intraspecific competitors, repeatedly reduced the fitness advantage of wild plants when considering seeds produced per reproductive plant and per emerged seedling, and F₂ plants often became indistinguishable from the wilds. Wild fitness remained superior when seedling emergence was also considered as part of fitness, but the fitness of F₂ hybrids relative to wild plants more than quadrupled with the addition of interspecific competitors and high densities of intraspecific competitors. Meanwhile, contrary to prediction, lower hybrid frequency reduced wild fitness advantage. These results emphasize the importance of taking a full life cycle perspective. Additionally, due to effects of exogenous selection, a given hybrid generation may be especially well-suited to hastening introgression under particular environmental conditions.     

RFLP Analysis of Chromosomal Segregation in Progeny from an Interspecific Hexaploid Somatic Hybrid between Solanum Brevidens and Solanum Tuberosum

Segregation of restriction fragment length polymorphism (RFLP) loci was monitored to determine the degree of homeologous pairing and recombination in a hexaploid somatic hybrid, A206, the result of protoplast fusion between Solanum tuberosum (PI 203900, a tetraploid cultivated potato) and Solanum brevidens (PI 218228), a diploid, sexually incompatible, distant relative harboring several traits for disease resistance. Somatic hybrid A206 was crossed to Katahdin, a tetraploid potato cultivar, to generate a segregating population of pentaploid progeny. Although the clones of the tetraploid S. tuberosum lines PI 203900 and Katahdin were highly polymorphic, the diploid S. brevidens clone was homozygous at all but two of the tested RFLP loci. Thus, homeologous recombination could be detected only when S. tuberosum and S. brevidens chromosomes paired and the S. brevidens homologs then segregated into separate gametes. A bias toward homologous pairing was observed for all 12 chromosomes. At least four and perhaps six chromosomes participated in homologous pairing only; each of 24 progeny contained all S. brevidens-derived RFLP markers for chromosomes 4, 8, 9 and 10. The remaining six chromosomes paired with their homolog(s) about twice as often as expected if hexaploid pairings were completely random. Where detectable with RFLPs, homeologous recombinations (both single and double) occurred at a frequency of 1.31 per chromosome. Cytological observations of meiosis I in the somatic hybrid indicated that homeologous pairing had occurred. Enhanced recombinational activity was observed for chromosome 2. A specific small deletion from chromosome 4 was detected in A206 and 11 other somatic hybrids out of 14 screened. These hybrids represent 13 independent fusion events between the same clones of S. brevidens and S. tuberosum. In one instance, this deletion occurred in one of two plants resulting from the same callus, indicating that the loss occurred in culture after fusion had taken place. It is possible that this deletion contributes to somaclonal variation.     

Breeding Potential of Introgression Lines Developed from Interspecific Crossing between Upland Cotton (Gossypium hirsutum) and Gossypium barbadense: Heterosis,Combining Ability and Genetic Effects

Upland cotton (Gossypium hirstum L.), which produces more than 95% of the world natural cotton fibers, has a narrow genetic base which hinders progress in cotton breeding. Introducing germplasm from exotic sources especially from another cultivated tetraploid G. barbadense L. can broaden the genetic base of Upland cotton. However, the breeding potential of introgression lines (ILs) in Upland cotton with G. barbadense germplasm integration has not been well addressed. This study involved six ILs developed from an interspecific crossing and backcrossing between Upland cotton and G. barbadense and represented one of the first studies to investigate breeding potentials of a set of ILs using a full diallel analysis. High mid-parent heterosis was detected in several hybrids between ILs and a commercial cultivar, which also out-yielded the high-yielding cultivar parent in F₁, F₂ and F₃ generations. A further analysis indicated that general ability (GCA) variance was predominant for all the traits, while specific combining ability (SCA) variance was either non-existent or much lower than GCA. The estimated GCA effects and predicted additive effects for parents in each trait were positively correlated (at P<0.01). Furthermore, GCA and additive effects for each trait were also positively correlated among generations (at P<0.05), suggesting that F₂ and F₃ generations can be used as a proxy to F₁ in analyzing combining abilities and estimating genetic parameters. In addition, differences between reciprocal crosses in F₁ and F₂ were not significant for yield, yield components and fiber quality traits. But maternal effects appeared to be present for seed oil and protein contents in F₃. This study identified introgression lines as good general combiners for yield and fiber quality improvement and hybrids with high heterotic vigor in yield, and therefore provided useful information for further utilization of introgression lines in cotton breeding.     

Next Generation Mapping of Enological Traits in an F2 Interspecific Grapevine Hybrid Family

In winegrapes (Vitis spp.), fruit quality traits such as berry color, total soluble solids content (SS), malic acid content (MA), and yeast assimilable nitrogen (YAN) affect fermentation or wine quality, and are important traits in selecting new hybrid winegrape cultivars. Given the high genetic diversity and heterozygosity of Vitis species and their tendency to exhibit inbreeding depression, linkage map construction and quantitative trait locus (QTL) mapping has relied on F₁ families with the use of simple sequence repeat (SSR) and other markers. This study presents the construction of a genetic map by single nucleotide polymorphisms identified through genotyping-by-sequencing (GBS) technology in an F₂ mapping family of 424 progeny derived from a cross between the wild species V. riparia Michx. and the interspecific hybrid winegrape cultivar, ‘Seyval’. The resulting map has 1449 markers spanning 2424 cM in genetic length across 19 linkage groups, covering 95% of the genome with an average distance between markers of 1.67 cM. Compared to an SSR map previously developed for this F₂ family, these results represent an improved map covering a greater portion of the genome with higher marker density. The accuracy of the map was validated using the well-studied trait berry color. QTL affecting YAN, MA and SS related traits were detected. A joint MA and SS QTL spans a region with candidate genes involved in the malate metabolism pathway. We present an analytical pipeline for calling intercross GBS markers and a high-density linkage map for a large F₂ family of the highly heterozygous Vitis genus. This study serves as a model for further genetic investigations of the molecular basis of additional unique characters of North American hybrid wine cultivars and to enhance the breeding process by marker-assisted selection. The GBS protocols for identifying intercross markers developed in this study can be adapted for other heterozygous species.     

A Hybrid Search Algorithm for Swarm Robots Searching in an Unknown Environment

This paper proposes a novel method to improve the efficiency of a swarm of robots searching in an unknown environment. The approach focuses on the process of feeding and individual coordination characteristics inspired by the foraging behavior in nature. A predatory strategy was used for searching; hence, this hybrid approach integrated a random search technique with a dynamic particle swarm optimization (DPSO) search algorithm. If a search robot could not find any target information, it used a random search algorithm for a global search. If the robot found any target information in a region, the DPSO search algorithm was used for a local search. This particle swarm optimization search algorithm is dynamic as all the parameters in the algorithm are refreshed synchronously through a communication mechanism until the robots find the target position, after which, the robots fall back to a random searching mode. Thus, in this searching strategy, the robots alternated between two searching algorithms until the whole area was covered. During the searching process, the robots used a local communication mechanism to share map information and DPSO parameters to reduce the communication burden and overcome hardware limitations. If the search area is very large, search efficiency may be greatly reduced if only one robot searches an entire region given the limited resources available and time constraints. In this research we divided the entire search area into several subregions, selected a target utility function to determine which subregion should be initially searched and thereby reduced the residence time of the target to improve search efficiency.     

甜瓜远缘群体果实糖含量相关性状遗传分析

以栽培甜瓜0246为母本,野生甜瓜Y101为父本,构建了P1、P2、F1、F2、B1、B26个世代,运用植物数量性状主基因+多基因混合遗传模型进行多世代联合分析,探讨了甜瓜果实糖含量相关性状的遗传特性。结果表明:果糖含量、葡萄糖含量和总糖含量遗传均受两对加性-显性-上位性主基因+加性-显性-上位性多基因模型控制(E-0),主基因在F2中的遗传率分别达到90.32%、82.42%和94.66%。蔗糖含量受一对加性主基因+加性-显性多基因模型控制(D-2),主基因在F2中的遗传率达到83.76%。甜瓜果实糖含量相关性状遗传体系中主基因具有重要作用且环境方差所占比例较小,适宜早代选择。     

Genetic Identification of Hyalodaphnia Species and Interspecific Hybrids

Species of the genus Daphnia, in particular the subgenus Hyalodaphnia, represent a taxonomically problematic group due to their phenotypic plasticity, local races and the formation of interspecific hybrids and backcrosses. In this study, we present a genetic approach utilising nuclear DNA to unequivocally identify species and interspecific hybrids. Several nuclear loci (ITS1-ITS2, CA14 and GA13) were amplified by PCR and products were subjected to diagnostic restriction enzymes (restriction fragment length polymorphism; RFLP). The application of this approach to several populations across Europe revealed that the markers are highly consistent and reproducible. In addition, we illustrate with a number of examples how this approach contributed to unravel previously unrecognised taxa, increased the sensitivity of biodiversity studies or contributed to the analysis of resting egg banks. Advantages and disadvantages of this approach compared to existing techniques are discussed and several empirical studies and their results are summarised.     

Qtl Analysis of Transgressive Segregation in an Interspecific Tomato Cross

Two accessions, representing the species Lycopersicon esculentum (cultivated tomato) and Lycopersicon pennellii (a wild relative), were evaluated for 11 quantitative traits and found to be significantly different for 10 of the traits. Transgressive segregation was observed for eight of the traits in a large interspecific F(2) population. When restriction fragment length polymorphism markers were used as probes for the quantitative trait loci (QTL) underlying the traits, 74 significant QTL (LOD > 2) were detected. Thirty-six percent of those QTL had alleles with effects opposite to those predicted by the parental phenotypes. These QTL were directly related to the appearance of transgressive individuals in the F(2) for those traits which showed transgressive segregration. However, the same types of QTL (with allelic effects opposite to those predicted by the parents) were also observed for traits that did not display transgressive segregation in the F(2). One such trait was dry weight accumulation. When two overdominant QTL (detected in the F(2)) for this trait were backcrossed into the L. esculentum genetic background, transgressive individuals were recovered and their occurrence was associated with the two QTL demonstrating the potential for transgressive segregation for all characters and implicating overdominance as a second cause of transgressive segregation. Epistasis was not implicated in transgressive segregation in either the F(2) or backcross generations. Results from this research not only reveal the basis of wide-cross transgressive segregation, but demonstrate that molecular markers can be used to identify QTL (from wild species) responsible for transgressive phenotypes and to selectively transfer them into crop species. This strategy might be used to improve many traits of economic importance including those for which wild species appear phenotypically inferior to their cultivated counterparts.     

一株种间融合的三倍体杂种酵母减数分裂产物的遗传学分析

通过原生质体融合技术将二倍体酿酒酵母（Ｓａｃｃｈａｒｏｍｙｃｅｓｃｅｒｅｖｉｓｉａｅｖａｒ．ｅｌｌｏｐｓｉｏｄｅｕｓ）与单倍体糖化酵母（Ｓａｃｃｈａｒｏｍｙｃｅｓｄｉａｓｔａｔｉｃｕｓ）构建成遗传上稳定的种间三倍体融合杂种。实验结果表明,这种融合杂种象有性杂种一样能诱导产孢;对其完整和非完整四分子的遗传分析,证明了通过遗传标记互补选择法获得的种间三倍体融合杂种ＨＵ－ＫＤＦ－２４０在产孢过程中,标记基因发生了分离和交换,出现了亲二型和重组类型;四分子对可溶性淀粉的发酵和不发酵分离比为１∶２,而原养型与营养缺陷型的分离比是１∶１。     

Interspecific Genetic Variability of the Oyster Mushroom Pleurotus ostreatusAs Revealed by Allozyme Gene Analysis

Allozyme variation in natural populations of basidiomycete fungus Pleurotus ostreatus (88 individuals) from three regions of central Russia was studied. The species was shown to have 92.86% of polymorphic allozyme loci and expected heterozygosity H _e = 0.49. The mean number of alleles per locus was 3.5. The genetic differences among populations were supported by F-statistics (F _ST = 0.750). The low level of inbreeding (F _IS = 0.018) suggests that the P. ostreatus populations are panmictic, and the main reproduction mode involves basidiospores dispersing at long distances. Using cluster analysis, geographically isolated populations and intersterile groups were differentiated within the complex P. ostreatus species.