Interspecific Hybrids Research Articles

Interspecific crossing in gooseberry breeding as the basis for the industrial-type varieties creation

For optimal cultivation of gooseberries, the presence of industrial-type cultivars plays an important role, therefore, the study of economically useful parameters, such as resistance to diseases and pests, productivity, high commercial qualities of berries, suitability for combine harvesting is relevant. Consequently, the goal of the present research was to study remote gooseberry hybrids obtained on the genetic basis of a mighty gooseberry species (Grossularia robusta) involved in hybridization according to the main economic and biological characteristics.Selected gooseberry forms obtained from the remote (interspecific) hybridization withGrossularia robustaspecies were the studied material.The degree of damage by the American powdery mildew, the quality of berries and suitability for machine harvesting were assessed. As a result of the long – term study of hybrid offspring obtained from interspecific crosses, promising selected formsF29-283-1(2) andF29-283-1(6) (seedlings from the open pollination from the family 142-x36-12 × Grossularia robusta) have been identified, which are of interest for further practical breeding of gooseberries when creating commercial cultivars of industrial type.

Spontaneous and Chemically Induced Genome Doubling and Polyploidization in Vegetable Crops

Plant ploidy manipulation is often required for breeding purposes. However, there is no comprehensive review covering genome doubling in vegetable crops despite the abundance of data for a large number of vegetable species. Similar to other species, genome doubling is required in vegetable crops to obtain doubled haploids (DHs). It is also utilized for the production of polyploids to overcome interspecific hybrid sterility and improve agricultural traits. Spontaneous haploid genome duplication (SHGD) occurs in many Apiaceae, Brassicaceae, Cucurbitaceae, and Solanaceae crops, allowing for the laborious treatment with antimitotic agents to be bypassed. SHGD mechanisms are not fully understood, but existing data suggest that SHGD can occur via nuclear fusion, endoreduplication, or other mechanisms during microspore or ovule early embryogenic development. Other studies show that SHGD can occur at later developmental stages during extended plant growth in vitro or ex vitro, possibly due to the presence of phytohormones in the medium and/or diploid cell competitive advantage. For unresponsive accessions and species with rare SHGD, such as onion (Allium cepa L.) and beet cultivars (Beta vulgaris subsp. vulgaris L.), antimitotic agent treatment has to be applied. Antimitotic agent application efficiency depends on the treatment conditions, especially the agent concentration and exposure time. Also, plant developmental stage is critical for agent accessibility and plant survival. The existing methods can be used to further improve genome doubling methodology for major vegetable crops and other species.

A novel wrinkled leaf vegetable germplasm (AACC) of interspecific hybrids between Tai-cai and Chinese kale

ABSTRACT Ruffled vegetables, having wrinkled leaves with a crispy and tender texture, are highly favored by consumers. However, the genetic resources of crinkled leaf vegetables in the Brassica genus are limited. In this study, distant hybridization was performed between ‘Mottle-leaf Tai-cai’ (Brassica campestris L. ssp. chinensis (L.) Makino var. tai-tsai Hort. AA, 2n = 20) and ‘Big Yellow Flower Chinese Kale’ (B. oleracea var. alboglabra Bailey. CC, 2n = 18) by hand emasculation followed by tissue culture. As a result, all obtained three embryos were identified as true hybrids (AC, 2n = 19) through morphology, cytology, and molecular markers. After chromosome doubling, an allotetraploid hybrid (AACC, 2n = 38) was obtained with a giant leaf, serrated leaf margin, and wrinkled leaf surface; therefore, its most agronomical characters were biased toward the female parent of ‘Mottle-leaf Tai-cai’. In comparison with diploid hybrid, the pollen stainability of allotetraploids were significantly improved and similar to their parents. Additionally, all 5 pairs of SSR primers showed the authenticity of the hybrids. Furthermore, the contents of soluble sugar, vitamin C, and cellulose in the hybrids increased when compared with their parents. Briefly, the obtained hybrid is interspecific euhybrid, and has wrinkle-leaf characteristics, improved nutritional quality, so it is a novel Brassica wrinkle-leaf vegetable germplasm.

Exploring interspecific hybridization dynamics in artificial forests of Pinus brutia and P. halepensis: Implications for sustainable afforestation.

Interspecific hybridization increases genetic diversity, which is essential for coping with changing environments. Hybrid zones, occurring naturally in overlapping habitats of closely related species, can be artificially established during afforestation. The resulting interspecific hybridization may promote sustainability in artificial forests, particularly in regions facing degradation due to climate change. Currently, there is limited evidence of hybridization during regeneration of artificial forests. Here, we studied the frequency of Pinus brutia Ten. × P. halepensis Mill. hybridization in five planted forests in Israel in three stages of forest regeneration: seeds before dispersal, emerged seedlings and recruited seedlings at the end of the dry season. We found hybrids on P. brutia, but not on P. halepensis trees due to asynchronous cone production phenology. Using 94 single-nucleotide polymorphism (SNP) markers, we found hybrids at all stages, most of which were hybrids of advanced generations. The hybrid proportions increased from 4.7 ± 2.1 to 8.2 ± 1.4 and 21.6 ± 6.4 per cent, from seeds to emerged seedlings and to recruited seedlings stages, respectively. The increased hybrid ratio implies an advantage of hybrids over P. brutia during forest regeneration. To test this hypothesis, we measured seedling growth rate and morphological traits under controlled conditions and found that the hybrid seedlings exhibited selected traits of the two parental species, which likely contributed to the fitness and survival of the hybrids during the dry season. This study highlights the potential contribution of hybrids to sustainable-planted forests and contributes to the understanding of genetic changes that occur during the regeneration of artificial forests.

On the Occurrence of Two Species of <i>Hypochoeris</i> Linn. in Nilgiris, South India

A chromosomal count of Hypochoeris plants collected at Ootacamund indicated the identity of those plants as H. radicata L., thus pointing to its presence in the Nilgiris, in addition to H. glabra L. reported in earlier works. This is confirmed by a detailed morphological study of living plants and herbarium specimens. A gradation in morphological characters between the two species leading to a possibility of interspecific hybridization is suggested. This may also account for the earlier misidentification of H. radicata with H. glabra. A table showing distinctive characters of the two species is provided.

Integrative transcriptomic and metabolomic analysis revealed the molecular mechanisms of fiber length difference between the micropylar end and chalazal end of ovule in interspecific hybrid cotton (Gossypium hirsutum × Gossypium barbadense)

Cotton fiber is an indispensable raw material in the textile industry. Fiber length is an important fiber quality index, and the research on fiber length is also quite abundant. However, on the same ovule, there are only a few studies on the difference in fiber length development between the micropylar end and the chalazal end of the ovule. We elucidate the mechanism of fiber length differences at both ends of the ovule through the phenomics, transcriptome, and metabolome. The results show that 20, 25, and 30 days post anthesis (DPA) are the pivotal stages to causing the difference in fiber length at two ends of the ovules. Through the KEGG annotation of differentially expressed genes (DEGs), it was found that flavonoid biosynthesis, plant hormone signal transduction, and phenylpropanoid biosynthesis are enriched in DEGs, and similar conclusions were drawn in the analysis of differential abundant metabolites (DAMs). The results of in vitro culture of ovules showed that chlorogenic acid in the flavonoid pathway and scopolin downstream of the phenylpropanoid pathway have significant effects on fiber growth. Our research provide insights into the mechanism of cotton fiber elongation.

Pollen and Floral Organ Morphology of 18 Oil-Tea Genotypes and Its Systematic Significance

Oil-tea belongs to the Camellia genus, an important oil crop in China. However, oil-tea is taxonomically challenging due to its morphological variation, polyploidy, and interspecific hybridization. Therefore, the present study aimed to investigate the flower organs’ morphology and pollen micro-morphology of 18 oil-tea genotypes in detail and discussed their significance for oil-tea taxonomy. The quantitative parameters of flowers were measured using Vernier caliper measurements. Pollen morphology was observed and photographed using scanning electron microscopy (SEM). The results indicated that the flower size varied significantly among the tested oil-tea genotypes, with the corolla diameter ranging from 42.25 μm in C. meiocarpa ‘LP’ to 89.51 μm in C. oleifera ‘ASX09’. The pollen grains of oil-tea are monads and medium grade in pollen size. There were two types of polar views, including triangular or subcircular, with a polar axis length (P) ranging from 27.5 μm in C. oleifera ‘CY67’ to 59.04 μm in C. mairei (H. Lév.) Melch. var. lapidea (Y.C. Wu) Sealy. The equatorial views exhibited oblate, spherical, or oblong shapes, with an equatorial axis length (E) of 21.32 to 41.62 μm. The pollen exine sculpture was perforate, verrucate, and reticulate. The perforation lumina diameter (D) ranged from 0.29 μm in C. magniflora Chang to 1.22 μm in C. yuhsienensis Hu, and the perforation width (W) varied from 0.77 μm in C. osmantha to 1.40 μm in C. gauchowensis ‘HM349’, respectively. Qualitative clustering analysis (Q-type cluster) and principal component analysis (PCA) were conducted using eleven indexes of flower and pollen morphology, and the 18 oil-tea genotypes were classified into three categories. In addition, the correlation analysis showed that there was a significant correlation between pollen size and flower morphology or pollen exine sculpture. These results offer valuable information on the classification and identification of the 18 oil-tea germplasm resources.

Obtaining and Characterization of an Interspecific Hybrid between Lilium callosum and ‘Snow Queen’ and Evaluation of the Botrytis Stress Response

To cultivate excellent lily germplasms, an interspecific hybrid (LC×SQ-01) was successfully obtained by using a cut-style pollination method in which the rare wild lily Lilium callosum was used as the female parent and the cut flower L. longiflorum ‘Snow Queen’ was used as the male parent. The morphological features of LC×SQ-01 included height, leaf length, and width, which were observed to be between those of the parents in the tissue-cultured seedlings. The height and leaf length of LC×SQ-01 were more similar to those of the male parent, and the width was between the widths of the parents for field-generated plants. The epidermal cell length and the guard cell and stoma sizes were between those of both parents in tissue-cultured and field-generated plants. In addition, the shapes of the epidermal cells and anticlinal wall in LC×SQ-01 were more analogous to those in the male parent, while the stoma morphology was different from that of both parents. Fourteen pairs of polymorphic SSR primers were identified in both parents, and the validity of LC×SQ-01 was demonstrated by PCR amplification using five pairs of SSR primers. Flow cytometry and root tip squashing assays revealed that LC×SQ-01 was a diploid plant, similar to its parents. Furthermore, the LC×SQ-01 hybrid was more resistant to B. cinerea than its parents, and it also showed much greater peroxidase (POD) and catalase (CAT) activity than the parents. These results lay a foundation for breeding a new high-resistance and ornamental lily variety.

Camelus knoblochi genome reveals the complex evolutionary history of Old World camels

Extant Old World camels (genus Camelus) contributed to the economic and cultural exchanges between the East and West for thousands of years.1,2 Although many remains have been unearthed,3,4,5 we know neither whether the prevalent hybridization observed between extant Camelus species2,6,7 also occurred between extinct lineages and the ancestors of extant Camelus species nor why some populations became extinct while others survived. To investigate these questions, we generated paleogenomic and stable isotope data from an extinct two-humped camel species, Camelus knoblochi. We find that in the mitochondrial phylogeny, all C.knoblochi form a paraphyletic group that nests within the diversity of modern, wild two-humped camels (Camelus ferus). In contrast, they are clearly distinguished from both wild and domesticated (Camelus bactrianus) two-humped camels on the nuclear level. Moreover, the divergence pattern of the three camel species approximates a trifurcation, because the most common topology is only slightly more frequent than the two other possible topologies. This mito-nuclear phylogenetic discordance likely arose due to interspecific gene flow between all three species, suggesting that interspecific hybridization is not exclusive to modern camels but a recurrent phenomenon throughout the evolutionary history of the genus Camelus. These results suggest that the genomic complexity of Old World camels' evolutionary history is underestimated when considering data from only modern species. Finally, we find that C.knoblochi populations began declining prior to the last glacial maximum and, by integrating palaeoecological evidence and stable isotope data, suggest that this was likely due to failure to adapt to a changing environment.

Genetic and epigenetic signatures for improved breeding of cultivated blueberry.

Blueberry belongs to the Vaccinium genus and is a highly popular fruit crop with significant economic importance. It was not until the early twentieth century that they began to be domesticated through extensive interspecific hybridization. Here, we collected 220 Vaccinium accessions from various geographical locations, including 154 from the United States, 14 from China, eight from Australia, and 29 from Europe and other countries, comprising 164Vaccinium corymbosum, 15Vaccinium ashei, 10 lowbush blueberries, seven half-high blueberries, and others. We present the whole-genome variation map of 220 accessions and reconstructed the hundred-year molecular history of interspecific hybridization of blueberry. We focused on the two major blueberry subgroups, the northern highbush blueberry (NHB) and southern highbush blueberry (SHB) and identified candidate genes that contribute to their distinct traits in climate adaptability and fruit quality. Our analysis unveiled the role of gene introgression from Vaccinium darrowii and V. ashei into SHB in driving the differentiation between SHB and NHB, potentially facilitating SHB's adaptation to subtropical environments. Assisted by genome-wide association studies, our analysis suggested VcTBL44 as a pivotal gene regulator governing fruit firmness in SHB. Additionally, we conducted whole-genome bisulfite sequencing on nine NHB and 12 SHB cultivars, and characterized regions that are differentially methylated between the two subgroups. In particular, we discovered that the β-alanine metabolic pathway genes were enriched for DNA methylation changes. Our study provides high-quality genetic and epigenetic variation maps for blueberry, which offer valuable insights and resources for future blueberry breeding.

Transposable Element Expression Profiles in Premalignant Pigment Cell Lesions and Melanoma of Xiphophorus.

Transposable elements (TEs) are characterized by their ability to change their genomic position. Through insertion or recombination leading to deletions and other chromosomal aberrations, they can cause genetic instability. The extent to which they thereby exert regulatory influence on cellular functions is unclear. To better characterize TEs in processes such as carcinogenesis, we used the well-established Xiphophorus melanoma model. By transcriptome sequencing, we show that an increasing total number in transposons correlates with progression of malignancy in melanoma samples from Xiphophorus interspecific hybrids. Further, by comparing the presence of TEs in the parental genomes of Xiphophorus maculatus and Xiphophorus hellerii, we could show that even in closely related species, genomic location and spectrum of TEs are considerably different.

Phylogenomics of mulberries (Morus, Moraceae) inferred from plastomes and single copy nuclear genes

Mulberries (genus Morus), belonging to the order Rosales, family Moraceae, are important woody plants due to their economic values in sericulture, as well as for nutritional benefits and medicinal values. However, the taxonomy and phylogeny of Morus, especially for the Asian species, remains challenging due to its wide geographical distribution, morphological plasticity, and interspecific hybridization. To better understand the evolutionary history of Morus, we combined plastomes and a large-scale nuclear gene analyses to investigate their phylogenetic relationships. We assembled the plastomes and screened 211 single-copy nuclear genes from 13 Morus species and related taxa. The plastomes of Morus species were relatively conserved in terms of genome size, gene content, synteny, IR boundary and codon usage. Using nuclear data, our results elucidated identical topologies based on coalescent and concatenation methods. The genus Morus was supported as monophyletic, with M. notabilis as the first diverging lineage and the two North American Morus species, M. microphylla and M. rubra, as sister to the other Asian species. In the Asian Morus species, interspecific relationships were completely resolved. However, cyto-nuclear discordances and gene tree-species tree conflicts were detected in the phylogenies of Morus, with multiple evidences supporting hybridization/introgression as the main cause of discordances between nuclear and plastid phylogenies, while gene tree-species tree conflicts were mainly caused by ILS.

Molecular genetic analysis of natural introgression to enhance chestnut blight resistance of Castanea henryi var. omeiensis

Castanea species have enormous potential for broad applications in the biomedical sciences and chemical wood industries. Due to the occurrence of fungal diseases, especially chestnut blight, the survival status of Castanea plants is seriously threatened. Castanea plants in China have natural tolerance to chestnut blight. This study investigated the genetic diversity and chestnut blight resistance of Castanea plants in China and searched for germplasm with high tolerance resistance. Cluster and population structure analysis revealed that wild Castanea plants in China could be divided into three groups with significant interspecific boundary, C. henryi var. omeiensis is located between C. mollissima and C. henryi var. henryi. The ABBA-BBAA test showed that significant gene introgression occurred between C. mollissima and C. henryi in Mount Emei, supporting the conclusion that C. henryi var. omeiensis as a natural hybrid resource. The results of disease resistance evaluation showed that the tolerance of wild C. mollissima to chestnut blight was the highest and significantly higher than that of wild C. henryi and C. seguinii. In particular, there is a strong association between disease tolerance in C. henryi var. omeiensis and the level of genetic introgression from C. mollissima. Then, the rIBD fragments of C. henryi var. omeiensis derived from C. mollissima were analyzed to reveal the source of disease resistance using whole genome resequencing data. A total of 203 rIBD segments containing 435 genes were identified. Finally, 41 candidate genes for chestnut blight resistance were selected through multiple omics. In conclusion, this study investigated a type of interspecific disease-resistant hybrid resources, identified a set of candidate genes for chestnut blight resistance, and provided new strategies for disease-resistant breeding of chestnut resources in the future.

Widening Genetic Diversity Using Embryo Rescue in Cucurbit Crops: A Review.

Embryo rescue is a vital technique in cucurbit breeding and propagation, addressing challenges such as embryo abortion, poor seed viability, and incompatibility barriers. This method involves the excision of immature embryos from seeds followed by their in vitro culture on a nutrient medium, providing an environment conducive to their growth and development. In cucurbits, embryo rescue has been extensively utilized to overcome barriers to hybridization, enabling the production of interspecific and intergeneric hybrids with desired traits. Various factors, including genotype, developmental stage of embryos, and culture conditions, influence the success of embryo rescue in cucurbits. Optimal nutrient formulations, growth regulators, and culture techniques are critical for promoting embryo germination, shoot elongation, and subsequent plantlet establishment. Additionally, embryo rescue facilitates the recovery of valuable genetic material from wild and exotic cucurbit species, expanding genetic diversity and developing novel cultivars with improved traits such as disease resistance, yield, and quality. This review highlights the principles, applications, and advancements in embryo rescue technology in cucurbits, emphasizing its significance in cucurbit breeding programs and crop improvement efforts.

Comparative chloroplast genomes: insights into the identification and phylogeny of rapid radiation genus Rhodiola.

Rhodiola L. is a genus exhibiting rapid radiation and represents a typical case for studying plastid gene adaptation in species that spread from high altitudes to low altitudes. In this study, 23 samples of 18 Rhodiola species were collected from the Qinghai-Tibetan Plateau and five scattered alpine areas, and the plastid genomes (plastomes) of these species were sequenced, annotated, and compared between high-altitude and widely distributed groups. The plastomes of Rhodiola were found to be highly conserved in terms of gene size, content, and order but highly variable in several lineage-specific features, such as codon usage bias, IR boundary shifting, and distinct repeat sequence structures binding to SSRs. Codon usage in the genes of photosystem II exhibited an obvious preference, reflecting significant environmental adaptation pressures. In this study, three repeat regions compounded with trinucleotide and mononucleotide repeats were found for the first time in R. forrestii, R. himalensis, and R. yunnanensis. High-variability regions such as ndhF, ycf1, trnH-psbA, and rpoC1-rpoB were screened, laying the foundation for the precise identification of these species. The phylogenetic analysis revealed the occurrence of cyto-nuclear discordance, likely originating from the frequent interspecific hybridization events observed within Rhodiola species during rapid radiation. Dioecious and hermaphrodite species can be broadly categorized into two subclades, probably they have different environmental adaptation strategies in response to climate change. In addition, the phylogenetic tree supported the monophyly of R. forrestii and R. yunnanensis, which compose R. Sect. Pseudorhodiola. In conclusion, plastome data enrich the genetic information available for the Rhodiola genus and may provide insight into species migration events during climate change.

Breeding value of potato hybrid clones from the VIR collection revealed in the environments of Kamchatka Territory

Background. Potato breeding involves planned artificial hybridization between previously selected parental lines. A way to make potato breeding more efficient is to use the diversity of the germplasm and broaden the gene pool of parental lines. Interspecific potato hybrids originated on the elite potato germplasm display a set of valuable traits. The current challenge is to assess the performance of potato hybrids under specific soil and climate conditions to clarify their breeding value.The objective of the study was to evaluate potato hybrids in the environments of Kamchatka Territory according to a set of traits, identify the best parental lines, develop new hybrid combinations, and select promising breeding material.Materials and methods. Eleven potato hybrids from VIR were studied over three years (2020–2022) in the fields of Kamchatka Research Institute of Agriculture. The hybrids were benchmarked against two reference potato cultivars, ‘Fresco’ and ‘Vulkan’, belonging to the early and mid-early maturity groups, respectively. Crosses between the hybrids and 28 potato cultivars were carried out in the greenhouse. The new hybrid material was tested in a preliminary trial nursery for yield and earliness.Results. Hybrid 117-2 was better in yield (899 g/plant) than cvs. ‘Vulkan’ and ‘Fresco’ (700–739 g/plant). Hybrids 94-5, 99-10- 1, 8-1-2004, 8-3-2004, 8-5-2004, 135-3-2005, 135-5-2005, 99-6-6, and 134-2-2006 in most traits matched the potato cultivars, manifesting good berry formation and seed setting when crossed. Out of 140 crosses between 11 hybrids and 28 cultivars, 35 crosses between 10 hybrids and 13 cultivars were successful. Most hybrids were effectively used in crossings as maternal forms.Conclusion. VIR’s hybrids 94-5, 8-1-2004, and 8-5-2004 proved the most promising as source material for the development of new early potatoes under the conditions of Kamchatka Territory.

Extra-long staple inter-specific cotton hybrid Phule Shubhra (RHB-1623): A genetic and agronomic breakthrough in cotton cultivation

Extra-long staple inter-specific cotton hybrid Phule Shubhra (RHB-1623): A genetic and agronomic breakthrough in cotton cultivation

The use of <i>in vitro</i> androgenesis for the involvement of interspecific hybrids between <i>Solanum tuberosum</i> L. and wild allotetraploid potato species <i>Solanum stoloniferum</i> Schltdl. et Bouché into breeding

Wild allotetraploid potato species Solanum stoloniferum Schltdl. & Bouché from Mexico is regarded as a valuable source of resistance genes for use in breeding. However, introgression of its resistance genes into breeding material is hampered by a set of reproductive barriers. The genomic difference between S. stoloniferum (genome ААВВ) and S. tuberosum L. (AAAA) is one of them. This makes questionable the possibility of transferring a variety of valuable genes of the wild species localized on the chromosomes of its genome B into the genome of cultivated potatoes. It is proposed to produce tetraploid (4x, AAAB) interspecific hybrids of S. stoloniferum, which are regarded as more promising for homoeological recombination than pentaploid (5x, ААААВ) hybrids commonly used in the introgression schemes. However, the effective ploidy of tetraploid hybrids (3EBN) hinders their backcrossing to cultivated potatoes (4 EBN). For instance, our attempts to involve the tetraploid hybrid of S. stoloniferum IGC16/36.1 obtained by us into hybridization with potato varieties were unsuccessful for a number of years. To solve this problem, we suggested a technique based on the production of 4x plants obtained in anther culture of this hybrid. The present research was aimed at assessing the efficiency of this approach.Thirty-one plants were obtained in anther culture (androgenic clones, androclones) of the hybrid IGC16/36.1 in 2018. Most of them exceeded the initial hybrid in habitus strength and flowering intensity. As a result of crosses made in 2019, 1039 hybrid seeds were obtained from crossing 21 androclones with the ‘Lemhi Russet’ variety (8.7 seeds/pollination), 1017 seeds (7.5 seeds/pollination) from crosses of 23 androclones with the ‘Quarta’ variety, and 716 seeds (12.3 seeds/pollination) from crosses of 11 androclones and a diploid potato line IGC 17n8 capable of producing fertile unreduced (2n) pollen. The hybrid seeds had good germination rate of 70-90%. Among the androclones that gave progeny in crosses with potato varieties, we identified genotypes carrying DNA markers of late blight (LB) resistance genes Rpi-sto1, R2 and R3b, PVY resistance genes Ryadg, Rysto and Rychc, and potato wart disease resistance gene Sen2 (these markers were found in the initial accession of S. stoloniferum PI 205522 and in the IGC 16/36.1 hybrid). Despite the complex nature of inheritance of the analyzed markers in progenies of backcrosses of androclones, a number of isolated hybrids carried several markers, including those of the Rpi-sto1, a broad-spectrum gene for high resistance to late blight. Hybrids with relatively high tuber productivity, features of cultivated potatoes such as regularly shaped tubers with small eyes, and high field resistance to late blight were selected.The prospects for using androclones of the tetraploid interspecific hybrid IGC 16/36.1 for increasing the frequency of homoeologous A/B recombination of chromosomes are discussed.

Determinants of microbiome composition: Insights from free-ranging hybrid zebras (Equus quagga × grevyi).

The composition of mammalian gut microbiomes is highly conserved within species, yet the mechanisms by which microbiome composition is transmitted and maintained within lineages of wild animals remain unclear. Mutually compatible hypotheses exist, including that microbiome fidelity results from inherited dietary habits, shared environmental exposure, morphophysiological filtering and/or maternal effects. Interspecific hybrids are a promising system in which to interrogate the determinants of microbiome composition because hybrids can decouple traits and processes that are otherwise co-inherited in their parent species. We used a population of free-living hybrid zebras (Equus quagga × grevyi) in Kenya to evaluate the roles of these four mechanisms in regulating microbiome composition. We analysed faecal DNA for both the trnL-P6 and the 16S rRNA V4 region to characterize the diets and microbiomes of the hybrid zebra and of their parent species, plains zebra (E. quagga) and Grevy's zebra (E. grevyi). We found that both diet and microbiome composition clustered by species, and that hybrid diets and microbiomes were largely nested within those of the maternal species, plains zebra. Hybrid microbiomes were less variable than those of either parent species where they co-occurred. Diet and microbiome composition were strongly correlated, although the strength of this correlation varied between species. These patterns are most consistent with the maternal-effects hypothesis, somewhat consistent with the diet hypothesis, and largely inconsistent with the environmental-sourcing and morphophysiological-filtering hypotheses. Maternal transmittance likely operates in conjunction with inherited feeding habits to conserve microbiome composition within species.

Epistasis, core-genome disharmony, and adaptation in recombining bacteria.

Recombination of short DNA fragments via horizontal gene transfer (HGT) can introduce beneficial alleles, create genomic disharmony through negative epistasis, and create adaptive gene combinations through positive epistasis. For non-core (accessory) genes, the negative epistatic cost is likely to be minimal because the incoming genes have not co-evolved with the recipient genome and are frequently observed as tightly linked cassettes with major effects. By contrast, interspecific recombination in the core genome is expected to be rare because disruptive allelic replacement is likely to introduce negative epistasis. Why then is homologous recombination common in the core of bacterial genomes? To understand this enigma, we take advantage of an exceptional model system, the common enteric pathogens Campylobacter jejuni and C. coli that are known for very high magnitude interspecies gene flow in the core genome. As expected, HGT does indeed disrupt co-adapted allele pairings, indirect evidence of negative epistasis. However, multiple HGT events enable recovery of the genome's co-adaption between introgressing alleles, even in core metabolism genes (e.g., formate dehydrogenase). These findings demonstrate that, even for complex traits, genetic coalitions can be decoupled, transferred, and independently reinstated in a new genetic background-facilitating transition between fitness peaks. In this example, the two-step recombinational process is associated with C. coli that are adapted to the agricultural niche.IMPORTANCEGenetic exchange among bacteria shapes the microbial world. From the acquisition of antimicrobial resistance genes to fundamental questions about the nature of bacterial species, this powerful evolutionary force has preoccupied scientists for decades. However, the mixing of genes between species rests on a paradox: 0n one hand, promoting adaptation by conferring novel functionality; on the other, potentially introducing disharmonious gene combinations (negative epistasis) that will be selected against. Taking an interdisciplinary approach to analyze natural populations of the enteric bacteria Campylobacter, an ideal example of long-range admixture, we demonstrate that genes can independently transfer across species boundaries and rejoin in functional networks in a recipient genome. The positive impact of two-gene interactions appears to be adaptive by expanding metabolic capacity and facilitating niche shifts through interspecific hybridization. This challenges conventional ideas and highlights the possibility of multiple-step evolution of multi-gene traits by interspecific introgression.