Genetic Analysis of Heterosis for Yield Influencing Traits in Brassica juncea Using a Doubled Haploid Population and Its Backcross Progenies

The exploitation of heterosis through hybrid breeding is one of the major breeding objectives for productivity increase in crop plants. This research analyzes the genetic basis of heterosis in Brassica juncea by using a doubled haploid (DH) mapping population derived from F1 between two heterotic inbred parents, one belonging to the Indian and the other belonging to the east European gene pool, and their two corresponding sets of backcross hybrids. An Illumina Infinium Brassica 90K SNP array-based genetic map was used to identify yield influencing quantitative trait loci (QTL) related to plant architecture, flowering, and silique- and seed-related traits using five different data sets from multiple trials, allowing the estimation of additive and dominance effects, as well as digenic epistatic interactions. In total, 695 additive QTL were detected for the 14 traits in the three trials using five data sets, with overdominance observed to be the predominant type of effect in determining the expression of heterotic QTL. The results indicated that the design in the present study was efficient for identifying common QTL across multiple trials and populations, which constitute a valuable resource for marker-assisted selection and further research. In addition, a total of 637 epistatic loci were identified, and it was concluded that epistasis among loci without detectable main effects plays an important role in controlling heterosis in yield of B. juncea.

Cytogenetic investigation of Arctic char × brook trout F1, F2 and backcross hybrids revealed remnants of the chromosomal rearrangements

Arctic char (Salvelinus alpinus) and brook trout (Salvelinus fontinalis) hybridize and their offspring is viable and fertile. This may be a real treat for the native European stocks of Arctic char which gene pools might be unintendedly contaminated with the genetic elements of brook trout. On the other hand, hybrids of these two species are appreciated by customers and have some potential for the aquaculture. Moreover, Salvelinus hybrids and backcross individuals are interesting models in the research focused on influence of hybridization on the genomic organization and chromosome rearrangements. Thus, the main goal of the present study was to examine chromosomes of Arctic char × brook trout F1, F2 hybrids and backcross individuals and compare with genomic information concerning parental species to recognize karyotypic changes provoked by the hybridization events. Application of conventional and molecular (FISH) techniques allow to identify characteristic chromosomes for both parental species in the hybrid progeny and show multiplicity of cytotypes among different types of crosses with variability in structure and number of chromosome (81–85) and chromosome arm (99–101). Chromosome fragment was detected in the karyotype of one F1 and one backcross individual and the presence of one triploid (3n) fish was documented. Occurrence of chromosomes containing internally located telomeric sequences (ITS) inherited after brook trout or both parental species was shown in F1 and backcross progeny. Moreover, additional CMA3-positive signal on chromosome from Arctic char pair no. 2 in F1 fish and interstitially located active NOR visible on subtelo-acrocentric (F2 hybrid) and acrocentric (Sf × H individual) chromosomes were detected. Described polymorphic chromosomes together with specific, interstitial location of CMA3-positive found in F2 and Sf × H hybrids and DAPI-positive regions observed in H × Sa fish at different uniarmed chromosomes pair presumably are remnants of chromosomal rearrangements. Provided results strongly indicate that the hybridization process influenced the genome organization in the Salvelinus hybrid progeny.

Clustering of loci controlling species differences in male chemical bouquets of sympatric Heliconius butterflies

The degree to which loci promoting reproductive isolation cluster in the genome – i.e. the genetic architecture of reproductive isolation - can influence the tempo and mode of speciation. Tight linkage between these loci can facilitate speciation in the face of gene flow. Pheromones play a role in reproductive isolation in many Lepidoptera species, and the role of endogenously-produced compounds as secondary metabolites decreases the likelihood of pleiotropy associated with many barrier loci. Heliconius butterflies use male sex pheromones to both court females (aphrodisiac wing pheromones) and ward off male courtship (male-transferred anti-aphrodisiac genital pheromones), and it is likely that these compounds play a role in reproductive isolation between Heliconius species. Using a set of backcross hybrids between H. melpomene and H. cydno, we investigated the genetic architecture of putative male pheromone compound production. We found a set of 40 significant quantitative trait loci (QTL) representing 33 potential pheromone compounds. QTL clustered significantly on two chromosomes, chromosome 8 for genital compounds and chromosome 20 for wing compounds, and chromosome 20 was enriched for potential pheromone biosynthesis genes. There was minimal overlap between pheromone QTL and known QTL for mate choice and color pattern. Nonetheless, we did detect linkage between a QTL for wing androconial area and optix, a color pattern locus known to play a role in reproductive isolation in these species. This tight clustering of putative pheromone loci might contribute to coincident reproductive isolating barriers, facilitating speciation despite ongoing gene flow.

Genomic Resources for Darters (Percidae: Etheostominae) Provide Insight into Postzygotic Barriers Implicated in Speciation

Comparative genomic approaches are increasingly being used to study the evolution of reproductive barriers in nonmodel species. Although numerous studies have examined prezygotic isolation in darters (Percidae), investigations into postzygotic barriers have remained rare due to long generation times and a lack of genomic resources. Orangethroat and rainbow darters naturally hybridize and provide a remarkable example of male-driven speciation via character displacement. Backcross hybrids suffer from high mortality, which appears to promote behavioral isolation in sympatry. To investigate the genomic architecture of postzygotic isolation, we used Illumina and PacBio sequencing to generate a chromosome-level, annotated assembly of the orangethroat darter genome and high-density linkage maps for orangethroat and rainbow darters. We also analyzed genome-wide RADseq data from wild-caught adults of both species and laboratory-generated backcrosses to identify genomic regions associated with hybrid incompatibles. Several putative chromosomal translocations and inversions were observed between orangethroat and rainbow darters, suggesting structural rearrangements may underlie postzygotic isolation. We also found evidence of selection against recombinant haplotypes and transmission ratio distortion in backcross hybrid genomes, providing further insight into the genomic architecture of genetic incompatibilities. Notably, regions with high levels of genetic divergence between species were enriched for genes associated with developmental and meiotic processes, providing strong candidates for postzygotic isolating barriers. These findings mark significant contributions to our understanding of the genetic basis of reproductive isolation between species undergoing character displacement. Furthermore, the genomic resources presented here will be instrumental for studying speciation in darters, the most diverse vertebrate group in North America.

Assessing a Bayesian Approach for Detecting Exotic Hybrids between Plantation and Native Eucalypts

Eucalyptus globulusis grown extensively in plantations outside its native range in Australia. Concerns have been raised that the species may pose a genetic risk to native eucalypt species through hybridisation and introgression. Methods for identifying hybrids are needed to enable assessment and management of this genetic risk. This paper assesses the efficiency of a Bayesian approach for identifying hybrids between the plantation speciesE. globulusandE. nitensand four at-risk native eucalypts. Range-wide DNA samples ofE. camaldulensis,E. cypellocarpa,E. globulus,E. nitens,E. ovataandE. viminalis, and pedigreed and putative hybrids (n= 606), were genotyped with 10 microsatellite loci. Using a two-way simulation analysis (two species in the model at a time), the accuracy of identification was 98% for first and 93% for second generation hybrids. However, the accuracy of identifying simulated backcross hybrids was lower (74%). A six-way analysis (all species in the model together) showed that as the number of species increases the accuracy of hybrid identification decreases. Despite some difficulties identifying backcrosses, the two-way Bayesian modelling approach was highly effective at identifyingF1s, which, in the context ofE. globulusplantations, are the primary management concern.