Species with Haploid or Doubled Haploid Protocols

Harnessing monocrop breeding strategies for intercrops

Intercropping is considered advantageous for many reasons, including increased yield stability, nutritional value and the provision of various regulating ecosystem services. However, intercropping also introduces diverse competition effects between the mixing partners, which can negatively impact their agronomic performance. Therefore, selecting complementary intercropping partners is the key to realizing a well-mixed crop production. Several specialized intercrop breeding concepts have been proposed to support the development of complementary varieties, but their practical implementation still needs to be improved. To lower this adoption threshold, we explore the potential of introducing minor adaptations to commonly used monocrop breeding strategies as an initial stepping stone towards implementing dedicated intercrop breeding schemes. While we acknowledge that recurrent selection for reciprocal mixing abilities is likely a more effective breeding paradigm to obtain genetic progress for intercrops, a well-considered adaptation of monoculture breeding strategies is far less intrusive concerning the design of the breeding programme and allows for balancing genetic gain for both monocrop and intercrop performance. The main idea is to develop compatible variety combinations by improving the monocrop performance in the two breeding pools in parallel and testing for intercrop performance in the later stages of selection. We show that the optimal stage for switching from monocrop to intercrop testing should be adapted to the specificity of the crop and the heritability of the traits involved. However, the genetic correlation between the monocrop and intercrop trait performance is the primary driver of the intercrop breeding scheme optimization process.

Embryogenesis induction of carrot (Daucus carota L.) in isolated microspore culture

Haploid technologies are used to create homozygous lines for accelerated breeding. We aimed to optimize the technology for using the isolated microspore culture in vitro to obtain doubled haploids of the carrot (Daucus carota L.). We studied two carrot varieties with different responsiveness to embryogenesis, Altajskaya lakomka and Breeding line 17. Carrot microspores were isolated from buds and cultivated in liquid nutrient media supplemented with an antibiotic and activated carbon in vitro. They were exposed to different thermal treatments. The experiment showed the benefits of combining cold pre-treatment of buds (5°C for 1 day) with heat shock of isolated microspores in vitro (32°C for 2 days). The induction of embryogenesis on the NLN-13 medium was twice as high as on the MSm-13 medium. The use of 1% activated carbon in 0.5% agarose increased the yield of embryoids by more than 1.5 times. 100 mg/dm3 of ampicillin was found to be the most efficient concentration. After 30 days of cultivation under optimized conditions, the yield was 161.3 and 44.0 embryoids per Petri dish for the cultivar Altajskaya lakomka and Breeding line 17, respectively. The induction of carrot embryogenesis is determined by the type and duration of thermal stress, the composition of the nutrient medium, the use of activated carbon as a sorbent, the addition of β-lactam antibiotics, and the type of explant exposed to thermal treatment. Our technology enabled us to obtain homozygous doubled haploid lines of carrots during a year, and these lines were included in the breeding process to create F1 hybrids.

Genome optimization via virtual simulation to accelerate maize hybrid breeding

The employment of doubled-haploid (DH) technology in maize has vastly accelerated the efficiency of developing inbred lines. The selection of superior lines has to rely on genotypes with genomic selection (GS) model, rather than phenotypes due to the high expense of field phenotyping. In this work, we implemented 'genome optimization via virtual simulation (GOVS)' using the genotype and phenotype data of 1404 maize lines and their F1 progeny. GOVS simulates a virtual genome encompassing the most abundant 'optimal genotypes' or 'advantageous alleles' in a genetic pool. Such a virtually optimized genome, although can never be developed in reality, may help plot the optimal route to direct breeding decisions. GOVS assists in the selection of superior lines based on the genomic fragments that a line contributes to the simulated genome. The assumption is that the more fragments of optimal genotypes a line contributes to the assembly, the higher the likelihood of the line favored in the F1 phenotype, e.g. grain yield. Compared to traditional GS method, GOVS-assisted selection may avoid using an arbitrary threshold for the predicted F1 yield to assist selection. Additionally, the selected lines contributed complementary sets of advantageous alleles to the virtual genome. This feature facilitates plotting the optimal route for DH production, whereby the fewest lines and F1 combinations are needed to pyramid a maximum number of advantageous alleles in the new DH lines. In summary, incorporation of DH production, GS and genome optimization will ultimately improve genomically designed breeding in maize. Short abstract: Doubled-haploid (DH) technology has been widely applied in maize breeding industry, as it greatly shortens the period of developing homozygous inbred lines via bypassing several rounds of self-crossing. The current challenge is how to efficiently screen the large volume of inbred lines based on genotypes. We present the toolbox of genome optimization via virtual simulation (GOVS), which complements the traditional genomic selection model. GOVS simulates a virtual genome encompassing the most abundant 'optimal genotypes' in a breeding population, and then assists in selection of superior lines based on the genomic fragments that a line contributes to the simulated genome. Availability of GOVS (https://govs-pack.github.io/) to the public may ultimately facilitate genomically designed breeding in maize.

Doubled Haploids in Eggplant

Eggplant is a solanaceous crop cultivated worldwide for its edible fruit. Eggplant breeding programs are mainly aimed to the generation of F1 hybrids by crossing two highly homozygous, pure lines, which are traditionally obtained upon several self crossing generations, which is an expensive and time consuming process. Alternatively, fully homozygous, doubled haploid (DH) individuals can be induced from haploid cells of the germ line in a single generation. Several attempts have been made to develop protocols to produce eggplant DHs principally using anther culture and isolated microspore culture. Eggplant could be considered a moderately recalcitrant species in terms of ability for DH production. Anther culture stands nowadays as the most valuable technology to obtain eggplant DHs. However, the theoretical possibility of having plants regenerated from somatic tissues of the anther walls cannot be ruled out. For this reason, the use of isolated microspores is recommended when possible. This approach still has room for improvement, but it is largely genotype-dependent. In this review, we compile the most relevant advances made in DH production in eggplant, their application to breeding programs, and the future perspectives for the development of other, less genotype-dependent, DH technologies.