Novel Sequencing and Genomic Technologies Revolutionized Rice Genomic Study and Breeding

Rice is one of the most important food crops worldwide. Population growth and climate change posed great challenges for further rice production. In the past decade, we have witnessed an explosive development in novel sequencing and genomic technologies. These technologies have been widely applied in rice genomic study and improvement processes, and contributed greatly to increase the efficiency and accuracy of rice breeding. On the other hand, novel sequencing and genomic technologies also promote the shift of breeding schemes from conventional field selection processes to genomic assisted breeding. These technologies have revolutionized almost every aspect of rice study and breeding. Here, we systematically sorted out and reviewed the progress and advancements of sequencing and genomic technologies. We further discussed how these technologies were incorporated into rice breeding practices and helped accelerate the rice improvement process. Finally, we reflected on how to further utilize novel sequencing and genomic technologies in rice genetic improvement, as well as the future trends of advancement for these technologies. It can be expected that, as the sequencing and genomic technologies will develop much more quickly in the future, and be combined with novel bioinformatics tools, rice breeding will move forward into the genomic assisted era.

Genetic Variability, Population Structure, and Relatedness Analysis of Meagre Stocks as an Informative Basis for New Breeding Schemes

This study evaluates the genetic diversity of different meagre broodstocks sampled in Greece. A multiplex of twelve microsatellite markers was used to genotype 946 fish from eleven stocks and batches used for broodstock selection, and the genetic data was used to calculate genetic population parameters as well as to investigate the genetic differentiation between stocks. The results from a relatedness analysis were used as the guiding lines for a fine-tuned and overall evaluation of the genetic distance between stocks, and the choice of candidate breeders from some of them. The approach implemented in this study uses well-established population genetics methods to evaluate the selection of breeder candidates in aquaculture commercial conditions utilizing a descriptive genetic data set based on microsatellite analyses, and to outline an efficient methodology for establishing the basis of new breeding schemes.

Pre-selection against a lethal recessive allele in breeding schemes with optimum-contribution selection or truncation selection

Background We tested the hypothesis that breeding schemes with a pre-selection step, in which carriers of a lethal recessive allele (LRA) were culled, and with optimum-contribution selection (OCS) reduce the frequency of a LRA, control rate of inbreeding, and realise as much genetic gain as breeding schemes without a pre-selection step. Methods We used stochastic simulation to estimate true genetic gain realised at a 0.01 rate of true inbreeding (ΔFtrue) by breeding schemes that combined one of four pre-selection strategies with one of three selection strategies. The four pre-selection strategies were: (1) no carriers culled, (2) male carriers culled, (3) female carriers culled, and (4) all carriers culled. Carrier-status was known prior to selection. The three selection strategies were: (1) OCS in which $$\Delta {\text{F}}_{{{\text{true}}}}$$ Δ F true was predicted and controlled using pedigree relationships (POCS), (2) OCS in which $$\Delta {\text{F}}_{{{\text{true}}}}$$ Δ F true was predicted and controlled using genomic relationships (GOCS), and (3) truncation selection of parents. All combinations of pre-selection strategies and selection strategies were tested for three starting frequencies of the LRA (0.05, 0.10, and 0.15) and two linkage statuses with the locus that has the LRA being on a chromosome with or without loci affecting the breeding goal trait. The breeding schemes were simulated for 10 discrete generations (t = 1, …, 10). In all breeding schemes, ΔFtrue was calibrated to be 0.01 per generation in generations t = 4, …, 10. Each breeding scheme was replicated 100 times. Results We found no significant difference in true genetic gain from generations t = 4, …, 10 between breeding schemes with or without pre-selection within selection strategy. POCS and GOCS schemes realised similar true genetic gains from generations t = 4, …, 10. POCS and GOCS schemes realised 12% more true genetic gain from generations t = 4, …, 10 than truncation selection schemes. Conclusions We advocate for OCS schemes with pre-selection against the LRA that cause animal suffering and high costs. At LRA frequencies of 0.10 or lower, OCS schemes in which male carriers are culled reduce the frequency of LRA, control rate of inbreeding, and realise no significant reduction in true genetic gain compared to OCS schemes without pre-selection against LRA.

Impact of Genomic and Transcriptomic Resources on Apiaceae Crop Breeding Strategies

The Apiaceae taxon is one of the most important families of flowering plants and includes thousands of species used for food, flavoring, fragrance, medical and industrial purposes. This study had the specific intent of reviewing the main genomics and transcriptomic data available for this family and their use for the constitution of new varieties. This was achieved starting from the description of the main reproductive systems and barriers, with particular reference to cytoplasmic (CMS) and nuclear (NMS) male sterility. We found that CMS and NMS systems have been discovered and successfully exploited for the development of varieties only in Foeniculum vulgare, Daucus carota, Apium graveolens and Pastinaca sativa; whereas, strategies to limit self-pollination have been poorly considered. Since the constitution of new varieties benefits from the synergistic use of marker-assisted breeding in combination with conventional breeding schemes, we also analyzed and discussed the available SNP and SSR marker datasets (20 species) and genomes (8 species). Furthermore, the RNA-seq studies aimed at elucidating key pathways in stress tolerance or biosynthesis of the metabolites of interest were limited and proportional to the economic weight of each species. Finally, by aligning 53 plastid genomes from as many species as possible, we demonstrated the precision offered by the super barcoding approach to reconstruct the phylogenetic relationships of Apiaceae species. Overall, despite the impressive size of this family, we documented an evident lack of molecular data, especially because genomic and transcriptomic resources are circumscribed to a small number of species. We believe that our contribution can help future studies aimed at developing molecular tools for boosting breeding programs in crop plants of the Apiaceae family.

Optimizing self-pollinated crop breeding employing genomic selection: from schemes to updating training sets

Long-term breeding schemes employing genomic selection (GS) can boost the response to selection per year. Although several studies show that GS delivers a higher response to selection, only a few analyze the best strategy to employ it, specifically how often and in what manner the training set (TS) should be updated. Therefore, we used stochastic simulation to compare in a long-term breeding program of a hypothetical self-pollinated crop five different strategies to implement GS in the line fixation stage and four methods and sizes to update the TS. Moreover, among breeding schemes, we proposed a new approach for using GS to select the best individuals in each F2 progeny based on genomic estimated breeding and divergence and crossed them to generate a new recombination event. Finally, we compared these schemes to the traditional phenotypic selection and drift. Our results showed that using GS in F2 followed by the phenotypic selection of new parentals in F4 was the best scenario. Furthermore, adding a new set of training data every cycle (over 800) to update the TS maintains the accuracy at satisfactory levels for many more generations, showing that more data is better than optimizing the genetic relationship between TS and the targeted population in a closed system. Hence, we believe that these results may help breeders optimize GS in their programs and improve genetic gain in long-term schemes.

Novel Genes Associated with Dairy Traits in Sarda Sheep

The aim of the present research was to analyze the variability of 45 SNPs from different genes involved in metabolism and innate immunity to perform an association analysis with the milk yield, composition and milk coagulation traits. A population of 1112 Sarda breed sheep was sampled. Genotyping was generated by a TaqMan Open ArrayTM. Thirty out of the 45 SNPs were polymorphic, and 12 displayed a minor allele frequency higher than 0.05. An association analysis showed that the variability at genes PRKAG3 and CD14 was significantly associated with the daily milk yield. The variability at PRKAG3 was also associated with the protein and casein content, somatic cell score and bacterial score. The variation at the PRKAA2 gene was associated with the milk lactose concentration. The SNPs at CD14 were also associated with the traditional milk coagulation properties, while the SNPs at GHR and GHRHR were associated with kSR, a derived coagulation parameter related to the rate of syneresis. The information provided here is new and increases our knowledge of genotype–phenotype interactions in sheep. Our findings might be useful in appropriate breeding schemes to be set up for the Sarda sheep breed, but these should be confirmed by further studies, possibly performed on independent populations.

Genealogical structure of the Belarusian black-and-white breed based on the microsatellite analysis of the lines bred at gene pool enterprises

The methods of molecular genetic analysis are widely used to assess the genetic structure and to study the dynamics of population-genetic processes in populations of domestic animals. I n particular, these are the highly polymorphic genetic markers – the microsatellites that are the most common molecular markers in genetic and genomic research. The aim of the research was to develop the genealogical structure of the Belarusian black-and-white breed based on the microsatellite analysis of the lines bred at a gene pool enterprise. The research was carried out with the animals bred at the JSC “SGC “Zarechye”. For the microsatellite analysis of boars of the Belarusian black-and-white breed, the DNA testing was carried out at 9 STR-loci (SО155, SО355, SО386, SО005, SW72, SW951, SО101, SW240, and SW857). In all studied lines, the largest number of effective alleles was at the SО005 locus – 4.00–5.14. The lines of animals with heterozygosity can be used in various breeding schemes, both in purebred breeding (in pedigree pig breeding) and in crossing (in industrial pig breeding). Polymorphism determines the degree of genetic variation in populations. The locus is classified as polymorphic when the frequency of the most common allele of this locus does not exceed 95% (р ≤ 95). The revealed polymorphism of loci in the lines Maket, Tik, and Veseliy indicates the presence of genetic variability in them, which allows using them in breeding and breed-forming processes. Based on the studies made, the genealogical structure of the Belarusian black-and-white breed, consisting of one subcluster and two branches, has been developed, which makes it possible to assess the state and degree of relation of structural units (lines), and reflects the prospect of their further use.

Estimation of Heterosis Among Potato (Solanum tuberosum L.) Crosses in Ethiopia

Determination of heterosis in tetraploid potato crosses is necessary for identification of superior genotypes for variety development or breeding program. However, producing heterotic potato genotypes through local crossing is not a common practice in Ethiopia. Hence, this study was conducted to estimate the magnitude of better, and standard check heteroses in potato clones that are produced from local crossing. This will help identify potential of hybrid for future breeding schemes. Heterosis of 75 clones were evaluated using a 9 x 9 Simple Lattice design. Results of the analysis of variance showed significant differences for all the growth characters, except medium-sized tubers and specific gravity of tuber. These results indicate the presence of genetic variability among the samples. The clones exhibited as high as 55.62 and 58.31 t.ha-1 marketable and total tuber yield, respectively. These clones also displayed mid, better parent and standard heterosis of 118.8%, 90.5% and 239.1%, respectively, for marketable tuber yield. This result indicates the presence of high magnitude heterosis which could be used to exploit the hybrid vigor. In addition, mid, better parent, and standard check heterosis were estimated at 79.36%, 61.04% and 209.17% for total tuber yield, respectively. Our results show the highest chance of getting heterotic offspring than parental and standard check varieties to developing new potato varieties. The information generated from this study would be valuable for researchers who intend to develop high-yielding varieties of potato

The genomes of precision edited cloned calves show no evidence for off-target events or increased de novo mutagenesis

Background Animal health and welfare are at the forefront of public concern and the agricultural sector is responding by prioritising the selection of welfare-relevant traits in their breeding schemes. In some cases, welfare-enhancing traits such as horn-status (i.e., polled) or diluted coat colour, which could enhance heat tolerance, may not segregate in breeds of primary interest, highlighting gene-editing tools such as the CRISPR-Cas9 technology as an approach to rapidly introduce variation into these populations. A major limitation preventing the acceptance of CRISPR-Cas9 mediated gene-editing, however, is the potential for off-target mutagenesis, which has raised concerns about the safety and ultimate applicability of this technology. Here, we present a clone-based study design that has allowed a detailed investigation of off-target and de novo mutagenesis in a cattle line bearing edits in the PMEL gene for diluted coat-colour. Results No off-target events were detected from high depth whole genome sequencing performed in precursor cell-lines and resultant calves cloned from those edited and non-edited cell lines. Long molecule sequencing at the edited site and plasmid-specific PCRs did not reveal structural variations and/or plasmid integration events in edited samples. Furthermore, an in-depth analysis of de novo mutations across the edited and non-edited cloned calves revealed that the mutation frequency and spectra were unaffected by editing status. Cells in culture, however, appeared to have a distinct mutation signature where de novo mutations were predominantly C > A mutations, and in cloned calves they were predominantly T > G mutations, deviating from the expected excess of C > T mutations. Conclusions We found no detectable CRISPR-Cas9 associated off-target mutations in the gene-edited cells or calves derived from the gene-edited cell line. Comparison of de novo mutation in two gene-edited calves and three non-edited control calves did not reveal a higher mutation load in any one group, gene-edited or control, beyond those anticipated from spontaneous mutagenesis. Cell culture and somatic cell nuclear transfer cloning processes contributed the major source of contrast in mutational profile between samples.