From Genome Sequencing to CRISPR-Based Genome Editing for Climate-Resilient Forest Trees

Due to the economic and ecological importance of forest trees, modern breeding and genetic manipulation of forest trees have become increasingly prevalent. The CRISPR-based technology provides a versatile, powerful, and widely accepted tool for analyzing gene function and precise genetic modification in virtually any species but remains largely unexplored in forest species. Rapidly accumulating genetic and genomic resources for forest trees enabled the identification of numerous genes and biological processes that are associated with important traits such as wood quality, drought, or pest resistance, facilitating the selection of suitable gene editing targets. Here, we introduce and discuss the latest progress, opportunities, and challenges of genome sequencing and editing for improving forest sustainability.

Selection for seed size has uneven effects on specialized metabolite abundance in oat (Avena sativa L)

Plant breeding strategies to optimize metabolite profiles are necessary to develop health-promoting food crops. In oats (Avena sativa L.), seed metabolites are of interest for their antioxidant properties, yet have not been a direct target of selection in breeding. In a diverse oat germplasm panel spanning a century of breeding, we investigated the degree of variation of these specialized metabolites and how it has been molded by selection for other traits, like yield components. We also ask if these patterns of variation persist in modern breeding pools. Integrating genomic, transcriptomic, metabolomic and phenotypic analyses for three types of seed specialized metabolites – avenanthramides, avenacins, and avenacosides – we found reduced heritable genetic variation in modern germplasm compared to diverse germplasm, in part due to increased seed size associated with more intensive breeding. Specifically, we found that abundance of avenanthramides increases with seed size, but additional variation is attributable to expression of biosynthetic enzymes. In contrast, avenacoside abundance decreases with seed size and plant breeding intensity. In addition, these different specialized metabolites do not share large-effect loci. Overall, we show that increased seed size associated with intensive plant breeding has uneven effects on the oat seed metabolome, but variation also exists independently of seed size to use in plant breeding. This work broadly contributes to our understanding of how plant breeding has influenced plant traits and tradeoffs between traits (like growth and defense) and the genetic bases of these shifts.

Characterization of Ribulose-1,5-Bisphosphate Carboxylase-Oxygenase Activase (Rca) Genes in Durum Wheat

Durum wheat is one of the most widely cultivated cereal crop in the Mediterranean area. Its production has been triggered by drought and rising temperature, both affecting the photosynthetic machinery. Rubisco is one of the most important enzymes in plants. Despite its major role in the control of carbon cycle it has a very low efficiency, which is restored by the action of Ribulose-1,5-bisphosphate carboxylase/oxygenase activase (Rca), a protein belonging to the AAA+ family. The main objective of our work was to isolate and characterize Rca genes in durum wheat and determine their phylogeny with other main crops and model species. Besides a genetic and physical position of Rca1 gene was allowed in a RIL mapping population previously developed. In silico analysis, performed in order to understand whether Rca1 gene was differentially expressed under stress condition, highlighted that homoeologous Rca1 genes have different expression levels especially after infections by Zymoseptoria, powdrey mildew and fusarium. A deeper knowledge of Rca genes structures as well as a better understanding of their physiological role in durum wheat might be of greater importance in panning future modern breeding programs to improve crop yield in adverse environmental condition.

Hormonal state of breeding bulls after a long winter period of operation in the conditions of the Udmurt Republic

Relevance. The study will help to identify new perspectives in breeding; get new data about the biological processes occurring in the body of animals according to the endogenous hormones of breeding bulls. The hormonal-immunobiological relationship in the body of bulls and their adaptive ability in different climatic conditions is a very important issue today.Methods. The work was performed in a temperate continental climate with a long, snowy winter and warm summer in the conditions of the Udmurt Republic in the period from 2020 to 2021 on breeding bulls (n = 27) of modern breeding at the age of 15–69 months. The state of endogenous hormones testosterone, estradiol, thyroxine and cortisol after a long winter period was studied, depending on the age, breed and selection in the normal physiological functioning of breeding bulls. The average serum values of estradiol — 0.517 nmol/l, testosterone — 25.7 nmol/l, thyroxine — 74.7 nmol/l, cortisol — 420 nmol/l, and their cholesterol precursor at the level of 3.2 nmol/l were established in the blood of breeding bulls located in this region. It was found that, depending on age, there are differences in all the studied indicators, however, there is a reliability for thyroxine and cortisol. The concentration of cortisol by selection significantly differs in imported bulls of European selection from the Netherlands at the level of p > 0.05, which characterizes the presence of a certain stress adaptation factor in this group. In terms of variability, a significant difference between min and max indicators was noted for the concentration of testosterone, which varied between 2.4 nmol/l and 60 nmol/l, indicating the individuality of these hormones in breeding bulls in this region.Results. Based on the data obtained, the need to take these data into account when operating breeding bulls and analyzing sperm products, taking into account the concentration of these hormones, as well as the implementation of appropriate preventive measures, is revealed.

Cultivation method for revitalized potato material in the system of original seed production

To arrange a system of virus-free potato seed production in the Sakhalin region, a series of studies undertaken to come up with a method towards potato material cultivation in film-gauze greenhouses. At the initial stage, the key agrotechnical methods were developed for growing test-tube microplants, including optimal planting plans – 70×15 cm (the highest yield derived from a standard mini-tuber fraction pcs/m2), 70×30 cm (for clone selection); spraying with insecticides (Aktellik – 3 l/ha, Rogor – 2 l/ha) and fungicides (Ridomil – 1 kg/ha, Tsineb – 2.4 kg/ha) to combat agents transmitting viral and fungal infections; chlorocholine chloride treatment (1.1%) to reduce the growth of the vegetative mass; serological analysis of plants for latent infection with viruses X, Y, S, M, F; burning tops with Reglon (2 l/ha) 2 weeks before harvesting. A set of agrotechnical methods used for producing healthy seed tubers on the Timiryazevskoye seed farm made it possible to reduce the elite cultivation cycle from 5 to 4 years, increase the yield by 57.2%, and reduce the production cost by 43.5%. Subsequently, the methods worked out for producing potato seeds were improved based on modern breeding varieties and phytoregulators (Azolen, Elena, Extrasol, Epin-Extra, Zircon) in spray mixtures with the fungicide Shirlan, contributing to an increased yield up to 34% and efficiency of a standard seed fraction up to 33%. Under production conditions, this method provided a conditionally net income of 450-700 thousand rubles/ha.

New proposals to strengthen the boom of agriculture in Peru: massive use of genetic resources and development of modern breeding programs

Peru is a place with abundant biological resources that should be employed for the benefit of society in general. However, to date, the use of Peruvian plant genetic resources was not fully exploited for the development of improved crops. This work was mostly conducted by the international private sector. The Climate Change Laboratory at Instituto Nacional de Innovación Agraria, and other laboratories at Universidad Nacional José Faustino Sánchez Carrión and Universidad Nacional Agraria La Molina together with other research programs of other institutions seek to promote the massive and sustainable use of plant genetic resources maintained in germplasm banks. It is planned to make use of modern molecular and morphological techniques. Moreover, infrastructure and human resources are being improved. As a result, we will be able to maintain the growth of the agricultural activity in Peru in terms of space and time.

PSXV-10 Study of allelic pattern of PLAG1 gene in the historical and modern populations of two oldest Russian dairy cattle breeds

Increasing animal stature is one of the goals of modern breeding programs for many dairy cattle breeds, because stature related to higher milk yield. The PLAG1 gene was shown to be a strong candidate responsible for stature in different cattle breeds. The polymorphic SNP BovineHD1400007259, located within PLAG1 gene, is considered as a causal mutation responsible for stature. The aim of our work was to evaluate the effect of long selection for the increased body height on the alterations of the allele’s frequencies of the PLAG1 gene in the historical and modern populations of the Russian Yaroslavl and Kholmogor dairy cattle breeds. The historical specimens of Yaroslavl (n = 22) and Kholmogor (n = 12) cattle dated by the first quarter of the 20th century were derived from the craniological collection of the E.F. Liskun Museum for Animal Husbandry. The modern representatives of Yaroslavl (n = 31) and Kholmogor (n = 25) breeds were used for comparison. All works with historical samples were performed in dedicated facility of the L.K. Ernst Research Center for Animal Husbandry. The samples were genotyped using high-density DNA arrays (Illumina Inc., USA). The historical DNA was treated by USER enzyme before genotyping to avoid the misincoporated nucleotides occurred due to postmortem DNA damage. We observed significant differences in allele frequencies of PLAG1 genes between historical and modern populations of both breeds. The frequencies of G allele, which is associated with higher stature, were increased from 0.114 in historical Yaroslavl cattle and from 0.167 in historical Kholmogor cattle to 0.633 and 0.860 in the modern breeds’ representatives, respectively. Our data suggest that PLAG1 gene was affected by artificial selection in studied cattle breeds. The research results will be useful for elucidation of the history of these two oldest Russian dairy cattle breeds. The study was funded by the RSF No. 21-66-00007.

A chromosome-level genome sequence of Chrysanthemum seticuspe, a model species for hexaploid cultivated chrysanthemum

Chrysanthemums are one of the most industrially important cut flowers worldwide. However, their segmental allopolyploidy and self-incompatibility have prevented the application of genetic analysis and modern breeding strategies. We thus developed a model strain, Gojo-0 (Chrysanthemum seticuspe), which is a diploid and self-compatible pure line. Here, we present the 3.05 Gb chromosome-level reference genome sequence, which covered 97% of the C. seticuspe genome. The genome contained more than 80% interspersed repeats, of which retrotransposons accounted for 72%. We identified recent segmental duplication and retrotransposon expansion in C. seticuspe, contributing to arelatively large genome size. Furthermore, we identified a retrotransposon family, SbdRT, which was enriched in gene-dense genome regions and had experienced a very recent transposition burst. We also demonstrated that the chromosome-level genome sequence facilitates positional cloning in C. seticuspe. The genome sequence obtained here can greatly contribute as a reference for chrysanthemum in front-line breeding including genome editing.

Frequent germplasm exchanges drive the high genetic diversity of Chinese-cultivated common apricot germplasm

The genetic diversity of germplasm is critical for exploring genetic and phenotypic resources and has important implications for crop-breeding sustainability and improvement. However, little is known about the factors that shape and maintain genetic diversity. Here, we assembled a high-quality chromosome-level reference of the Chinese common apricot ‘Yinxiangbai’, and we resequenced 180 apricot accessions that cover four major ecogeographical groups in China and other accessions from occidental countries. We concluded that Chinese-cultivated common apricot germplasms possessed much higher genetic diversity than those cultivated in Western countries. We also detected seven migration events among different apricot groups, where 27% of the genome was identified as being introgressed. Remarkably, we demonstrated that these introgressed regions drove the current high level of germplasm diversity in Chinese-cultivated common apricots by introducing different genes related to distinct phenotypes from different cultivated groups. Our results highlight the consideration that introgressed regions may provide an important reservoir of genetic resources that can be used to sustain modern breeding programs.

The Gossypium anomalum genome as a resource for cotton improvement and evolutionary analysis of hybrid incompatibility

Cotton is an important crop that has been the beneficiary of multiple genome sequencing efforts, including diverse representatives of wild species for germplasm development. Gossypium anomalum is a wild African diploid species that harbors stress-resistance and fiber-related traits with potential application to modern breeding efforts. In addition, this species is a natural source of cytoplasmic male sterility and a resource for understanding hybrid lethality in the genus. Here, we report a high-quality de novo genome assembly for G. anomalum and characterize this genome relative to existing genome sequences in cotton. In addition, we use the synthetic allopolyploids 2(A2D1) and 2(A2D3) to discover regions in the G. anomalum genome potentially involved in hybrid lethality, a possibility enabled by introgression of regions homologous to the D3 (Gossypium davidsonii) lethality loci into the synthetic 2(A2D3) allopolyploid.