Domestication Process Research Articles

Agricultural innovations in the Ancient Near East and beyond

There is a rich and diverse body of research dedicated to understanding the cultural and biological processes that led to plant domestication and the development of agriculture in both the Old and New Worlds. Work continues to refine and challenge proposed models for the process of plant domestication, the likely centres of origin and subsequent spread of plant crops and agricultural innovations. This research is taking place in the light of new archaeobotanical evidence and the development and application of novel scientific techniques. As such, publications that bring together new lines of research and evidence, and how these inform our current understanding of plant domestication and agriculture, are an important resource for both specialist and non-specialist audiences.

Taking the Deer by the Antlers: Deer in Material Culture in the Balkan Neolithic

Prehistoric communities had strong ties with the animal world that surrounded them—animals were prey, sources of food, and raw materials, but also threats and mysteries, and certain animals often had an important place in the symbolic realm. With the process of domestication and the switch to animal husbandry as the main source of animal food, these relations changed considerably, and a certain dichotomy between “the domestic” and “the wild” may be noted in numerous past communities. When it comes to the Neolithic period in the Balkans, domestic animals had an important place in subsistence and economy, and it seems that cattle had a particularly prominent symbolic role. Wild species preserved some of their significance in both subsistence and symbolic realms, especially cervids (red deer, roe deer, and fallow deer). In this paper, the place of deer in the material culture of the Neolithic communities in the Balkans will be analysed: skeletal elements of deer were used for the production of diverse items, including non-utilitarian ones, or were part of ritual depositions, and deer representations are encountered in other materials, such as clay figurines. The symbolic meaning of deer cannot be reconstructed with certainty; however, it is probable that deer were tied with territoriality and the landscape.

The Evolution, Expression Patterns, and Domestication Selection Analysis of the Annexin Gene Family in the Barley Pan-Genome.

Plant annexins constitute a conserved protein family that plays crucial roles in regulating plant growth and development, as well as in responses to both biotic and abiotic stresses. In this study, a total of 144 annexin genes were identified in the barley pan-genome, comprising 12 reference genomes, including cultivated barley, landraces, and wild barley. Their chromosomal locations, physical-chemical characteristics, gene structures, conserved domains, and subcellular localizations were systematically analyzed to reveal the certain differences between wild and cultivated populations. Through a cis-acting element analysis, co-expression network, and large-scale transcriptome analysis, their involvement in growth, development, and responses to various stressors was highlighted. It is worth noting that HvMOREXann5 is only expressed in pistils and anthers, indicating its crucial role in reproductive development. Based on the resequencing data from 282 barley accessions worldwide, genetic variations in thefamily were investigated, and the results showed that 5 out of the 12 identified HvMOREXanns were affected by selection pressure. Genetic diversity and haplotype frequency showed notable reductions between wild and domesticated barley, suggesting that a genetic bottleneck occurred on the annexin family during the barley domestication process. Finally, qRT-PCR analysis confirmed the up-regulation of HvMOREXann7 under drought stress, along with significant differences between wild accessions and varieties. This study provides some insights into the genome organization and genetic characteristics of the annexin gene family in barley at the pan-genome level, which will contribute to better understanding its evolution and function in barley and other crops.

Chromosome-level reference genome and resequencing of 322 accessions reveal evolution, genomic imprint and key agronomic traits in adzuki bean.

Adzuki bean (Vigna angularis) is an important legume crop cultivated in over 30 countries worldwide. We developed a high-quality chromosome-level reference genome of adzuki bean cultivar Jingnong6 by combining PacBio Sequel long-read sequencing with short-read and Hi-C technologies. The assembled genome covers 97.8% of the adzuki bean genome with a contig N50 of approximately 16 Mb and a total of 32 738 protein-coding genes. We also generated a comprehensive genome variation map of adzuki bean by whole-genome resequencing (WGRS) of 322 diverse adzuki beans accessions including both wild and cultivated. Furthermore, we have conducted comparative genomics and a genome-wide association study (GWAS) on key agricultural traits to investigate the evolution and domestication. GWAS identified several candidate genes, including VaCycA3;1, VaHB15, VaANR1 and VaBm, that exhibited significant associations with domestication traits. Furthermore, we conducted functional analyses on the roles of VaANR1 and VaBm in regulating seed coat colour. We provided evidence for the highest genetic diversity of wild adzuki (Vigna angularis var. nipponensis) in China with the presence of the most original wild adzuki bean, and the occurrence of domestication process facilitating transition from wild to cultigen. The present study elucidates the genetic basis of adzuki bean domestication traits and provides crucial genomic resources to support future breeding efforts in adzuki bean.

Determining the genetic basis of ginsenosides variation during ginseng domestication by evolutionary transcriptomics

Ginsenosides, the primary medicinally active substances in ginseng, are consistently used to treat a variety of diseases. Cultivated ginseng was domesticated from wild ginseng, for which the mode of domestication and the changes in the content of ginsenosides and their regulatory mechanisms during the domestication process were unclear. Here, transcriptome sequencing and metabolomic analysis were used to compare wild and cultivated ginsengs to gain insight into the genetic and ginsenosides content changes associated with domestication. Genetic structure analysis revealed that ginseng might have undergone independent domestication in China and Korea, respectively. A slightly reduced genetic diversity occurred in wild and cultivated ginsengs and ginseng was domesticated about 2000 years ago in China. 330 genes were identified as signatures of selective sweeps that occurred during ginseng domestication, including bZIP051, GARP222, HMGCS058, and UGTs225. The content of ginsenosides in leaves of cultivated ginseng was higher than leaves of wild ginseng, while substantial monomers content in wild ginseng was significantly higher than that in cultivated ginseng. The content of ginsenosides was higher in leaves than in roots and stems of both wild and cultivated ginsengs. Module-trait association analysis suggested abundant TFs, including MYB, AP2/ERF, NAC, and bZIP, were highly associated with expression level of ginsenosides synthetic genes and monomer content. The occurrence of alternative splicing events in genes was significantly reduced during ginseng domestication, with ginsenosides synthesis genes being particularly susceptible to alternative splicing. The variation of ginsenosides content was independently regulated by alternative splicing and transcription factors between cultivated and wild ginsengs. This study provided valuable genetic sources of ginsenosides that could contribute to ginseng breeding.

Root microbiota analysis of Oryza rufipogon and Oryza sativa reveals an orientation selection during the domestication process.

The root-associated microbiota has a close relation to the life activities of plants, and its composition is affected by the rhizospheric environment and plant genotypes. Rice (Oryza sativa) was domesticated from the ancestor species Oryza rufipogon. Many important agricultural traits and adversity resistance of rice have changed during a long time of natural domestication and artificial selection. However, the influence of rice genotypes on root microbiota in important agricultural traits remains to be explained. In this study, we performed 16S rRNA and internal transcribed spacer (ITS) gene amplicon sequencing to generate bacterial and fungal community profiles of O. rufipogon and O. sativa, both of which were planted in a farm in Guangzhou and had reached the reproductive stage. We compared their root microbiota in detail by alpha diversity, beta diversity, different species, core microbiota, and correlation analyses. We found that the relative abundance of bacteria was significantly higher in the cultivated rice than in the common wild rice, while the relative abundance of fungi was the opposite. Significant differences in agricultural traits between O. rufipogon and O. sativa showed a high correlation with core microorganisms in the two Oryza species, which only existed in either or had obviously different abundance in both two species, indicating that rice genotype/phenotype had a strong influence on recruiting specific microorganisms. Our study provides a theoretical basis for the in-depth understanding of rice root microbiota and the improvement of rice breeding from the perspective of the interaction between root microorganisms and plants.IMPORTANCEPlant root microorganisms play a vital role not only in plant growth and development but also in responding the biotic and abiotic stresses. Oryza sativa is domesticated from Oryza rufipogon which has many excellent agricultural traits especially containing resistance to biotic and abiotic stresses. To improve the yield and resistance of cultivated rice, it is particularly important to deeply research on differences between O. sativa and O. rufipogon and find beneficial microorganisms to remodel the root microbiome of O. sativa.

Resistance to platformization: Palantir in the Norwegian police

ABSTRACT In 2016, the Norwegian police signed a contract with Palantir Technology for the provision of the surveillance platform Gotham, a platform that enables agencies to integrate data stored in different databases from internal and external sources. The project was to be ready for operation in 2018. In February 2020, the Norwegian Police Directorate announced the project had ended. When they signed off the contract, they had spent around NOK 100 million for nothing. Drawing on documents and interviews with police managers and officers involved in the Gotham project, we explore how platformization represented a conflicting institutional logic which collided with the dominant one and threatened established power structures. Platformization, understood as an organizational process, competes with professionalism and bureaucracy as established institutional logics in the police to control and coordinate work. The analysis of conflicting institutional logics stemming from socio-technical and material objects, reveals how police staff experiences of the symbolic, material and cognitive aspects of logics are of importance in domestication processes. The struggle for market dominance also fueled the conflict between established and new suppliers. The totalizing tendencies of platform policing may explain why the project went on for so long before it was terminated. To a certain degree, our findings show data becoming a major currency, and there is a calculative logic in this type of policing. Platform policing has user activity as its source, and non-use stops the business.

Resequencing of reindeer genomes provides clues to their docile habits.

Reindeer have long been served as vital subsistence resources for inhabitants of Arctic and subarctic regions owing to their domestication. However, the evolutionary relationships and divergence times among different reindeer populations, genetic traits that distinguish domesticated reindeer, and factors that contribute to their relative docility compared with that of other Cervidae specie, remain unclear. In this study, we sequenced the genomes of 32 individuals from wild and domestic reindeer populations that inhabit Arctic and subarctic regions. We found that reindeer experienced 2 or more independent domestication events characterized by weak artificial selection pressure and limited significant differences in genomic parameters between wild and domestic populations. Alterations in conserved noncoding elements in the reindeer genomes, particularly those associated with nervous system development, may have contributed to their domestication by rendering the nervous system less responsive. Together, our results suggest that inherent species-specific traits, rather than intense artificial selection, may have played a significant role in the relatively docile behavior of reindeer and offer valuable insights into the domestication process of these animals.

Mudjair: Intellectual Progress and Fisheries Innovation in the Dutch Colonial Period

Several historical studies that exist today have reviewed how the fishing industry developed during the colonial period. However, generally existing studies focus more on aspects of marine and port fisheries. The inland or freshwater fisheries aspect is not highlighted much. One of the results of the development of inland fisheries knowledge and technology is the innovation of mudjair fish. This paper tries to dig deeper into the innovators of mudjair fish both in terms of background knowledge and domestication methods. The method used in this paper is the historical method. Based on the results of the study, Mudjair's knowledge as an innovator is based on informal knowledge. The series of fish domestication processes he used were scientific organic knowledge. This is evidence of intellectual progress and innovation in the field of fisheries.

Research on soil‐borne diseases of ginseng due to root exudates

AbstractIn a monocropping pattern for the crop domestication process, the interspecific and intraspecific interaction modes can be changed. In domesticated crops, the intraspecific interactions may have detrimental effects. Moreover, soil‐borne diseases in consecutive monocropped medicinal crops can be a critical challenge that has been difficult to solve. This study has been conducted to evaluate the effect of monoculture and intercropped cultivation on soil‐borne diseases caused by root secretions in American ginseng. The results of the correlation analysis showed that the polyethylenes in the roots had a more negative correlation with the occurrence of soil‐borne diseases than ginsenosides. Therefore, polyethylenes can be considered as an important factor in replanting failure of American ginseng. Furthermore, polyethylenes were able to remain in the soil and have a greater impact on the incidence of soil‐borne diseases than ginsenosides.

Identification of the domestication gene GmCYP82C4 underlying the major quantitative trait locus for the seed weight in soybean.

A major quantitative trait locus (QTL) for the hundred-seed weight (HSW) was identified and confirmed in the two distinct soybean populations, and the target gene GmCYP82C4 underlying this locus was identified that significantly associated with soybean seed weight, and it was selected during the soybean domestication and improvement process. Soybean is a major oil crop for human beings and the seed weight is a crucial goal of soybean breeding. However, only a limited number of target genes underlying the quantitative trait loci (QTLs) controlling seed weight in soybean are known so far. In the present study, six loci associated with hundred-seed weight (HSW) were detected in the first population of 573 soybean breeding lines by genome-wide association study (GWAS), and 64 gene models were predicted in these candidate QTL regions. The QTL qHSW_1 exhibits continuous association signals on chromosome four and was also validated by region association study (RAS) in the second soybean population (409 accessions) with wild, landrace, and cultivar soybean accessions. There were seven genes in qHSW_1 candidate region by linkage disequilibrium (LD) block analysis, and only Glyma.04G035500 (GmCYP82C4) showed specifically higher expression in flowers, pods, and seeds, indicating its crucial role in the soybean seed development. Significant differences in HSW trait were detected when the association panels are genotyped by single-nucleotide polymorphisms (SNPs) in putative GmCYP82C4 promoter region. Eight haplotypes were generated by six SNPs in GmCYP82C4 in the second soybean population, and two superior haplotypes (Hap2 and Hap4) of GmCYP82C4 were detected with average HSW of 18.27g and 18.38g, respectively. The genetic diversity of GmCYP82C4 was analyzed in the second soybean population, and GmCYP82C4 was most likely selected during the soybean domestication and improvement process, leading to the highest proportion of Hap2 of GmCYP82C4 both in landrace and cultivar subpopulations. The QTLs and GmCYP82C4 identified in this study provide novel genetic resources for soybean seed weight trait, and the GmCYP82C4 could be used for soybean molecular breeding to develop desirable seed weight in the future.

Biodegradation of chloroxylenol by an aerobic enrichment consortium and a newly identified Rhodococcus strain.

Chloroxylenol is a commonly used antimicrobial agent in antibacterial and disinfection products, which has been detected in various environments, such as wastewater treatment plants, rivers, seawater, and even drinking water, with concentrations ranging from ng/L to mg/L. However, the biodegradation of chloroxylenol received limited attention with only sporadic reports available so far. In this study, an efficient chloroxylenol-degrading consortium, which could degrade 20 mg/L chloroxylenol within two days, was obtained after five months of enrichment. Amplicon sequencing analysis revealed a decrease in the α-diversity (e.g., Shannon index and Inv_Simpson index) of the community during the domestication process. Microbial community dynamics were uncovered, with sequences affiliated to Achromobacter, Pseudomonas, and Rhodococcus identified as the most abundant taxonomic groups. From the consortium, five pure isolates were obtained; however, it was found that only one strain of Rhodococcus could degradechloroxylenol. Strain Rhodococcus sp. DMU2021 could degrade chloroxylenol efficiently under the conditions of temperature 30-40 °C, and neutral/alkaline conditions. Chloroxylenol was toxic to strain DMU2021 and triggered both enzymatic and non-enzymatic antioxidant systems in response. This study provides novel insights into the biodegradation process of chloroxylenol, as well as valuable bioresources for bioremediation.

Wild Otherness Within: A Jungian and Zen Approach to the Untamed Self in the Ten Oxherding Pictures

The Ten Oxherding Pictures are an ancient allegory for the process of enlightenment. This article analyzes the series of ten paintings through the lenses of Jungian psychology and alterity studies to suggest an unorthodox interpretation of the images. This interpretation highlights the relationship between the oxherd and the ox, suggesting that the ox is a wild other that seeks intersubjective understanding. In questioning the meaning of domestication in these images, this investigation deconstructs the traditional allegory of enlightenment as a process of domestication, suggesting that these images instead point towards the importance of releasing the appropriative attitude. Ultimately, the oxherd in the series must surrender his perceptual lens to make space for what seems untamed and unencompassable to speak to and through him.

Systematic identification of wheat spike developmental regulators by integrated multi-omics, transcriptional network, GWAS, and genetic analyses

The spike architecture of wheat plays a crucial role in determining grain number, making it a key trait for optimization in wheat breeding programs. In this study, we used a multi-omic approach to analyze the transcriptome and epigenome profiles of the young spike at eight developmental stages, revealing coordinated changes in chromatin accessibility and H3K27me3 abundance during the flowering transition. We constructed a core transcriptional regulatory network (TRN) that drives wheat spike formation and experimentally validated a multi-layer regulatory module involving TaSPL15, TaAGLG1, and TaFUL2. By integrating the TRN with genome-wide association studies, we identified 227 transcription factors, including 42 with known functions and 185 with unknown functions. Further investigation of 61 novel transcription factors using multiple homozygous mutant lines revealed 36 transcription factors that regulate spike architecture or flowering time, such as TaMYC2-A1, TaMYB30-A1, and TaWRKY37-A1. Of particular interest, TaMYB30-A1, downstream of and repressed by WFZP, was found to regulate fertile spikelet number. Notably, the excellent haplotype of TaMYB30-A1, which contains a C allele at the WFZP binding site, was enriched during wheat breeding improvement in China, leading to improved agronomic traits. Finally, we constructed a free and open access Wheat Spike Multi-Omic Database (http://39.98.48.156:8800/#/). Our study identifies novel and high-confidence regulators and offers an effective strategy for dissecting the genetic basis of wheat spike development, with practical value for wheat breeding.

Breeding approaches for improvement of temperate fruit crops and nuts - a review

Fruit breeding is an ancient technology with dynamic current technology and an exciting future (Janick and Moore, 1975, 1996). In its broadest sense, fruit breeding refers to the purposeful genetic improvement of fruit crops through various techniques including selection, hybridization, mutation induction, and molecular techniques. Its origins trace to the domestication process in prehistory and antiquity, where useful species were chosen and cultivated, and improved by continuous selection (Janick, 2005, 2011). Much of the world fruit industry is still based on grower selection from chance seedlings as well as mutations (sports) and as a result many fruit species are characterized by a narrow germplasm base. Spontaneous hybridization between wild plants and cultivated clones was critical to the early domestication of fruits. The lengthy juvenile period and the large field space required to grow temperate fruits have imposed major limitations on conventional breeding and various molecular biological techniques have been employed to make fruit breeding easier. (Igarashi et al.2016). Marker-assisted selection (MAS) uses DNA markers to provide an early DNA-based evaluation of genetic performance potential of seedlings, with the aim of improving cost and/or genetic efficiency of seedling selection (Ru, et al., 2015). Transgenic technology has facilitated the development of fruit trees with resistance to fungal or bacterial diseases, improved fruit quality, or root stocks with better rooting or dwarfing ability. In recent years, new technologies for genetic improvement, such as transgrafting, and genome-editing, have emerged. (Mudge, et al. 2009; Jia and Wang 2014). Using these techniques, no foreign genes are present in the final product, and some of them show considerable promise for application to apple breeding. Furthermore, genome editing, by which only the target gene can be accurately modified, is emerging as a novel breeding technology. These new technologies will undoubtedly facilitate fruit breeding, and yield novel and attractive fruit cultivars.

Population comparative genomics discovers gene gain and loss during grapevine domestication.

Plant domestication are evolutionary experiments conducted by early farmers since thousands years ago, during which the crop wild progenitors are artificially selected for desired agronomic traits along with dramatic genomic variation in the course of moderate to severe bottlenecks. However, previous investigations are mainly focused on small-effect variants, while changes in gene contents are rarely investigated due to the lack of population-level assemblies for both the crop and its wild relatives. Here, we applied comparative genomic analyses to discover gene gain and loss during grapevine domestication using long-read assemblies of representative population samples for both domesticated grapevines (V. vinifera ssp. vinifera) and their wild progenitors (V. vinifera ssp. sylvestris). Only ∼7% of gene families were shared by 16 Vitis genomes while ∼8% of gene families were specific to each accession, suggesting dramatic variations of gene contents in grapevine genomes. Compared to wild progenitors, the domesticated accessions exhibited an increased presence of genes associated with asexual reproduction, while the wild progenitors showcased a higher abundance of genes related to pollination, revealing the transition from sexual reproduction to clonal propagation during domestication processes. Moreover, the domesticated accessions harbored fewer disease-resistance genes than wild progenitors. The SVs occurred frequently in aroma and disease-resistance related genes between domesticated grapevines and wild progenitors, indicating the rapid diversification of these genes during domestication. Our study provides insights and resources for biological studies and breeding programs in grapevine.

The functional divergence of homologous GPAT9 genes contributes to the erucic acid content of Brassica napus seeds

BackgroundThe early allopolyploid Brassica napus was a hybrid of two Brassica species, that had undergone a whole genome duplication event followed by genome restructuring, including deletions and small scale duplications. A large number of homologous genes appeared functional divergence during species domestication. Due to the high conservation of de novo glycerolipid biosynthesis, multiple homologues of glycerol-3-phosphate acyltransferases (GPATs) have been found in B. napus. Moreover, the functional variances among these homologous GPAT-encoding genes are unclear.ResultsIn this study, four B. napus homologous genes encoding glycerol-3-phosphate acyltransferase 9 (BnaGPAT9) were characterized. Although a bioinformatics analysis indicated high protein sequence similarity, the homologues demonstrated tissue-specific expression patterns and functional divergence. Yeast genetic complementation assays revealed that BnaGPAT9-A1/C1 homologues but not BnaGPAT9-A10/C9 homologues encoded functional GPAT enzymes. Furthermore, a single nucleotide polymorphism of BnaGPAT9-C1 that occurred during the domestication process was associated with enzyme activity and contributed to the fatty acid composition. The seed-specific expression of BnGPAT9-C11124A increased the erucic acid content in the transformant seeds.ConclusionsThis study revealed that BnaGPAT9 gene homologues evolved into functionally divergent forms with important roles in erucic acid biosynthesis.

Exploring perceptions of gender roles amongst sexually active adolescents in rural KwaZulu-Natal, South Africa.

Traditional gender and social norms reinforce asymmetrical power relations, increase the risk of experiencing gender-based violence and mediate poor engagement with sexual and reproductive health services. This study explored gender norms and expectations amongst cisgender adolescents in rural KwaZulu-Natal, South Africa. A purposive sample of 29 adolescents aged 16-19 years old were enrolled as part of a longitudinal qualitative study. The current analysis reports on the first round of in-depth interviews, which focused on the role of men and women in their community. A theoretically informed thematic analysis identified three broad themes: 1) Adolescent interpretation and understanding of gender identity, 2) Gendered essentialism and Gender roles (two sub-themes: Young men: Power through providing, and Young women: The domestication process which highlighted that gender roles were defined by being the provider for men, and the successful fulfilment of traditional domestic behaviours amongst women), 3) Gender and fertility highlighted how participants highly valued fertility as affirming of manhood/womanhood. These norms reinforce gender roles that maintain asymmetrical power relations, carrying them over into adulthood. The subtle social pressure to prove fertility could have unintended consequences for driving teenage pregnancy. Structural, gender-based interventions emphasising positive gender-role development in early childhood are needed.

Whole-genome resequencing of major populations revealed domestication-related genes in yaks

BackgroundThe yak is a symbol of the Qinghai-Tibet Plateau and provides important basic resources for human life on the plateau. Domestic yaks have been subjected to strong artificial selection and environmental pressures over the long-term. Understanding the molecular mechanisms of phenotypic differences in yak populations can reveal key functional genes involved in the domestication process and improve genetic breeding.Material and methodHere, we re-sequenced 80 yaks (Maiwa, Yushu, and Huanhu populations) to identify single-nucleotide polymorphisms (SNPs) as genetic variants. After filtering and quality control, remaining SNPs were kept to identify the genome-wide regions of selective sweeps associated with domestic traits. The four methods (π, XPEHH, iHS, and XP-nSL) were used to detect the population genetic separation.ResultsBy comparing the differences in the population stratification, linkage disequilibrium decay rate, and characteristic selective sweep signals, we identified 203 putative selective regions of domestic traits, 45 of which were mapped to 27 known genes. They were clustered into 4 major GO biological process terms. All known genes were associated with seven major domestication traits, such as dwarfism (ANKRD28), milk (HECW1, HECW2, and OSBPL2), meat (SPATA5 and GRHL2), fertility (BTBD11 and ARFIP1), adaptation (NCKAP5, ANTXR1, LAMA5, OSBPL2, AOC2, and RYR2), growth (GRHL2, GRID2, SMARCAL1, and EPHB2), and the immune system (INPP5D and ADCYAP1R1).ConclusionsWe provided there is an obvious genetic different among domestic progress in these three yak populations. Our findings improve the understanding of the major genetic switches and domestic processes among yak populations.

Comparative transcriptomic insights into the domestication of Pleurotus abieticola for coniferous cultivation.

Introduction: Pleurotus abieticola, a promising edible fungus in the Pleurotaceae family, especially its ability to utilize coniferous substrate, holds significant potential for commercial cultivation. However, few reports on the adaptation of P. abieticola to coniferous substrate from the perspective of omics. Methods: This study explores the biological characteristics, domestication process, and nutritional composition of P. abieticola, along with its adaptability to coniferous substrates using transcriptomics. We assessed biological characteristics, optimizing mycelial growth on agar medium with varied carbon and nitrogen sources, temperature, and pH. Additionally, the optimization process extended to fruiting bodies, where impact on the differentiation were evaluated under varying light conditions. Fruiting body nutrient composition was analyzed per the Chinese National Food Safety Standard. Transcriptome sequencing focused on P. abieticola mycelial colonized coniferous and broadleaved substrates. Results and Discussion: The optimal conditions for mycelial growth were identified: dextrin (carbon source), diammonium hydrogen phosphate (nitrogen source), 25°C (temperature), and pH 7.0. White light promoted fruiting body growth and differentiation. Larch substrate exhibited superior yield (190g) and biological efficiency (38.0%) compared to oak (131g, 26.2%) and spruce (166g, 33.2%). P. abieticola showcased high dietary fiber, protein, and total sugar content, low fat, and sufficient microelements. Transcriptome analysis revealed significant key genes involved in lignocellulose degradation, stress-resistant metabolism, and endocytosis metabolism, underscoring their pivotal for coniferous adaptation. This study offers valuable insights for the commercial development and strain breeding of P. abieticola, efficiently leveraging conifer resources. The findings underscore its potential as a valuable source for food, medicinal products, and biotechnological applications.