http://www.cell.com/article/S0092867421014288/pdf

The Chinese pine genome and methylome unveil key features of conifer evolution

Abstract Potato ( Solanum tuberosum L.) is the world’s most important non-cereal food crop, and the vast majority of commercially grown cultivars are highly heterozygous tetraploids. Advances in diploid hybrid breeding based on true seeds have the potential to revolutionize future potato breeding and production 1–4 . So far, relatively few studies have examined the genome evolution and diversity of wild and cultivated landrace potatoes, which limits the application of their diversity in potato breeding. Here we assemble 44 high-quality diploid potato genomes from 24 wild and 20 cultivated accessions that are representative of Solanum section Petota , the tuber-bearing clade, as well as 2 genomes from the neighbouring section, Etuberosum . Extensive discordance of phylogenomic relationships suggests the complexity of potato evolution. We find that the potato genome substantially expanded its repertoire of disease-resistance genes when compared with closely related seed-propagated solanaceous crops, indicative of the effect of tuber-based propagation strategies on the evolution of the potato genome. We discover a transcription factor that determines tuber identity and interacts with the mobile tuberization inductive signal SP6A. We also identify 561,433 high-confidence structural variants and construct a map of large inversions, which provides insights for improving inbred lines and precluding potential linkage drag, as exemplified by a 5.8-Mb inversion that is associated with carotenoid content in tubers. This study will accelerate hybrid potato breeding and enrich our understanding of the evolution and biology of potato as a global staple food crop. 

https://www.nature.com/articles/s41586-022-04822-x.pdf

Genome evolution and diversity of wild and cultivated potatoes

Tracing the genetic footprints of vertebrate landing in non-teleost ray-finned fishes.

Fish biology has been developed for more than 100 years, but some important breakthroughs have been made in the last decade. Early studies commonly concentrated on morphology, phylogenetics, development, growth, reproduction manipulation, and disease control. Recent studies have mostly focused on genetics, molecular biology, genomics, and genome biotechnologies, which have provided a solid foundation for enhancing aquaculture to ensure food security and improving aquatic environments to sustain ecosystem health. Here, we review research advances in five major areas: (1) biological innovations and genomic evolution of four significant fish lineages including non-teleost ray-finned fishes, northern hemisphere sticklebacks, East African cichlid fishes, and East Asian cyprinid fishes; (2) evolutionary fates and consequences of natural polyploid fishes; (3) biological consequences of fish domestication and selection; (4) development and innovation of fish breeding biotechnologies; and (5) applicable approaches and potential of fish genetic breeding biotechnologies. Moreover, five precision breeding biotechniques are examined and discussed in detail including gene editing for the introgression or removal of beneficial or detrimental alleles, use of sex-specific markers for the production of mono-sex populations, controllable primordial germ cell on-off strategy for producing sterile offspring, surrogate broodstock-based strategies to accelerate breeding, and genome incorporation and sexual reproduction regain-based approach to create synthetic polyploids. Based on these scientific and technological advances, we propose a blueprint for genetic improvement and new breed creation for aquaculture species and analyze the potential of these new breeding strategies for improving aquaculture seed industry and strengthening food security.

Rethinking fish biology and biotechnologies in the challenge era for burgeoning genome resources and strengthening food security

Fish biology has been developed for more than 100 years, but some important breakthroughs have been made in the last decade. Early studies commonly concentrated on morphology, phylogenetics, development, growth, reproduction manipulation, and disease control. Recent studies have mostly focused on genetics, molecular biology, genomics, and genome biotechnologies, which have provided a solid foundation for enhancing aquaculture to ensure food security and improving aquatic environments to sustain ecosystem health. Here, we review research advances in five major areas: (1) biological innovations and genomic evolution of four significant fish lineages including non-teleost ray-finned fishes, northern hemisphere sticklebacks, East African cichlid fishes, and East Asian cyprinid fishes; (2) evolutionary fates and consequences of natural polyploid fishes; (3) biological consequences of fish domestication and selection; (4) development and innovation of fish breeding biotechnologies; and (5) applicable approaches and potential of fish genetic breeding biotechnologies. Moreover, five precision breeding biotechniques are examined and discussed in detail including gene editing for the introgression or removal of beneficial or detrimental alleles, use of sex-specific markers for the production of mono-sex populations, controllable primordial germ cell on-off strategy for producing sterile offspring, surrogate broodstock-based strategies to accelerate breeding, and genome incorporation and sexual reproduction regain-based approach to create synthetic polyploids. Based on these scientific and technological advances, we propose a blueprint for genetic improvement and new breed creation for aquaculture species and analyze the potential of these new breeding strategies for improving aquaculture seed industry and strengthening food security. 

Jue Ruan

Papers

African lungfish genome sheds light on the vertebrate water-to-land transition.