Polyploidization, pervasive among higher plant species, enhances adaptation to water deficit, but the physiological and molecular advantages need to be investigated widely. Long non-coding RNAs (lncRNAs) are involved in drought tolerance in various crops. Herein, we demonstrate that tetraploidy potentiates tolerance to drought stress in cassava (Manihot esculenta Crantz). Autotetraploidy reduces transpiration by lesser extent increasing of stomatal density, smaller stomatal aperture size, or greater stomatal closure, and reducing accumulation of H2O2 under drought stress. Transcriptome analysis of autotetraploid samples revealed down-regulation of genes involved in photosynthesis under drought stress, and less down-regulation of subtilisin-like proteases involved in increasing stomatal density. UDP-glucosyltransferases were increased more or reduced less in dehydrated leaves of autotetraploids compared with controls. Strand-specific RNA-seq data (validated by quantitative real time PCR) identified 2372 lncRNAs, and 86 autotetraploid-specific lncRNAs were differentially expressed in stressed leaves. The co-expressed network analysis indicated that LNC_001148 and LNC_000160 in autotetraploid dehydrated leaves regulated six genes encoding subtilisin-like protease above mentioned, thereby result in increasing the stomatal density to a lesser extent in autotetraploid cassava. Trans-regulatory network analysis suggested that autotetraploid-specific differentially expressed lncRNAs were associated with galactose metabolism, pentose phosphate pathway and brassinosteroid biosynthesis, etc. Tetraploidy potentiates tolerance to drought stress in cassava, and LNC_001148 and LNC_000160 mediate drought tolerance by regulating stomatal density in autotetraploid cassava.

• A total of 508 metabolites were identified in three cassava cultivars. • White-fleshed cassava had the highest contents of amino acids and organic acids. • Yellow-fleshed cassava was enriched in metabolites related to specific pathways. • Several pathways were found to be regulated at the transcriptional level.

Cassava is a crucial crop that makes a significant contribution to ensuring human food security. However, high-quality telomere-to-telomere cassava genomes have not been available up to now, which has restricted the progress of haploid molecular breeding for cassava. In this study, we constructed two nearly complete haploid resolved genomes and an integrated, telomere-to-telomere gap-free reference genome of an excellent cassava variety, ‘Xinxuan 048’, thereby providing a new high-quality genomic resource. Furthermore, the evolutionary history of several species within the Euphorbiaceae family was revealed. Through comparative analysis of haploid genomes, it was found that two haploid genomes had extensive differences in linear structure, transcriptome features, and epigenetic characteristics. Genes located within the highly divergent regions and differentially expressed alleles are enriched in the functions of auxin response and the starch synthesis pathway. The high heterozygosity of cassava ‘Xinxuan 048’ leads to rapid trait segregation in the first selfed generation. This study provides a theoretical basis and genomic resource for molecular breeding of cassava haploids.

Pueraria lobata var. thomsonii (hereinafter abbreviated as Podalirius thomsonii), a member of the legume family, is one of the important traditional Chinese herbal medicines, and its puerarin extract is widely used in the health and pharmaceutical industry. Here, we assembled a high-quality genome of P. thomsonii using long-read single-molecule sequencing and Hi-C technologies. The genome assembly is ~1.37 Gb in size and consists of 5145 contigs with a contig N50 of 593.70 kb, further clustered into 11 pseudochromosomes. Genome structural annotation resulted in ~869.33 Mb (~62.70% of the genome) repeat regions and 45 270 protein-coding genes. Genome evolution analysis revealed that P. thomsonii is most closely related to soybean and underwent two ancient whole-genome duplication events; one was in the common ancestor shared by legume species and the other occurred independently at around 7.2 million years ago, after its speciation. A total of 2373 gene families were found to be unique in P. thomsonii compared with five other legume species. Genes and metabolites related to puerarin content in tuberous tissues were characterized. A total of 572 genes that were upregulated in the puerarin biosynthesis pathway were identified, and 235 candidate genes were further enriched by omics data. Furthermore, we identified six 8-C-glucosyltransferase (8-C-GT) candidate genes significantly involved in puerarin metabolism. Our study filled a key genomic gap in the legume family, and provided valuable multi-omic resources for the genetic improvement of P. thomsonii.

Cassava (Manihot esculenta Crantz) is a staple food of 800 million people in the tropical and subtropical regions of the world. Its industrial utilization for bioethanol, animal feed, and starch are still continuously expanding. It was not until the 1970s that significant scientific efforts were undertaken to improve cassava, despite its considerable economic and social significance. Shortening the breeding cycle and improving the breeding efficiency are always the focus of the cassava breeding study. In this review, we provide a global perspective on the current status of cassava germplasm resources and explore the diverse applications of cassava breeding methods from hybridization, polyploidy, and inbreeding to genomic selection and gene editing. Additionally, we overview at least six nearly complete cassava genome sequences established based on modern genomic techniques. These achievements have substantially supported the advancing of gene discovery and breeding of new cassava varieties. Furthermore, we provide a summary of the advancements in cassava’s functional genomics, concentrating on important traits such as starch quality and content, dry matter content, tolerance to postharvest physiological deterioration, nutritional quality, and stress resistance. We also provide a comprehensive summary of the milestone events and key advancements in cassava genetic improvement over the past 50 years. Finally, we put forward the perspective of developing genomic selection breeding model and super-hybrids of cassava through building inbreeding population and emphasize the generation of triploid cassavas, as well as using gene editing technology allowing cassava to be a tropical model plant to serve for basic biological research and molecular breeding.