Plant-on-chip: Core morphogenesis processes in the tiny plant Wolffia australiana.

A plant can be thought of as a colony comprising numerous growth buds, each developing to its own rhythm. Such lack of synchrony impedes efforts to describe core principles of plant morphogenesis, dissect the underlying mechanisms, and identify regulators. Here, we use the minimalist known angiosperm to overcome this challenge and provide a model system for plant morphogenesis. We present a detailed morphological description of the monocot Wolffia australiana, as well as high-quality genome information. Further, we developed the plant-on-chip culture system and demonstrate the application of advanced technologies such as single-nucleus RNA-sequencing, protein structure prediction, and gene editing. We provide proof-of-concept examples that illustrate how W. australiana can decipher the core regulatory mechanisms of plant morphogenesis.

Divergent improvement of two cultivated allotetraploid cotton species.

Interspecific genomic variation can provide a genetic basis for local adaptation and domestication. A series of studies have presented its role of interspecific haplotypes and introgressions in adaptive traits, but few studies have addressed their role in improving agronomic character. Two allotetraploid Gossypium species, Gossypium barbadense (Gb) and G. hirsutum (Gh) originating from the Americas, are cultivated independently. Here, through sequencing and the comparison of one GWAS panel in 229 Gb accessions and two GWAS panels in 491 Gh accessions, we found that most associated loci or functional haplotypes for agronomic traits were highly divergent, representing the strong divergent improvement between Gb and Gh. Using a comprehensive interspecific haplotype map, we revealed that six interspecific introgressions from Gh to Gb were significantly associated with the phenotypic performance of Gb, which could explain 5%-40% of phenotypic variation in yield and fibre qualities. In addition, three introgressions overlapped with six associated loci in Gb, indicating that these introgression regions were under further selection and stabilized during improvement. A single interspecific introgression often possessed yield-increasing potential but decreased fibre qualities, or the opposite, making it difficult to simultaneously improve yield and fibre qualities. Our study not only has proved the importance of interspecific functional haplotypes or introgressions in the divergent improvement of Gb and Gh, but also supports their potential value in further human-mediated hybridization or precision breeding.

Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton.

Allotetraploid cotton is an economically important natural-fiber-producing crop worldwide. After polyploidization, Gossypium hirsutum L. evolved to produce a higher fiber yield and to better survive harsh environments than Gossypium barbadense, which produces superior-quality fibers. The global genetic and molecular bases for these interspecies divergences were unknown. Here we report high-quality de novo-assembled genomes for these two cultivated allotetraploid species with pronounced improvement in repetitive-DNA-enriched centromeric regions. Whole-genome comparative analyses revealed that species-specific alterations in gene expression, structural variations and expanded gene families were responsible for speciation and the evolutionary history of these species. These findings help to elucidate the evolution of cotton genomes and their domestication history. The information generated not only should enable breeders to improve fiber quality and resilience to ever-changing environmental conditions but also can be translated to other crops for better understanding of their domestication history and use in improvement.

Identifying Functional Genes Influencing Gossypium hirsutum Fiber Quality.

Fiber quality is an important economic index and a major breeding goal in cotton, but direct phenotypic selection is often hindered due to environmental influences and linkage with yield traits. A genome-wide association study (GWAS) is a powerful tool to identify genes associated with phenotypic traits. In this study, we identified fiber quality genes in upland cotton (Gossypium hirsutum L.) using GWAS based on a high-density CottonSNP80K array and multiple environment tests. A total of 30 and 23 significant single nucleotide polymorphisms (SNPs) associated with five fiber quality traits were identified across the 408 cotton accessions in six environments and the best linear unbiased predictions, respectively. Among these SNPs, seven loci were the same, and 128 candidate genes were predicted in a 1-Mb region (±500 kb of the peak SNP). Furthermore, two major genome regions (GR1 and GR2) associated with multiple fiber qualities in multiple environments on chromosomes A07 and A13 were identified, and within them, 22 candidate genes were annotated. Of these, 11 genes were expressed [log2(1 + FPKM)>1] in the fiber development stages (5, 10, 20, and 25 dpa) using RNA-Seq. This study provides fundamental insight relevant to identification of genes associated with fiber quality and will accelerate future efforts toward improving fiber quality of upland cotton.