A reference-grade genome assembly for Gossypium bickii and insights into its genome evolution and formation of pigment glands and gossypol.

The pigment gland is a morphological characteristic of Gossypium and its related genera. Gossypium bickii (G1) is characterized by delayed pigment gland morphogenesis in the cotyledons. In this study, a reference-grade genome of G1 was generated, and comparative genomics analysis showed that G1 was closest to Gossypium australe (G2), followed by A- and D-genome species. Two large fragment translocations in chromosomes 5 and 13 were detected between the G genome and other Gossypium genomes and were unique to the G1 and G2 genomes. Compared with the G2 genome, two large fragment inversions in chromosomes 12 and 13 were detected in G1. According to the phylogeny, divergence time, and similarity analysis of nuclear and chloroplast genomes, G1 was formed by hybridization between Gossypium sturtianum (C1) and a common ancestor of G2 and Gossypium nelsonii (G3). The coordinated expression patterns of pigment gland formation (GoPGF) and gossypol biosynthesis genes in G1 were verified to be consistent with its phenotype, and nine genes that were related to the process of pigment gland formation were identified. A novel gene, GbiCYP76B6, regulated by GoPGF, was found to affect gossypol biosynthesis. These findings offer insights into the origin and evolution of G1 and its mechanism of pigment gland formation and gossypol biosynthesis.

Genome-wide characterization on MT family and their expression in response to environmental cues in upland cotton (Gossypium hirsutum L.).

Metallothioneins (MTs) are believed as key metal chelators and scavengers of reactive oxygen species (ROS), which are involved in tolerance and de-toxicity to multiple environmental stresses in plants. The MT gene family was characterized from upland cotton (Gossypium hirsutum L.), compared with its putative genome donors G. arboretum and raimondii. Subsequently, gene functions were predicted by promoter analysis. Moreover, gene expressions subjecting to exogenous stimuli, as well as in terms of developments, were studied. The main findings were shown as follows: 1) 19 GhMTs were identified from G. hirsutum, and the family completely included all four sub-types, namely p1, p2, p3, and pec. Sub-type p2 GhMTs were most conservative in protein motif compositions, gene structures, phylogenic relationships, and group numbers, while p3 GhMTs demonstrated much more diversiform and distant genetic relationships. 2) The GhMT family experienced apparent gene expansion, and the members from the D sub-genome were subjected to stronger environmental selection. 3) GhMTs played differential and overlapped roles in response to environmental cues. 4) GhMT6, GhMT8, and GhMT14 were involved in both vegetative and reproductive developments. These findings must provide valuable insights into understanding the plant MT gene family and novel gene resources for cotton breeding for environmental stresses, phytoremediation, and beyond.

Whole-genome resequencing of 240 Gossypium barbadense accessions reveals genetic variation and genes associated with fiber strength and lint percentage.

KEY MESSAGE: Genetic variation in a G. barbadense population was revealed using resquencing. GWAS on G.barbadense population identified several candidate genes associated with fiber strength and lint percentage. Gossypium barbadense is the second-largest cultivated cotton species planted in the world, which is characterized by high fiber quality. Here, we described the global pattern of genetic polymorphisms for 240 G. barbadense accessions based on the whole-genome resequencing. A total of 3,632,231 qualified single-nucleotide polymorphisms (SNPs) and 221,354 insertion-deletions (indels) were obtained. We conducted a genome-wide association study (GWAS) on 12 traits under four environments. Two traits with more stable associated variants, fiber strength and lint percentage, were chosen for further analysis. Three putative candidate genes, HD16 orthology (GB_D11G3437), WDL2 orthology (GB_D11G3460) and TUBA1 orthology (GB_D11G3471), on chromosome D11 were found to be associated with fiber strength, and one gene orthologous to Arabidopsis Receptor-like protein kinase HERK 1 (GB_A07G1034) was predicated to be the candidate gene for the lint percentage improvement. The identified genes may serve as promising targets for genetic engineering to accelerate the breeding process for G. barbadense and the high-density genome variation map constructed in this work may facilitate our understanding of the genetic architecture of cotton traits.