Genome resources for three modern cotton lines guide future breeding efforts.

Cotton (Gossypium hirsutum L.) is the key renewable fibre crop worldwide, yet its yield and fibre quality show high variability due to genotype-specific traits and complex interactions among cultivars, management practices and environmental factors. Modern breeding practices may limit future yield gains due to a narrow founding gene pool. Precision breeding and biotechnological approaches offer potential solutions, contingent on accurate cultivar-specific data. Here we address this need by generating high-quality reference genomes for three modern cotton cultivars ('UGA230', 'UA48' and 'CSX8308') and updating the 'TM-1' cotton genetic standard reference. Despite hypothesized genetic uniformity, considerable sequence and structural variation was observed among the four genomes, which overlap with ancient and ongoing genomic introgressions from 'Pima' cotton, gene regulatory mechanisms and phenotypic trait divergence. Differentially expressed genes across fibre development correlate with fibre production, potentially contributing to the distinctive fibre quality traits observed in modern cotton cultivars. These genomes and comparative analyses provide a valuable foundation for future genetic endeavours to enhance global cotton yield and sustainability.

QTL mapping and identification of candidate genes linked to red rot resistance in sugarcane.

Sugarcane (Saccharum species hybrid) is one of the most important commercial crops cultivated worldwide for products like white sugar, bagasse, ethanol, etc. Red rot is a major sugarcane disease caused by a hemi-biotrophic fungus, Colletotrichum falcatum Went., which can potentially cause a reduction in yield up to 100%. Breeding for red rot-resistant sugarcane varieties has become cumbersome due to its complex genome and frequent generation of new pathotypes of red rot fungus. In the present study, a genetic linkage map was developed using a selfed population of a popular sugarcane variety CoS 96268. A QTL linked to red rot resistance (qREDROT) was identified, which explained 26% of the total phenotypic variation for the trait. A genotype-phenotype network analysis performed to account for epistatic interactions, identified the key markers involved in red rot resistance. The differential expression of the genes located in the genomic region between the two flanking markers of the qREDROT as well as in the vicinity of the markers identified through the genotype-phenotype network analysis in a set of contrasting genotypes for red rot infection further confirmed the mapping results. Further, the expression analysis revealed that the plant defense-related gene coding 26S protease regulatory subunit is strongly associated with the red rot resistance. The findings can help in the screening of disease resistant genotypes for developing red rot-resistant varieties of sugarcane. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03481-7.

Correction to: Improved lint yield under field conditions in cotton over-expressing transcription factors regulating fibre initiation.

Due to an unfortunate misunderstanding, an extra middle initial erroneously appeared in the original publication and the full name of the first author should read Shi Ming Liu.

Improved lint yield under field conditions in cotton over-expressing transcription factors regulating fibre initiation.

Only a few transcription factors (TFs) regulating which cells of the ovule epidermis differentiate into lint fibres have been identified in cotton (Gossypium hirsutum L.). In this study, the effect on lint yield and fibre quality of over-expressing three TFs in cotton, GhHD-1, GhMYB25 and GhMYB25Like, and their double and triple combinations, were evaluated in field experiments over two seasons. The expression of single or stacked TFs were all driven either by an ovule-specific promoter, FBP 7, or a constitutive promoter, Stunt 7, in a Coker 315 background. TF type, either singly or in combination, was found to be the most significant factor affecting lint yield. Among 64 transgenic lines tested, seven were higher yielding than null segregant lines in one or both seasons and were all from the sets with single and double over-expressed TF combinations. A reduced yield was associated with the set of triple combinations. The two most stable high yielding lines across the seasons recorded 12-22% higher yields than the nulls, although were not competitive to locally adapted commercial controls. Over-expression of TFs singly or in combination did not significantly alter fibre length and strength, but sometimes increased fibre micronaire. There were positive relationships between lint yield and lint percentage and lint yield and fibre density amongst the transgenic lines. Our preliminary results suggest that manipulating TF expression, either singly or in pairs, can increase the density of fibres initiated on developing seeds and fibre yields under field conditions while maintaining overall fibre quality.