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Verticillium wilt (VW) is an important and widespread disease of cotton and once established is long-lived and difficult to manage. In Australia, the non-defoliating pathotype of Verticillium dahliae is the most common, and extremely virulent. Breeding cotton varieties with increased VW resistance is the most economical and effective method of controlling this disease and is greatly aided by understanding the genetics of resistance. This study aimed to investigate VW resistance in 240 F7 recombinant inbred lines (RIL) derived from a cross between MCU-5, which has good resistance, and Siokra 1–4, which is susceptible. Using a controlled environment bioassay, we found that resistance based on plant survival or shoot biomass was complex but with major contributions from chromosomes D03 and D09, with genomic prediction analysis estimating a prediction accuracy of 0.73 based on survival scores compared to 0.36 for shoot biomass. Transcriptome analysis of MCU-5 and Siokra 1–4 roots uninfected or infected with V. dahliae revealed that the two cultivars displayed very different root transcriptomes and responded differently to V. dahliae infection. Ninety-nine differentially expressed genes were located in the two mapped resistance regions and so are potential candidates for further identifying the genes responsible for VW resistance. [ABSTRACT FROM AUTHOR]

Numerous genetic loci and several functionally characterized genes have been linked to determination of lint percentage (lint%), one of the most important cotton yield components, but we still know little about the major genetic components underlying lint%. Here, we first linked the genetic loci containing MYB25-like_At and HD1_At to the fiberless seed trait of 'SL1-7-1' and found that MYB25-like_At and HD1_At were very lowly expressed in 'SL1-7-1' ovules during fiber initiation. We then dissected the genetic components involved in determination of lint% using segregating populations derived from crosses of fuzzless mutants and intermediate segregants with different lint%, which not only confirmed the HD1_At locus but identified the HD1_Dt locus as being the major genetic components contributing to fiber initiation and lint%. The segregating populations also allowed us to evaluate the relative contributions of MYB25-like_At , MYB25-like_Dt , HD1_At , and HD1_Dt to lint%. Haplotype analysis of an Upland cotton (Gossypium hirsutum) population with 723 accessions (including 81 fuzzless seed accessions) showed that lint% of the accessions with the LP allele (higher lint%) at MYB25-like_At , MYB25-like_Dt , or HD1_At was significantly higher than that with the lp allele (lower lint%). The lint% of the Upland cotton accessions with 3 or 4 LP alleles at MYB25-like and HD1 was significantly higher than that with 2 LP alleles. The results prompted us to propose a strategy for breeding high-yielding cotton varieties, i.e. pyramiding the LP alleles of MYB25-like and HD1 with new lint% LP alleles without negative impact on seed size and fiber quality. [ABSTRACT FROM AUTHOR]

Cotton is one of the most important multiple-usage crops, including fiber, oil, protein, and even ornament. Anthocyanins are the main chromogenic substances in plants, giving the floral organs of ornamental plants their bright colors. Here, we characterized a cotton accession (Gossypium hirsutum L.) showing pink petals with red spot at the base of petal. The pink flower (PF) accession is thought to be derived from interspecific cross between G. hirsutum and a diploid wild cotton species G. bickii native to Australia. We mapped the genetic region underlying the PF trait using bulked segregant RNA sequencing (BSR-Seq) and demonstrated introgression of a genomic region from G. bickii based on re-sequencing of the PF accession and comparative genomic analyses. The introgression fragment contains an R2R3-MYB gene (GH_A07G0851 or GhPF) homologous to GbBM regulating the formation of the red spots at the base of petals in G. barbadense. The coding region of GH_A07G0851 from the PF accession has a 15-bp deletion found only in Australian diploid wild cotton species, G. bickii , and G. australe , which possess light pink flowers with red spots at the base of petals. The temporal expression pattern of GH_A07G0851 tightly correlates with coloration of pink flowers during their development. The results demonstrate the importance of MYB gene in regulation of biosynthesis and accumulation of anthocyanins in cotton flowers and provide candidate gene for manipulating flower color, an important attribute that can facilitate the production of hybrid seeds through attracting pollinators for efficient pollen transfer so to enhance utilization of heterosis in cotton. • Based on bulked segregant RNA sequencing and genotyping by target sequencing, the pink flower gene GhPF was mapped. • It was confirmed that, a region with GhPF was introduced from G.bickii into upland cotton through distant hybridization. • A 15-bp deletion in the coding region of GH_A07G0851 from the pink flower found only in G.bickii and G.australe). • The deletion sites is completely co-segregating with the PF phenotype. • The spatiotemporal expression pattern of GH_A07G0851 correlates with coloration of pink flowers during their development. [ABSTRACT FROM AUTHOR]

Comprehensive utilization of cottonseeds is limited by the presence of pigment glands and its inclusion gossypol. The ideal cotton has glandless seeds but a glanded plant, a trait found in only a few Australian wild cotton species, including Gossypium bickii. Introgression of this trait into cultivated species has proved to be difficult. Understanding the biological processes toward pigment gland morphogenesis and the associated underlying molecular mechanisms will facilitate breeding of cultivated cotton varieties with the trait of glandless seeds and glanded plant. In this study, single-cell RNA sequencing (scRNA-seq) was performed on 12 222 protoplasts isolated from cotyledons of germinating G. bickii seeds 48 h after imbibition. Clustered into 14 distinct clusters unsupervisedly, these cells could be grouped into eight cell populations with the assistance of known cell marker genes. The pigment gland cells were well separated from others and could be separated into pigment gland parenchyma cells, secretory cells, and apoptotic cells. By integrating the pigment gland cell developmental trajectory, transcription factor regulatory networks, and core transcription factor functional validation, we established a model for pigment gland formation. In this model, light and gibberellin were verified to promote the formation of pigment glands. In addition, three novel genes, GbiERF114 (ETHYLENE RESPONSE FACTOR 114), GbiZAT11 (ZINC FINGER OF ARABIDOPSIS THALIANA 11), and GbiNTL9 (NAC TRANSCRIPTION FACTOR-LIKE 9), were found to affect pigment gland formation. Collectively, these findings provide new insights into pigment gland morphogenesis and lay the cornerstone for future cotton scRNA-seq investigations., (Copyright © 2023 The Author. Published by Elsevier Inc. All rights reserved.)