Dataset Information

Genome assembly of two nematode-resistant cotton lines (Gossypium hirsutum L.).

ABSTRACT: Upland cotton (Gossypium hirsutum L.) is susceptible to damage by the root-knot and the reniform nematodes, causing yield losses greater than 4% annually in the United States. In addition, these nematodes are synergistic with seeding disease and root rot pathogens that exacerbate diseases and subsequent yield losses. Production practices to minimize nematode damage include crop rotation and nematicides, but these techniques need to be repeated and are expensive. The use of resistant cultivars is deemed the most effective and economical approach for managing nematodes in cotton. Here, we describe the genomes of two nematode-resistant lines of cotton, BARBREN-713 and BAR 32-30. These genomes may expedite the development of DNA markers that can be used to efficiently introduce nematode resistance into commercially valuable Upland lines.

SUBMITTER: Perkin LC

PROVIDER: S-EPMC8527472 | biostudies-literature | 2021 Oct

REPOSITORIES: biostudies-literature

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Genome assembly of two nematode-resistant cotton lines (Gossypium hirsutum L.).

Perkin Lindsey C LC Bell Al A Hinze Lori L LL Suh Charles P-C CP Arick Mark A MA Peterson Daniel G DG Udall Joshua A JA

G3 (Bethesda, Md.) 20211001 11

Upland cotton (Gossypium hirsutum L.) is susceptible to damage by the root-knot and the reniform nematodes, causing yield losses greater than 4% annually in the United States. In addition, these nematodes are synergistic with seeding disease and root rot pathogens that exacerbate diseases and subsequent yield losses. Production practices to minimize nematode damage include crop rotation and nematicides, but these techniques need to be repeated and are expensive. The use of resistant cultivars is ...[more]

PMID: 34849785

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Project description:BackgroundHow to develop new cotton varieties possessing high yield traits of Upland cotton and superior fiber quality traits of Sea Island cotton remains a key task for cotton breeders and researchers. While multiple attempts bring in little significant progresses, the development of Chromosome Segment Substitution Lines (CSSLs) from Gossypium barbadense in G. hirsutum background provided ideal materials for aforementioned breeding purposes in upland cotton improvement. Based on the excellent fiber performance and relatively clear chromosome substitution segments information identified by Simple Sequence Repeat (SSR) markers, two CSSLs, MBI9915 and MBI9749, together with the recurrent parent CCRI36 were chosen to conduct transcriptome sequencing during the development stages of fiber elongation and Secondary Cell Wall (SCW) synthesis (from 10DPA and 28DPA), aiming at revealing the mechanism of fiber development and the potential contribution of chromosome substitution segments from Sea Island cotton to fiber development of Upland cotton.ResultsIn total, 15 RNA-seq libraries were constructed and sequenced separately, generating 705.433 million clean reads with mean GC content of 45.13% and average Q30 of 90.26%. Through multiple comparisons between libraries, 1801 differentially expressed genes (DEGs) were identified, of which the 902 up-regulated DEGs were mainly involved in cell wall organization and response to oxidative stress and auxin, while the 898 down-regulated ones participated in translation, regulation of transcription, DNA-templated and cytoplasmic translation based on GO annotation and KEGG enrichment analysis. Subsequently, STEM software was performed to explicate the temporal expression pattern of DEGs. Two peroxidases and four flavonoid pathway-related genes were identified in the "oxidation-reduction process", which could play a role in fiber development and quality formation. Finally, the reliability of RNA-seq data was validated by quantitative real-time PCR of randomly selected 20 genes.ConclusionsThe present report focuses on the similarities and differences of transcriptome profiles between the two CSSLs and the recurrent parent CCRI36 and provides novel insights into the molecular mechanism of fiber development, and into further exploration of the feasible contribution of G. barbadense substitution segments to fiber quality formation, which will lay solid foundation for simultaneously improving fiber yield and quality of upland cotton through CSSLs.

Project description:BackgroundGossypium raimondii Ulbr is a diploid wild cotton (2n = 26, D5D5) that originated in west-central Peru of South America and possesses desirable characteristics that are absent in the Upland cotton G. hirsutum. Many beneficial genes were lost from G. hirsutum in the process of domestication, leading to a narrowed genetic base and greater vulnerability to biotic and abiotic stresses. This genetic base can be expanded through distant hybridization using the superior genes of G. raimondii.ResultsIn this study, putative hexaploid F1 plants of G. hirsutum - G. raimondii were generated by interspecific hybridization. Analysis of its mitotic metaphase plates revealed the presence of 78 chromosomes, with each of the six chromosome-specific fluorescence in situ hybridization (FISH) probes (3D5, 5D5, 6D5, 7D5, 9D5, and 10D5) of G. raimondii exhibiting bright and distinct signals on its respective pair of chromosomes. Then, the fertile hexaploid F1 plants were continuously backcrossed with G. hirsutum and a set of G. hirsutum - G. raimondii monosomic alien addition lines (MAALs) were developed using SSR markers in successive backcrosses and self-crossing from BC2F1 to BC4F2. These MAALs were confirmed by chromosome-specific anchored SSRs and FISH. This set of MAALs exhibited abundant variation in morphological traits, agronomic characteristics, yield, and fiber quality traits, as well as in drought and salt resistance at seedling stage. Notably, MAAL_9D5 and MAAL_10D5 demonstrated excellent fiber length (FL), fiber uniformity (FU), fiber strength (FS), micronaire value, and fiber elongation (FE); At seeding stage, MAAL_8D5, MAAL9D5, MAAL_10D5, MAAL_12D5, and MAAL_13D5 showed salt resistance potential; while MAAL_1D5, MAAL_3D5, MAAL_4D5, MAAL_7D5, MAAL_8D5, MAAL_12D5, and MAAL_13D5 exhibited drought resistance potential. These MAALs will provide important genetic bridge materials for gene transfer from G. raimondii as well as for the study of Gossypium species genomes and their evolution.ConclusionsA set of Gossypium hirsutum - Gossypium raimondii MAALs were developed and they showed abundant variation in morphological, agronomic, yield, and fiber quality traits, as well as in drought and salt resistance at seedling stage.

Dataset Information

Genome assembly of two nematode-resistant cotton lines (Gossypium hirsutum L.).

Publications

Genome assembly of two nematode-resistant cotton lines (Gossypium hirsutum L.).

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