Chromosome Painting Based on Bulked Oligonucleotides in Cotton

Liu, Yuling; Wang, Xiuyuan; Wei, Yangyang; Liu, Zhen; Lú, Quánwěi; Liu, Fang; Zhang, Tao; Peng, Renhai

doi:10.3389/fpls.2020.00802

Cited by 9 publications

(4 citation statements)

References 55 publications

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“…There is limited information on molecular cytogenetics of kenaf despite its economic value. In contrast, the techniques have been employed leading to the development of cytogenetic maps and karyotypes of major crops including soybean (Findley et al 2010; 2017), potatoes (Dong et al 2000), maize (Danilova & Birchler 2008; Mondin et al 2014) and cotton (Gan et al 2013; Lu et al 2018; Liu et al 2020).…”

Section: Discussionmentioning

confidence: 99%

Comparative cytogenetics of kenaf (Hibiscus cannabinusL.) breeding lines reveal chromosomal variability and instability

Ankrah,

El-nagish,

Breitenbach

et al. 2023

Preprint

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Kenaf (Hibiscus cannabinus), a native warm-seasonal crop in Africa, is being considered for genetic improvement for local bast fiber production. To expedite its genetic improvement through breeding, kenaf genotypes from Ghana were assessed for genomic diversity regarding their chromosomal composition and ploidy levels. To gain insight into the repetitive DNA fractions in kenaf, the organization of 5S and 35S rRNA genes, as well as telomeric signal patterns were studied by a molecular cytogenetic approach.Using multi-color fluorescentin situhybridization, distinct rDNA loci andArabidopsis-type telomeres were revealed. The 5S rRNA genes were conserved in kenaf and localized in interstitial regions of two chromosomes across all accessions. The 35S rRNA genes were variable across the kenaf accessions and localized at sub-terminal ends and rarely interstitially in eight or six chromosome arms. Telomeric signals were observed at terminal ends of all chromosomes, with smaller signals also interstitially. The chromosome configuration of Ghana kenaf accessions was confirmed to be 2n=2x=36, each. We discuss the chromosomal variability and the likely genomic instability in the kenaf breeding lines from Ghana.To our knowledge, this is the first report on molecular cytogenetics on kenaf and thus, provides valuable insights into the genome of kenaf that will be useful for breeding. Additionally, this study provides a basis for further studies to analyze the repetitive DNA sequences and develop reference karyotypes to reveal genetic and evolutionary relationships between cultivated and wildHibiscusspecies.

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Section: Discussionmentioning

confidence: 99%

Comparative cytogenetics of kenaf (Hibiscus cannabinusL.) breeding lines reveal chromosomal variability and instability

Ankrah,

El-nagish,

Breitenbach

et al. 2023

Preprint

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“…in ICR-CAAS: AD5-07)—were harvested from circa 6-d-old incubator-grown seedlings. Root tips were pretreated using 0.089 mM cycloheximide at 20 °C for 80 min, fixed in methanol-acetic acid (3:1), and then stored at 4 °C for 24 h. Chromosome preparations of metaphase chromosomes were created according to a previously reported method ( 108 ). The protocol of ND-FISH using synthesized probes was described by Tang et al.…”

Section: Methodsmentioning

confidence: 99%

Evolutionary divergence of duplicated genomes in newly described allotetraploid cottons

Peng

Tian

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

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Allotetraploid cotton ( Gossypium ) species represents a model system for the study of plant polyploidy, molecular evolution, and domestication. Here, chromosome-scale genome sequences were obtained and assembled for two recently described wild species of tetraploid cotton, Gossypium ekmanianum [(AD) 6 , Ge ] and Gossypium stephensii [(AD) 7 , Gs ], and one early form of domesticated Gossypium hirsutum , race punctatum [(AD) 1 , Ghp ]. Based on phylogenomic analysis, we provide a dated whole-genome level perspective for the evolution of the tetraploid Gossypium clade and resolved the evolutionary relationships of Gs , Ge , and domesticated G. hirsutum . We describe genomic structural variation that arose during Gossypium evolution and describe its correlates—including phenotypic differentiation, genetic isolation, and genetic convergence—that contributed to cotton biodiversity and cotton domestication. Presence/absence variation is prominent in causing cotton genomic structural variations. A presence/absence variation-derived gene encoding a phosphopeptide-binding protein is implicated in increasing fiber length during cotton domestication. The relatively unimproved Ghp offers the potential for gene discovery related to adaptation to environmental challenges. Expanded gene families enoyl-CoA δ isomerase 3 and RAP2-7 may have contributed to abiotic stress tolerance, possibly by targeting plant hormone-associated biochemical pathways. Our results generate a genomic context for a better understanding of cotton evolution and for agriculture.

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“…Root tips of ve cotton species: Gossypium hirsutum (cultivar: TM-1), Gossypium barbadense (cultivar: 3-79), Gossypium tomentosum (accession number in ICR-CAAS: AD3-LZ), Gossypium mustelinum (accession number in ICR-CAAS: AD4-LZ), and Gossypium darwinii accession (accession number in ICR-CAAS: AD5-07), were harvested from circa 6-day-old incubator-grown seedlings. Root tips were pretreated using 25 ppm cycloheximide at 20°C for 80 min, xed in methanol-acetic acid (3:1), and then stored at 4°C for 24 h. Chromosome preparations of metaphase chromosomes were created according to previously reported methods [101]. The protocol of ND-FISH using synthesized probes was described by Tang et al…”

Section: Fish Analysis Of Rga-derived Oligo Probesmentioning

confidence: 99%

Comparative genomics and polyploid dynamics in tetraploid cotton (Gossypium)

Peng

Liu

et al. 2021

Preprint

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Allotetraploid species of cotton (Gossypium) represent a model system for the study of plant polyploidy, molecular evolution and domestication. In this study three high-quality draft assemblies of tetraploid cottons are presented, comprising one early form of domesticated Gossypium hirsutum (AD1-genome, Gh), i.e., Gossypium hirsutum race punctatum (GhP), and two recently described wild species of tetraploid cotton, G. ekmanianum (AD6, Ge) and G. stephensii (AD7, Gs). Using comparative phylogenomics, we confirm a monophyletic origin of tetraploid Gossypium and provide a dated whole-genome level perspective for the evolution of the clade. Recombination and patterns of selection are asymmetric between the two co-resident genomes in the allopolyploid nucleus. Considerable gene structural variation occurs widely within homoeologous genomes and between heterologous genomes during evolution and domestication. Despite few large-scale chromosomal structure variations among tetraploid cotton, frequent homoeologous exchanges between subgenomes in all species have contributed to diversity and asymmetrically between subgenomes. Abiotic and biotic adaptive evolution was driven by various evolutionary forces, leading to transcriptome change and gene family expansion. Our study marks a milestone in modern polyploid crop research, completing genome sequencing for all species of polyploid Gossypium, and will facilitate a better understanding of the genomic landscape and crop improvement dynamics of polyploids.

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Chromosome Painting Based on Bulked Oligonucleotides in Cotton

Cited by 9 publications

References 55 publications

Comparative cytogenetics of kenaf (Hibiscus cannabinusL.) breeding lines reveal chromosomal variability and instability

Comparative cytogenetics of kenaf (Hibiscus cannabinusL.) breeding lines reveal chromosomal variability and instability

Evolutionary divergence of duplicated genomes in newly described allotetraploid cottons

Comparative genomics and polyploid dynamics in tetraploid cotton (Gossypium)

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