Extensive intraspecific gene order and gene structural variations in upland cotton cultivars

Yang, Zhaoen; Ge, Xianping; Yang, Zuoren; Qin, Wenqiang; Sun, Gaofei; Wang, Zhi; Li, Zhi; Ji, Liu; Wu, Jie; Wang, Ye; Lu, Lili; Wang, Peng; Mo, Huijuan; Zhang, Xueyan; Li, Fuguang

doi:10.1038/s41467-019-10820-x

Cited by 175 publications

(168 citation statements)

References 78 publications

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“…Multiple genome assemblies of cotton (tetraploids and their diploid ancestors) are now available, but the effects of domestication and genetic improvement on chromosomes within single species are largely unknown. To address this question, our team assembled new reference genomes of two different genotypes of G. hirsutum [24]. In these genomes, sequence contiguity improved significantly compared with previous studies (Figure 1).…”

Section: Extension Of Cotton Reference Genomesmentioning

confidence: 97%

“…Further, genomic comparisons showed that large-scale inversions exist on different chromosomes between G. hirsutum and G. barbadense ( Figure IA). The genetic effects of inversions have been well studied in Arabidopsis [93] and Gossypium [24]. Inversions suppress the recombination of an inverted region and its neighboring regions, decreasing population diversity and resulting in population divergence.…”

Section: Box 2 a Model For Genetic Breakdown Of Interspecific Hybridmentioning

confidence: 99%

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Gossypium Genomics: Trends, Scope, and Utilization for Cotton Improvement

Yang

Qanmber

Wang

et al. 2020

Trends in Plant Science

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114

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Cotton (Gossypium spp.) is the most important natural fiber crop worldwide. The diversity of Gossypium species also provides an ideal model for investigating evolution and domestication of polyploids. However, the huge and complex cotton genome hinders genomic research. Technical advances in high-throughput sequencing and bioinformatics analysis have now largely overcome these obstacles, bringing about a new era of cotton genomics. Here, we review recent progress in Gossypium genomics based on whole genome sequencing, resequencing, and comparative genomics, which have provided insights about the genomic basis of fiber biogenesis and the landscape of cotton functional genomics. We address current challenges and present multidisciplinary genomics-enabled breeding strategies covering the breadth of high fiber yield, quality, and environmental resilience for future cotton breeding programs. Gossypium Genomics at a Glance As the world's most important fiber crop and a major source of seed oil and protein, cotton is cultivated in more than 75 countries around the globe [1]. Cotton fibers are seed trichomes, up to 65 mm long, composed of almost pure cellulose, and provide a unique single-celled model system for studying cell elongation and cell wall biogenesis [2]. The Gossypium genus is extraordinarily diverse, with eight diploid genome groups (A-G, and K) and one allopolyploid group (AD) [3,4]. Hybridization and polyploidization of two parental diploids, an A genome-like species with a D genome-like species, has resulted in at least seven allotetraploid species. Two allotetraploid species, Gossypium hirsutum and Gossypium barbadense, evolved independently; these two account for over 90% of annual commercial fiber production. Gossypium is ideal for investigating the origin, evolution, and domestication of polyploids [5-7]. Highlights Cotton is an important natural fiber crop cultivated worldwide that also provides an ideal model for investigating evolution and domestication of polyploids Combinations of the latest technologies, such as optical mapping, high-throughput chromosome conformation capture (Hi-C), and Pacific Biosciences (PacBio) long-reads, have been used to generate multiple high-quality reference genomes of diploid and allotetraploid cotton. Comparative population genomics illuminated the genetic history of cotton domestication and identified the genomic variation determining fiber yield, quality, and stress resistance.

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Section: Extension Of Cotton Reference Genomesmentioning

confidence: 97%

Section: Box 2 a Model For Genetic Breakdown Of Interspecific Hybridmentioning

confidence: 99%

Gossypium Genomics: Trends, Scope, and Utilization for Cotton Improvement

Yang

Qanmber

Wang

et al. 2020

Trends in Plant Science

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114

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“…5). It is possible that structural variation among the genomes of the parents of mapping populations used in this study has contributed to variation in the recombination rates between progeny of different populations such as has occurred in Arabidopsis 98 , banana 99 and cotton 100 .…”

Section: Crossover Frequency and Recombination Varied Between Maps Dmentioning

confidence: 99%

Maximising recombination across macadamia populations to generate linkage maps for genome anchoring

Langdon

King

Baten

et al. 2020

Sci Rep

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the proteaceae genus Macadamia has a recent history of domestication as a commercial nut crop. We aimed to establish the first sequence-based haploid-correlated reference genetic linkage maps for this primarily outcrossing perennial tree crop, with marker density suitable for genome anchoring. Four first generation populations were used to maximise the segregation patterns available within full-sib, biparental and self-pollinated progeny. This allowed us to combine segregation data from overlapping subsets of >4,000 informative sequence-tagged markers to increase the effective coverage of the karyotype represented by the recombinant crossover events detected. All maps had 14 linkage groups, corresponding to the Macadamia haploid chromosome number, and enabled the anchoring and orientation of sequence scaffolds to construct a pseudo-chromosomal genome assembly for macadamia. Comparison of individual maps indicated a high level of congruence, with minor discrepancies satisfactorily resolved within the integrated maps. The combined set of maps significantly improved marker density and the proportion (70%) of the genome sequence assembly anchored. Overall, increasing our understanding of the genetic landscape and genome for this nut crop represents a substantial advance in macadamia genetics and genomics. The set of maps, large number of sequence-based markers and the reconstructed genome provide a toolkit to underpin future breeding that should help to extend the macadamia industry as well as provide resources for the long term conservation of natural populations in eastern Australia of this unique genus.

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“…These tissues were collected from ZM24 (also as CCRI24) cotton plants,which was obtained from the Institute of Cotton Research, the Chinese Academy of Agricultural Sciences and grown under field conditions in Zhengzhou China [51,52]. ZM24 is a national certified species of China (No.…”

Section: Plant Material Rna Extraction and Qrt-pcr Analysismentioning

confidence: 99%

Genome-wide characterization and expression analysis of geranyl geranyl diphosphate synthase genes of cotton (Gossypium spp.) in plant development and abiotic stresses

Ali

Qanmber

Wei

et al. 2020

Preprint

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Background: GGPP (geranyl geranyl diphosphate) is produced in the isoprenoid pathway and mediates the function of various plant metabolites, which is synthesized by GGPPS (GGPP synthases) in plants. GGPPS characterization has not been performed in any plant species except Arabidiosis thaliana. Here, we performed a complete computational and bioinformatics analysis of GGPPS and detected their transcription expression pattern in Gossypium hirsutum for the first time in order to explore their evolutionary relationship and potential functions. We unravel evolutionary relationship, conserved sequence logos, gene duplication and potential involvement in plant development and abiotic stresses tolerance of GGPPS genes in G. hirsutum.Results: A total of 134 GGPPS genes from 17 plant species were identified. Evolutionary analysis divided GGPPS genes into five groups and indicated their divergence from a common ancestor.Further, GGPPS family genes were conserved during evolution and underwent segmental duplication.25 GhGGPPS genes identified showed diverse expression pattern particularly in ovule and fiber development indicating their vital and divers roles in the fiber development. Additionally, GhGGPPS genes exhibited wide range of responses when subjected to abiotic (heat, cold, NaCl and PEG) and hormonal (BL, GA, IAA, SA and MeJA) stresses. Conclusions:Collectively, GGPPS genes are evolutionary conserved, may are involved in different development stages and stress signaling pathways, some potential key genes (e.g. GhGGPP4, GhGGPP9, GhGGPP15) were suggested and provide valuable source for cotton breeding in fiber quality and resistant to various stresses. BackgroundIsoprenoids represent the largest group of biologically active specialized metabolites in plants. Many Isoprenoids provides protection to plants from pathogens and herbivores [1]. Isoprenoids also have important functions in plant photosynthesis and respiration process and involve many hormonal pathways (abscisic acid, brassinosteroids, cytokinin, gibberellin, and strigolactones) important for development and growth regulation in plants [1][2][3][4].In isoprenoid pathway, prenyl diphosphate synthases are active with important isozymes for 4 isoprenoid metabolism, use isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) as substrates in the mevalonate (MVA) or methylerythritol (MEP) pathway. In general, they are represented by three enzymes such as geranyl diphosphate (GPP) synthase, farnesyldiphosphate (FPP) synthase and geranylgeranyl diphosphate (GGPP) synthase in plants [4].GGPPS is an essential enzyme among three isoprenoids for primary and secondary isoprenoid compounds synthesis such as chlorophylls, carotenoids and derivatives including different hormones (e.g. abscisic acid (ABA), strigolactones and gibberellins), and proteins (e.g. plastoquinones, ubiquinones, phylloquinones, tocopherols, diterpenoids, polyprenols, dolichols, and prenylated) [4].GGPPS catalyzes successive additions of IPP to DMAPP, GPP and FPP as a homodimer [5] an...

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Extensive intraspecific gene order and gene structural variations in upland cotton cultivars

Cited by 175 publications

References 78 publications

Gossypium Genomics: Trends, Scope, and Utilization for Cotton Improvement

Gossypium Genomics: Trends, Scope, and Utilization for Cotton Improvement

Maximising recombination across macadamia populations to generate linkage maps for genome anchoring

Genome-wide characterization and expression analysis of geranyl geranyl diphosphate synthase genes of cotton (Gossypium spp.) in plant development and abiotic stresses

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