The genome sequence of Sea-Island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres

Yuan, Daojun; Tang, Zhonghui; Wang, Maojun; Gao, Wenhui; Tu, Lili; Jin, Xin; Chen, Lingling; He, Yonghui; Zhang, Lin; Zhu, Longfu; Yang, Li; Liang, Qiqi; Lin, Zhenhua; Yang, Xiyan; Liu, Nian; Jin, Shuangxia; Yang, Lei; Ding, Yuanhao; Li, Guoliang; Ruan, Xiaoan; Ruan, Yijun; Zhang, Xianlong

doi:10.1038/srep17662

Cited by 250 publications

(239 citation statements)

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“…A line between two genes indicates a paralog genes during growth and development of G. hirsutum plant. The transcription levels in various tissues or organs of RNA-seq data from NCBI and COTTONFGD (http:// www.cottonfgd.org/) were downloaded and analyzed (Yuan et al 2015;Yang et al 2017), including the vegetative (root, stem, and leaf) and reproductive (torus, petal, stamen, pistil, calycle, − 3 and − 1 days post anthesis (DPA) ovule, 0, 1, 3, 5, 10, 20, 25, and 35 days post anthesis (DPA) seed) tissues as well as in the fiber (5, 10, 20, and 25 DPA), and germinating seeds at 0 h, 5 h,10 h and from roots and cotyledons at 24 h, 48 h, 72 h, 96 h, and 120 h after imbibition. Their expression levels were varied (Figs.…”

Section: Expression Patterns Of Sweet Genes In Different Tissuesmentioning

confidence: 99%

“…The RNA-seq data was downloaded from the NCBI Sequence Read Archive (SRA: PRJNA248163, http:// www.ncbi.nlm.nih.gov/sra/?term=PRJNA248163) and CottonFGD website (Yuan et al 2015;Zhu et al 2017). The fragments per kilobase million (FPKM) values denoting the expression levels of SWEET genes were isolated from a comprehensive profile of the TM-1 transcriptome data (Trapnell et al 2012).…”

Section: Transcriptome Data Analysis Of Sweet Gene Expression From Hementioning

confidence: 99%

“…With the release of genomes sequences of two diploid cotton (A2, D5) and two allotetraploid cotton (AD1, AD2) (Phillips et al 2017;Li et al 2014;Paterson et al 2012;Wang et al 2012;Li et al 2015;Zhang et al 2015;Yuan et al 2015;Liu et al 2015) facilitates the survey of SWEETs in cotton. In this study, we identified the SWEETs in four cotton species by genome-wide analysis.…”

Section: Introductionmentioning

confidence: 99%

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A genome-wide analysis of SWEET gene family in cotton and their expressions under different stresses

et al. 2018

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Background: The SWEET (Sugars will eventually be exported transporters) gene family plays multiple roles in plant physiological activities and development process. It participates in reproductive development and in the process of sugar transport and absorption, plant senescence and stress responses and plant-pathogen interaction. However, thecomprehensive analysis of SWEET genes has not been reported in cotton.

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Section: Expression Patterns Of Sweet Genes In Different Tissuesmentioning

confidence: 99%

Section: Transcriptome Data Analysis Of Sweet Gene Expression From Hementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A genome-wide analysis of SWEET gene family in cotton and their expressions under different stresses

et al. 2018

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“…Restriction-site associated DNA sequencing (RAD-seq) is a powerful and cost-effective method for detecting genetic variations [22, 23] and has become widely applied in plants [24–28]. Moreover, landmark breakthroughs in genome sequencing of cotton species such as G. raimondii [29, 30] G. arboretum [31], G. barbadense [32, 33] and G. hirsutum L. [34, 35], have been achieved and will facilitate the detection of SNP markers.…”

Section: Introductionmentioning

confidence: 99%

High-density linkage map construction and QTL analysis for earliness-related traits in Gossypium hirsutum L

et al. 2016

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Background Gossypium hirsutum L., or upland cotton, is an important renewable resource for textile fiber. To enhance understanding of the genetic basis of cotton earliness, we constructed an intra-specific recombinant inbred line population (RIL) containing 137 lines, and performed linkage map construction and quantitative trait locus (QTL) mapping.ResultsUsing restriction-site associated DNA sequencing, a genetic map composed of 6,434 loci, including 6,295 single nucleotide polymorphisms and 139 simple sequence repeat loci, was developed from RIL population. This map spanned 4,071.98 cM, with an average distance of 0.63 cM between adjacent markers. A total of 247 QTLs for six earliness-related traits were detected in 6 consecutive years. In addition, 55 QTL coincidence regions representing more than 60 % of total QTLs were found on 22 chromosomes, which indicated that several earliness-related traits might be simultaneously improved. Fine-mapping of a 2-Mb region on chromosome D3 associated with five stable QTLs between Marker25958 and Marker25963 revealed that lines containing alleles derived from CCRI36 in this region exhibited smaller phenotypes and earlier maturity. One candidate gene (EMF2) was predicted and validated by quantitative real-time PCR in early-, medium- and late-maturing cultivars from 3- to 6-leaf stages, with highest expression level in early-maturing cultivar, CCRI74, lowest expression level in late-maturing cultivar, Bomian1.ConclusionsWe developed an SNP-based genetic map, and this map is the first high-density genetic map for short-season cotton and has the potential to provide deeper insights into earliness. Cotton earliness-related QTLs and QTL coincidence regions will provide useful materials for QTL fine mapping, gene positional cloning and MAS. And the gene, EMF2, is promising for further study.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3269-y) contains supplementary material, which is available to authorized users.

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“…G. darwinii has many excellent traits, such as drought tolerance, finer fibre fineness, Fusarium wilt and Verticillium wilt resistance [5]. In addition, with the rapid development of next-generation sequencing (NGS) technologies, the recent publications on the genome sequence of the tetraploid AD 1 -genome [6, 7] and AD 2 -genome [8] and the diploid A-genome [9] and D-genome [10, 11] have improved the development of new analyses and comparative approaches for the genomics of both diploid and polyploid cottons.…”

Section: Introductionmentioning

confidence: 99%

Uncovering SNP and indel variations of tetraploid cottons by SLAF-seq

et al. 2017

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BackgroundCotton (Gossypium spp.), as the world’s most utilized textile fibre source, is an important, economically valuable crop worldwide. Understanding the genomic variation of tetraploid cotton species is important for exploitation of the excellent characteristics of wild cotton and for improving the diversity of cotton in breeding. However, the discovery of DNA polymorphisms in tetraploid cotton genomes has lagged behind other important crops.ResultsA total of 111,795,823 reads, 467,735 specific length amplified fragment (SLAF) tags and 139,176 high-quality DNA polymorphisms were identified using specific length amplified fragment sequencing (SLAF-seq), including 132,880 SNPs and 6,296 InDels between the reference genome (TM-1) and the five tetraploid cotton species. Intriguingly, gene ontology (GO) enrichment analysis revealed that a number of significant terms were related to reproduction in G. barbadense acc. 3–79. Based on the new data sets, we reconstructed phylogenetic trees that showed a high concordance to the phylogeny of diploid and polyploid cottons. A large amount of interspecific genetic variations were identified, and some of them were validated by the single-strand conformation polymorphism (SSCP) method, which will be applied in introgression genetics and breeding with G. hirsutum cv. Emian22 as the receptor and the other species as donors.ConclusionsUsing SLAF-seq, a large number of DNA polymorphisms were identified. The comprehensive analysis of DNA polymorphisms provided invaluable insights into the different tetraploid cotton species. More importantly, the identification of numerous interspecific genetic variations provides the basis and is very practical for future introgression breeding. The results presented herein provide a valuable genomic resource for new insights into the genetics and breeding of cotton.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3643-4) contains supplementary material, which is available to authorized users.

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The genome sequence of Sea-Island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres

Cited by 250 publications

References 71 publications

A genome-wide analysis of SWEET gene family in cotton and their expressions under different stresses

A genome-wide analysis of SWEET gene family in cotton and their expressions under different stresses

High-density linkage map construction and QTL analysis for earliness-related traits in Gossypium hirsutum L

Uncovering SNP and indel variations of tetraploid cottons by SLAF-seq

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