Gossypium barbadense genome sequence provides insight into the evolution of extra-long staple fiber and specialized metabolites

Liu, Xia; Zhao, Bo; Zheng, Huajun; Hu, Yan; Lü, Gang; Yang, Changqing; Chen, Jiedan; Chen, Jun-Jian; Chen, Dian-Yang; Zhang, Liang; Zhou, Yan; Wang, Ling-Jian; Guo, Wangzhen; Bai, Yulin; Ruan, Ju-Xin; Shangguan, Xiao-Xia; Mao, Ying‐Bo; Shan, Chun-Min; Jiang, Jianping; Zhu, Yaping; Jin, Lan; Kang, Hui; Chen, Shu-Ting; He, Xu-Lin; Wang, Rui; Wang, Yuezhu; Chen, Jie; Wang, Lijun; Yu, Shuting; Wang, Biyun; Wei, Jia; Song, Sichao; Lu, Xinyan; Gao, Zhixing; Gu, Wenyi; Deng, Xiao; Ma, Dan; Wang, Sen; Liang, Wan; Fang, Lei; Cai, Caiping; Zhu, Xiefei; Zhou, Baoliang; Chen, Z. Jeffrey; Xu, Shuhua; Zhang, Yugao; Wang, Shengyue; Zhang, Tianzhen; Zhao, Guoping; Chen, Xiaoya

doi:10.1038/srep14139

Cited by 219 publications

(218 citation statements)

References 69 publications

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“…Recent advances in our increased knowledge of the sequence, structure, and organization of the cotton genomes (Paterson et al, 2012;Wang et al, 2012;Li et al, 2014Li et al, , 2015Liu et al, 2015;Zhang et al, 2015;) will facilitate such efforts. This study suggests that MD 15 contains and transmits unique, additive alleles associated with improved fiber quality, especially fiber strength.…”

Section: Discussionmentioning

confidence: 99%

Genetic Variation for Agronomic and Fiber Quality Traits in a Population Derived from High‐Quality Cotton Germplasm

Campbell

Greene

et al. 2016

Crop Science

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Genetic improvement of fiber quality is necessary to meet the requirements of processors and users of upland cotton (Gossypium hirsutum L.) fiber. To foster genetic improvement of cotton fiber quality, adequate genetic variation for the quantitatively inherited physical properties of cotton is required. Additionally, knowledge of the genetic architecture of fiber quality is needed to design effective breeding strategies to further improve fiber quality. In this study, our objective was to estimate genetic variance components and predict genetic effects for agronomic and fiber quality traits in a population derived from four known genotypic sources of high fiber quality. The majority of genetic variation present in a half‐diallel population derived from these four sources of high fiber quality was due to additive effects. Predicted genetic effects demonstrated that one of the four parents, MD 15, provides a unique genetic source of high fiber quality alleles that behave additively.

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Section: Discussionmentioning

confidence: 99%

Genetic Variation for Agronomic and Fiber Quality Traits in a Population Derived from High‐Quality Cotton Germplasm

Campbell

Greene

et al. 2016

Crop Science

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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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“…The commercially cropped cotton is almost entirely of the species Gossypium hirsutum, derived from a few cultivars of the species, consequently of narrow genetic base (Moiana et al 2015). Gossypium barbadense is the second most cultivated species, known for the best fiber quality (Liu et al 2015). The Amazon basin is a center of diversity for cotton, and comprises the "kidney" cotton, classified as variety brasiliense, whose seeds are fused to each other in the capsule.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity of Gossypium barbadense from the central Brazilian Amazon

et al. 2018

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The Amazon Basin is a center of diversity of Gossypium barbadense and the strategy for conservation of this genetic resource depends on the knowledge of the diversity maintained in Amazonas State. During two expeditions, in 2012 and 2014, plants were collected in ten municipalities in the state of Amazonas, in the central Brazilian Amazon region. The molecular diversity was estimated by SSR markers for 50 samples collected in 2012. The morphological diversity of 24 plants collected in 2014 was assessed ex situ and compared to that of 50 plants of the same and other cotton varieties from other Brazilian states. Most of plants evaluated in situ in Amazonas had purple petioles and veins (82%), associated to medicinal use, and kidney seeds (78%). The ex situ morphological analysies showed that G. barbadense plants from the Amazonas state: i) presented higher similarity to cotton plants from other northern Brazilian states, and ii) were grouped separately from those of other northern Brazilian states by descriptor analysis. Both the molecular (H=0.41) and morphological (H=0.38±0.02) diversity among the collected plants was considered intermediary. Our study indicates the distinctiveness of Amazon cottons, and contributes to demonstrate the discrimination power of multicategorical traits.KEYWORDS: conservation, genetic resources, cotton tree, phenotypic characterization Diversidade genética de Gossypium barbadense coletado na Amazônia central RESUMOA bacia Amazônica é um centro de diversidade de Gossypium barbadense e a estratégia de manutenção desse recurso genético depende do conhecimento da diversidade da espécie mantida no Estado do Amazonas. Em 2012 e 2014 plantas desta espécie foram coletadas em dez municípios na região centro-leste do Estado. A diversidade molecular por marcadores microssatélites foi mensurada para 50 amostras da coleta de 2012. A diversidade morfológica de 24 plantas coletadas em 2014 foi medida ex situ e comparada com a de 50 amostras desta e de outras variedades de algodão de outros estados do Brasil. A maioria das plantas do Amazonas apresentou folhas arroxeadas (82%), associadas a uso medicinal, e sementes unidas, do tipo rim-de-boi (78%). A análise morfológica ex situ mostrou que G. barbadense coletado no estado do Amazonas: i) tem maior similaridade com plantas da mesma espécie de outros estados da Região Norte do Brasil e ii) se agrupam entre si de forma diferenciada das plantas de outros estados. A diversidade molecular (H = 0,41) e morfológica (H = 0,38 ± 0,02) entre os acessos foi considerada intermediária. Nosso estudo indica o caráter distintivo dos algodões amazônicos, e contribui para demonstrar o poder de discriminação de variáveis multicategóricas.

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Gossypium barbadense genome sequence provides insight into the evolution of extra-long staple fiber and specialized metabolites

Cited by 219 publications

References 69 publications

Genetic Variation for Agronomic and Fiber Quality Traits in a Population Derived from High‐Quality Cotton Germplasm

Genetic Variation for Agronomic and Fiber Quality Traits in a Population Derived from High‐Quality Cotton Germplasm

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

Genetic diversity of Gossypium barbadense from the central Brazilian Amazon

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