$\require{mediawiki-texvc}$

연합인증

연합인증 가입 기관의 연구자들은 소속기관의 인증정보(ID와 암호)를 이용해 다른 대학, 연구기관, 서비스 공급자의 다양한 온라인 자원과 연구 데이터를 이용할 수 있습니다.

이는 여행자가 자국에서 발행 받은 여권으로 세계 각국을 자유롭게 여행할 수 있는 것과 같습니다.

연합인증으로 이용이 가능한 서비스는 NTIS, DataON, Edison, Kafe, Webinar 등이 있습니다.

한번의 인증절차만으로 연합인증 가입 서비스에 추가 로그인 없이 이용이 가능합니다.

다만, 연합인증을 위해서는 최초 1회만 인증 절차가 필요합니다. (회원이 아닐 경우 회원 가입이 필요합니다.)

연합인증 절차는 다음과 같습니다.

최초이용시에는
ScienceON에 로그인 → 연합인증 서비스 접속 → 로그인 (본인 확인 또는 회원가입) → 서비스 이용

그 이후에는
ScienceON 로그인 → 연합인증 서비스 접속 → 서비스 이용

연합인증을 활용하시면 KISTI가 제공하는 다양한 서비스를 편리하게 이용하실 수 있습니다.

Resequencing a core collection of upland cotton identifies genomic variation and loci influencing fiber quality and yield

Nature genetics, v.50 no.6, 2018년, pp.803 - 813  

Ma, Zhiying (North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, China. mzhy@hebau.edu.cn) ,  He, Shoupu (State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China) ,  Wang, Xingfen (North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, China. cotton@hebau.edu.cn) ,  Sun, Junling (State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China) ,  Zhang, Yan (North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, China) ,  Zhang, Guiyin (North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, China) ,  Wu, Liqiang (North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, China) ,  Li, Zhikun (North China Key Laboratory for Crop Germplasm Resources o) ,  Liu, Zhihao ,  Sun, Gaofei ,  Yan, Yuanyuan ,  Jia, Yinhua ,  Yang, Jun ,  Pan, Zhaoe ,  Gu, Qishen ,  Li, Xueyuan ,  Sun, Zhengwen ,  Dai, Panhong ,  Liu, Zhengwen ,  Gong, Wenfang ,  Wu, Jinhua ,  Wang, Mi ,  Liu, Hengwei ,  Feng, Keyun ,  Ke, Huifeng ,  Wang, Junduo ,  Lan, Hongyu ,  Wang, Guoning ,  Peng, Jun ,  Wang, Nan ,  Wang, Liru ,  Pang, Baoyin ,  Peng, Zhen ,  Li, Ruiqiang ,  Tian, Shilin ,  Du, Xiongming

Abstract ▼ AI-Helper 아이콘AI-Helper

Upland cotton is the most important natural-fiber crop. The genomic variation of diverse germplasms and alleles underpinning fiber quality and yield should be extensively explored. Here, we resequenced a core collection comprising 419 accessions with 6.55-fold coverage depth and identified approxima...

참고문헌 (64)

  1. Crop Sci JF Zhang 54 1 2014 10.2135/cropsci2012.12.0710 Zhang, J. F., Fang, H., Zhou, H. P., Sanogo, S. & Ma, Z. Y. Genetics, breeding, and marker-assisted selection for Verticillium wilt resistance in cotton. Crop Sci. 54, 1-15 (2014). 

    상세보기 crossref

  2. Proc. Natl. Acad. Sci. USA JF Wendel 86 4132 1989 10.1073/pnas.86.11.4132 Wendel, J. F. New World tetraploid cottons contain Old World cytoplasm. Proc. Natl Acad. Sci. USA 86, 4132-4136 (1989). 

    상세보기 crossref

  3. Plant Physiol. ZJ Chen 145 1303 2007 10.1104/pp.107.107672 Chen, Z. J. et al. Toward sequencing cotton (Gossypium) genomes. Plant Physiol. 145, 1303-1310 (2007). 

    상세보기 crossref

  4. J. Plant Genetic Resour P Dai 17 961 2016 Dai, P. et al. Construction of core collection of upland cotton based on phenotypic data. J. Plant Genetic Resour. 17, 961-968 (2016). 

  5. China Agr. History (Lond.) RH Wang 2 81 1992 Wang, R. H. A brief history of the introduction of American cotton cultivars into China. Zhongguo Nong Ye Ke Xue 4, 30-35 (1983). 

  6. Nat. Genet. L Fang 49 1089 2017 10.1038/ng.3887 Fang, L. et al. Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits. Nat. Genet. 49, 1089-1098 (2017). 

    상세보기 crossref

  7. Nat. Genet. M Wang 49 579 2017 10.1038/ng.3807 Wang, M. et al. Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication. Nat. Genet. 49, 579-587 (2017). 

    상세보기 crossref

  8. Plant Biotechnol. J. C Huang 15 1374 2017 10.1111/pbi.12722 Huang, C. et al. Population structure and genetic basis of the agronomic traits of upland cotton in China revealed by a genome-wide association study using high-density SNPs. Plant Biotechnol. J. 15, 1374-1386 (2017). 

    상세보기 crossref

  9. Plant Biotechnol. J. Z Sun 15 982 2017 10.1111/pbi.12693 Sun, Z. et al. Genome-wide association study discovered genetic variation and candidate genes of fibre quality traits in Gossypium hirsutum L. Plant Biotechnol. J. 15, 982-996 (2017). 

    상세보기 crossref

  10. Brown, A. H. D. The case for core collection. in The Use of Plant Genetic Resources (eds. Brown, A. H. D. et al.) 136-156 (Cambridge Univ. Press, Cambridge, 1989). 

  11. J. Cotton Sci J Foulk 13 212 2009 Foulk, J., Meredith, W., Mcalister, D. & Luke, D. Fiber and yarn properties improve with new cotton cultivar. J. Cotton Sci. 13, 212-220 (2009). 

  12. Nat. Genet. X Huang 42 961 2010 10.1038/ng.695 Huang, X. et al. Genome-wide association studies of 14 agronomic traits in rice landraces. Nat. Genet. 42, 961-967 (2010). 

    상세보기 crossref

  13. Nature X Huang 490 497 2012 10.1038/nature11532 Huang, X. et al. A map of rice genome variation reveals the origin of cultivated rice. Nature 490, 497-501 (2012). 

    상세보기 crossref

  14. Nat. Genet. K Yano 48 927 2016 10.1038/ng.3596 Yano, K. et al. Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice. Nat. Genet. 48, 927-934 (2016). 

    상세보기 crossref

  15. Nat. Genet. H Li 45 43 2013 10.1038/ng.2484 Li, H. et al. Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels. Nat. Genet. 45, 43-50 (2013). 

    상세보기 crossref

  16. Nat. Commun. ES Mace 4 2013 10.1038/ncomms3320 Mace, E. S. et al. Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum. Nat. Commun. 4, 2320 (2013). 

    상세보기 crossref

  17. Nat. Genet. G Jia 45 957 2013 10.1038/ng.2673 Jia, G. et al. A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica). Nat. Genet. 45, 957-961 (2013). 

    상세보기 crossref

  18. Annu. Rev. Plant Biol. X Huang 65 531 2014 10.1146/annurev-arplant-050213-035715 Huang, X. & Han, B. Natural variations and genome-wide association studies in crop plants. Annu. Rev. Plant Biol. 65, 531-551 (2014). 

    상세보기 crossref

  19. Nat. Genet. K Wang 44 1098 2012 10.1038/ng.2371 Wang, K. et al. The draft genome of a diploid cotton Gossypium raimondii. Nat. Genet. 44, 1098-1103 (2012). 

    상세보기 crossref

  20. Zhongguo Nong Ye Ke Xue P Dai 49 3694 2016 Dai, P. et al. Comprehensive evaluation and genetic diversity analysis of phenotypic traits of core collection in upland cotton. Zhongguo Nong Ye Ke Xue 49, 3694-3708 (2016). 

    상세보기

  21. Nat. Biotechnol. T Zhang 33 531 2015 10.1038/nbt.3207 Zhang, T. et al. Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nat. Biotechnol. 33, 531-537 (2015). 

    상세보기 crossref

  22. Nat. Genet. Y Jiao 44 812 2012 10.1038/ng.2312 Jiao, Y. et al. Genome-wide genetic changes during modern breeding of maize. Nat. Genet. 44, 812-815 (2012). 

    상세보기 crossref

  23. Nat. Commun. X Wei 6 2015 10.1038/ncomms9609 Wei, X. et al. Genetic discovery for oil production and quality in sesame. Nat. Commun. 6, 8609 (2015). 

    상세보기 crossref

  24. Nat. Genet. F Li 46 567 2014 10.1038/ng.2987 Li, F. et al. Genome sequence of the cultivated cotton Gossypium arboreum. Nat. Genet. 46, 567-572 (2014). 

    상세보기 crossref

  25. Nat. Biotechnol. Z Zhou 33 408 2015 10.1038/nbt.3096 Zhou, Z. et al. Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat. Biotechnol. 33, 408-414 (2015). 

    상세보기 crossref

  26. Genome Biol. L Fang 18 2017 10.1186/s13059-017-1167-5 Fang, L. et al. Genomic insights into divergence and dual domestication of cultivated allotetraploid cottons. Genome Biol. 18, 33 (2017). 

    상세보기 crossref

  27. Evolution M Kopp 60 1537 2006 10.1111/j.0014-3820.2006.tb00499.x Kopp, M. & Hermisson, J. The evolution of genetic architecture under frequency-dependent disruptive selection. Evolution 60, 1537-1550 (2006). 

    상세보기 crossref

  28. Pflanzenschutz-Nachrichten Bayer T Arioli 58 140 2005 Arioli, T. Genetic engineering for cotton fiber improvement. Pflanzenschutz-Nachrichten Bayer 58, 140-150 (2005). 

    상세보기

  29. Plant Physiol. HJ Kim 127 1361 2001 10.1104/pp.010724 Kim, H. J. & Triplett, B. A. Cotton fiber growth in planta and in vitro: models for plant cell elongation and cell wall biogenesis. Plant Physiol. 127, 1361-1366 (2001). 

    상세보기 crossref

  30. Cell XW Deng 71 791 1992 10.1016/0092-8674(92)90555-Q Deng, X. W. et al. COP1, an Arabidopsis regulatory gene, encodes a protein with both a zinc-binding motif and a G beta homologous domain. Cell 71, 791-801 (1992). 

    상세보기 crossref

  31. Biol. Chem S Albert 381 453 2000 10.1515/BC.2000.059 Albert, S. & Gallwitz, D. Msb4p, a protein involved in Cdc42p-dependent organization of the actin cytoskeleton, is a Ypt/Rab-specific GAP. Biol. Chem 381, 453-456 (2000). 

    상세보기 crossref

  32. Annu. Rev. Plant Biol. PJ Hussey 57 109 2006 10.1146/annurev.arplant.57.032905.105206 Hussey, P. J., Ketelaar, T. & Deeks, M. J. Control of the actin cytoskeleton in plant cell growth. Annu. Rev. Plant Biol. 57, 109-125 (2006). 

    상세보기 crossref

  33. Curr. Opin. Plant Biol. CJ Staiger 9 554 2006 10.1016/j.pbi.2006.09.013 Staiger, C. J. & Blanchoin, L. Actin dynamics: old friends with new stories. Curr. Opin. Plant Biol. 9, 554-562 (2006). 

    상세보기 crossref

  34. Plant Cell XB Li 17 859 2005 10.1105/tpc.104.029629 Li, X. B., Fan, X. P., Wang, X. L., Cai, L. & Yang, W. C. The cotton ACTIN1 gene is functionally expressed in fibers and participates in fiber elongation. Plant Cell 17, 859-875 (2005). 

    상세보기 crossref

  35. Trends Plant Sci L Serna 11 274 2006 10.1016/j.tplants.2006.04.008 Serna, L. & Martin, C. Trichomes: different regulatory networks lead to convergent structures. Trends Plant Sci. 11, 274-280 (2006). 

    상세보기 crossref

  36. Plant Physiol. T Jégu 161 1694 2013 10.1104/pp.112.212357 Jégu, T. et al. Multiple functions of Kip-related protein5 connect endoreduplication and cell elongation. Plant Physiol. 161, 1694-1705 (2013). 

    상세보기 crossref

  37. Plant Cell YH Shi 18 651 2006 10.1105/tpc.105.040303 Shi, Y. H. et al. Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fiber cell elongation. Plant Cell 18, 651-664 (2006). 

    상세보기 crossref

  38. Science CA Beasley 179 1003 1973 10.1126/science.179.4077.1003 Beasley, C. A. Hormonal regulation of growth in unfertilized cotton ovules. Science 179, 1003-1005 (1973). 

    상세보기 crossref

  39. Am. J. Bot. CA Beasley 61 188 1974 10.1002/j.1537-2197.1974.tb06045.x Beasley, C. A. & Ting, I. P. Effects of plant growth substances on in vitro fiber development from unfertilized cotton ovules. Am. J. Bot. 61, 188-194 (1974). 

    상세보기 crossref

  40. J. Cotton Sci S Gialvalis 5 252 2001 Gialvalis, S. & Seagull, R.W. Plant hormones alter fiber initiation in unfertilized, cultured ovules of Gossypium hirsutum. J. Cotton Sci. 5, 252-258 (2001). 

  41. J. Cotton Sci RW Seagull 8 105 2004 Seagull, R. W. & Giavalis, S. Pre- and post-anthesis application of exogenous hormones alters fiber production in Gossypium hirsutum L. cultivar Maxxa GTO. J. Cotton Sci. 8, 105-111 (2004). 

  42. Nat. Biotechnol. M Zhang 29 453 2011 10.1038/nbt.1843 Zhang, M. et al. Spatiotemporal manipulation of auxin biosynthesis in cotton ovule epidermal cells enhances fiber yield and quality. Nat. Biotechnol. 29, 453-458 (2011). 

    상세보기 crossref

  43. Plant Physiol TS Tseng 126 1250 2001 10.1104/pp.126.3.1250 Tseng, T. S., Swain, S. M. & Olszewski, N. E. Ectopic expression of the tetratricopeptide repeat domain of SPINDLY causes defects in gibberellin response. Plant Physiol. 126, 1250-1258 (2001). 

    상세보기 crossref

  44. J. Exp. Bot Z Lin 59 4271 2008 10.1093/jxb/ern276 Lin, Z. et al. SlTPR1, a tomato tetratricopeptide repeat protein, interacts with the ethylene receptors NR and LeETR1, modulating ethylene and auxin responses and development. J. Exp. Bot. 59, 4271-4287 (2008). 

    상세보기 crossref

  45. J. Exp. Bot Z Lin 60 3697 2009 10.1093/jxb/erp209 Lin, Z., Ho, C. W. & Grierson, D. AtTRP1 encodes a novel TPR protein that interacts with the ethylene receptor ERS1 and modulates development inArabidopsis. J. Exp. Bot. 60, 3697-3714 (2009). 

    상세보기 crossref

  46. Plant J. M Zhang 83 582 2015 10.1111/tpj.12911 Zhang, M. et al. A tetratricopeptide repeat domain-containing protein SSR1 located in mitochondria is involved in root development and auxin polar transport in Arabidopsis. Plant J. 83, 582-599 (2015). 

    상세보기 crossref

  47. Crop Sci. OL May 35 1570 1995 10.2135/cropsci1995.0011183X003500060009x May, O. L., Bowman, D. T. & Calhoun, D. S. Genetic diversity of U.S. upland cotton cultivars released between 1980 and 1990. Crop Sci. 35, 1570-1574 (1995). 

    상세보기 crossref

  48. Crop Sci. GA Esbroeck Van 38 33 1998 10.2135/cropsci1998.0011183X003800010006x Van Esbroeck, G. A., Bowman, D. T., Calhoun, D. S. & May, O. L. Changes in the genetic diversity of cotton in the USA from 1970 to 1995. Crop Sci. 38, 33-37 (1998). 

    상세보기 crossref

  49. Acta Genet. Sin G Chen 33 733 2006 10.1016/S0379-4172(06)60106-6 Chen, G. & Du, X. M. Genetic diversity of source germplasm of upland cotton in China as determined by SSR marker analysis. Acta Genet. Sin. 33, 733-745 (2006). 

    상세보기 crossref

  50. Euphytica DD Fang 191 391 2013 10.1007/s10681-013-0886-2 Fang, D. D. et al. A microsatellite-based genome-wide analysis of genetic diversity and linkage disequilibrium in upland cotton (Gossypium hirsutum L.) cultivars from major cotton-growing countries. Euphytica 191, 391-401 (2013). 

    상세보기 crossref

  51. Theor. Appl. Genet. P Tyagi 127 283 2014 10.1007/s00122-013-2217-3 Tyagi, P. et al. Genetic diversity and population structure in the US upland cotton (Gossypium hirsutum L.). Theor. Appl. Genet. 127, 283-295 (2014). 

    상세보기 crossref

  52. New Phytol PK Ingvarsson 189 909 2011 10.1111/j.1469-8137.2010.03593.x Ingvarsson, P. K. & Street, N. R. Association genetics of complex traits in plants. New Phytol. 189, 909-922 (2011). 

    상세보기 crossref

  53. Plant Methods A Korte 9 2013 10.1186/1746-4811-9-29 Korte, A. & Farlow, A. The advantages and limitations of trait analysis with GWAS: a review. Plant Methods 9, 29 (2013). 

    상세보기 crossref

  54. Genome Res. AD Long 9 720 1999 10.1101/gr.9.8.720 Long, A. D. & Langley, C. H. The power of association studies to detect the contribution of candidate genetic loci to variation in complex traits. Genome Res. 9, 720-731 (1999). 

    상세보기 crossref

  55. Genome Res. A McKenna 20 1297 2010 10.1101/gr.107524.110 McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303 (2010). 

    상세보기 crossref

  56. Nucleic Acids Res. K Wang 38 e164 2010 10.1093/nar/gkq603 Wang, K., Li, M. & Hakonarson, H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 38, e164 (2010). 

    상세보기 crossref

  57. Bioinformatics H Li 26 589 2010 10.1093/bioinformatics/btp698 Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589-595 (2010). 

    상세보기 crossref

  58. Bioinformatics P Danecek 27 2156 2011 10.1093/bioinformatics/btr330 Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156-2158 (2011). 

    상세보기 crossref

  59. Am. J. Hum. Genet. S Purcell 81 559 2007 10.1086/519795 Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559-575 (2007). 

    상세보기 crossref

  60. Nat. Genet. X Zhou 44 821 2012 10.1038/ng.2310 Zhou, X. & Stephens, M. Genome-wide efficient mixed-model analysis for association studies. Nat. Genet. 44, 821-824 (2012). 

    상세보기 crossref

  61. Proc. Natl. Acad. Sci. USA JA Poland 108 6893 2011 10.1073/pnas.1010894108 Poland, J. A., Bradbury, P. J., Buckler, E. S. & Nelson, R. J. Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize. Proc. Natl Acad. Sci. USA 108, 6893-6898 (2011). 

    상세보기 crossref

  62. Nucleic Acids Res. MW Pfaffl 29 e45 2001 10.1093/nar/29.9.e45 Pfaffl, M. W. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 29, e45 (2001). 

    상세보기 crossref

  63. Nat. Protoc. M Senthil-Kumar 9 1549 2014 10.1038/nprot.2014.092 Senthil-Kumar, M. & Mysore, K. S. Tobacco rattle virus-based virus-induced gene silencing in Nicotiana benthamiana. Nat. Protoc. 9, 1549-1562 (2014). 

    상세보기 crossref

  64. Nat. Protoc. C Trapnell 7 562 2012 10.1038/nprot.2012.016 Trapnell, C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 7, 562-578 (2012). 

    상세보기 crossref

관련 콘텐츠

섹션별 컨텐츠 바로가기

AI-Helper ※ AI-Helper는 오픈소스 모델을 사용합니다.

AI-Helper 아이콘
AI-Helper
안녕하세요, AI-Helper입니다. 좌측 "선택된 텍스트"에서 텍스트를 선택하여 요약, 번역, 용어설명을 실행하세요.
※ AI-Helper는 부적절한 답변을 할 수 있습니다.

선택된 텍스트

맨위로