دورية أكاديمية
أعرض في EDS

Bulked sample analysis in genetics, genomics and crop improvement.

التفاصيل البيبلوغرافية
العنوان: Bulked sample analysis in genetics, genomics and crop improvement.
المؤلفون: Zou C; Institute of Crop Science, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China., Wang P; Institute of Crop Science, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China., Xu Y; Institute of Crop Science, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China. y.xu@cgiar.org.; International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico. y.xu@cgiar.org.
المصدر: Plant biotechnology journal [Plant Biotechnol J] 2016 Oct; Vol. 14 (10), pp. 1941-55. Date of Electronic Publication: 2016 Apr 28.
نوع المنشور: Journal Article; Review; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Wiley on behalf of the Society for Experimental Biology, Association of Applied Biologists Country of Publication: England NLM ID: 101201889 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1467-7652 (Electronic) Linking ISSN: 14677644 NLM ISO Abbreviation: Plant Biotechnol J Subsets: MEDLINE
أسماء مطبوعة: Publication: 2014- : Oxford Wiley on behalf of the Society for Experimental Biology, Association of Applied Biologists
Original Publication: [Oxford] : Blackwell Pub., c2003-
مواضيع طبية MeSH: Crops, Agricultural/*genetics , Genomics/*methods, Breeding ; Crops, Agricultural/physiology ; Genetics ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA
مستخلص: Biological assay has been based on analysis of all individuals collected from sample populations. Bulked sample analysis (BSA), which works with selected and pooled individuals, has been extensively used in gene mapping through bulked segregant analysis with biparental populations, mapping by sequencing with major gene mutants and pooled genomewide association study using extreme variants. Compared to conventional entire population analysis, BSA significantly reduces the scale and cost by simplifying the procedure. The bulks can be built by selection of extremes or representative samples from any populations and all types of segregants and variants that represent wide ranges of phenotypic variation for the target trait. Methods and procedures for sampling, bulking and multiplexing are described. The samples can be analysed using individual markers, microarrays and high-throughput sequencing at all levels of DNA, RNA and protein. The power of BSA is affected by population size, selection of extreme individuals, sequencing strategies, genetic architecture of the trait and marker density. BSA will facilitate plant breeding through development of diagnostic and constitutive markers, agronomic genomics, marker-assisted selection and selective phenotyping. Applications of BSA in genetics, genomics and crop improvement are discussed with their future perspectives.
(© 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.)
References: Proteome Sci. 2011 Feb 11;9:10. (PMID: 21314956)
Nat Genet. 2009 Feb;41(2):166-7. (PMID: 19169256)
Nat Genet. 2012 Jan 15;44(2):217-20. (PMID: 22246502)
Theor Appl Genet. 1990 Aug;80(2):205-8. (PMID: 24220897)
PLoS Genet. 2011 Apr;7(4):e1001372. (PMID: 21533022)
New Phytol. 2012 Jan;193(1):96-108. (PMID: 21973035)
Nature. 2010 Apr 15;464(7291):1039-42. (PMID: 20393561)
BMC Plant Biol. 2014 Mar 27;14:81. (PMID: 24673936)
Biotechniques. 1997 Sep;23(3):504-11. (PMID: 9298224)
Analyst. 2014 Feb 7;139(3):528-42. (PMID: 24326290)
Trends Plant Sci. 2014 Jan;19(1):52-61. (PMID: 24139902)
Genetics. 1994 Dec;138(4):1365-73. (PMID: 7896115)
BMC Genomics. 2013 Sep 17;14:628. (PMID: 24330545)
Genetics. 2004 Dec;168(4):2285-93. (PMID: 15611192)
Proteomics. 2015 Jan;15(2-3):218-31. (PMID: 25266292)
Proteomics. 2015 Jan;15(2-3):462-73. (PMID: 25195567)
Cancer Cell. 2003 Apr;3(4):317-25. (PMID: 12726858)
BMC Plant Biol. 2012 Jan 26;12:14. (PMID: 22280551)
Plant J. 2009 Jan;57(2):373-85. (PMID: 18786180)
PLoS Genet. 2013;9(8):e1003683. (PMID: 23966868)
Curr Opin Plant Biol. 2007 Apr;10(2):156-61. (PMID: 17291822)
Mol Biotechnol. 2003 Feb;23(2):97-106. (PMID: 12632694)
Genome Res. 2009 Jun;19(6):1068-76. (PMID: 19420380)
Nat Biotechnol. 2012 Jan 22;30(2):174-8. (PMID: 22267009)
Genes Dev. 2009 Jan 1;23(1):80-92. (PMID: 19095804)
Theor Appl Genet. 2014 Jul;127(7):1491-9. (PMID: 24845123)
BMC Plant Biol. 2011 Nov 17;11:163. (PMID: 22094046)
PLoS Genet. 2009 Jul;5(7):e1000551. (PMID: 19593375)
Plant J. 2011 Aug;67(4):715-25. (PMID: 21518053)
Theor Appl Genet. 2015 Nov;128(11):2289-99. (PMID: 26215184)
New Phytol. 2013 Oct;200(1):276-283. (PMID: 23790109)
PLoS Genet. 2010 May 06;6(5):e1000940. (PMID: 20463887)
Nat Methods. 2013 Dec;10(12):1177-84. (PMID: 24185837)
Theor Appl Genet. 2014 Nov;127(11):2503-13. (PMID: 25208646)
BMC Genomics. 2014 Sep 29;15:823. (PMID: 25266061)
Nat Rev Genet. 2014 Nov;15(11):749-63. (PMID: 25246196)
Reproduction. 2007 Jan;133(1):95-106. (PMID: 17244736)
PLoS One. 2013 Jul 30;8(7):e68433. (PMID: 23935868)
BMJ. 2008 Sep 29;337:a1655. (PMID: 18824488)
Mol Plant. 2012 Jul;5(4):865-75. (PMID: 22147755)
Genetics. 1989 Jan;121(1):185-99. (PMID: 2563713)
Mol Cell Proteomics. 2012 Apr;11(4):M111.011460. (PMID: 22171321)
PLoS Comput Biol. 2011 Nov;7(11):e1002255. (PMID: 22072954)
Nature. 2008 Oct 30;455(7217):1251-4. (PMID: 18820680)
Science. 2000 Mar 10;287(5459):1816-20. (PMID: 10710308)
Science. 2002 Apr 5;296(5565):92-100. (PMID: 11935018)
Theor Appl Genet. 2009 Jan;118(2):347-58. (PMID: 18854970)
PLoS One. 2011 May 04;6(5):e19379. (PMID: 21573248)
Chem Rev. 1996 Jun 20;96(4):1519-1532. (PMID: 11848801)
Nat Methods. 2008 Feb;5(2):175-7. (PMID: 18204456)
PLoS One. 2011;6(12):e28334. (PMID: 22174790)
Plant J. 2013 Apr;74(1):174-83. (PMID: 23289725)
Nat Genet. 2010 Nov;42(11):961-7. (PMID: 20972439)
Science. 2011 Oct 7;334(6052):83-6. (PMID: 21980108)
Plant J. 2012 Mar;69(6):1052-63. (PMID: 22098111)
Proc Natl Acad Sci U S A. 2013 Jan 8;110(2):453-8. (PMID: 23267105)
PLoS One. 2011 Jan 27;6(1):e15993. (PMID: 21297997)
BMC Genet. 2011 Oct 18;12:89. (PMID: 22008150)
Trends Plant Sci. 2014 Jun;19(6):390-8. (PMID: 24491827)
Biotechniques. 2011 Jan;50(1):32-40. (PMID: 21231920)
Mol Biotechnol. 2013 May;54(1):1-12. (PMID: 22476870)
Cell. 2012 Dec 7;151(6):1358-69. (PMID: 23217716)
Nat Biotechnol. 2009 Jul;27(7):633-41. (PMID: 19561596)
Nucleic Acids Res. 2008 Apr;36(6):e35. (PMID: 18276640)
Mech Ageing Dev. 2007 Jan;128(1):161-7. (PMID: 17126887)
Nat Genet. 2012 Jun 03;44(7):812-5. (PMID: 22660547)
Nat Genet. 2012 Jun 03;44(7):808-11. (PMID: 22660546)
Theor Appl Genet. 2007 Feb;114(4):669-81. (PMID: 17165081)
PLoS One. 2013 May 17;8(5):e62137. (PMID: 23690931)
Theor Appl Genet. 2016 Apr;129(4):653-673. (PMID: 26932121)
Theor Appl Genet. 2015 Mar;128(3):539-47. (PMID: 25575840)
PLoS Genet. 2013 Jun;9(6):e1003534. (PMID: 23754958)
Mol Biosyst. 2011 Mar;7(3):773-83. (PMID: 21132161)
Mol Biol Rep. 2011 Nov;38(8):5037-53. (PMID: 21161392)
Nat Biotechnol. 2015 May;33(5):445-9. (PMID: 25798936)
Nat Methods. 2009 Aug;6(8):550-1. (PMID: 19644454)
Genetics. 2010 Jan;184(1):19-26. (PMID: 19884313)
Ann Bot. 2002 Jun;89 Spec No:941-63. (PMID: 12102519)
Curr Protoc Protein Sci. 2011 Apr;Chapter 27:Unit27.2. (PMID: 21488044)
Nat Biotechnol. 2002 Feb;20(2):163-70. (PMID: 11821862)
Genetics. 2008 Jan;178(1):539-51. (PMID: 18202393)
J Exp Bot. 2012 Jun;63(10):3749-64. (PMID: 22442426)
Nat Biotechnol. 2011 Jun 19;29(7):635-43. (PMID: 21685905)
Nat Rev Genet. 2009 Jan;10(1):57-63. (PMID: 19015660)
Proc Natl Acad Sci U S A. 2007 Mar 13;104(11):4730-5. (PMID: 17360592)
Mol Cell Proteomics. 2004 Dec;3(12):1154-69. (PMID: 15385600)
Front Plant Sci. 2014 Sep 30;5:484. (PMID: 25324846)
Theor Appl Genet. 1987 Feb;73(4):556-62. (PMID: 24241113)
Theor Appl Genet. 2014 Oct;127(10):2183-92. (PMID: 25119870)
Nature. 2014 Nov 27;515(7528):554-7. (PMID: 25252978)
Genome Biol. 2013 Jun 17;14(6):R61. (PMID: 23773572)
Nucleic Acids Res. 1991 Dec 11;19(23):6553-8. (PMID: 1684420)
Drug Discov Today. 2005 Jun 1;10(11):789-94. (PMID: 15922937)
Nat Rev Genet. 2011 Feb;12(2):87-98. (PMID: 21191423)
Nat Biotechnol. 1999 Oct;17(10):994-9. (PMID: 10504701)
Plant Biotechnol J. 2014 Aug;12(6):709-17. (PMID: 24602056)
Curr Opin Biotechnol. 2008 Feb;19(1):4-9. (PMID: 18207731)
Nat Protoc. 2014 Jan;9(1):90-103. (PMID: 24336473)
Heredity (Edinb). 2015 Mar;114(3):291-9. (PMID: 25407079)
Theor Appl Genet. 2013 Feb;126(2):443-9. (PMID: 23052026)
Nat Methods. 2010 Sep;7(9):681-5. (PMID: 20805795)
Anal Chem. 2011 Jun 15;83(12):4407-26. (PMID: 21491952)
PLoS One. 2008;3(10):e3376. (PMID: 18852878)
New Phytol. 2013 Mar;197(4):1332-1343. (PMID: 23252608)
Electrophoresis. 2009 Jun;30 Suppl 1:S122-32. (PMID: 19441019)
Plant Mol Biol. 2002 Jan;48(1-2):143-54. (PMID: 11862971)
Plant Sci. 2011 Mar;180(3):461-9. (PMID: 21421393)
BMC Genomics. 2014 Oct 16;15:903. (PMID: 25326146)
Sci Rep. 2013;3:1827. (PMID: 23661174)
Nat Genet. 2010 Mar;42(3):260-3. (PMID: 20101244)
Nat Rev Genet. 2014 Oct;15(10):662-76. (PMID: 25139187)
Plant J. 2015 Nov;84(3):587-96. (PMID: 26386250)
Mol Cell Proteomics. 2007 Dec;6(12):2058-71. (PMID: 17848588)
Nucleic Acids Res. 2008 Nov;36(19):e122. (PMID: 18753151)
Plant Cell. 2014 Apr 11;26(4):1382-1397. (PMID: 24728647)
PLoS One. 2012;7(5):e36406. (PMID: 22586469)
Plant Cell. 2011 Sep;23(9):3374-91. (PMID: 21949153)
PLoS Biol. 2011 Aug;9(8):e1001125. (PMID: 21857804)
Methods Mol Biol. 2008;424:113-23. (PMID: 18369857)
PLoS One. 2014 Jan 06;9(1):e83675. (PMID: 24400075)
Plant Biotechnol J. 2015 Jun;13(5):613-24. (PMID: 25382230)
Theor Appl Genet. 2014 Sep;127(9):2005-9. (PMID: 25112203)
Adv Healthc Mater. 2014 Mar;3(3):412-23. (PMID: 23966175)
Proc Natl Acad Sci U S A. 1991 Nov 1;88(21):9828-32. (PMID: 1682921)
Trends Genet. 2013 Aug;29(8):479-87. (PMID: 23769209)
Theor Appl Genet. 2009 Dec;120(1):177-90. (PMID: 19841886)
Theor Appl Genet. 2014 Oct;127(10):2243-52. (PMID: 25119873)
Front Physiol. 2012 Sep 19;3:347. (PMID: 23049510)
Genet Epidemiol. 2010 Jul;34(5):479-91. (PMID: 20552648)
Curr Opin Chem Biol. 2003 Feb;7(1):55-63. (PMID: 12547427)
Nat Commun. 2013;4:2832. (PMID: 24343161)
Plant Physiol. 2013 Jun;162(2):553-66. (PMID: 23606598)
J Med Food. 2014 Nov;17(11):1239-46. (PMID: 25184943)
J Proteomics. 2010 Oct 10;73(11):2064-77. (PMID: 20685252)
Nat Genet. 2011 Dec 04;44(1):32-9. (PMID: 22138690)
Nat Biotechnol. 2011 Jun 19;29(7):625-34. (PMID: 21685906)
Genetics. 1987 May;116(1):113-25. (PMID: 3596228)
فهرسة مساهمة: Keywords: DNA-seq; RNA-seq; breeding; bulked sample analysis; bulked segregant analysis; chips; microarrays; protein-seq
تواريخ الأحداث: Date Created: 20160319 Date Completed: 20170601 Latest Revision: 20240326
رمز التحديث: 20240326
مُعرف محوري في PubMed: PMC5043468
DOI: 10.1111/pbi.12559
PMID: 26990124
قاعدة البيانات: MEDLINE
الوصف
تدمد:1467-7652
DOI:10.1111/pbi.12559