Vai ai contenuti. | Spostati sulla navigazione | Spostati sulla ricerca | Vai al menu | Contatti | Accessibilità

| Crea un account

Kerschbamer, Emanuela (2015) Identification of selective sweeps in domesticated apple (Malus × domestica Borkh.). [Tesi di dottorato]

Full text disponibile come:

[img]
Anteprima
Documento PDF
12Mb

Abstract (inglese)

The domesticated apple (Malus × domestica) is one of the most cultivated plant over the world and is one of the most genetically polymorphic agricultural species.
Studying the genetic diversity of the apple germplasm could provide important hints about the domestication process as giving a valuable resource for high resolution genetic mapping, QTL analysis and breeding programs. Advances in next generation sequencing technologies have driven the costs of DNA sequencing down to the point that whole genome re-sequencing (WGS) is now feasible for high diversity, large genome species. The aim of this work is to gain information on genome-wide genetic variability patterns in apple and to identify regions of the genome that may have been selected during the process of plant domestication.
SNPs were called from Illumina short reads for 63 apple cultivars representative of European germplasm diversity. The identified SNPs (over 15 millions) were filtered for quality and to avoid repeated and paralogous regions. Additional filters (minor allele frequency and Hardy-Weinberg equilibrium) were applied to discard variants derived from genotyping errors resulting in a final number of 426,321 SNPs . The SNPs kept after the quality filters were used to study the population structure and the genetic diversity. A weak stratification of the analyzed population emerged both from the principal component analysis (PCA) and a model based clustering approach performed using fastStructure. This analysis showed the presence of three subpopulations with a high level of admixture. FST between each couple of sub-groups was 0.055, 0.083 and 0.096 that indicate a moderate differentiation.
Two different approaches were used to identify selective sweeps. The first is based on allelic frequencies and the site frequency spectrum (SFS) and it is implemented in the software SweeD. The second is based on linkage disequilibrium patterns and the omega statistic and it is implemented in the software OmegaPlus.
Regions that were identified by both softwares were merged and used as candidate regions for positive selection resulting in 1,194 sweeps on the whole genome. A total of 153 gene predictions were extracted from these candidate regions and annotated using Gene Ontology terms and mapping on the KEGG pathway database. Similarity searches were also performed against plant databases to find gene orthologs and to better understand the function of candidates. The annotation revealed that genes under positive selection are involved in pathways like photosynthesis, protein ubiquitination, plant hormone signal transduction and starch and sucrose metabolism. In particular for the plant hormone signal transduction, were identified the auxin influx carrier and a SAUR family protein that lead to cell enlargement and plant growth and the ethylene insensitive protein 2 that leads to fruit ripening and senescence. The genes identified in regions under positive selection that were functionally annotated are consistent with the domestication traits for a better fruit: bigger, tastier and sweeter

Abstract (italiano)

Il melo domestico (Malus × domestica) è una delle piante più coltivate al mondo ed è tra le specie agricole geneticamente più polimorfiche. Studiare la diversità genetica in melo può dare importanti suggerimenti sul processo di domesticazione e valide risorse per creare mappe genetiche ad alta risoluzione, per analisi di QTL e nei programmi di breeding. I miglioramenti nelle tecnologie di sequenziamento del DNA, dette NGS, hanno ridotto di molto i costi del sequenziamento al punto che i risequenziamenti completi di genomi sono ora fattibili anche per specie ad alta diversità genetica e dal genoma molto grande.
Lo scopo di questo lavoro è l'analisi della variabilità genetica dell’intero genoma di melo e l'identificazione di regioni genomiche sottoposte a selezione durante il processo di domesticazione.
A tale scopo 63 cultivar di melo, rappresentanti l’intera diversità del germoplasma europeo, sono state sequenziate con teconolgia Illumina. Dalle sequenze sono stati predetti oltre 15 milioni di SNP che sono stati filtrati eliminare le predizioni scadenti o legate a regioni ripetute e paraloghe. Ulteriori filtri (minor allele frequency e Hardy-Weinberg equilibrium) sono stati applicati per eliminare gli SNP derivati da errori di genotipizzazione. Il numero finale degli SNP filtrati è risultato di 426'321.
Gli SNP rimasti dopo i filtri di qualità sono stati usati per studiare la struttura di popolazione e la diversità genetica. Dall'analisi delle componenti principali e da un metodo di clusterizzazione implementato in fastStructure, è emersa una debole stratificazione della popolazione analizzata. Questa analisi ha mostrato la presenza di tre sottopopolazioni con un alto livello di admixture. L’FST tra ogni coppia di sottopopolazioni è risultato di 0,055, 0,083 and 0,096 indicando un livello di differenziazione moderato. Due diversi approcci sono stati usati per identificare 'selective sweep'. Il primo è basato sulle frequenze alleliche e sul 'site frequency spectrum' (SFS) ed è implementato nel software SweeD. Il secondo è basato sui pattern di 'linkage disequilibrium' e la statistica ω ed è implementato nel software OmegaPlus. Le regioni del genoma che sono state identificate da entrambi i software sono state usate come regioni candidate sotto selezione positiva. In tutto il genoma le regioni sotto selezione sono risultate 1'194.
In totale 153 predizioni geniche sono state estratte dalle regioni candidate e annotate usando i termini della Gene Ontology e con i pathway metabolici descritti nel database KEGG. Ricerche di similarità in database di piante sono state fatte per trovare geni ortologhi e per capire meglio la funzione dei geni candidati.
L'annotazione ha rivelato che i geni sotto selezione positiva sono coinvolti in vari processi quali la fotosintesi, l'ubiquitinazione di proteine, la trasduzione del segnale ormonale delle piante o il metobolismo di amidi e zuccheri. In particolare, per la trasduzione del segnale, sono stati identificati l'importatore dell'auxina e una proteina della famiglia SAUR che agiscono sull'aumento della dimensione cellulare e sulla crescita della pianta e la proteina 2 insensibile all'etilene che porta alla maturazione del frutto e alla senescenza. Le annotazioni funzionali disponibili ascrivono i geni identificati a ruoli fisiologici coerenti con i tratti fenotipici attesi per un processo di domesticazione. Per esempio i tratti legati al miglioramento delle caratterisitche del frutto come la dimensione, il gusto e la dolcezza

Statistiche Download - Aggiungi a RefWorks
Tipo di EPrint:Tesi di dottorato
Relatore:Valle , Giorgio
Dottorato (corsi e scuole):Ciclo 27 > scuole 27 > BIOSCIENZE E BIOTECNOLOGIE > BIOTECNOLOGIE
Data di deposito della tesi:04 Febbraio 2015
Anno di Pubblicazione:04 Febbraio 2015
Parole chiave (italiano / inglese):apple, Malus x domestica, selective sweep, domestication, selection
Settori scientifico-disciplinari MIUR:Area 05 - Scienze biologiche > BIO/11 Biologia molecolare
Area 05 - Scienze biologiche > BIO/18 Genetica
Struttura di riferimento:Dipartimenti > Dipartimento di Biologia
Codice ID:8021
Depositato il:12 Nov 2015 16:40
Simple Metadata
Full Metadata
EndNote Format

Bibliografia

I riferimenti della bibliografia possono essere cercati con Cerca la citazione di AIRE, copiando il titolo dell'articolo (o del libro) e la rivista (se presente) nei campi appositi di "Cerca la Citazione di AIRE".
Le url contenute in alcuni riferimenti sono raggiungibili cliccando sul link alla fine della citazione (Vai!) e tramite Google (Ricerca con Google). Il risultato dipende dalla formattazione della citazione.

1] Ferree DC, Warrington IJ: Apples. Botany, Production and Uses. CAB International 2003. Cerca con Google

[2] Sansavini S, Donati F, Costa F, Tartarini S: Advances in apple breeding for enhanced fruit quality and resistance to biotic stresses: new varieties for the european market. Journal of Fruit and Ornamental Plant Research 2004, 12. Cerca con Google

[3] Van Nerum I, Keulemans J: Update on and Review of the Incompatibility ( S-) Genotypes of Apple Cultivars. HortScience 2004, 39(5):943–947. Cerca con Google

[4] Considine MJ, Wan Y, D’Antuono MF, Zhou Q, Han M, Gao H, Wang M: Molecular genetic features of polyploidization and aneuploidization reveal unique patterns for genome duplication in diploid Malus. PloS one 2012, 7:e29449. Cerca con Google

[5] Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, Coppola G, Costa F, Cova V, Dal Ri A, Goremykin V, Komjanc M, Longhi S, Magnago P, Malacarne G, Malnoy M, Micheletti D, Moretto M, Perazzolli M, Si-Ammour A, Vezzulli Cerca con Google

S, Zini E, Eldredge G, Fitzgerald LM, Gutin N, Lanchbury J, Macalma T, Mitchell JT, Reid J, Wardell B, Kodira C, Chen Z, Desany B, Niazi F, Palmer M, Koepke T, Jiwan D, Schaeffer S, Krishnan V, Wu C, Chu VT, King ST, Vick J, Tao Q, Mraz A, Stormo A, Stormo K, Bogden R, Ederle D, Stella A, Vecchietti A, Kater MM, Masiero S, Lasserre P, Lespinasse Y, Allan AC, Bus V, Chagnè D, Crowhurst RN, Gleave AP, Lavezzo E, Cerca con Google

Fawcett Ja, Proost S, Rouzè P, Sterck L, Toppo S, Lazzari B, Hellens RP, Durel CE, Gutin A, Bumgarner RE, Gardiner SE, Skolnick M, Egholm M, Van de Peer Y, Salamini F, Viola R: The genome of the domesticated apple (Malus domestica Borkh.). Nature genetics 2010, 42(10):833–9. Cerca con Google

[6] Potter D, Eriksson T, Evans RC, Oh S, Smedmark JEE, Morgan DR, Kerr M, Robertson KR, Arsenault M, Dickinson Ta, Campbell CS: Phylogeny and classification of Rosaceae. Plant Systematics and Evolution 2007, 266(1-2):5–43. Cerca con Google

[7] Campbell CS, Donoghue MJ, Baldwin BG, F WM: Phylogenetic Relationships in Maloideae (Rosaceae) Evidence from sequences of the internal transcriped spacers. American journal of botany 1995, 82(7):903–918. Cerca con Google

[8] Shulaev V, Korban SS, Sosinski B, Abbott AG, Aldwinckle HS, Folta KM, Iezzoni A, Main D, Ar ́s u P, Dandekar AM, Lewers K, Brown SK, Davis TM, Gardiner SE, Potter Cerca con Google

D, Veilleux RE: Multiple models for Rosaceae genomics. Plant physiology 2008,147(3):985–1003. Cerca con Google

[9] Campbell CS, Evans RC, Morgan DR, Dickinson Ta, Arsenault MP: Phylogeny of subtribe Pyrinae (formerly the Maloideae, Rosaceae): Limited resolution of a complex evolutionary history. Plant Systematics and Evolution 2007, 266(1-2):119– 145. Cerca con Google

[10] Wolfe J, Wehr W: Rosaceous Chamaebatiaria-like foliage from the Paleogene of Cerca con Google

western North America. Aliso (USA) 1988, 12:177–200. Cerca con Google

[11] Tuskan G, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao R, Bhalerao R, Blaudez Cerca con Google

D, Boerjan W, Brun A, Brunner A, Busov V: The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 2006, 313(5793)::1596. Cerca con Google

[12] Salse J, Bolot S, Throude M, Jouffe V, Piegu B, Quraishi UM, Calcagno T, Cooke R, Delseny M, Feuillet C: Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution. The Plant cell 2008, 20:11–24. Cerca con Google

[13] Doyle J, Flagel L, Paterson A, Rapp R, Soltis D, Soltis P, Wendel J: Evolutionary genetics of genome merger and doubling in plants. Annual review of genetics 2008, 42(443):461. Cerca con Google

[14] Janick J, Cummins J, Brown S, Hemmat M: Apples. Fruit breeding. 1996. Cerca con Google

[15] Zohary D, Hopf M: Domestication of Plants in the Old World. Oxford University Press, Cerca con Google

third edition 2000. Cerca con Google

[16] White KD: Roman farming. (Aspects of Greek and Roman life). Cornell un edition 1970. Cerca con Google

[17] Nagy S, Shaw PE, Veldhuis MK: Citrus Science and Technology. Avi publis edition 1977. Cerca con Google

[18] Ellison R, Renfrew J, Brothwell D, Seeley N: Some food offerings from Ur, excavated Cerca con Google

by Sir Leonard Woolley, and previously unpublished. Journal of Archaeological Cerca con Google

Science 1978, 5(2):167–177. Cerca con Google

[19] Korban S, Skirvin R: Nomenclature of the cultivated apple. HortScience 1984, 19(2):177–180. Cerca con Google

[20] Hokanson SC, McFerson JR, Forsline PL, Lamboy WF: Collecting and Managing Wild Malus Germplasm in its Center of Diversity. HortScience 1997, 32(2):173–176. Cerca con Google

[21] Robinson JP, Harris Sa, Juniper BE: Taxonomy of the genus Malus Mill. (Rosaceae) with emphasis on the cultivated apple, Malus domestica Borkh. Plant Systematics and Evolution 2001, 226(1-2):35–58. Cerca con Google

[22] Harris Sa, Robinson JP, Juniper BE: Genetic clues to the origin of the apple. Trends Cerca con Google

in genetics : TIG 2002, 18(8):426–30. Cerca con Google

[23] Morgan J, Richards A: The New Book Of Apples. Brogdale Horticultural Trust, Ebury Cerca con Google

Press 2002. Cerca con Google

[24] Coart E, Van Glabeke S, De Loose M, Larsen aS, Rold ́n-Ruiz a Cerca con Google

I: Chloroplast diversity Cerca con Google

in the genus Malus: New insights into the relationship between the European Cerca con Google

wild apple (Malus sylvestris (L.) Mill.) and the domesticated apple (Malus Cerca con Google

domestica Borkh.). Molecular Ecology 2006, 15:2171–2182. Cerca con Google

[25] Cornille A, Giraud T, Smulders MJM, Rold ́n-Ruiz a Cerca con Google

I, Gladieux P: The domestication Cerca con Google

and evolutionary ecology of apples. Trends in genetics : TIG 2013, :1–9. Cerca con Google

[26] Cornille A, Gladieux P, Smulders MJM, Rold ́n-Ruiz a Cerca con Google

I, Laurens F, Le Cam B, Nersesyan Cerca con Google

A, Clavel J, Olonova M, Feugey L, Gabrielyan I, Zhang XG, Tenaillon MI, Giraud T: Cerca con Google

New insight into the history of domesticated apple: secondary contribution Cerca con Google

of the European wild apple to the genome of cultivated varieties. PLoS genetics Cerca con Google

2012, 8(5):e1002703. Cerca con Google

[27] Gupta PK, Roy JK, Prasad M: Single nucleotide polymorphisms: A new paradigm Cerca con Google

for molecular marker technology and DNA polymorphism detection with em- Cerca con Google

phasis on their use in plants. Current Science 2001, 80(4):524–535. Cerca con Google

[28] Ding C, Jin S: High throughput methods for SNP genotyping. Methods in Molec- Cerca con Google

ular Biology 2009, (578):245–25. Cerca con Google

[29] Pushkarev D, Neff NF, Quake SR: Single-molecule sequencing of an individual Cerca con Google

human genome. Nature biotechnology 2009, 27(9):847–850. Cerca con Google

[30] Clark RM, Schweikert G, Toomajian C, Ossowski S, Zeller G, Shinn P, Warthmann N, Hu Cerca con Google

TT, Fu G, Hinds DA, Chen H, Frazer KA, Huson DH, Nordborg M, Ecker JR, Weigel D: Cerca con Google

Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis Cerca con Google

thaliana. Science 2007, 317(July):338–342. Cerca con Google

[31] Velasco R, Zharkikh A, Troggio M, Cartwright Da, Cestaro A, Pruss D, Pindo M, Fitzger- Cerca con Google

ald LM, Vezzulli S, Reid J, Malacarne G, Iliev D, Coppola G, Wardell B, Micheletti Cerca con Google

D, Macalma T, Facci M, Mitchell JT, Perazzolli M, Eldredge G, Gatto P, Oyzerski R, Cerca con Google

Moretto M, Gutin N, Stefanini M, Chen Y, Segala C, Davenport C, Dematt` e Cerca con Google

L, Mraz A, Cerca con Google

Battilana J, Stormo K, Costa F, Tao Q, Si-Ammour A, Harkins T, Lackey A, Perbost C, Cerca con Google

Taillon B, Stella A, Solovyev V, Fawcett Ja, Sterck L, Vandepoele K, Grando SM, Toppo Cerca con Google

S, Moser C, Lanchbury J, Bogden R, Skolnick M, Sgaramella V, Bhatnagar SK, Fontana Cerca con Google

P, Gutin A, Van de Peer Y, Salamini F, Viola R: A high quality draft consensus Cerca con Google

sequence of the genome of a heterozygous grapevine variety. PloS one 2007, Cerca con Google

2(12):e1326. Cerca con Google

[32] Arai-Kichise Y, Shiwa Y, Nagasaki H, Ebana K, Yoshikawa H, Yano M, Wakasa K: Dis- Cerca con Google

covery of Genome-wide DNA Polymorphisms in a Landrace Cultivar of Japon- Cerca con Google

ica Rice by Whole-genome Sequencing. Plant & cell physiology 2011, 52(2):274. Cerca con Google

[33] Br ̈utigam a Cerca con Google

A, Gowik U: What can next generation sequencing do for you? Next Cerca con Google

generation sequencing as a valuable tool in plant research. Plant biology 2010, Cerca con Google

12(6):831–41. Cerca con Google

[34] Elshire RJ, Glaubitz JC, Sun Q, Poland Ja, Kawamoto K, Buckler ES, Mitchell SE: A Cerca con Google

robust, simple genotyping-by-sequencing (GBS) approach for high diversity Cerca con Google

species. PloS one 2011, 6(5):e19379. Cerca con Google

[35] Davey JW, Hohenlohe Pa, Etter PD, Boone JQ, Catchen JM, Blaxter ML: Genome- Cerca con Google

wide genetic marker discovery and genotyping using next-generation sequenc- Cerca con Google

ing. Nature reviews. Genetics 2011, 12(7):499–510. Cerca con Google

[36] Wood AR, Tuke MA, Nalls M, Hernandez D, Gibbs JR, Lin H, Xu CS, Li Q, Shen J, Jun Cerca con Google

G, Almeida M, Tanaka T, Perry JRB, Gaulton K, Rivas M, Pearson R, Curran JE, John- Cerca con Google

son MP, G ̈ring o Cerca con Google

HHH, Duggirala R, Blangero J, Mccarthy MI, Bandinelli S, Weedon MN, Cerca con Google

Singleton A, Melzer D, Ferrucci L, Frayling TM: Whole-genome sequencing to un- Cerca con Google

derstand the genetic architecture of common gene expression and biomarker Cerca con Google

phenotypes. Human molecular genetics 2014, (November):1–9. Cerca con Google

[37] Devlin B, Risch N: A comparison of linkage disequilibrium measures for fine- Cerca con Google

scale mapping. Genomics 1995, 29:311–322. Cerca con Google

[38] Lewontin RC: The interactions of selection and linkage II. Optimus models. Cerca con Google

Genetics 1964, 50(4)(1956):49–67. Cerca con Google

[39] Weir BS: Genetic data analysis II: methods for discrete population genetic data. 1996. Cerca con Google

[40] Hill WG, Robertson a: Linkage disequilibrium in finite populations. TAG. Theo- Cerca con Google

retical and applied genetics. Theoretische und angewandte Genetik 1968, 38:226–31. Cerca con Google

[41] Fisher R: The Logic of Inductive Inference. Journal of the Royal Statistical Society Cerca con Google

1934, 98:39–82. Cerca con Google

[42] Flint-garcia SA, Thornsberry JM, Buckler ESI: STRUCTURE OF LINKAGE DIS- Cerca con Google

EQUILIBRIUM IN PLANTS. Annu. Rev. Plant Biol. 2003, 54:357–374. Cerca con Google

[43] Stich B, Melchinger AE, Piepho HP, Heckenberger M, Maurer HP, Reif JC: A new test Cerca con Google

for family-based association mapping with inbred lines from plant breeding Cerca con Google

programs. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik Cerca con Google

2006, 113:1121–1130. Cerca con Google

[44] Yu J, Buckler ES: Genetic association mapping and genome organization of Cerca con Google

maize. Current Opinion in Biotechnology 2006, 17:155–160. Cerca con Google

[45] Bel ́ o Cerca con Google

A, Zheng P, Luck S, Shen B, Meyer DJ, Li B, Tingey S, Rafalski A: Whole genome Cerca con Google

scan detects an allelic variant of fad2 associated with increased oleic acid levels Cerca con Google

in maize. Molecular Genetics and Genomics 2008, 279:1–10. Cerca con Google

[46] Ravel C, Praud S, Murigneux A, Canaguier A, Sapet F, Samson D, Balfourier F, Dufour Cerca con Google

P, Chalhoub B, Brunel D, Beckert M, Charmet G: Single-nucleotide polymorphism Cerca con Google

frequency in a set of selected lines of bread wheat (Triticum aestivum L.). Cerca con Google

Genome 2006, 49:1131–1139. Cerca con Google

[47] Rhon ́ e Cerca con Google

B, Raquin AL, Goldringer I: Strong linkage disequilibrium near the selected Cerca con Google

Yr17 resistance gene in a wheat experimental population. Theoretical and Applied Cerca con Google

Genetics 2007, 114:787–802. Cerca con Google

[48] Tommasini L, Schnurbusch T, Fossati D, Mascher F, Keller B: Association mapping of Cerca con Google

Stagonospora nodorum blotch resistance in modern European winter wheat Cerca con Google

varieties. Theoretical and Applied Genetics 2007, 115:697–708. Cerca con Google

[49] Myles S, Peiffer J, Brown PJ, Ersoz ES, Zhang Z, Costich DE, Buckler ES: Association Cerca con Google

mapping: critical considerations shift from genotyping to experimental design. Cerca con Google

The Plant cell 2009, 21(8):2194–202. Cerca con Google

[50] Mackay I, Powell W: Methods for linkage disequilibrium mapping in crops. Trends Cerca con Google

in Plant Science 2007, 12(2):57–63. Cerca con Google

[51] Nielsen R: Molecular signatures of natural selection. Annual review of genetics Cerca con Google

2005, 39:197–218. Cerca con Google

[52] Nielsen R, Hellmann I, Hubisz M, Bustamante C, Clark AG: Recent and ongoing Cerca con Google

selection in the human genome. Nature reviews. Genetics 2007, 8(11):857–68. Cerca con Google

[53] Maynard Smith J, Haigh J: The hitch-hiking effect of a favourable gene. Genetical Cerca con Google

Research 1974, 23:23–35. Cerca con Google

[54] Olsen KM, Caicedo AL, Polato N, McClung A, McCouch S, Purugganan MD: Selection Cerca con Google

under domestication: evidence for a sweep in the rice waxy genomic region. Cerca con Google

Genetics 2006, 173(2):975–83. Cerca con Google

[55] Tajima F: Statistical Method for Testing the Neutral Mutation Hypothesis by Cerca con Google

DNA Polymorphism. Genetics 1989, 595(3):585–595. Cerca con Google

[56] Fu YX, Li Wh: Statistical Tests of Neutrality of Mutations. Genetics 1992, Cerca con Google

(133):693–709. Cerca con Google

[57] Fay JC, Wu Ci: Hitchhiking Under Positive Darwinian Selection. Genetics 2000, Cerca con Google

(155):1405–1413. Cerca con Google

[58] Kim Y, Stephan W: Detecting a local signature of genetic hitchhiking along a Cerca con Google

recombining chromosome. Genetics 2002, 160(2):765–77. Cerca con Google

[59] Beaumont Ma, Nichols Ra: Evaluating Loci for Use in the Genetic Analysis of Cerca con Google

Population Structure. Proceedings of the Royal Society B: Biological Sciences 1996, Cerca con Google

263:1619–1626. Cerca con Google

[60] Majewski J, Cohan FM: Adapt globally, act locally: The effect of selective sweeps Cerca con Google

on bacterial sequence diversity. Genetics 1999, 152(January):1459–1474. Cerca con Google

[61] Akey JM, Zhang G, Zhang K, Jin L, Shriver MD: Interrogating a High-Density SNP Cerca con Google

Map for Signatures of Natural Selection. Genome research 2002, 12:1805–1814. Cerca con Google

[62] Sabeti PC, Reich DE, Higgins JM, Levine HZP, Richter DJ, Schaffner SF, Gabriel SB, Cerca con Google

Platko JV, Patterson NJ, Mcdonald GJ, Ackerman HC, Campbell SJ, Altshuler D, Cooper Cerca con Google

R, Kwiatkowski D, Ward R, Lander ES: Detecting recent positive selection in the Cerca con Google

human genome from haplotype structure. Nature 2002, 419(October):832–837. Cerca con Google

[63] Voight BF, Kudaravalli S, Wen X, Pritchard JK: A map of recent positive selection Cerca con Google

in the human genome. PLoS biology 2006, 4(3):e72. Cerca con Google

[64] Wang ET, Kodama G, Baldi P, Moyzis RK: Global landscape of recent inferred Cerca con Google

Darwinian selection for Homo sapiens. Proceedings of the National Academy of Cerca con Google

Sciences of the United States of America 2006, 103:135–40. Cerca con Google

[65] Kim Y, Nielsen R: Linkage disequilibrium as a signature of selective sweeps. Cerca con Google

Genetics 2004, 167(3):1513–24. Cerca con Google

[66] Homer N, Merriman B, Nelson SF: BFAST: an alignment tool for large scale Cerca con Google

genome resequencing. PloS one 2009, 4(11):e7767. Cerca con Google

[67] Smith T, Waterman M: Identification of common molecular subsequences. Journal Cerca con Google

of Molecular Biology 1981, 147:195–197. Cerca con Google

[68] Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Cerca con Google

Durbin R: The Sequence Alignment/Map format and SAMtools. Bioinformatics Cerca con Google

(Oxford, England) 2009, 25(16):2078–9. Cerca con Google

[69] Danecek P, Auton A, Abecasis G, Albers Ca, Banks E, DePristo Ma, Handsaker RE, Cerca con Google

Lunter G, Marth GT, Sherry ST, McVean G, Durbin R: The variant call format and Cerca con Google

VCFtools. Bioinformatics (Oxford, England) 2011, 27(15):2156–8. Cerca con Google

[70] Bianco L, Cestaro A, Sargent DJ, Banchi E, Derdak S, Di Guardo M, Salvi S, Jansen Cerca con Google

J, Viola R, Gut I, Laurens F, Chagn ́ e Cerca con Google

D, Velasco R, van de Weg E, Troggio M: De- Cerca con Google

velopment and Validation of a 20K Single Nucleotide Polymorphism (SNP) Cerca con Google

Whole Genome Genotyping Array for Apple (Malus domestica Borkh). PloS Cerca con Google

one 2014, 9(10):e110377. Cerca con Google

[71] Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MaR, Bender D, Maller J, Sklar Cerca con Google

P, de Bakker PIW, Daly MJ, Sham PC: PLINK: a tool set for whole-genome associ- Cerca con Google

ation and population-based linkage analyses. American journal of human genetics Cerca con Google

2007, 81(3):559–75. Cerca con Google

[72] Raj A, Stephens M, Pritchard JK: fastSTRUCTURE: Variational Inference of Cerca con Google

Population Structure in Large SNP Data Sets. Genetics 2014, 197(2):573–589. Cerca con Google

[73] Jakobsson M, Rosenberg Na: CLUMPP: a cluster matching and permutation Cerca con Google

program for dealing with label switching and multimodality in analysis of Cerca con Google

population structure. Bioinformatics (Oxford, England) 2007, 23(14):1801–6. Cerca con Google

[74] Nei M, Li WH: Mathematical model for studying genetic variation in terms Cerca con Google

of restriction endonucleases. Proceedings of the National Academy of Sciences 1979, Cerca con Google

76(10):5269–5273. Cerca con Google

[75] Wright S: Genetical structure of populations. Nature 1950, 4215:247–249. Cerca con Google

[76] Schaid DJ: Linkage Disequilibrium Testing when Linkage Phase is Unknown. Cerca con Google

Genetics 2004, 166(January):505–512. Cerca con Google

ˇ Cerca con Google

[77] Pavlidis P, Zivkovic D, Stamatakis A, Alachiotis N: SweeD: likelihood-based detec- Cerca con Google

tion of selective sweeps in thousands of genomes. Molecular biology and evolution Cerca con Google

2013, 30(9):2224–34. Cerca con Google

[78] Nielsen R, Williamson S, Kim Y, Hubisz MJ, Clark AG, Bustamante C: Genomic scans Cerca con Google

for selective sweeps using SNP data. Genome research 2005, 15(11):1566–75. Cerca con Google

[79] Altschul S, Gish W, Miller W, Myers E, Lipman D: Basic local alignment search Cerca con Google

tool. Journal of Molecular Biology 1990, 215(3):403–410. Cerca con Google

[80] Baird Na, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis Za, Selker EU, Cresko Cerca con Google

Wa, Johnson Ea: Rapid SNP discovery and genetic mapping using sequenced Cerca con Google

RAD markers. PLoS ONE 2008, 3(10):1–7. Cerca con Google

[81] Pfender WF, Saha MC, Johnson Ea, Slabaugh MB: Mapping with RAD (restriction- Cerca con Google

site associated DNA) markers to rapidly identify QTL for stem rust resistance Cerca con Google

in Lolium perenne. Theoretical and Applied Genetics 2011, 122:1467–1480. Cerca con Google

[82] Ward Ja, Bhangoo J, Fern ́ndez-Fern ́ndez a Cerca con Google

a Cerca con Google

F, Moore P, Swanson JD, Viola R, Velasco Cerca con Google

R, Bassil N, Weber Ca, Sargent DJ: Saturated linkage map construction in Rubus Cerca con Google

idaeus using genotyping by sequencing and genome-independent imputation. Cerca con Google

BMC genomics 2013, 14:2. Cerca con Google

[83] Liu H, Bayer M, Druka A, Russell JR, Hackett Ca, Poland J, Ramsay L, Hedley PE, Waugh R: An evaluation of genotyping by sequencing (GBS) to map the Breviaristatum-e (ari-e) locus in cultivated barley. BMC genomics 2014, 15:104. Cerca con Google

[84] Poland Ja, Brown PJ, Sorrells ME, Jannink JL: Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by- sequencing approach. PLoS ONE 2012, 7(2). Cerca con Google

[85] Chutimanitsakun Y, Nipper RW, Cuesta-Marcos A, Cistu ́ e Cerca con Google

L, Corey A, Filichkina T, Cerca con Google

Johnson Ea, Hayes PM: Construction and application for QTL analysis of a Re- Cerca con Google

striction Site Associated DNA (RAD) linkage map in barley. BMC genomics Cerca con Google

2011, 12:4. Cerca con Google

[86] Yang H, Tao Y, Zheng Z, Zhang Q, Zhou G, Sweetingham MW, Howieson JG, Li C: Cerca con Google

Draft Genome Sequence, and a Sequence-Defined Genetic Linkage Map of Cerca con Google

the Legume Crop Species Lupinus angustifolius L. PLoS ONE 2013, 8(5). Cerca con Google

[87] Arnold B, Corbett-Detig RB, Hartl D, Bomblies K: RADseq underestimates diver- Cerca con Google

sity and introduces genealogical biases due to nonrandom haplotype sampling. Cerca con Google

Molecular Ecology 2013, 22:3179–3190. Cerca con Google

[88] Pina A, Urrestarazu J, Errea P: Analysis of the genetic diversity of local apple Cerca con Google

cultivars from mountainous areas from Aragon (Northeastern Spain). Scientia Cerca con Google

Horticulturae 2014, 174:1–9. Cerca con Google

[89] Liang W, Dondini L, De Franceschi P, Paris R, Sansavini S, Tartarini S: Genetic Diver- Cerca con Google

sity , Population Structure and Construction of a Core Collection of Apple Cerca con Google

Cultivars from Italian Germplasm. Plant Molecular Biology Reporter 2014, :1–16. Cerca con Google

[90] Glaszmann JC, Kilian B, Upadhyaya HD, Varshney RK: Accessing genetic diversity Cerca con Google

for crop improvement. Current Opinion in Plant Biology 2010, 13:167–173. Cerca con Google

[91] Jones E, Chu WC, Ayele M, Ho J, Bruggeman E, Yourstone K, Rafalski A, Smith OS, Cerca con Google

McMullen MD, Bezawada C, Warren J, Babayev J, Basu S, Smith S: Development of Cerca con Google

single nucleotide polymorphism (SNP) markers for use in commercial maize Cerca con Google

(Zea mays L.) germplasm. Molecular Breeding 2009, 24:165–176. Cerca con Google

[92] Yamamoto T, Nagasaki H, Yonemaru Ji, Ebana K, Nakajima M, Shibaya T, Yano M: Cerca con Google

Fine definition of the pedigree haplotypes of closely related rice cultivars by Cerca con Google

means of genome-wide discovery of single-nucleotide polymorphisms. BMC Cerca con Google

genomics 2010, 11:267. Cerca con Google

[93] Brown GR, Gill GP, Kuntz RJ, Langley CH, Neale DB: Nucleotide diversity and Cerca con Google

linkage disequilibrium in loblolly pine. Proceedings of the National Academy of Cerca con Google

Sciences of the United States of America 2004, 101(42):15255–60. Cerca con Google

[94] Gilchrist EJ, Haughn GW, Ying CC, Otto SP, Zhuang J, Cheung D, Hamberger B, Cerca con Google

Aboutorabi F, Kalynyak T, Johnson L, Bohlmann J, Ellis BE, Douglas CJ, Cronk QCB: Cerca con Google

Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation Cerca con Google

in wild populations of Populus trichocarpa. Molecular Ecology 2006, 15:1367–1378. Cerca con Google

[95] Jiang D, Ye QL, Wang FS, Cao L: The Mining of Citrus EST-SNP and Its Applica- Cerca con Google

tion in Cultivar Discrimination. Agricultural Sciences in China 2010, 9(2):179–190. Cerca con Google

[96] Wu SB, Wirthensohn MG, Hunt P, Gibson JP, Sedgley M: High resolution melting analysis of almond SNPs derived from ESTs. Theoretical and Applied Genetics 2008, 118:1–14. Cerca con Google

[97] Lima LS, Gramacho KP, Carels N, Novais R, Gaiotto Fa, Lopes UV, Gesteira aS, Zaidan Ha, Cascardo JCM, Pires JL, Micheli F: Single nucleotide polymorphisms from Theobroma cacao expressed sequence tags associated with witches’ broom disease in cacao. Genetics and Molecular Research 2009, 8(3):799–808. Cerca con Google

[98] Vezzulli S, Micheletti D, Riaz S, Pindo M, Viola R, This P, Walker MA, Troggio M, Cerca con Google

Velasco R: A SNP transferability survey within the genus Vitis. BMC plant Cerca con Google

biology 2008, 8:128. Cerca con Google

[99] Lijavetzky D, Cabezas JA, Ib ́nez a ̃ A, Rodr ́ıguez V, Mart ınez-Zapater JM: High throughput SNP discovery and genotyping in grapevine (Vitis vinifera L.) by combining a re-sequencing approach and SNPlex technology. BMC genomics 2007, 8:424. Cerca con Google

[100] Chagn ́ e D, Gasic K, Crowhurst RN, Han Y, Bassett HC, Bowatte DR, Lawrence TJ, Rikkerink EHa, Gardiner SE, Korban SS: Development of a set of SNP markers present in expressed genes of the apple. Genomics 2008, 92:353–358. Cerca con Google

[101] Han Y, Chagn ́ e Cerca con Google

D, Gasic K, Rikkerink EHa, Beever JE, Gardiner SE, Korban SS: BAC- Cerca con Google

end sequence-based SNPs and Bin mapping for rapid integration of physical Cerca con Google

and genetic maps in apple. Genomics 2009, 93(3):282–288. Cerca con Google

[102] A map of human genome variation from population-scale sequencing 2010. Cerca con Google

[103] Tenaillon MI, Sawkins MC, Long aD, Gaut RL, Doebley JF, Gaut BS: Patterns of DNA Cerca con Google

sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays Cerca con Google

L.). Proceedings of the National Academy of Sciences of the United States of America 2001, 98(16):9161–9166. Cerca con Google

[104] Kota R, Varshney RK, Prasad M, Zhang H, Stein N, Graner a: EST-derived single nucleotide polymorphism markers for assembling genetic and physical maps of the barley genome. Functional and Integrative Genomics 2008, 8:223–233. Cerca con Google

[105] Zhu Q, Zheng X, Luo J, Gaut BS, Ge S: Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: Severe bottleneck during domestication of rice. Molecular Biology and Evolution 2007, 24:875–888. Cerca con Google

[106] Cao K, Zheng Z, Wang L, Liu X, Zhu G, Fang W, Cheng S, Zeng P, Chen C, Wang X, Xie M, Zhong X, Wang X, Zhao P, Bian C, Zhu Y, Zhang J, Ma G, Chen C, Li Y, Hao F, Li Y, Huang G, Li Y, Li H, Guo J, Xu X, Wang J: Comparative population genomics reveals the domestication history of the peach, Prunus persica, and human influences on perennial fruit crops. Genome Biology 2014, 15(7):415. Cerca con Google

[107] Crisci JL, Poh YP, Mahajan S, Jensen JD: The impact of equilibrium assumptions on tests of selection. Frontiers in genetics 2013, 4(November):235. Cerca con Google

[108] Alachiotis N, Stamatakis a, Pavlidis P: OmegaPlus: a scalable tool for rapid detection of selective sweeps in whole-genome datasets. Bioinformatics (Oxford, England) 2012, 28(17):2274–5. Cerca con Google

[109] Lyu J, Li B, He W, Zhang S, Gou Z, Zhang J, Meng L, Li X, Tao D, Huang W, Hu F, Wang W: A genomic perspective on the important genetic mechanisms of upland adaptation of rice. BMC plant biology 2014, 14:160. Cerca con Google

[110] Gore Ma, Chia JM, Elshire RJ, Sun Q, Ersoz ES, Hurwitz BL, Peiffer Ja, McMullen MD, Grills GS, Ross-Ibarra J, Ware DH, Buckler ES: A first-generation haplotype map of maize. Science (New York, N.Y.) 2009, 326(5956):1115–7. Cerca con Google

[111] Jiao Y, Zhao H, Ren L, Song W, Zeng B, Guo J, Wang B, Liu Z, Chen J, Li W, Zhang M, Xie S, Lai J: Genome-wide genetic changes during modern breeding of maize. Nature genetics 2012, 44(7):812–5. Cerca con Google

[112] Huang X, Kurata N, Wei X, Wang ZX, Wang A, Zhao Q, Zhao Y, Liu K, Lu H, Li W, Guo Y, Lu Y, Zhou C, Fan D, Weng Q, Zhu C, Huang T, Zhang L, Wang Y, Feng L, Furuumi H, Kubo T, Miyabayashi T, Yuan X, Xu Q, Dong G, Zhan Q, Li C, Fujiyama A, Toyoda A, Lu T, Feng Q, Qian Q, Li J, Han B: A map of rice genome variation reveals the origin of cultivated rice. Nature 2012, 490(7421):497–501. Cerca con Google

[113] Morris GP, Ramu P, Deshpande SP, Hash CT, Shah T, Upadhyaya HD, Riera-Lizarazu O, Brown PJ, Acharya CB, Mitchell SE, Harriman J, Glaubitz JC, Buckler ES, Kresovich S: Population genomic and genome-wide association studies of agroclimatic traits in sorghum. Proceedings of the National Academy of Sciences of the United Cerca con Google

States of America 2013, 110(2):453–8. Cerca con Google

[114] Wang M, Yu Y, Haberer G, Marri PR, Fan C, Goicoechea JL, Zuccolo A, Song X, Kudrna D, Ammiraju JSS, Cossu RM, Maldonado C, Chen J, Lee S, Sisneros N, de Baynast K, Golser W, Wissotski M, Kim W, Sanchez P, Ndjiondjop MN, Sanni K, Long M, Carney Cerca con Google

J, Panaud O, Wicker T, Machado Ca, Chen M, Mayer KFX, Rounsley S, Wing Ra: The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nature Genetics 2014, 46(9):982–988. Cerca con Google

[115] Schmutz J, McClean PE, Mamidi S, Wu GA, Cannon SB, Grimwood J, Jenkins J, Shu S, Song Q, Chavarro C, Torres-Torres M, Geffroy V, Moghaddam SM, Gao D, Abernathy B, Barry K, Blair M, Brick Ma, Chovatia M, Gepts P, Goodstein DM, Gonzales M, Hellsten Cerca con Google

U, Hyten DL, Jia G, Kelly JD, Kudrna D, Lee R, Richard MMS, Miklas PN, Osorno JM, Rodrigues J, Thareau V, Urrea Ca, Wang M, Yu Y, Zhang M, Wing Ra, Cregan PB, Rokhsar DS, Jackson Sa: A reference genome for common bean and genome-wide analysis of dual domestications. Nature genetics 2014, 46(7):707–713. Cerca con Google

Download statistics

Solo per lo Staff dell Archivio: Modifica questo record