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Candidate genes and genetic architecture of symbiotic and agronomic traits revealed by whole-genome, sequence-based association genetics in Medicago truncatula.

Stanton-Geddes J, Paape T, Epstein B, Briskine R, Yoder J, Mudge J, Bharti AK, Farmer AD, Zhou P, Denny R, May GD, Erlandson S, Yakub M, Sugawara M, Sadowsky MJ, Young ND, Tiffin P.

PLoS One. 2013 May 31;8(5):e65688. doi: 10.1371/journal.pone.0065688. Print 2013.


Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula.

Branca A, Paape TD, Zhou P, Briskine R, Farmer AD, Mudge J, Bharti AK, Woodward JE, May GD, Gentzbittel L, Ben C, Denny R, Sadowsky MJ, Ronfort J, Bataillon T, Young ND, Tiffin P.

Proc Natl Acad Sci U S A. 2011 Oct 18;108(42):E864-70. doi: 10.1073/pnas.1104032108. Epub 2011 Sep 26.


DNA polymorphisms and haplotype patterns of transcription factors involved in barley endosperm development are associated with key agronomic traits.

Haseneyer G, Stracke S, Piepho HP, Sauer S, Geiger HH, Graner A.

BMC Plant Biol. 2010 Jan 8;10:5. doi: 10.1186/1471-2229-10-5.


Population genomic analysis of Tunisian Medicago truncatula reveals candidates for local adaptation.

Friesen ML, Cordeiro MA, Penmetsa RV, Badri M, Huguet T, Aouani ME, Cook DR, Nuzhdin SV.

Plant J. 2010 Aug;63(4):623-35. doi: 10.1111/j.1365-313X.2010.04267.x.


Genome-wide association studies for agronomical traits in a world wide spring barley collection.

Pasam RK, Sharma R, Malosetti M, van Eeuwijk FA, Haseneyer G, Kilian B, Graner A.

BMC Plant Biol. 2012 Jan 27;12:16. doi: 10.1186/1471-2229-12-16.


Genome-wide association studies using single nucleotide polymorphism markers developed by re-sequencing of the genomes of cultivated tomato.

Shirasawa K, Fukuoka H, Matsunaga H, Kobayashi Y, Kobayashi I, Hirakawa H, Isobe S, Tabata S.

DNA Res. 2013 Dec;20(6):593-603. doi: 10.1093/dnares/dst033. Epub 2013 Jul 31.


Single-nucleotide polymorphism discovery and diversity in the model legume Medicago truncatula.

Loridon K, Burgarella C, Chantret N, Martins F, Gouzy J, Prospéri JM, Ronfort J.

Mol Ecol Resour. 2013 Jan;13(1):84-95. doi: 10.1111/1755-0998.12021. Epub 2012 Sep 27.


Genomic signature of adaptation to climate in Medicago truncatula.

Yoder JB, Stanton-Geddes J, Zhou P, Briskine R, Young ND, Tiffin P.

Genetics. 2014 Apr;196(4):1263-75. doi: 10.1534/genetics.113.159319. Epub 2014 Jan 17.


High-throughput genomics in sorghum: from whole-genome resequencing to a SNP screening array.

Bekele WA, Wieckhorst S, Friedt W, Snowdon RJ.

Plant Biotechnol J. 2013 Dec;11(9):1112-25. doi: 10.1111/pbi.12106. Epub 2013 Aug 7.


Mapping the genetic basis of symbiotic variation in legume-rhizobium interactions in Medicago truncatula.

Gorton AJ, Heath KD, Pilet-Nayel ML, Baranger A, Stinchcombe JR.

G3 (Bethesda). 2012 Nov;2(11):1291-303. doi: 10.1534/g3.112.003269. Epub 2012 Nov 1.


Population- and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum L.).

Chao S, Dubcovsky J, Dvorak J, Luo MC, Baenziger SP, Matnyazov R, Clark DR, Talbert LE, Anderson JA, Dreisigacker S, Glover K, Chen J, Campbell K, Bruckner PL, Rudd JC, Haley S, Carver BF, Perry S, Sorrells ME, Akhunov ED.

BMC Genomics. 2010 Dec 29;11:727. doi: 10.1186/1471-2164-11-727.


A genome-wide association study of seed protein and oil content in soybean.

Hwang EY, Song Q, Jia G, Specht JE, Hyten DL, Costa J, Cregan PB.

BMC Genomics. 2014 Jan 2;15:1. doi: 10.1186/1471-2164-15-1.


Molecular adaptation in flowering and symbiotic recognition pathways: insights from patterns of polymorphism in the legume Medicago truncatula.

De Mita S, Chantret N, Loridon K, Ronfort J, Bataillon T.

BMC Evol Biol. 2011 Aug 1;11:229. doi: 10.1186/1471-2148-11-229.


Novel genomic approaches unravel genetic architecture of complex traits in apple.

Kumar S, Garrick DJ, Bink MC, Whitworth C, Chagné D, Volz RK.

BMC Genomics. 2013 Jun 12;14:393. doi: 10.1186/1471-2164-14-393.


Genome-wide association studies of 14 agronomic traits in rice landraces.

Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, Li C, Zhu C, Lu T, Zhang Z, Li M, Fan D, Guo Y, Wang A, Wang L, Deng L, Li W, Lu Y, Weng Q, Liu K, Huang T, Zhou T, Jing Y, Li W, Lin Z, Buckler ES, Qian Q, Zhang QF, Li J, Han B.

Nat Genet. 2010 Nov;42(11):961-7. doi: 10.1038/ng.695. Epub 2010 Oct 24.


Patterns of linkage disequilibrium and association mapping in diploid alfalfa (M. sativa L.).

Sakiroglu M, Sherman-Broyles S, Story A, Moore KJ, Doyle JJ, Charles Brummer E.

Theor Appl Genet. 2012 Aug;125(3):577-90. doi: 10.1007/s00122-012-1854-2. Epub 2012 Apr 5.


Adaptation of maize to temperate climates: mid-density genome-wide association genetics and diversity patterns reveal key genomic regions, with a major contribution of the Vgt2 (ZCN8) locus.

Bouchet S, Servin B, Bertin P, Madur D, Combes V, Dumas F, Brunel D, Laborde J, Charcosset A, Nicolas S.

PLoS One. 2013 Aug 30;8(8):e71377. doi: 10.1371/journal.pone.0071377. eCollection 2013.


High-density genome-wide association mapping implicates an F-box encoding gene in Medicago truncatula resistance to Aphanomyces euteiches.

Bonhomme M, André O, Badis Y, Ronfort J, Burgarella C, Chantret N, Prosperi JM, Briskine R, Mudge J, Debéllé F, Navier H, Miteul H, Hajri A, Baranger A, Tiffin P, Dumas B, Pilet-Nayel ML, Young ND, Jacquet C.

New Phytol. 2014 Mar;201(4):1328-42. doi: 10.1111/nph.12611. Epub 2013 Nov 28.


A genome-wide survey for SNPs altering microRNA seed sites identifies functional candidates in GWAS.

Richardson K, Lai CQ, Parnell LD, Lee YC, Ordovas JM.

BMC Genomics. 2011 Oct 13;12:504. doi: 10.1186/1471-2164-12-504.


The genomic architecture and association genetics of adaptive characters using a candidate SNP approach in boreal black spruce.

Prunier J, Pelgas B, Gagnon F, Desponts M, Isabel N, Beaulieu J, Bousquet J.

BMC Genomics. 2013 Jun 1;14:368. doi: 10.1186/1471-2164-14-368.

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