SpringerLink
Log in

Association map** of agronomic traits on chromosome 2A of wheat

  • Published:
Genetica Aims and scope Submit manuscript

Abstract

Association map** is a method to test the association between molecular markers and quantitative trait loci (QTL) based on linkage disequilibrium (LD). In this study, the collection of 108 wheat germplasm accessions form China were evaluated for their plant heights, spike length, spikelets per spike, grains per spike, thousand kernel weight and spikelets density in 3 years at three locations. And they were genotyped with 85 SSR markers and 40 EST-SSR markers. The population structure was inferred on the basis of unlinked 48 SSR markers and 40 EST-SSR markers. The extent of LD on chromosome 2A was 2.3 cM. Association of 37 SSR loci on chromosomes 2A with six agronomic traits was analysed with a mixed linear model. A total of 14 SSR loci were significantly associated with agronomic traits. Some of the associated markers were located in the QTL region detected in previous linkage map** analysis. Our results demonstrated that association map** can enhance QTL information and achieves higher resolution with short LD extent.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price includes VAT (Germany)

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Agrama HA, Eizenga GC, Yan W (2007) Association map** of yield and its components in rice cultivars. Mol Breed 19:341–356. doi:10.1007/s11032-006-9066-6

    Article  Google Scholar 

  • Blanco A, Bellomo MP, Lotti C, Maniglio T, Pasqualone A, Simeone R, Troccoli A, Di Fonzo N (1998) Genetic map** of sedimentation volume across environments using recombinant inbred lines of durum wheat. Plant Breed 117:413–417. doi:10.1111/j.1439-0523.1998.tb01965.x

    Article  Google Scholar 

  • Börner A, Schumann E, Fürste A, Cöster H, Leithold B, Röder S, Weber E (2002) Map** of quantitative trait loci determining agronomic important characters in hexaploid wheat (Triticum aestivum L.). Theor Appl Genet 105:921–936. doi:10.1007/s00122-002-0994-1

    Article  PubMed  Google Scholar 

  • Breseghello F, Sorrells MS (2006) Association map** of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172:1165–1177. doi:10.1534/genetics.105.044586

    Article  PubMed  Google Scholar 

  • Camus-Kulandaivelu L, Veyricras JB, Madur D, Combes V, Fourmann M, Barraud S, Dubreuil P, Gouesnard B, Manicacci D, Charcosset A (2006) Maize adaptation to temperate climate: relationship with population structure and polymorphism in the Dwarf8 gene. Genetics 172:2449–2463. doi:10.1534/genetics.105.048603

    Article  PubMed  CAS  Google Scholar 

  • Ching A, Caldwell KS, Jung M, Dolan M, Smith OS, Tingey S, Morgante M, Rafalski A (2002) SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet 3:1–14. doi:10.1186/1471-2156-3-19

    Article  Google Scholar 

  • Flint-Garcia SA, Thuillet AC, Yu JM, Pressoir G, Romero SM, Mitchell SE, Doebley J, Kresovich S, Goodman MM, Buckler ES (2005) Maize association population, a high-resolution platform for quantitative trait locus dissection. Plant J 44:1054–1064. doi:10.1111/j.1365-313X.2005.02591.x

    Article  PubMed  CAS  Google Scholar 

  • Garris A, McCouch SR, Kresovich S (2003) Population structure and its effect on haplotype diversity and linkage disequilibrium surrounding the xa5 locus of rice (Oryza sativa L.). Genetics 165:759–769

    PubMed  Google Scholar 

  • Gervais L, Dedryver F, Morlais JY, Bodusseau V, Negre S, Bilous M, Groos C, Trottet M (2003) Map** of quantitative trait loci for field resistance to Fusarium head blight in an European winter wheat. Theor Appl Genet 106:961-970

    PubMed  CAS  Google Scholar 

  • Hanocq E, Niarquin M, Heumez E, Rousset M, Gouis J (2004) Detection and map** of QTL for earliness components in a bread wheat recombinant inbred lines population. Theor Appl Genet 110:106–115. doi:10.1007/s00122-004-1799-1

    Article  PubMed  CAS  Google Scholar 

  • Hill WG, Robertson A (1968) Linkage disequilibrium in finite populations. Theor Appl Genet 38:226–231. doi:10.1007/BF01245622

    Article  Google Scholar 

  • Huang XQ, Kempf H, Ganal MW, Röder MS (2004) Advanced backcross QTL analysis in progenies derived from a cross between a German elite winter wheat variety and synthetic wheat (Triticum aestivum L.). Theor Appl Genet 109:933–943. doi:10.1007/s00122-004-1708-7

    Article  PubMed  CAS  Google Scholar 

  • Jannink JL, Bink M, Jansen RC (2001) Using complex plant pedigrees to map valuable genes. Trends Plant Sci 6:337–342. doi:10.1016/S1360-1385(01)02017-9

    Article  PubMed  CAS  Google Scholar 

  • Jones LE, Rybka K, Lukaszewski AJ (2002) The effect of a deficiency and a deletion on recombination in chromosome 1BL in wheat. Theor Appl Genet 104:1204–1208. doi:10.1007/s00122-002-0876-6

    Article  PubMed  CAS  Google Scholar 

  • José C, Juan B, Susanne D, Mateo V, Sybil A, Herrera F, Morten L, Ravi PS, Richard T, Marilyn W, Jorge F, Matthew R, Jonathan HC, Rodomiro O (2007) Association analysis of historical bread wheat germplasm using additive genetic covariance of relatives and population structure. Genetics 177(3):1889–1913. doi:10.1534/genetics.107.078659

    Article  CAS  Google Scholar 

  • Kato K, Miura H, Sawada S (2000) Map** QTLs controlling grain yield and its components on chromosome 5A of wheat. Theor Appl Genet 101:1114–1121. doi:10.1007/s001220051587

    Article  CAS  Google Scholar 

  • Khan A, Procunier DJ, Humphreys GD, Tranquilli G, Schlatter AR, Marcucci-Poltri S, Frohberg R, Dubcovsky J (2000) Development of PCR-based marker for a high grain protein content gene from Triticum turgidum ssp. dicoccoides transferred to bread wheat. Crop Sci 40:518–524

    Article  CAS  Google Scholar 

  • Kraakman AT, Niks RE, Van den Berg PM, Stam P, Van Eeuwijk FA (2004) Linkage disequilibrium map** of yield and yield stability in modern spring barley cultivars. Genetics 168:435–446. doi:10.1534/genetics.104.026831

    Article  PubMed  CAS  Google Scholar 

  • Kraft T, Hansen M, Nilsson N-O (2000) Linkage disequilibrium and fingerprinting in sugar beet. Theor Appl Genet 101:323–326. doi:10.1007/s001220051486

    Article  Google Scholar 

  • Kumar N, Kulwal PL, Balyan HS, Gupta PK (2007) QTL map** for yield and yield contributing traits in two map** populations of bread wheat. Mol Breed 19:163–177. doi:10.1007/s11032-006-9056-8

    Article  Google Scholar 

  • Lewis CM (2002) Genetic association studies: design, analysis and interpretation. Brief Bioinform 3:146–153. doi:10.1093/bib/3.2.146

    Article  PubMed  CAS  Google Scholar 

  • Maccaferri M, Sanguineti MC, Noli E, Tuberosa R (2005) Population structure and long-range linkage disequilibrium in a durum wheat elite collection. Mol Breed 15:271–289. doi:10.1007/s11032-004-7012-z

    Article  CAS  Google Scholar 

  • Navabi A, Tewari JP, Singh RP, McCallum B, Laroche A, Briggs KG (2005) Inheritance and QTL analysis of durable resistance to stripe and leaf rusts in an Australian cultivar, Triticum aestivum ‘Cook’. Genome 48:97–107. doi:10.1139/g04-100

    Article  PubMed  CAS  Google Scholar 

  • Olmos S, Distelfeld A, Chicaiza O, Schlatter AR, Fahima T, Echenique V, Dulxovsky J (2003) Precise map** of a locus affecting grain protein content in durum wheat. Theor Appl Genet 107:1243–1251. doi:10.1007/s00122-003-1377-y

    Article  PubMed  CAS  Google Scholar 

  • Otto CD, Kianian SF, Elias EM, Stack RW, Joppa LR (2002) Genetic dissection of a major Fusarium head blight QTL in tetraploid wheat. Plant Mol Biol 48:625–632. doi:10.1023/A:1014821929830

    Article  PubMed  CAS  Google Scholar 

  • Palaisa KA, Morgante M, Williams M, Rafalski A (2003) Contrasting effects of selection on sequence diversity and linkage disequilibrium at two phytoene synthase loci. Plant Cell 15:1795–1806. doi:10.1105/tpc.012526

    Article  PubMed  CAS  Google Scholar 

  • Peng JH, Ronin Y, Fahima T, Röder MS, Li YC, Nevo E, Korol A (2003) Domestication quantitative trait loci in Triticum dicoccoides, the progenitor of wheat. Proc Natl Acad Sci USA 100:2489–2494. doi:10.1073/pnas.252763199

    Article  PubMed  CAS  Google Scholar 

  • Perretant M, Cadalen T, Charmet G, Sourdille P, Nicolas P, Boeuf C, Tixier MH, Branlard G, Bernard S, Bernard M (2000) QTL analysis of bread-making quality in wheat using a doubled haploid population. Theor Appl Genet 100:1167–1175. doi:10.1007/s001220051420

    Article  CAS  Google Scholar 

  • Prasad M, Kumar N, Kulwal PL, Röder MS, Balyan HS, Dhaliwal HS, Gupta PK (2003) QTL analysis for grain protein content using SSR markers and validation studies using NILs in bread wheat. Theor Appl Genet 106:659–667

    PubMed  CAS  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    PubMed  CAS  Google Scholar 

  • Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5:94–100. doi:10.1016/S1369-5266(02)00240-6

    Article  PubMed  CAS  Google Scholar 

  • Ravel C, Praud S, Murigneux A, Linossier L, Dardevet M, Balfourier F, Dufour P, Brunel D, Charmet G (2006) Identification of Glu-B1-1 as a candidate gene for the quantity of high-molecularweight glutenin in bread wheat (Triticum aestivum L.) by means of an association study. Theor Appl Genet 112:738–743. doi:10.1007/s00122-005-0178-x

    Article  PubMed  CAS  Google Scholar 

  • Remington DL, Thornsberry JM, Matsuola Y, Wilson LM, Whitt SR, Doebley J, Kresovich S, Goodman MM, Buckler ES (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci USA 98:11479–11484. doi:10.1073/pnas.201394398

    Article  PubMed  CAS  Google Scholar 

  • Rhoné B, Raquin AL, Goldringer I (2006) Strong linkage disequilibrium near the selected Yr17 resistance gene in a wheat experimental population. Theor Appl Genet 114:787–802. doi:10.1007/s00122-006-0477-x

    Article  PubMed  CAS  Google Scholar 

  • Risch NJ (2000) Searching for genetic determinants in the new millennium. Nature 405:847–856. doi:10.1038/35015718

    Article  PubMed  CAS  Google Scholar 

  • Risch N, Merikangas K (1996) The future of genetic studies of complex human diseases. Science 273:1516–1517. doi:10.1126/science.273.5281.1516

    Article  PubMed  CAS  Google Scholar 

  • Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal DNA spacer length polymorphisms in barley: Mendelian inheritance, chromosomal location and population dynamics. Proc Natl Acad Sci USA 81:8014–8018. doi:10.1073/pnas.81.24.8014

    Article  PubMed  CAS  Google Scholar 

  • Salvi S, Tuberosa R (2005) To clone or not to clone plant QTLs, present and future challenges. Trends Plant Sci 10:297–304. doi:10.1016/j.tplants.2005.04.008

    Article  PubMed  CAS  Google Scholar 

  • Somers DJ, Isaac P, Edwards K (2004) A high-density microsatellite consensus map for bread wheat (Triticum aestivum L.). Theor Appl Genet 109:1105–1114. doi:10.1007/s00122-004-1740-7

    Article  PubMed  CAS  Google Scholar 

  • Stachel M, Lelley T, Grausgruber H, Vollmann J (2000) Application of microsatellites in wheat (Triticum aestivum L.) for studying genetic differentiation caused by selection for adaptation and use. Theor Appl Genet 100:242–248. doi:10.1007/s001220050032

    Article  Google Scholar 

  • Stich B, Melchinger AE, Frisch M, Maurer HP, Heckenberger M, Reif JC (2005) Linkage disequilibrium in European elite maize germplasm investigated with SSRs. Theor Appl Genet 111:723–730. doi:10.1007/s00122-005-2057-x

    Article  PubMed  Google Scholar 

  • Szalma SJ, Buckler ES, Snook ME, McMullen MD (2005) Association analysis of candidate genes for maysin and chlorogenic acid accumulation in maize silks. Theor Appl Genet 110:1324–1333. doi:10.1007/s00122-005-1973-0

    Article  PubMed  CAS  Google Scholar 

  • Tenaillon M, Sawkins MC, Long AD, Gaut RL, Doebley JF, Gaut BS (2001) Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc Natl Acad Sci USA 98:9161–9166. doi:10.1073/pnas.151244298

    Article  PubMed  CAS  Google Scholar 

  • Thornsberry JM, Goodman MM, Docbley J, Stephen Kresovich S, Nielsen D, Buckler ES (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28:286–289. doi:10.1038/90135

    Article  PubMed  CAS  Google Scholar 

  • Tommasini L, Schnurbusch T, Fossati D, Mascher F, Keller B (2007) Association map** of Stagonospora nodorum blotch resistance in modern European winter wheat varieties. Theor Appl Genet 115:697–708. doi:10.1007/s00122-007-0601-6

    Article  PubMed  CAS  Google Scholar 

  • Toth B, Galiba G, Feher E, Sutka J, Snape JW (2003) Map** genes affecting flowering time and frost resistance on chromosome SB of wheat. Theor Appl Genet 107:509–514. doi:10.1007/s00122-003-1275-3

    Article  PubMed  CAS  Google Scholar 

  • Yu J, Pressoir G, Briggs WH, Bi IV, Yamasaki M, Doebley J, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES (2006) A unified mixed-model method for association map** that accounts for multiple levels of relatedness. Nat Genet 38:203–208. doi:10.1038/ng1702

    Article  PubMed  CAS  Google Scholar 

  • Zondervan KT, Cardon LR (2004) The complex interplay among factors that influence allelic association. Nat Rev Genet 5:89–100. doi:10.1038/nrg1270

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

This research was supported by a grant of “863” programme from the Chinese Ministry of Science and Technology (No. 2006AA100102).

Author information

Authors and Affiliations

  1. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, China

    Ji Yao, Lihua Liu & Yonglian Zheng

  2. Bei**g Hybrid Wheat Research Centre, Bei**g Academy of Agricultural and Forestry Sciences, 100097, Bei**g, China

    Ji Yao, Lixin Wang, Lihua Liu & Chang** Zhao

Authors
  1. Ji Yao
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Lixin Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Lihua Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Chang** Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yonglian Zheng
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Chang** Zhao or Yonglian Zheng.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Yao, J., Wang, L., Liu, L. et al. Association map** of agronomic traits on chromosome 2A of wheat. Genetica 137, 67–75 (2009). https://doi.org/10.1007/s10709-009-9351-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10709-009-9351-5

Keywords

Search

Navigation