Abstract
Grain number (GN) is one of three major yield-related components in wheat. We used the Chinese wheat mini core collection to undertake a genome-wide association analysis of grain number using 531 SSR markers randomly located on all 21 chromosomes. Grain numbers of all accessions were measured in four trials, i.e. two environments in four growing seasons. Association analysis based on a mixed linear model (MLM) revealed that 27 SSR loci were significantly associated with mean GN (MGN) estimated by the best linear unbiased predictor (BLUP) method. These included numerous breeder favorable alleles with strong positive effects at 23 loci. Significant or extremely significant differences were detected on MGN between varieties conveying favored allele and varieties with other alleles. Moreover, statistical simulation showed that the favored alleles have additive genetic effects. Although modern varieties combined larger numbers of favored alleles, the numbers of favored alleles were not significantly different from those in landraces, especially those alleles contributing mostly to the phenotypic variation. These results indicate that there is still considerable genetic potential for use of markers for genome selection of GN for high yield in wheat.
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Abbreviations
- GN:
-
Grain number
- MLM:
-
Mixed linear model
- BLUP:
-
Best linear unbiased predictor
- MGN:
-
Mean grain number
- SNS:
-
Spikelet number per spike
- SL:
-
Spike length
- GNS:
-
Grain number per spike
- TKW:
-
Thousand kernel weight
- MCC:
-
Mini core collection
References
Agrama HA, Eizenga GC, Yan W (2007) Association mapping of yield and its components in rice cultivars. Mol Breeding 19:341–356
Araki E, Miura H, Sawada S (1999) Identification of genetic loci affecting amylose content and agronomic traits on chromosome 4A of wheat. Theor Appl Genet 98:977–984
Atwell S, Huang YS, Vilhjálmsson BJ, Willems G, Horton M, Li Y, Meng D, Platt A, Tarone AM, Hu T, Jiang R, Muliyati NW, Zhang X, Amer MA, Baxter I, Benjamin B, Chory J, Dean C, Debieu M, Meaux J, Ecker JR, Faure N, Kniskern JM, Jones Jonathan DG, Michael T, Nemri A, Roux F, Salt DE, Tang C, Todesco M, Brian TM, Weigel D, Marjoram P, Borevitz JO, Bergelson J, Nordborg M (2010) Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465:627–631
Aycicek M, Yildirim T (2006) Path coefficient analysis of yield and yield components in bread wheat (Triticum aestivum L.) genotypes. Pak J Bot 38:417–424
Bernardo R (1996a) Test cross additive and dominance effects in best linear unbiased prediction of maize single-cross performance. Theor Appl Genet 93:1098–1102
Bernardo R (1996b) Marker-based estimate of identity by descent and alikeness in state among maize inbreds. Theor Appl Genet 93:262–267
Bernardo R (1996c) Best linear unbiased prediction of maize single-cross performance. Crop Sci 36:50–56
Börner A, Schumann E, Fürste A, Cöster H, Leithold B, Röder MS, Weber WE (2002) Mapping of quantitative trait loci determining agronomic important characters in hexaploid wheat. Theor Appl Genet 105:921–936
Bradbury PJ, Zhang ZW, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635
Brancourt-Hulme M, Doussinault G, Lecomte C, Bérard P, Le Buanec B, Trottet M (2003) Genetic improvement of agronomic traits of winter wheat cultivars released in France from 1946 to 1992. Crop Sci 43:37–45
Breseghello F, Sorrells ME (2006) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172:1165–1177
Buckler ES, Thornsberry JM (2002) Plant molecular diversity and applications to genomics. Curr Opin Plant Biol 5:107–111
Clark RM (2010) Genome-wide association studies coming of age in rice. Nat Genet 42:926–927
Cockram J, White J, Zuluaga DL, Smith D, Comadran J, Macaulay M, Luo ZW, Kearsey MJ, Werner P, Harrap D, Tapsell C, Liu H, Hedley PE, Stein N, Schulte D, Steuernagel B, Marshall DF, Thomas WTB, Ramsay L, Mackay L, Balding DJ (2010) Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome. Proc Natl Accad Sci USA 107:21611–21616
Cuthbert JL, Somers DJ, Brǔlé-Babel AL, Brown PD, Crow GH (2008) Molecular mapping of quantitative trait loci for yield and yield components in spring wheat (Triticum aestivum L.). Theor Appl Genet 117:595–608
Deng SM, Wu XR, Wu YY, Zhou RH, Wang HG, Jia JZ, Liu SB (2011) Characterization and precise mapping of a QTL increasing spike number with pleiotropic effects in wheat. Theor Appl Genet 122:281–289
Donmez E, Sears RG, Shroyer JP, Paulsen GM (2001) Genetic gain in yield attributes of winter wheat in the great plains. Crop Sci 41:1412–1419
Frisch M, Thiemann A, Fu J, Schrag TA, Scholten S, Melchinger AE (2010) Transcriptome-based distance measures for grouping of germplasm and prediction of hybrid performance in maize. Theor Appl Genet 120:709–720
Gaju O, Reynolds MP, Sparkes DL, Foulkes MJ (2009) Relationships between large-spike phenotype, grain number, and yield potential in spring wheat. Crop Sci 49:961–973
Gupta PK, Mir RR, Mohan A, Kumar J (2008) Wheat genomics: present status and future prospects. Int J Plant Genomics 2008:896451
Hai L, Guo HJ, Wagner C, Xiao SH, Friedt W (2008) Genomic regions for yield and yield parameters in Chinese winter wheat (Triticum aestivum L.) genotypes tested under varying environments correspond to QTL in widely different wheat materials. Plant Sci 175:226–232
Hao CY, Dong YC, Wang LF, You GX, Zhang HN, Ge HM, Jia JZ, Zhang XY (2008) Genetic diversity and construction of core collection in Chinese wheat genetic resources. Chin Sci Bull 53:1518–1526
Hao CY, Wang LF, Ge HM, Dong YC, Zhang XY (2011) Genetic diversity and linkage disequilibrium in Chinese bread wheat (Triticum aestivum L.) revealed by SSR markers. PLoS One 6(2):e17279
Hardy OJ, Vekemans X (2002) SPAGeDi: a versatile computer program to analyze spatial genetic structure at the individual or population levels. Mol Ecol Notes 2:618–620
Harjes CE, Rocheford TR, Bai L, Brutnell TP, Bermudez Kandianis C, Sowinski SG, Stapleton AE, Vallabhaneni R, Williams M, Wurtzel ET, Yan JB, Buckler ES (2008) Natural genetic variation in lycopene epsilon cyclase tapped for maize biofortification. Science 319:330–333
Hu YJ, Zhao TF (1995) Studies on the effect of grain weight in breeding of high-yield wheat. Acta Agron Sin 21:671–678
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 a synthetic wheat (Triticum aestivum L.). Theor Appl Genet 109:933–943
Huang XH, Wei XH, Sang T, Zhao Q, Feng Q, Zhao Y, Li CY, Zhu CR, Lu TT, Zhang ZW, Li M, Fan DL, Guo YL, Wang AH, Wang L, Deng LW, Li WJ, Lu YQ, Weng QJ, Liu KY, Huang T, Zhou TY, Jing YF, Li W, Lin Z, Buckler ES, Qian Q, Zhang QF, Li JY, Han B (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42:961–965
Jia JZ (1984) The statistical analysis for correlation factors in kernel weight and plant characters in wheat (T. aestivum L.). Acta Agron Sin 10:201–205
Kato K, Miura H, Sawada S (2000) Mapping QTLs controlling grain yield and its components on chromosome 5A of wheat. Theor Appl Genet 101:1114–1121
Koebner RMD, Snape JW (1999) Actual and potential contributions of biotechnology to wheat breeding. In: Satorre EH, Slafer GA (eds) Wheat: ecology and physiology of yield determination, Food Products Press, p 441–460
Kumar N, Kulwal PL, Balyan HS, Gupta PK (2007) QTL mapping for yield and yield contributing traits in two mapping populations of bread wheat. Mol Breeding 19:163–177
Li WL, Nelson JC, Chu CY, Shi LH, Huang SH, Liu DJ (2002) Chromosomal locations and genetic relationship of tiller and spike characters in wheat. Euphytica 125:357–366
Li SS, Jia JZ, Wei XY, Zhang XC, Li LZ, Chen HM, Fan YD, Sun HY, Zhao XH, Lei TD, Xu YF, Jiang FS, Wang HG, Li LH (2007) A intervarietal genetic map and QTL analysis for yield traits in wheat. Mol Breeding 20:67–178
Loiselle BA, Sork VL, Nason J, Graham C (1995) Spatial genetic structure of a tropical understory shrub, Psychotria officinalis (Rubiaceae). Am J Bot 82:1420–1425
Marza F, Bai GH, Carver BF, Zhou WC (2006) Quantitative trait loci for yield and related traits in the wheat population Ning7840 × Clark. Theor Appl Genet 112:688–698
Myles S, Peiffer J, Brown PJ (2009) Association mapping: critical considerations shift from genotyping to experimental design. Plant Cell 21:2194–2202
Narasimhamoorthy B, Gill BS, Fritz AK, Nelson JC, Brown-Guedira GL (2006) Advanced backcross QTL analysis of a hard winter wheat × synthetic wheat population. Theor Appl Genet 112:787–796
Neumann K, Kobiljski B, Denčić S, Varshney RK, Börner A (2011) Genome-wide association mapping: a case study in bread wheat (Triticum aestivum L.). Mol Breeding 27:37–58
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
Pritchard JK, Rosenberg NA (1999) Use of unlinked genetic markers to detect population stratification in association chain will tend to get stuck moving among very similar studies. Am J Hum Genet 65:220–228
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959
Qian MM, Sun HW, Song CH, Yang XM (1989) Study on evolution of agronomic characters in northern winter wheat region. Chin Seeds 1:3–5
Röder MS, Korzun V, Wendehake K, Plaschke J, Tixier MH, Leroy P, Ganal MW (1998) A microsatellite map of wheat. Genetics 149:2007–2023
Sharp PJ, Chao S, Desai S, Gale MD (1989) The isolation, characterization and application in Triticeae of a set of wheat RFLP probes identifying each homoeologous chromosome arm. Theor Appl Genet 78:342–348
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
Su ZQ, Hao CY, Wang LF, Dong YC, Zhang XY (2011) Identification and development of a functional marker of TaGW2 associated with grain weight in bread wheat (Triticum aestivum L.). Theor Appl Genet 122:211–223
Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ES (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28:286–289
Tian XM (1991) Studies on evolution and its tendency of agronomic character of winter wheat during cultivar alternation in Xinjiang. Acta Agron Sin 17:297–303
Ting SK (1979) Investigation on ways of selecting wheat varieties with a yield over 1,500 jin per mu. Sci Agri Sin 3:8–16
Wang ZL, Cao WX, Dai TB (2001) Genotypic differences in formation of kernel number per spike and analysis of improvement approaches in wheat. Acta Agron Sin 27:236–242
Wang RX, Hai L, Zhang XY, You GX, Yan CS, Xiao SH (2009) QTL mapping for grain filling rate and yield-related traits in RILs of the Chinese winter wheat population Heshangmai × Yu8679. Theor Appl Genet 118:313–325
Wang LF, Ge HM, Hao CY, Dong YS, Zhang XY (2012) Identifying loci influencing 1,000-kernel weight in wheat by microsatellite screening for evidence of selection during breeding. PLoS One 7(2):e29432. doi:10.1371/journal.pone.0029432
Wilson LM, Whitt SR, Ibanez AM, Rocheford TR, Goodman MM, Buckler ES (2004) Dissection of maize kernel composition and starch production by candidate gene association. Plant Cell 16:2719–2733
Yao J, Wang L, Liu L, Zhao C, Zheng Y (2009) Association mapping of agronomic traits on chromosome 2A of wheat. Genetica 137:67–75
Yu JM, Pressoir G, Briggs WH, Bi IV, Yamasaki M, Doebley JF, Mcmullen MD, Gaut B, Nielsen DM, Holland JB, Kresovich S, Buckler ES (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38:203–208
Zhang N, Xu Y, Akash M, McCouch S, Oard JH (2005) Identification of candidate markers associated with agronomic traits in rice using discriminant analysis. Theor Appl Genet 110:721–729
Zhang XY, Tong YP, You GX, Hao CY, Ge HM, Wang LF, Li B, Dong YS, Li ZS (2007) Hitchhiking effect mapping: a new approach for discovering agronomically important genes. Agri Sci China 6:255–264
Zhang LY, Liu DC, Guo XL, Yang WL, Sun JZ, Wang DW, Zhang AM (2010a) Genomic distribution of quantitative trait loci for yield and yield-related traits in common wheat. J Int Plant Biol 52:996–1007
Zhang ZW, Ersoz E, Lai CQ, Fodhunter RJ, Tiwari HK, Gore MA, Bradbury PJ, Yu JM, Arnett DK, Ordovas JM, Buckler ES (2010b) Mixed linear model approach adapted for genome-wide association studies. Nat Genet 42:355–360
Zhu C, Gore M, Buckler E, Yu J (2008) Status and prospects of association mapping in plants. Plant Genome 1:5–20
Acknowledgments
The authors are grateful to HN Zhang, YH Tian, J Lin and YJ Wang for excellent genotyping and phenotyping of the mini core collection. We also gratefully acknowledge help from Prof. Robert A McIntosh, University of Sydney, with English editing. This work was supported by the Chinese Ministry of Science and Technology (2010CB125900) and Chinese Agricultural Research System, Ministry of Agriculture (CARS-3-1-2) and the National High Technology Research and Development Program of China (2006AA10Z1F2).
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D. Zhang and C. Hao contributed equally to this work.
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Zhang, D., Hao, C., Wang, L. et al. Identifying loci influencing grain number by microsatellite screening in bread wheat (Triticum aestivum L.). Planta 236, 1507–1517 (2012). https://doi.org/10.1007/s00425-012-1708-9
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DOI: https://doi.org/10.1007/s00425-012-1708-9