Identifying loci influencing 1,000-kernel weight in wheat by microsatellite screening for evidence of selection during breeding

PLoS ONE

Volumn 7, Issue 2, 2012, Pages

  Wang, Lanfen ^a   Ge, Hongmei ^a   Hao, Chenyang ^a   Dong, Yushen ^a   Zhang, Xueyong ^a  

^a INSTITUTE OF PLANT PROTECTION   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; GENE FREQUENCY; GENE FUNCTION; GENE IDENTIFICATION; GENE LOCATION; GENE LOCUS; GENETIC ASSOCIATION; GENETIC LINE; GENETIC SCREENING; GENETIC SELECTION; GENOTYPE; GEOGRAPHIC DISTRIBUTION; HEREDITY; LANDRACE; MICROSATELLITE MARKER; NONHUMAN; PHENOTYPIC VARIATION; PLANT BREEDING; PLANT GENE; PLANT YIELD; POPULATION STRUCTURE; SEED KERNEL; SEED WEIGHT; SIMPLE SEQUENCE REPEAT; STATISTICAL MODEL; STRUCTURE ANALYSIS; WHEAT; ALLELE; BREEDING; GENETIC VARIABILITY; GENETICS; PLANT GENOME;

TRITICUM AESTIVUM;

MICROSATELLITE DNA;

ALLELES; BREEDING; GENETIC VARIATION; GENOME, PLANT; MICROSATELLITE REPEATS; TRITICUM;

EID: 84856649156     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0029432     Document Type: Article

References (65)

1. He ZH, Bonjean APA, (2010) Cereals in China D.F., Mexico CIMMYT.
2. Xiao SH, He ZH, (2003) Wheat yield and end use quality improvement in China (Chapter 13). In: Zhuang QS, editors. published by China Agricultural Publish Press In: Chinese wheat improvement and pedigree analysis.
3. Wright SI, Bi IV, Schroeder SG, Yamasaki M, Doebley JF, et al. (2005) The effects of artificial selection on the maize genome. Science 308: 1310-1314.
4. Andolfatto P, (2001) Adaptive hitchhiking effects on genome variability. Curr Opin in Genet Dev 11: 635-641.
5. Schlötterer C, (2003) Hitchhiking mapping - functional genomics from the population genetics perspective. Trend Genet 19: 32-38.
6. Zhang XY, Tong YP, You GX, Hao CY, Ge HM, et al. (2007) Hitchhiking effect mapping: A new approach for discovering agronomically important genes. Agri Sci China 6: 255-264.
7. Flint-Garcia SA, Thornsberry JM, Buckler ES, (2003) Structure of linkage disequilibrium in plants. Ann Rev Plant Biol 54: 357-374.
8. Breseghello F, Sorrells ME, (2006) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172: 1165-1177.
9. Crossa J, Burgueño J, Dreisigacker S, Vargas M, Herrera-Foessel SA, et al. (2007) Association analysis of historical bread wheat germplasm using additive genetic covariance of relatives and population structure. Genetics 177: 1889-1913.
10. Barrero RA, Bellgard M, Zhang XY, (2011) Diverse approaches to achieving grain yield in wheat. Funct Integr Genomics 11: 27-48.
11. Hao CY, Dong YC, Wang LF, You GX, Zhang HN, et al. (2008) Genetic diversity and construction of core collection in Chinese wheat genetic resources. Chinese Sci Bull 53: 1518-1526.
12. Dong YS, Cao YS, Zhang XY, Wang LF, Li LH, et al. (2003) Establishment of candidate core collections in Chinese common wheat germplasm. J Plant Genet Res 4: 1-8.
13. 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 Doi:10.1371/journal.pone.0017279.
14. Wang J, Sun JZ, Liu DC, Yang WL, Wang DW, et al. (2008) Analysis of Pina and Pinb in the mini core collections of Chinese wheat germplasm by ecotilling and identification of a novel Pinb allele. J Cereal Sci 48: 836-842.
15. Guo ZA, Song YX, Zhou RH, Ren ZL, Jia JZ, (2009) Discovery, evaluation and distribution of haplotypes of the wheat Ppd-D1 gene. New Phytol 185: 841-851.
16. Jiang QY, Hou J, Hao CY, Wang LF, Ge HM, et al. (2011) The wheat (T. aestivum) sucrose synthase 2 gene (TaSus2) active in endosperm development is associated with yield traits. Funct Integr Genomics 11: 49-61.
17. Li XP, Zhao XQ, He X, Zhao GY, Li B, et al. (2011) Haplotype analysis of the genes encoding glutamine synthetase chloroplast isoformes and their association with nitrogen-use- and yield-related traits in bred wheat. New Phytol 189: 449-458.
18. 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.
19. Ersoz E, Yu JM, Buckler ES, (2009) Applications of linkage disequilibrium and association mapping in maize. In: Kriz AL, Larkins BA, editors. Biotechnology in Agriculture and Forestry Volume 63, III Springer-Verlag Berlin Heideberg, Germany pp. 173-195 In: Molecular Genetic Approaches to Maize Improvement.
20. Zhuang QS, (2003) Chinese wheat improvement and pedigree analysis. Agricultural Press, Beijing (in Chinese).
21. Yu JM, Pressoir G, Briggs WH, Bi IV, Yamasaki M, et al. (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38: 203-208.
22. 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.
23. Quarrie SA, Quarrie SP, Radosevic R, Rancic D, Kaminska A, et al. (2006) Dissecting a wheat QTL for yield present in a range of environments: from the QTL to candidate genes. J Exp Bot 57: 2627-2637.
24. Cuthbert JL, Somers DJ, Brule-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.
25. Sun XC, Marza F, Ma HX, Carver BF, Bai GH, (2010) Mapping quantitative trait loci for quality factors in an inter-class cross of US and Chinese wheat. Theor Appl Genet 120: 1041-1051.
26. Tsilo TJ, Hareland GA, Simsek S, Chao S, Anderson JA, (2010) Genome mapping of kernel characteristics in hard red spring wheat breeding lines. Theor Appl Genet 121: 717-730.
27. Nordborg M, Weigel D, (2008) Next-generation genetics in plants. Nature 456: 720-723.
28. Yan JB, Shah T, Warburton M, Buckler ES, McMullen MD, et al. (2009) Genetic characterization of a global maize collection using SNP markers. PloS One 4 (12): e8451.
29. Yan JB, Warburton M, Crouch J, (2011) Association mapping for enhancing maize (Zea mays L.) genetic improvement. Crop Sci 51: 433-449.
30. Horvath A, Didier A, Koenig J, Exbrayat F, Charmet G, et al. (2009) Analysis of diversity and linkage disequilibrium along chromosome 3B of bread wheat (Triticum aestivum L.). Theor Appl Genet 119: 1523-1537.
31. Doebley JF, Gaut BS, Smith BD, (2006) The molecular genetics of crop domestication. Cell 127: 1309-1321.
32. Mackay TFC, Stone EA, Ayroles JF, (2009) The genetics of quantitative traits: challenges and prospects. Nat Rev Genet 10: 565-577.
33. Ott A, Trautschold B, Sandhu D, (2011) Using microsatellites to understand the physical distribution of recombination on soybean chromosomes. PLoS ONE 6 (7): e22306 doi:10.1371/journal.pone.0022306.
34. Gupta PK, Rustig S, Kumar N, (2006) Genetic and molecular basis of grain size and grain number and its relevance to grain productivity in higher plants. Genome 49: 565-571.
35. Sun XY, Wu K, Zhao Y, Kong FM, Han GZ, et al. (2008) QTL analysis of kernel shape and weight using recombinant inbred lines in wheat. Euphytica 165: 615-624.
36. Wang RX, Hai L, Zhang XY, You GX, Yan CX, et al. (2009) QTL mapping for grain filling rate and yield-related traits in RILs of the Chinese winter wheat population Heshangmai 3× Yu8679. Theor Appl Genet 118: 313-325.
37. Groos C, Robert N, Bervas E, Charmet G, (2003) Genetic analysis of grain protein-content, grain yield and thousand-kernel weight in bread wheat. Theor Appl Genet 106: 1032-1040.
38. Snape JW, Foulkes MJ, Simmonds J, Leverington M, Fish LJ, et al. (2007) Dissecting gene×environmental effects on wheat yields via QTL and physiological analysis. Euphytica 154: 401-408.
39. Röder MS, Huang XQ, Börner A, (2008) Fine mapping of the region on wheat chromosome 7D controlling grain weight. Funct Integr Genomic 8: 79-86.
40. Koebner RMD, Summers RW, (2003) 21st century wheat breeding: Plot selection or plate detection. Trends Biotechnol 21: 59-63.
41. Heffner EL, Sorrells ME, Jannink JL, (2009) Genomic selection for crop improvement. Crop Sci 49: 1-12.
42. Tester M, Langridge P, (2010) Breeding technologies to increase crop production in a changing world. Science 327: 818-822.
43. Frisch M, Thiemann A, Fu J, Schrag TA, Scholten S, et al. (2010) Transcriptome-based distance measures for grouping of germplasm and prediction of hybrid performance in maize. Theor Appl Genet 120: 709-720.
44. Reynolds MP, Calderini DF, Condon AG, Rajaram S, (2001) Physiological basis of yield gains in wheat associated with the LR19 translocation from Agropyron elongatum. Euphytica 119: 137-141.
45. Glaszmann JC, Kilian B, Upadhyaya HD, Varshney RK, (2010) Accessing genetic diversity for crop improvement. Curr Opin Plant Biol 13: 167-173.
46. Gennaro A, Koebner RMD, Ceoloni C, (2009) A candidate for Lr19, an exotic gene conditioning leaf rust resistance in wheat. Func Integr Genomic 9: 325-334.
47. Wang LF, Balfourier F, Exbrayat-Vinson F, Hao CY, Dong YS, et al. (2007) Comparison of genetic diversity level between European and East-Asian wheat collections using SSR markers. Sci Agric Sin 40: 2667-2678.
48. Song XJ, Huang W, Shi M, Zhu MZ, Lin HX, (2007) A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet 39: 623-630.
49. Xue WY, Xin YZ, Wen XY, Zhao Y, Tang WJ, et al. (2008) Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet 40: 761-767.
50. Bernardo R, (1996) Test cross additive and dominance effects in best linear unbiased prediction of maize single-cross performance. Theor Appl Genet 93: 1098-1102.
51. Bernardo R, (1996) Marker-based estimate of identity by descent and alikeness in state among maize inbreds. Theor Appl Genet 93: 262-267.
52. Bernardo R, (1996) Best linear unbiased prediction of maize single-cross performance. Crop Sci 36: 50-56.
53. 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.
54. Röder MS, Korzun V, Wendehake K, Plaschke J, Tixier MH, et al. (1998) A microsatellite map of wheat. Genetics 149: 2007-2023.
55. 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.
56. 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.
57. Pritchard JK, Stephens M, Donnelly P, (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
58. Evanno G, Regnaut S, Goudet J, (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14: 2611-2620.
59. 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.
60. 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.
61. Bradbury PJ, Zhang ZW, Kroon DE, Casstevens TM, Ramdoss Y, et al. (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23: 2633-2635.
62. Zhang ZW, Ersoz E, Lai CQ, Fodhunter RJ, Tiwari HK, et al. (2010) Mixed linear model approach adapted for genome-wide association studies. Nat Genet 42: 355-360.
63. Agrama HA, Eizenga GC, Yan W, (2007) Association mapping of yield and its components in rice cultivars. Mol Breeding 19: 341-356.
64. Ge HM, You GX, Wang LF, Hao CY, Dong YC, et al. (2011) Genome selection sweep and association analysis shed light on future breeding by design in wheat. Crop Sci In press.
65. Quarrie SA, Steed A, Calestani C, Semikhodskii A, Lebreton C, et al. (2005) A high-density genetic map of hexaploid wheat (Triticum aestivum L.) from the cross Chinese Spring×SQ1 and its use to compare QTLs for grain yield across a range of environments. Theor Appl Genet 110: 865-880.