SNP identification and allelic-specific PCR markers development for TaGW2, a gene linked to wheat kernel weight

Theoretical and Applied Genetics

Volumn 125, Issue 5, 2012, Pages 1057-1068

  Yang, Zibo ^a   Bai, Zhiyuan ^a   Li, Xiaolin ^a   Wang, Pei ^a   Wu, Qingxia ^a   Yang, Lin ^a   Li, Liqun ^a   Li, Xuejun ^a  

^a NORTHWEST A F UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ASSOCIATION ANALYSIS; BREAD WHEAT; CHINESE SPRINGS; CLONING AND SEQUENCING; CODING SEQUENCES; FULL-LENGTH CDNA; FUNCTION DOMAIN; KERNEL SIZE; MUTATED ALLELES; ORTHOLOGOUS GENES; PCR MARKERS; PROTEIN SEQUENCES; SDS-PAGE; SINGLE-NUCLEOTIDE POLYMORPHISMS; SPLICE SITE; TRITICUM AESTIVUM; WHEAT KERNELS; WILD TYPES;

AMINO ACIDS; DNA SEQUENCES; GENETIC ENGINEERING; GRAIN (AGRICULTURAL PRODUCT);

GENES;

PLANT DNA;

ALLELE; AMINO ACID SEQUENCE; ARTICLE; CHROMOSOME MAP; GENETIC MARKER; GENETICS; GENOTYPE; GROWTH, DEVELOPMENT AND AGING; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHENOTYPE; PLANT CHROMOSOME; PLANT GENE; PLANT SEED; POLYACRYLAMIDE GEL ELECTROPHORESIS; POLYMERASE CHAIN REACTION; SEQUENCE HOMOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM; WHEAT;

ALLELES; AMINO ACID SEQUENCE; BASE SEQUENCE; CHROMOSOME MAPPING; CHROMOSOMES, PLANT; DNA, PLANT; ELECTROPHORESIS, POLYACRYLAMIDE GEL; GENES, PLANT; GENETIC MARKERS; GENOTYPE; MOLECULAR SEQUENCE DATA; PHENOTYPE; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; SEEDS; SEQUENCE HOMOLOGY, AMINO ACID; SEQUENCE HOMOLOGY, NUCLEIC ACID; TRITICUM;

TRITICUM AESTIVUM;

EID: 84865584531     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-012-1895-6     Document Type: Article

References (52)

1. Ahn S, Anderson JA, Sorrells ME, Tanksley SD (1993) Homoeologous relationships of rice, wheat and maize chromosomes. Mol Gen Genet 241: 483-490.
2. Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9: 208-218.
3. Börner A, Schumann E, Fürste A, Cöster H, Leithold B, Röder MS, Weber E (2002) Mapping of quantitative trait loci determining agronomic important characters in hexaploid wheat (Triticum aestivum L.). Theor Appl Genet 105: 921-936.
4. Bornstein P, McKay J, Morishima JK, Devarayalu S, Gelinas RE, Oprian DD, Molday RS (1987) Regulatory elements in the first intron contribute to transcriptional control of the human αl(I) collagen gene. Proc Natl Acad Sci USA 84: 8869-8873.
5. Breseghello F, Sorrells ME (2006) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172: 1165-1177.
6. Breseghello F, Sorrells ME (2007) QTL analysis of kernel size and shape in two hexaploid wheat mapping population. Field Crops Res 101: 172-179.
7. Chen DH, Ronald PC (1999) A rapid DNA minipreparation method suitable for AFLP and other PCR applications. Plant Mol Biol Rep 17: 53-57.
8. de Roos A (2007) Conserved intron positions in ancient protein modules. Biol Direct 2: 7.
9. Dholakia BB, Ammiraju JSS, Singh H, Lagu MD, Röder MS, Rao VS, Dhaliwal HS, Ranjekar PK, Gupta VS (2003) Molecular marker analysis of kernel size and shape in bread wheat. Plant Breed 122: 392-395.
10. Distelfeld A, Uauy C, Olmos S, Schlatter A, Dubcovsky J, Fahima T (2004) Microcolinearity between a 2-cM region encompassing the kernel protein content locus Gpc-6B1 on wheat chromosome 6B and a 350-kb region on rice chromosome 2. Funct Integr Genomics 4: 59-66.
11. Fan C, Xing Y, Mao H, Lu T, Han B, Xu C, Li X, Zhang Q (2006) GS3, a major QTL for kernel length and weight and minor QTL for kernel width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet 112: 1164-1171.
12. Fedorov A, Merican AF, Gilbert W (2002) Large-scale comparison of intron positions among animal, plant, and fungal genes. Proc Natl Acad Sci USA 99: 16128-16133.
13. Flavell RB, Bennett MD, Smith JB, Smith DB (1974) Genome size and proportion of repeated nucleotide sequence DNA in plant. Biochem Genet 12: 257-269.
14. Fu D, Uauy C, Distelfeld A, Blechl A, Epstein L, Chen X, Sela H, Fahima T, Dubcovsky J (2009) A kinase-START gene confers temperature-dependent resistance to wheat stripe rust. Science 323: 1357-1360.
15. Gale MD, Devos KM (1998) Comparative genetics in the grasses. Proc Natl Acad Sci USA 95: 1971-1974.
16. Gegas VC, Nazari A, Griffiths S, Simmonds J, Fish L, Orford S, Sayers L, Doonan JH, Snape JW (2010) A genetic framework for kernel size and shape variation in wheat. Plant Cell 22: 1046-1056.
17. Groos C, Robert N, Bervas E, Charmet G (2003) Genetic analysis of kernel protein-content, kernel yield and thousand-kernel weight in bread wheat. Theor Appl Genet 106: 1032-1040.
18. Hayashi K, Hashimoto N, Daigen M, Ashikawa I (2004) Development of PCR-based SNP markers for rice blast resistance genes at the Piz locus. Theor Appl Genet 108: 1212-1220.
19. Hayden MJ, Tabone T, Mather DE (2009) Development and assessment of simple PCR markers for SNP genotyping in barley. Theor Appl Genet 119: 939-951.
20. Jenkins S, Gibson N (2002) High-throughput SNP genotyping. Comp Funct Genom 3: 57-66.
21. Jeong SC, Maroof MAS (2004) Detection and genotyping of SNPs tightly linked to two disease resistance loci, Rsv1 and Rsv3, of soybean. Plant Breed 123: 305-310.
22. Kojima S, Takahashi Y, Kobayashi Y, Monna L, Sasaki T, Araki T, Yano M (2002) Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions. Plant Cell Physiol 43: 1096-1105.
23. Kumar N, Kulwal PL, Gaur A, Tyagi AK, Khurana JP, Khurana P, Balyan HS, Gupta PK (2006) QTL analysis for kernel weight in common wheat. Euphytica 151: 135-144.
24. Kwok P (2001) Methods for genotyping single nucleotide polymorphisms. Annu Rev Genomics Hum Genet 2: 235-258.
25. Lavett DK (1984) A model for transcriptional regulation based upon homology between introns and promoter regions and secondary structure in the promoter regions: the human globins. J Theor Biol 107: 1-36.
26. Li SS, Jia JZ, Wei XY, Zhang XC, Li LZ, Chen HM, Fan YD, Sun HY, Zhao XH, Lei TD et al (2007) A intervarietal genetic map and QTL analysis for yield traits in wheat. Mol Breed 20: 167-178.
27. Li Q, Yang XH, Bai GH, Warburton ML, Mahuku G, Gore M, Dai JR, Li JS, Yan JB (2010) Cloning and characterization of a putative GS3 ortholog involved in maize kernel development. Theor Appl Genet 120: 753-763.
28. Li YB, Fan CC, Xing YZ, Jiang YH, Luo LJ, Sun L, Shao D, Xu CJ, Li XH, Xiao JH, He YQ, Zhang QF (2011) Natural variation in GS5 plays an important role in regulating kernel size and yield in rice. Nat Genet 43: 1266-1269.
29. McCartney CA, Somers DJ, Humphreys DJ, Lukow O (2005) Mapping quantitative trait loci controlling agronomic traits in the spring wheat cross RL 4452 × AC 'Domain'. Genome 48: 870-883.
30. Nabila Y, Payorm S, Robert D, Dudler Robert, Keller Beat (2004) Genome analysis at different ploidy levels allows cloning of t he powdery mildew resistance gene Pm3b from hexaploid wheat. Plant J 37: 528-538.
31. Newton CR, Graham A, Heptinstall LE (1989) Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucl Acids Res 17: 2503-2516.
32. Quarrie SA, Steed A, Calestani C, Semikhodskii A, Lebreton C, Chinoy 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 kernel yield across a range of environments. Theor Appl Genet 110: 865-880.
33. Ramya P, Chaubal A, Kulkarni K, Gupta L, Kadoo N, Dhaliwal HS, Chhuneja P, Lagu M, Gupta V (2010) QTL mapping of 1000-kernel weight, kernel length, and kernel width in bread wheat (Triticum aestivum L.). J Appl Genet 51: 421-429.
34. Semagn K, Bjornstad A, Ndjiondjop M (2006) An overview of molecular marker methods for plants. Afr J Biotechnol 5: 2540-2568.
35. Shomura A, Lzawa T, Ebana K, Ebitani T, Kanegae H, Konishi S, Yano M (2008) Deletion in a gene associated with kernel size increased yields during rice domestication. Nat Genet 40: 1023-1028.
36. Snape JW, Foulkes MJ, Simmonds J, Leverington M, Fish LJ, Wang YK, Ciavarrella M (2007) Dissection gene X environmental effects on wheat yields via QTL and physiological analysis. Euphytica 154: 401-408.
37. Song XJ, Huang W, Shi M, Zhu MZ, Lin HX (2007) A QTL for rice kernel width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet 39: 623-630.
38. Sorrells ME, La Rota M, Bermudez-Kandianis CE, Greene RA, Kantety R, Munkvold JD, Miftahudin Mahmoud A, Ma X, Gustafson PJ et al (2003) Comparative DNA sequence analysis of wheat and rice genomes. Genome Res 13: 1818-1827.
39. Su ZQ, Hao CY, Wang LF, Dong YC, Zhang XY (2011) Identification and development of a functional marker of TaGW2 associated with kernel weight in bread wheat (Triticum aestivum L.). Theor Appl Genet 122: 211-223.
40. Sun XY, Wu K, Zhao Y, Kong FM, Han GZ, Jiang HM, Huang XJ, Li RJ, Wang HG, Li SS (2009) QTL analysis of kernel shape and weight using recombinant inbred families in wheat. Euphytica 165: 615-624.
41. Takano-Kai N, Jiang H, Kubo T, Sweeney M, Matsumoto T, Kanamori H, Padhukasahasram B, Bustamante C, Yoshimura A, Doi K, McCouch S (2009) Evolutionary history of GS3, a gene conferring kernel length in rice. Genetics 182: 1323-1334.
42. Varshney RK, Sigmund R, Börner A, Korzun V, Stein N, Sorrells ME, Langridge P, Graner A (2005) Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice. Plant Sci 168: 195-202.
43. Wang ET, Wang JJ, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH (2008) Control of rice kernel filling and yield by a gene with a potential signature of domestication. Nat Genet 40: 1370-1374.
44. Wang CR, Chen S, Yu S (2011a) Functional markers developed from multiple loci in GS3 for fine marker-assisted selection of grain length in rice. Theor Appl Genet 122: 905-913.
45. Wang SW, Yang JH, Zhang MF (2011b) Developments of functional markers for Fom-2-mediated fusarium wilt resistance based on single nucleotide polymorphism in melon (Cucumis melo L.). Mol Breed 27: 385-393.
46. Weng JF, Gu SH, Wan XY, Gao H, Guo T, Su N, Lei CL, Zhang X, Cheng ZJ, Guo XP, Wang JL, Jiang L, Zhai HQ, Wan JM (2008) Isolation and initial characterization of GW5, a major QTL associated with rice kernel width and weight. Cell Res 18: 1199-1209.
47. Xu JY, Xue QZ, Luo LJ, Li ZK (2002) Genetic dissection of kernel weight and its related traits in rice (Oryza sativa L.). Chin J Rice Sci 16: 6-10 (in Chinese with an English abstract).
48. Xue WY, Xing YZ, Weng XY, Zhao Y, Tang WJ, Wang L, Zhou HJ, Yu SB, Xu CG, Li XH, Zhang QF (2008) Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet 40: 761-767.
49. Yan L, Loukoianov A, Tranquilli G, Helguera M, Fahima T, Dubcovsky J (2000) Positional cloning of the wheat vernalization gene VRN1. Proc Natl Acad Sci USA 100: 6263-6268.
50. Yan L, Loukoianov A, Blechl A, Tranquilli G, Ramakrishna W, SanMiguel P, Bennetzen Jeffrey L, Echenique V, Dubcovsky J (2004) The wheat VRN2 gene is a flowering repressor down-regulated by vernalization. Science 303: 1640-1644.
51. Ylä-Herttuala S, Palinski W, Rosenfeld ME, Parthasarathy S, Carew TE, Butler S, Witztum JL, Steinberg D (1989) Evidence for the presence of oxidatively modified low density lipoprotein in atherosclerotic lesions of rabbit and man. J Clin Invest 84: 1086-1095.
52. Zhao XL, Ma W, Gale KR, Lei ZS, He ZH, Sun QX, Xia XC (2007) Identification of SNPs and development of functional markers for LMW-GS genes at Glu-D3 and Glu-B3 loci in bread wheat (Triticum aestivum L.). Mol Breed 20: 223-231.