Analysis of a single nucleotide polymorphism that controls the cooking quality of rice using a non-gel based assay

被引:8
作者
Bormans, CA
Rhodes, RB
Kephart, DD
McClung, AM
Park, WD [1 ]
机构
[1] Texas A&M Univ, Dept Biochem & Biophys, Borlaug Ctr So Crop Improvement, College Stn, TX 77843 USA
[2] Promega Corp, Madison, WI 53711 USA
[3] USDA ARS, Beaumont, TX 77713 USA
关键词
amylose; granule-bound starch synthase; READIT (TM) assay; single-nucleotide polymorphism; waxy gene;
D O I
10.1023/A:1020883827053
中图分类号
S3 [农学(农艺学)];
学科分类号
0901 ;
摘要
The waxy gene encoding granule-bound starch synthase (GBSS) is responsible for the synthesis of amylose in developing grain. Recent work has shown that a G-T polymorphism in the leader intron 5' splice site of GBSS plays a key role in determining the cooking and processing quality of rice. Cultivars with sequence AGGTATA at this location splice GBSS pre-mRNA efficiently and produce relatively large amounts of amylose. These varieties generally a have firm texture when cooked and the grains remain separate. In contrast, GBSS pre-mRNA splicing is temperature sensitive and generally less efficient in cultivars with the sequence AGTTATA. As a result, these cultivars generally have lower amylose content and produce soft and sticky cooked rice. We have used the READIT(TM) assay, a non-gel based assay that uses the ability of DNA polymerase to perform pyrophosphoralysis, the reverse of DNA polymerization, to screen the critical G-T polymorphism in more than 750 samples from U. S. and Asian germplasm. We observed complete concordance between the results obtained using DNA sequencing or restriction enzyme digestion and the READIT(TM) assay. It also gave accurate results with both heterozygous plants and with complex mixtures as might result when grain from advanced generation plants is pooled to obtain larger samples.
引用
收藏
页码:261 / 267
页数:7
相关论文
共 10 条
  • [1] Microsatellites and a single-nucleotide polymorphism differentiate apparent amylose classes in an extended pedigree of US rice germ plasm
    Ayres, NM
    McClung, AM
    Larkin, PD
    Bligh, HFJ
    Jones, CA
    Park, WD
    [J]. THEORETICAL AND APPLIED GENETICS, 1997, 94 (6-7) : 773 - 781
  • [2] Use of alternate splice sites in granule-bound starch synthase mRNA from low-amylose rice varieties
    Bligh, HFJ
    Larkin, PD
    Roach, PS
    Jones, CA
    Fu, HY
    Park, WD
    [J]. PLANT MOLECULAR BIOLOGY, 1998, 38 (03) : 407 - 415
  • [3] Single-nucleotide polymorphism identification assays using a thermostable DNA polymerase and delayed extraction MALDI-TOF mass spectrometry
    Haff, LA
    Smirnov, IP
    [J]. GENOME RESEARCH, 1997, 7 (04): : 378 - 388
  • [4] Juliano B. O., 1985, RICE CHEM TECHNOLOGY
  • [5] Transcript accumulation and utilization of alternate and non-consensus splice sites in rice granule-bound starch synthase are temperature-sensitive and controlled by a single-nucleotide polymorphism
    Larkin, PD
    Park, WD
    [J]. PLANT MOLECULAR BIOLOGY, 1999, 40 (04) : 719 - 727
  • [6] High-throughput genotyping for a polymorphism linked to soybean cyst nematode resistance gene Rhg4 by using Taqman™ probes
    Meksem, K
    Ruben, E
    Hyten, DL
    Schmidt, ME
    Lightfoot, DA
    [J]. MOLECULAR BREEDING, 2001, 7 (01) : 63 - 71
  • [7] Fine mapping of the Co-4 locus of common bean reveals a resistance gene candidate, COK-4, that encodes for a protein kinase
    Melotto, M
    Kelly, JD
    [J]. THEORETICAL AND APPLIED GENETICS, 2001, 103 (04) : 508 - 517
  • [9] Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp mays L.)
    Tenaillon, MI
    Sawkins, MC
    Long, AD
    Gaut, RL
    Doebley, JF
    Gaut, BS
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2001, 98 (16) : 9161 - 9166
  • [10] Multicolor molecular beacons for allele discrimination
    Tyagi, S
    Bratu, DP
    Kramer, FR
    [J]. NATURE BIOTECHNOLOGY, 1998, 16 (01) : 49 - 53