Improvement of marker-based predictability of Apparent Amylose Content in japonica rice through GBSSI allele mining

被引:72
作者
Biselli, Chiara [1 ,2 ]
Cavalluzzo, Daniela [1 ]
Perrini, Rosaria [1 ]
Gianinetti, Alberto [2 ]
Bagnaresi, Paolo [2 ]
Urso, Simona [2 ]
Orasen, Gabriele [1 ]
Desiderio, Francesca [2 ]
Lupotto, Elisabetta [3 ]
Cattivelli, Luigi [2 ]
Vale, Giampiero [1 ,2 ]
机构
[1] CRA Consiglio Ric & Sperimentaz Agr, Rice Res Unit, I-13100 Vercelli, Italy
[2] CRA Consiglio Ric & Sperimentaz Agr, Genom Res Ctr, I-29017 Fiorenzuola Darda, Piacenza, Italy
[3] CRA Consiglio Ric & Sperimentaz Agr, Dept Plant Biol & Crop Prod, Rome, Italy
关键词
Apparent amylose content; Grain shape characters; Marker-Assisted Selection (MAS); Molecular markers; Re-sequencing; Rice (Oryza sativa L.); SINGLE NUCLEOTIDE POLYMORPHISMS; BOUND STARCH SYNTHASE; WAXY GENE; MOLECULAR CHARACTERIZATION; GRAIN QUALITY; SPLICE SITES; TEMPERATURE; ENDOSPERM; SEQUENCE; LOCUS;
D O I
10.1186/1939-8433-7-1
中图分类号
S3 [农学(农艺学)];
学科分类号
0901 ;
摘要
Background: Apparent Amylose Content (AAC), regulated by the Waxy gene, represents the key determinant of rice cooking properties. In occidental countries high AAC rice represents the most requested market class but the availability of molecular markers allowing specific selection of high AAC varieties is limited. Results: In this study, the effectiveness of available molecular markers in predicting AAC was evaluated in a collection of 127 rice accessions (125 japonica ssp. and 2 indica ssp.) characterized by AAC values from glutinous to 26%. The analyses highlighted the presence of several different allelic patterns identifiable by a few molecular markers, and two of them, i.e., the SNPs at intron1 and exon 6, were able to explain a maximum of 79.5% of AAC variation. However, the available molecular markers haplotypes did not provide tools for predicting accessions with AAC higher than 24.5%. To identify additional polymorphisms, the re-sequencing of the Waxy gene and 1kbp of the putative upstream regulatory region was performed in 21 genotypes representing all the AAC classes identified. Several previously un-characterized SNPs were identified and four of them were used to develop dCAPS markers. Conclusions: The addition of the SNPs newly identified slightly increased the AAC explained variation and allowed the identification of a haplotype almost unequivocally associated to AAC higher than 24.5%. Haplotypes at the waxy locus were also associated to grain length and length/width (L/W) ratio. In particular, the SNP at the first intron, which identifies the Wx(a) and Wx(b) alleles, was associated with differences in the width of the grain, the L/W ratio and the length of the kernel, most likely as a result of human selection.
引用
收藏
页数:18
相关论文
共 53 条
  • [1] EFFECT OF ENVIRONMENTAL-TEMPERATURE AT THE MILKY STAGE ON AMYLOSE CONTENT AND FINE-STRUCTURE OF AMYLOPECTIN OF WAXY AND NONWAXY ENDOSPERM STARCHES OF RICE (ORYZA-SATIVA-L)
    ASAOKA, M
    OKUNO, K
    FUWA, H
    [J]. AGRICULTURAL AND BIOLOGICAL CHEMISTRY, 1985, 49 (02): : 373 - 379
  • [2] 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
  • [3] Nucleotide diversity in starch synthase IIa and validation of single nucleotide polymorphisms in relation to starch gelatinization temperature and other physicochemical properties in rice (Oryza sativa L.)
    Bao, J. S.
    Corke, H.
    Sun, M.
    [J]. THEORETICAL AND APPLIED GENETICS, 2006, 113 (07) : 1171 - 1183
  • [4] BENNETT GL, 1980, GENETICS, V94, P763
  • [5] An improved method for using a microsatellite in the rice waxy gene to determine amylose class
    Bergman, CJ
    Delgado, JT
    McClung, AM
    Fjellstrom, RG
    [J]. CEREAL CHEMISTRY, 2001, 78 (03) : 257 - 260
  • [6] 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
  • [7] A microsatellite sequence closely linked to the Waxy gene of Oryza sativa
    Bligh, HFJ
    Till, RI
    Jones, CA
    [J]. EUPHYTICA, 1995, 86 (02) : 83 - 85
  • [8] Characterization of an Italian rice germplasm collection with genetic markers useful for breeding to improve eating and cooking quality
    Caffagni, A.
    Albertazzi, G.
    Gavina, G.
    Ravaglia, S.
    Gianinetti, A.
    Pecchioni, N.
    Milc, J.
    [J]. EUPHYTICA, 2013, 194 (03) : 383 - 399
  • [9] Aberrant splicing of intron 1 leads to the heterogeneous 5′ UTR and decreased expression of waxy gene in rice cultivars of intermediate amylose content
    Cai, XL
    Wang, ZY
    Xing, YY
    Zhang, JL
    Hong, MM
    [J]. PLANT JOURNAL, 1998, 14 (04) : 459 - 465
  • [10] Waxy gene haplotypes:: Associations with apparent amylose content and the effect by the environment in an international rice germplasm collection
    Chen, Ming-Hsuan
    Bergman, Christine
    Pinson, Shannon
    Fjellstrom, Robert
    [J]. JOURNAL OF CEREAL SCIENCE, 2008, 47 (03) : 536 - 545