Identification and characterization of a novel Waxy allele from a Yunnan rice landrace.
Low amylose content (AC) is a desirable trait for rice (Oryza sativa L.) cooking quality and is selected in soft rice breeding. To gain a better understanding of the molecular mechanism controlling AC formation, we screened 83 Yunnan rice landraces in China and identified a rice variety, Haopi, with low AC. Genetic analyses and transgenic experiments revealed that low AC in Haopi was controlled by a novel allele of the Wx locus, Wx(hp), encoding a granule-bound starch synthase (GBSSI). Sequence comparisons of Wx(hp) and Wx(b) alleles (from Nipponbare) showed several nucleotide changes in the upstream regulatory regions (including the promoter, 5'-untranslated region, and first intron 5' splicing junction site). Interestingly, these changes had no obvious effect on the expression level and splicing efficiency of Wx transcripts. In addition, an examination of the coding region revealed that the Wx(hp) allele carries an A-to-G change at nucleotide position +497 from the start codon, resulting in an Asp(165)/Gly(165) substitution. The amino acid substitution had no detectable effects on GBSSI activity in vitro; however, it notably reduced the binding of GBSSI to starch granules, resulting in a reduction of AC in rice seeds. Moreover, three other Yunnan landraces with low AC also carry a nucleotide substitution identical to Haopi at the +497 position of the Wx gene, suggesting common ancestry. Based on the single-nucleotide polymorphism, we have developed a new derived cleaved amplified polymorphic sequence marker for use in breeding practice to manipulate AC in rice endosperm.
Liu
Linglong
L
State Key Laboratory for Crop Genetics & Germplasm Enhancement, Jiangsu Provincial Center of Plant Gene Engineering, Nanjing Agricultural University, Weigang 1, 210095 Nanjing, China.
Ma
Xiaodong
X
Liu
Shijia
S
Zhu
Changlan
C
Jiang
Ling
L
Wang
Yihua
Y
Shen
Yi
Y
Ren
Yulong
Y
Dong
Hui
H
Chen
Liangming
L
Liu
Xi
X
Zhao
Zhigang
Z
Zhai
Huqu
H
Wan
Jianmin
J
D000483:Alleles; D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D000688:Amylose / Q000235:genetics / Q000378:metabolism; D018745:Genome, Plant; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics* / Q000378:metabolism / Q000648:ultrastructure; D010641:Phenotype; D010940:Plant Proteins / Q000235:genetics*; D011110:Polymorphism, Genetic; D012639:Seeds / Q000235:genetics / Q000378:metabolism / Q000648:ultrastructure; D016415:Sequence Alignment; D013213:Starch / Q000378:metabolism; D013214:Starch Synthase / Q000235:genetics*; D014170:Transformation, Genetic
D010940:Plant Proteins; C060756:waxy protein, plant; D013213:Starch; D000688:Amylose; D013214:Starch Synthase