Rice quality is determined by starch, which is composed of two polysaccharides: amylose and amylopectin. Despite many studies that have attempted to improve rice quality ( Aluko et al., 2004 Zhou et al., 2010 Nelson et al., 2011), the genetic mechanism that controls quality remains ambiguous, and only a few quality-related genes have been identified ( Li et al., 2011, 2014 Wang et al., 2012). However, with the constantly increasing demands from society, rice quality cannot meet the requirements of consumers. Rice yield has increased significantly over the past decade due to the introduction of semi-dwarfness and the exploitation of heterosis. The combined effects of different SNPs of Wx are very important for rice quality breeding. TT-AA-CC and TT-AA-TT had a low AAC and a soft GC. In1T-E圆A-Ex10C and In1T-E圆A-Ex10T were classified as being low AAC type. The combined effects of three SNPs had a significant influence on all ECQs and RVA profile parameters, except for gelatinization temperature. The apparent amylose content (AAC) was mainly controlled by the In1G/T SNP, and rice gel consistency (GC) was regulated by the Ex10C/T SNP. Wx a had a dominant epistasis to SSIII-2 because the effect of SSIII-2 was masked by the massive synthesis of GBSS under Wx a. There was no obvious difference between different SSIII-2 alleles under the same background of Wx a, whereas there was a significant diversity under the same background of Wx b. The results revealed various effects of SSIII-2 on rice quality under different backgrounds of Wx alleles. The genotypes of SSIII-2 and the single nucleotide polymorphisms (SNPs) on intron1, exon6, and exon10 of Wx, and the physicochemical indicators and rapid visco analyzer (RVA) profile characteristics were analyzed. To investigate the effects of Wx and its interaction with SSIII-2 on grain ECQs, a population from a hybrid combination was established as a research material. SSIII-2 (SSIIIa), a member of the soluble starch synthases, is responsible for the synthesis of long chains of amylopectin. The Wx gene encodes a granule-bound starch synthase (GBSS) and plays a key role in determining rice eating and cooking qualities (ECQs).
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