PJB-2018-1587
Development of functional markers for quantitative trait locus underlying rice quality components
Ting Mao, Xu Li, Zhengjin Xu, Jiayu Wang, Liang Tang, Hai Xu, Shukun Jiang, Zhan Zhang and Zhenyu Li
Abstract
Three locus (GS3, Chalk5 and Wx) controlling grain size, grain chalkiness and amylose content (AC) have been cloned and can be used to improve rice quality by molecular marker-assisted selection (MAS). At present, identification of the above-mentioned alleles need DNA sequencing or restriction enzyme digestion, which were laborious, time-consuming tasks. Developing functional markers harboring the advantage of rapid, simple and low cost will contribute to rice quality improvement by MAS. Tetra-primer ARMS-PCR technology is an economical method for single nucleotide polymorphisms (SNP) scoring, however, its utilization is limited due to low amplification efficiency and inaccuracy extension caused by distinct melting temperature (Tm) difference existing between four primers in one PCR system. In this paper, we developed a set of functional markers using tetra-primer ARMS-PCR technology, and we also put forward corresponding solving schemes on low amplification efficiency and inaccuracy extension caused by Tm difference. The results showed that five markers were developed through adjusting the location of deliberate mismatch bases introduced, three markers (GS3ac-ARMS, Chalk5tc-ARMS, Waxygt-ARMS) could identify different alleles for each loci holding the advantage of rapid, simple and low cost. Further, we analyzed the alleles distribution on rice varieties derived from Northeast China. All of these works could provide foundations for rice quality improvement utilizing the suitable genes (QTLs) by MAS.
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