Parama Praphasanobol, Putut Rakhmad Purnama, Supaporn Junbuathong, Somsong Chotechuen, Peerapon Moung-Ngam, Waraluk Kasettranan, Chanita Paliyavuth, Luca Comai, Monnat Pongpanich, Teerapong Buaboocha, Supachitra Chadchawan

Plants (Basel); 2023 Sep 17; 12(18):3290. doi: 10.3390/plants12183290.

Figure: Manhattan plot of SNPs associated with the AAC trait with the most significant SNPs on chromosomes 1, 6, and 11.

Abstract

Rice (Oryza sativa L.) is the main source of energy for humans and a staple food of high cultural significance for much of the world's population. Rice with highly resistant starch (RS) is beneficial for health and can reduce the risk of disease, especially type II diabetes. The identification of loci affecting starch properties will facilitate breeding of high-quality and health-supportive rice. A genome-wide association study (GWAS) of 230 rice cultivars was used to identify candidate loci affecting starch properties. The apparent amylose content (AAC) among rice cultivars ranged from 7.04 to 33.06%, and the AAC was positively correlated with RS (R² = 0.94) and negatively correlated with rapidly available glucose (RAG) (R² = -0.73). Three loci responsible for starch properties were detected on chromosomes 1, 6, and 11. On chromosome 6, the most significant SNP corresponded to LOC_Os06g04200 which encodes granule-bound starch synthase I (GBSSI) or starch synthase. Two novel loci associated with starch traits were LOC_Os01g65810 and LOC_Os11g01580, which encode an unknown protein and a sodium/calcium exchanger, respectively. The markers associated with GBSSI and LOC_Os11g01580 were tested in two independent sets of rice populations to confirm their effect on starch properties. The identification of genes associated with starch traits will further the understanding of the molecular mechanisms affecting starch in rice and may be useful in the selection of rice varieties with improved starch.

See https://pubmed.ncbi.nlm.nih.gov/37765454/

Figure 4. Manhattan plot (left) displaying the single nucleotide polymorphisms (SNPs) in a population of 230 rice cultivars associated with the following starch traits: (A) AAC, (B) RAG, (C) SAG, (D) RS, (E) HI, and (F) GI. The locations of SNPs on the chromosome and the association test (−log₁₀(p)) are plotted on the x-axis and y-axis, respectively. The red line indicates the Bonferroni correction at p < 0.05. The chart (right) presents the quantile–quantile (Q–Q) plot of the observed and expected p-values from the association analyses.