Genetic Dissection of qPCG1 for a Quantitative Trait Locus for Percentage of Chalky Grain in Rice (Oryza sativa L.)

Abstract

Rice is a pivotal cereal crop that provides the staple food for more than half of the world’s population. Along with improvements in the standard of living, people not only pay attention to the grain yield but also to the grain quality. Chalkiness is one of the most important index of grain quality. In this study, qPCG1, a QTL for percentage of chalky grain, was mapped in an interval with a physical distance about 139 kb on chromosome 1 by residual heterozygous line (RHL) method. qPCG1 was incomplete dominant and the additive effect plays a major role and explained 6.8–21.9% of phenotypic variance within the heterogeneous region on chromosome 1. The effect of allele from Zhonghui9308 was decreasing the percentage of chalky grains (PCG). Microscope observation results indicated that there are great differences in the shape, structure and arrangement of starch granule between the chalky part and transparent part. Analysis of starch physicochemical properties showed that the total starch content, amylose content and chain length distribution of amylopectin changed while the protein contents were not apparently affected with the changed chalkiness. qPCG1 had little influence on main agronomic traits and it might be useful in rice breeding for it did not bring negative effect on grain yield while reducing the chalkiness.

Bin-based genome-wide association studies reveal superior alleles for improvement of appearance quality using a 4-way MAGIC population in rice

“…In the last decade, four chalkiness QTLs of qPGWC-7 [2] , qACE9 [7] , qPGWC8 [4] and qPGC1 [8] were fine-mapped in rice. In this investigation, the detected chalkiness QTLs were located in chromosomes 2, 3, 5, 6 and 8.…”

“…varieties, and qACE9 was fine mapped to a 22-kb genomic region on chromosome 9 [7] . Recently, qPCG1 was fine mapped to a 139-kb region on chromosome 1 using a residual heterozygous line [8] . Currently, only one major QTL ( Chalk5 ) encoding a vacuolar H ++ -translocating pyrophosphatase has been cloned as a positive regulator on chromosome 5, and upregulation of Chalk5 expression increased chalkiness in the endosperm [9] .…”

Genetic Mapping and Validation of Quantitative Trait Loci (QTL) for the Grain Appearance and Quality Traits in Rice (Oryza sativa L.) by Using Recombinant Inbred Line (RIL) Population

“…The use of the marker-assisted breeding and the completion of rice genome sequencing have greatly facilitated the discovery and mapping of QTLs and genes for grain dimension. To date, several QTLs were reported for the dynamic shape of rice grain attributed traits in the various genetic background of mapping populations in rice [ 9 , 10 , 27 ]. However, different grain visualization traits regarding paddy, brown, and head rice grain appearance QTL information have not been reported.…”

“…To date, several researchers had identified QTLs that were associated with physical appearance and grain quality traits and were located majorly on chromosomes 1, 3, 4, 5, 6, 7, and 10 [ 5 , 10 , 27 , 36 , 39 ]. In the present study, paddy, brown, and head grain rice appearance trait-related QTLs and polymorphic SSR markers were effectively compared with previously reported QTLs and linkages maps.…”

“…Many of these traits are highly complex governed by quantitative trait loci (QTLs) that are influenced by environmental factors and showed genetic variation to be polygenic in segregating progeny of intervarietal crosses, natural populations as landraces, and among inbred lines. The efficiency of molecular markers for the improvement of grain appearance and nutritional quality traits has been successfully utilized in various genetic backgrounds, mapping populations, and landraces of rice genotypes [ 10 , 23 – 27 ]. Among the various types of molecular markers, SSR, STS, and SNP markers are highly useful when they are located within a gene of interest or in linkage disequilibrium with the gene throughout a population.…”