Abstract
Rice seed storage protein (SSP) is an important source of nutrition and energy. Understanding the genetic basis of SSP content and mining favorable alleles that control it will be helpful for breeding new improved cultivars. An association analysis for SSP content was performed to identify underlying genes using 527 diverse Oryza sativa accessions grown in two environments. We identified more than 107 associations for five different traits, including the contents of albumin (Alb), globulin (Glo), prolamin (Pro), glutelin (Glu), and total SSP (Total). A total of 28 associations were located at previously reported QTLs or intervals. A lead SNP sf0709447538, associated for Glu content in the indica subpopulation in 2015, was further validated in near isogenic lines NIL(Zhenshan97) and NIL(Delong208), and the Glu phenotype had significantly difference between two NILs. The association region could be target for map-based cloning of the candidate genes. There were 13 associations in regions close to grain-quality-related genes; five lead single nucleotide polymorphisms (SNPs) were located less than 20 kb upstream from grain-quality-related genes (PG5a, Wx, AGPS2a, RP6, and, RM1). Several starch-metabolism-related genes (AGPS2a, OsACS6, PUL, GBSSII, and ISA2) were also associated with SSP content. We identified favorable alleles of functional candidate genes, such as RP6, RM1, Wx, and other four candidate genes by haplotype analysis and expression pattern. Genotypes of RP6 and RM1 with higher Pro were not identified in japonica and exhibited much higher expression levels in indica group. The lead SNP sf0601764762, repeatedly detected for Alb content in 2 years in the whole association population, was located in the Wx locus that controls the synthesis of amylose. And Alb content was significantly and negatively correlated with amylose content and the level of 2.3 kb Wx pre-mRNA examined in this study. The associations or candidate genes identified would provide new insights into the genetic basis of SSP content that will help in developing rice cultivars with improved grain nutritional quality through marker-assisted breeding.
Highlights
Rice is one of the major staple cereal foods and is an important source of total protein in human food
The results shown here promote our understanding of the genetic basis of the storage protein groups, should be of use for breeders attempting to improve nutritional quality by means of marker assisted selection
Glu accounted for approximately 80% of total seed storage protein (SSP); Alb and Pro each accounted for about 5%; and Glo accounted for about 10% (Figure 1F)
Summary
Rice is one of the major staple cereal foods and is an important source of total protein in human food. The SSP in rice can be classified into four fractions: albumin, globulin, prolamin, and glutelin, according to differences in solubility. Glutelin encoded by 15 genes accounts for as much as 80% of the total SSPs and is concentrated in the milled fraction, whereas prolamin, the most evenly distributed protein, accounts for less than 5% (Yamagata et al, 1982). Based on the molecular mass, prolamins classified into three groups: 10 kDa prolamin (RP10), 13 kDa prolamin (RM1, RM2, RM4, and RM9), and 16 kDa prolamin (RP16) (Yamagata et al, 1982; Kawakatsu et al, 2008) Both albumin and globulin are concentrated in the bran and polishing during milling removes a major portion of these proteins (Shewry, 2007). Emphasis in rice breeding should be on the concentration, and on the quality of rice protein
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