| Rice (Oryza sativa L.) is one of the most important crops, rice varieties with high yield, good eating and nutritional quality is the main objective of breeders. In the present study, one recombinant inbred lines (RILs) population, which were constructed by two indica varieties, JY293 (small grain and high apparent amylose content (AAC)) and M201 (big grain and low AAC), and one association population were used to uncover the genetics of rice grain yield related traits, starch properties and brown rice nutritional qualities. The research results are as follows:(1) Rapid identification of quantitative trait loci (QTLs) for grain weight was carried out by the combination of specific locus amplified fragments sequencing (SLAF-Seq) technology and the linkage mapping. qTGW3.1, qTGW3.2 and qTGW3.3 are corresponding to previous cloned or fine mapped QTLs, GS3, qGL3, and qTGW3.3. According to contribution analysis, we constructed two strategies to produce big size grain varieties, one is to use the major qTGW3.2 alone by crossing with maintenance lines to produce hybrid rice, and the other one is to pyramid the two minor-effect QTLs together.(2) QTL mapping for rice yield related traits was carried out by using a RIL population. According to two years (2012 and 2013) QTL mapping results, we totally detected 37 QTLs, and 14 of them were detected in both years. Four clustered QTLs corresponding to known genes/QTLs (GW2, GS3, qGL3 and qTGW3.2) were revealed on chromosomes 2 and 3, which had pleiotropic effects on grain weight and plant architecture traits. Three new QTLs, qTGW3.0, qGL2.2 and qETN4, were detected in both years.(3) QTL mapping of eating and cooking (ECQ) quality parameters was conducted using the RILs population and two divided Wx-genotype based subpopulations. In the whole RIL population mapping, a total of 29 QTLs were detected, and Wx gene is the major QTL for apparent amylose content (AAC) and most RVA properties. The two subpopulations detected 10 QTLs, four of them (qPRO3.1, qPV9, qHPV9, and qCS7) were also detected in the whole RIL QTL mapping. In addition, A QTL cluster on chromosome 9 for peak viscosity, hot paste viscosity and cool paste viscosity was detectable in both subpopulations, and was close to the isoamylase 3 (ISA3) locus. A QTL cluster for both peak time and pasting temperature on chromosome 6 was near to the starch synthase I (SSI) locus, and was potentially a new QTL with minor effect for peak time and pasting temperature.(4) Genome wide association study (GWAS) of 10 eating and cooking qualities were performed in one original and four derived panels with high quality resequencing data. Using the MLM method, based on the P+K model, we totally detected 29,24,16,17, and 29 QTLs in each of the five panels. Besides Wx gene, there were 12,3, and 2 QTLs (for the same trait) were detected in 2,3, and 4 panels, respectively. One previously detected QTL (chr.11:22240707-22563596) for protein content and one new association QTL (chr.5:7756614-8042699) for peak viscosity (PV), hot paste viscosity (HPV), and peak time (PeT) detected in more than two panels are valuable QTLs for gene cloning. Some of the QTLs are close to starch synthase related genes (SSRGs), such as isoamylase 3 (ISA3) gene, starch synthase â…£-1 (SSIV-1), and ADP-glucose pyrophosphorylase large subunit 2 (AGPL2). The QTL (chr.7:1118122-1967247) for BD detected in whole panel andjaponica panel, and the QTL (chr.7:25312126-26540950) for BD and SB detected in whole panel and indica panel, might be specific gene alleles in japonica or indica panels.(5) GWAS was carried out for polyphenol and their antioxidant capacities with high quality SNPs in the whole, white, and red grain panels. We qualified and quantified 9 and 8 bound phenolic compounds in 32 red and 88 white pericarp accessions, respectively. The phenotype of free phenolic acid content (FPC) in red grain panel is significant higher than that in white grain panel, but the concentration of bound phenolic acid compounds varied in varieties, not in colors. The FPC (45.87 mg GAE/100 g) is similar to bound phenolic acid content (BPC) (48.60 mg GAE/100 g) in white grain panel, but FPC (471.05 mg GAE/100 g) is 7 times of the BPC (61.7mg GAE/100 g) in red grain panel. A total of 30 and 22 QTLs were detected in the whole panel and white grain panel, respectively. No QTL was detected in the red grain panel. Rc is the major QTL detected for FP and their antioxidant capacities in the whole panel. Two new QTLs (chr.2:24392269; chr.9:6670223) detected in the whole population and 2 new QTLs (chr.4: 34120529; chr.11:28947480) in the white grain panel for free phenolic related traits, and one QTL (chr.11:23220681) for ferulic acid detected in two panels. |
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