Genome-Wide Association Studies Of Rice Quality Traits And Genetic Dissection Of Quality Genes

As a staple food for more than half the world's population,rice is one of the most important food crops and has significant research value.With people's living quality improving,the main objective of rice breeding has changed from achieving high yield to high yield and high quality.The quality of rice consists of processing quality,appearance quality,cooking and eating quality and nutrition quality.A total of 533 core germplasm materials collected in our lab were constructed to carry out genome wide association study?GWAS?of the 17 main quality traits of rice and further to analyze the genetic mechanism of main quality traits.Based on the genetic mapping of the RILs crossed by ZS97B and Nanyangzhan,we located a major QTL,qGT3,on chromosome3.Then we constructed a near isogenic line?NIL?with the genetic background of ZS97B for fine mapping qGT3.The major results of the research are as follows:1.Genome wide association study was performed to identify loci associated with17 major quality traits:Brown rice rate?BRR?,milled rice ratio?MRR?,head rice rate?HRR?,milled rice length?MRL?,milled rice width?MRW?,length-width ratio?LWR?,chalkiness degree?CD?,chalky rice rate?CRR?,amylose content?AC?,gel consistency?GC?,alkali value?AV?and 7 viscosity coefficients.A total of 212 significant loci were detected for rice quality,and among them were several cloned genes included Waxy,GS3,qSW5/GW5,ALK,etc.These detected loci between indica rice and japonica rice had significant difference,indicating that there was a large genetic differentiation.2.By comparing phenotype data in core germplasm,we found in processing quality,brown rice rate and milled rice rate had a significant positive correlation,but the positive correlation between brown rice rate and head rice rate was not that significant.As for processing quality and appearance quality,there was a significant correlation between them.Milled rice width and head rice rate had a significant positive correlation,but milled rice length and head rice rate had a negative correlation.Grain shape and chalkiness also had a significant positive correlation,especially for grain width and chalkiness.For cooking and eating quality,amylose content and appearance quality had a significant or extremely significant correlation with other eating and cooking quality.Gel consistency had a significant correlation with all viscosity value trait,but alkali value was only significantly correlated with hot viscosity and cool paste viscosity.Among different viscosity coefficients,most of these traits had significant correlations,especially between hot viscosity and cool paste viscosity,while the pasting temperature had a less correlation with other elements of viscosity.3.By comparing the correlation between amylose content,gel consistency and alkali value and viscosity in different amylose content,we found that in low and middle amylose content,amylose content had a significant correlation with viscosity coefficient?r=0.19**⁰.66**?,while in high and waxy amylose content,amylose content had no significant correlation with viscosity?r=0.02⁰.18?.In rice varieties containing high,middle and low amylose content,gel consistency had significant correlation with viscosity coefficient?r=0.18**⁰.78**?,while in waxy rice there was no correlation between them.Viscosity coefficient only had a significant correlation with Alkali value?r=0.36**?.Alkali value had a significant correlation with viscosity coefficient in rice varieties containing different amylose content?r=0.23**⁰.78**?.4.Amylose content as the key element of rice,its synthesis was mainly regulated by OsAPS2,OsAPL1,OsAPL3,OsAPL3,OsSSI,OsSSIIIa,Wx,ALK and OsBEIIb.Based on the information of SNP from Ricevarmap,we conducted the haplotype analysis of Wx,ALK which were important genes affecting quality traits,and compared Wx,ALK with amylose content,gel consistency and alkali value.We observed the phenotype of the three quality traits among different Wx haplotype materials had a significant difference.The four haplotypes of ALK gene had a significant influence on the cooking taste quality,especially on Alkali value.We took an evolutionary analysis and EHH analysis of Wx and ALK,and found that different haplotypes of Wx and ALK might be selected in the breeding process.5.Utilizing linear regression to analyze the relationship between main genes for starch synthesis and three main quality traits of rice?amylose content,gel consistency and alkali value?,6 of them were correlated to 3 major rice quality traits?amylose content,gel consistency and gel temperature?.Wx had a significant correlation with the3 rice quality traits?amylose content,gel consistency and alkali value?,ALK had a significant correlation with gel consistency and gel temperature,OsSSI had a significant correlation with amylose content and gel consistency,and OsAPS2 had a significant correlation with gel consistency.6.In order to dissect the genetic basis of the large grain shape in‘Nanyangzhan',a recombinant inbred line?RIL?population derived from Nanyangzhan?NYZ?and Zhenshan 97B?ZS97?was used to map quantitative trait loci?QTLs?for grain length?GL?,width?GW?,thickness?GT?,length-to-width ratio?LWR?and kilo-grain weight?KGW?.A total of 53 QTLs were detected.Among them,QTLs for GW and GL showed a concentrated distribution on chromosome 2 and chromosome 3,respectively.NYZ,the parent with large grain shape,carried 44 alleles showing positive effects on the studied traits.7.Among the 53 QTLs,a total of 17 QTLs for GL,12 QTLs for GW,8 QTLs for LWR,11 QTLs for KGW and 5 QTLs for GT were detected in 2 years.8.Based on former research,a major QTL for grain thickness was located in the interval between RM545 and RM517 on chromosome 3.NYZ as male parent and ZS97B as recurrent parent were constructed near-isogenic lines.And 255 individuals randomly selected from BC₃F₂ isolated population was made interval linkage mapping and verified the genetic effect of qGT3.qGT3 was located between SSR molecular markers RM517 and RM7576 by Mapmaker mapping,and the genetic variation rate of grain thickness explained by qGT3 in random population was 59.9%.In the near-isogenic lines,the grain thickness phenotype of qGT3^NYZ,a genotype derived from NYZ had an increase of 0.12mm when it was compared with that of qGT3^ZS97B,a genotype derived from ZS97B,9.A large BC₃F₂ segregation population of 3000 individuals was used to identify recombinants.A total of 37 recombinant plants were identified.The recombinant plants were made a progeny testing,finally the qGT3 was located within the range of 38.6kb.