Effects Of Ecological Environment And Genetic Characteristics On Quality And Yield Traits Of Indica And Japonica Hybrid Rice

In this study,a RIL population of F9 generation was established with Japonica super rice variety,Shennong 265(SN265),as female parent and Indica rice,Luhui 99(R99),as male parent.The population was evaluated for 14 qulity traits and 11 yield related traits in four typical rice cultivated areas: the Rice Research Institute of Shenyang Agricultural University(SY,N41°,E123°),the sub base of China National Hybrid Rice R&D Center in Jiangsu Province(JS,N32°,E120°),the Academy of Agricultural Sciences of Sichuan Province(SC,N32°,E104°),and the Agricultural Genomics Institute at Shenzhen(SZ,N22°,E114°)for two growing seasons during 2015–2016.At the same time,10 environmental factors were recorded by portable weather station.In addition,the genetic map of the RIL population was constructed using whole genome resequencing,and assembled the parental genome using the thirdgeneration sequencing combined with second-generation sequencing.Effects of IndicaJaponica specific SNP ratio on yield and quality traits were analyzied.We also conducted the QTL mapping for 15 yield and quality traits using the RIL population and the functions of related candidate genes were analyzed as well.The main results are as follows:1.The average brown rice ratio and milled rice ratio were the highest in SC with 76.51% and 68.86%,respectively,while the lowest in SZ with 72.41% and 65.18%,respectively.The average chalkiness ratio and chalkiness level of the RIL population in JS were 18.26% and 5.20 respectively,both were lower than those in other regions.The average head rice ratio of the RIL population is the highest in JS with 58.81%,while the grain length was the shortset with averagely 5.39 cm and the grain width was the narrowest with averagely 2.43 cm.The amylose and protein content of the RIL population in four regions was ranked as SZ < SC < JS < SY,and SY < SC < JS < SZ,separately.2.The environmental conditions had a stronger effect on head rice ratio,grain length,alkali consumption amylose and protein content.And the affects were dynamic throughout the growth period.For example,the air temperature was negatively correlated with the brown rice ratio before 20 days,but was significantly positively correlated after 20 days.Compared to light and humidity,temperature was more stable and predictable,and night temperature showed a stronger correlation efficiency to cooking quality than day temperature,and the daily temperature range had contrary effects compared to day and night temperature on grain quality.3.The Indica pedigree percentage showed a significant positive correlation to panicle length and grain shape(the ratio of grain length to grain width)and a negative correlation to head rice ratio in all three of the areas.With increasing latitude,the correlation efficiency between indica pedigree percentage and grain shape became larger,and the correlation efficiency of indica pedigree percentage to panicle length and head rice ratio became smaller.In JS,the indica pedigree percentage also has a significant positive correlation to grain number and a significant negative correlation to amylose content.4.We genotyped the RIL population with the whole genome resequencing method,and 1,456,445 SNP were obtained.The genome was further divided into 3,289 bin markers,and the final genetic map distance was 1737.13 cm.A total of 79 QTLs related to 15 agronomic traits were identified,which explained 14.66% of the phenotypic varations averagely.Finemapping of QTLs for eight QTL clusterings on Chr.1,3,4,5,8,9,12 were conducted using the genome assembly of the two parental lines,and eight candidate genes related to rice quality and yield related traits were identified.5.At the same time,we found that with the change of ecological environment,some genes changed functionally: with increasing latitude,the effect of Gn1 a,SDG708,SD1,GW5 became stronger,while the effect of PHYB and DEP1 became weaker,and DTH8 had higher effect in the middle latitudes but the effect became lower at lower and higher latitudes.We also found that gene function also differs with genetic background: the combination of the indica-type gw5 and dep1 alleles can simultaneously improve grain yield and morphological traits.The combination of the japonica-type allele of DEP1,GW5,and indica-type of Gn1 a is associated with the highest grain yield per plant in all three of the areas.6.Moreover,we validated the involvement of one candidate gene,DEP1,in determining panicle length,using CRISPR/Cas9 gene editing.In the RIL population,the average ear length of the materials with mutant genotype(R99)was significantly higher than those of the materials without mutation(SN265 genotype).Through gene editing,ear length of the materials with deletion mutation were significantly higher than those of the control material Sasanishiki and the ear length of the materials with single base mutation was slightly lower than that of the control,but the difference was not significant.