Studies To Protection Mechanism Of Yunnan Rice Landraces And Association Mapping Of Main Agronomic Traits Of Japonica Rice

Rice is the first food crop in China, the staple food of people about2/3is rice in China.With the development and applications of agricultural science and technology, rice yield is themomentum of continuous increment in recent years. However, the genetic basis of varieties ismore and more narrow while breeders are pursuing high-yielding varieties at the same time.Unexpected disaster, such as diseases, pests, etc. may result in incalculable losses and seriousconsequences. It is important to sustainable development of rice production for broadeningthe genetic basis of the varieties and nurturing the complex genetic background, high-yield,high-quality rice varieties. Landraces is the product of long-term choice by natural andman-made in rice production and domestication. Compared with breeding rice, landraces havemore complex genetic background, richer genetic diversity and heterogeneity, and strongeradaptability to the environment. It is an inexhaustible source for breeders to nurture all kindsof varieties which contain many excellent genes such as high yield, high-quality, disease andinsect resistance, stress tolerance etc. Therefore, the effective protection of rice landraces issignificant for sustainable development of rice production in China.By breeders oriented cultivation of generation to generation, bred varieties is a polymerof many excellent yields, good qualities, tolerance, resistance to insect pests and other genes.Bred varieties plays important roles in cereals production and meeting human demand. Bredvarieties are also the core of genetic resources for breeding and improvement. It is importantto discover excellent genes using bred varieties come from different geographical orecological places.In this study, Yunnan rice landraces and japonica varieties from around the world as testmaterial, we studied to protection mechanism of Yunnan rice landraces and associationmapping of main agronomic traits of japonica rice. The main results were summarized asfollows:1. Genetic diversity within populations of16rice landraces and2advanced cultivarsfrom Yunnan were analyzed using20SSR markers. The results showed that the SSR markerpolymorphism within populations for87.5%of rice landraces was higher than that ofadvanced cultivars, while the SSR marker polymorphism within populations for12.5%of landraces was similar with that of advanced cultivars. The number of alleles (Na) and Nei'sgenetic diversity index (He) were showed that81.2%of rice landraces were higher than thoseof advanced cultivars, and18.8%of landraces were same or slightly smaller than advancedcultivars. The He within populations of rice landraces were significantly different, rangedfrom0.0146to0.5117, while HBS-2, MXG-1and MXG-2were the highest with0.4214,0.5117and0.4489, respectively. Compared heterozygosity within rice varieties,87.5%of ricelandraces were significantly higher than improved cultivars. AMOVA showed that1/4geneticdifference among rice landraces were from within populations of rice landraces (P<0.001).Compared the polymorphism, Ne, He and percentage of variation within populations of ricelandraces among20SSR markers, RM333, RM257and RM180were higher than others. Itspeculated that RM333, RM257and RM180were suitable to testing genetic diversity withinrice landraces of Yunnan.2. The phenotypic differences eight pairs of rice landraces from in situ (collected in2007)and ex situ (collected in1980) conservation programs with single-origin were studied. Surveyof7agronomic traits, in addition to the FLW variation range of1980population was greaterthan that of2007population, the remaining six traits showed that the2007population wasmore than1980population. the coefficient of variation showed that JYN, XG, DBN and MXGwere6agronomic traits which2007populations was higher than1980populations, andJGN and LSG was4. Compared the average coefficient of variation between8pairsagronomic characters of rice landraces populations collected in1980and2007, six agronomictraits showed that2007population was higher than1890population except for PE. Theseresults indicate that the phenotypic variation within Yunnan rice landraces of in situconservation programs was higher than that of ex situ conservation programs.3. The genetic structure and diversity of eight singer-origin pairs of rice landraces fromin situ and ex situ conservation programs were studied using20pairs of microsatellitemarkers with high polymorphism. The number of alleles detected in the populations from insitu conservation ranged from43to88with the mean number of alleles per locus rangingfrom2.15to4.40, while the number of alleles detected in the populations from ex situconservation ranged from33to65, and the mean of alleles per locus ranged from1.65to3.25.Compared to the ex situ populations, the number of alleles, the number of specific alleles andthe genetic diversity index showed a significant increase in the in situ populations. Further,the numbers of specific alleles from in situ populations were2.1to5.0times greater than inex situ populations except for rice landrace QTG. An AMOVA showed that thewithin-landrace genetic structure differed significantly between in situ and ex situ conservation treatments with differences exceeding20%. The analysis of genetic similarityreached similar conclusions to those of the AMOVA. Compared with ex situ conservationprograms, the rice landraces under in situ conservation programs had more alleles and highergenetic diversity in Yunnan of China.4. Selected JGN, LSG and QTG with smaller He and MXG with higher He, geneticdifferences were analyzed among20,40,60,80,100populations (randomly selected fromoriginal populations respectively) and original populations.40to60populations can contain98%alleles, and80populations can be detected in all alleles compared the originalpopulations of alleles frequency more than2%. Compared alleles more than5%of originalpopulations,40populations can be detected98%alleles while60can be fully detected.Changes of Ne and He showed that JGN, LSG and QTG with low genetic diversity in thereproduction need40populations to keep Ne and He of original populations while MXG withhigh genetic diversity need80populations. The results showed that the number of populationsto contain genetic integrity in updating was affected by the heterogeneity of the rice landraces.In our study,40～80populations can effectively maintain the genetic integrity of ricelandraces to update using SSR markers.5. Selected2rice landraces of Yunnan with significant differences in genetic diversity,120single plants of populations were planted four times consecutively using a bulk systemgetting seeds. Genetic differences among populations were analyzed. The number of alleleswere significant difference, but this change mainly caused by increasing or disappearing rarealleles with low frequency. The Ne and He changed within the small fluctuations, and nosignificant difference among populations. MXG with high heterogeneity floating range wasbigger than that of LSG, this indicated that rice landraces with high heterogeneity are moreprone to genetic erosion. Similarity coefficient of rice landraces planting4times were0.98and0.99, respectively. Analyzed similarity coefficients among40and80populations(randomly selected from the original populations) and the original populations planted2to4times,40populations of LSG and80populations of MXG were above0.99. It was provedthat40to80populations can be kept genetic similarity of the original groups to planting4times continuously. The result showed that using120individuals to update rice landraces canmaintain the genetic integrity of original populations.40to80individual populations containsimilarity among4times planting. It speculated that used of40to80individual populationscan maintain genetic diversity for repeatedly breeding.6. Association mapping of347japonica varieties using the main agronomic traits andSSR markers. Analysis of Phenotype showed that the agronomic traits and coefficient of variation of varieties from different national or regional were large variations. Coefficient ofvariation of traits from5.46to27.36except for MD, accounted for the average ratios from67.7to149.6%. Analysis of Structure showed that the tested groups divided into three subsets,the variety of similar areas or ecological types classified in same subgroup. Agronomic traitswith2years data and148SSR markers were associated mapping using GLM model ofTASSEL software. LD was detected extensively not only among syntenic markers but alsoamong nonsyntenic ones, while the loci pairs with r2>0.5accounted for only5.83%of thetotal ones.76sites totaling216(times) were significantly agronomic traits while50(times)associated2years data at the same time within148loci. Among76loci, MD associated with31loci, PH is19, PL is22, PPP is28,1000-GW is20, SPP and Ssr is24respectively.46lociwere associated with two or more traits. Some loci located in this paper were the same orclose to the loci of QTL mapping by previous. The results showed that association mappingmethod is an effective complement to traditional QTL mapping, and combine the twomethods is the effective way to map and excavate rice complex gene.