A clear subdivision between lowland and upland accessions was apparent, thereby indicating the presence. Author summary genomic selection is a promising breeding technique that aims to improve the efficiency and speed of the breeding process. Wed like to understand how you use our websites in order to improve them. In order to find new chromosomal regions associated with the different ability of rice to elongate the coleoptile under submergence, we used genome. Association mapping of stigma and spikelet characteristics in rice oryza sativa l.
Here, we report the development of an association mapping panel consisting of 1,568 diverse inbred rice varieties and a genotyping data set generated using a highdensity rice array hdra. These rice landraces were further screened with 274 simple sequence repeat markers, and association mapping was performed using a mixed linear model approach. Genotyping of diagnostic markers revealed the rhtd1b mutant allele in 58% of the investigated varieties, while the rhtb1b mutant was only present in 7% of the varieties. Open access resources for genomewide association mapping. The 91 accessions were recently added to the usdaars national plant germplasm system. The genotypes of the genes for the resulting traits indicated that association mapping supports screening suitable experimental materials for developing mapping populations. Minor qtls will be localized using a bc4f8 population. Elite genes for aluminum al tolerance might exist in rice landraces. Pdf association mapping for yield and grain quality traits in rice. Association mapping, also known as linkage disequilibrium mapping, is a method of mapping quantitative trait loci qtls that takes advantage of linkage disequilibrium to link phenotypes to genotypes. Linkage qtl mapping and association studies are usually applied to genetically dissect related traits, which could be further facilitated by high. Genomewide and genebased association mapping for rice eating. Bucklera,b,c a institute for genomic diversity, cornell university, ithaca, new york 148532703 b department of plant breeding and genetics, cornell university, ithaca, new york 14853. While it has been shown to be effective in crops such as wheat and corn, it has not yet been applied to rice breeding.
We conducted genomewide association studies gwas using a multiparent advanced generation intercross magic plus population to identify qtls and snp markers that could potentially be integrated in biofortification and disease resistance. Genome wide association mapping of grain and straw. The mapping results showed that a total of 23 significant p traitmarker associations were detected for al tolerance. Dissection of coleoptile elongation in japonica rice under. Nested association mapping nam is a technique designed by the labs of edward buckler, james holland, and michael mcmullen for identifying and dissecting the genetic architecture of complex traits in corn.
High yield in rice mainly depends on large grain weight, ideal plant architecture and proper flowering time adapting to various geographic regions. Mineral elements in brown rice grain play an important role in human health. The development of genomewide association studies gwas in crops has made it possible to mine interesting alleles hidden in gene bank resources. Hydroponics enables an easy observation of the root system but does not permit to assess root growth reaction in response to drought. Agrama2, aaron jackson3, kathleen yeater5, xiaobai li1, bihu huang6, biaolin hu7, anna mcclung3, dianxing wu1 1state key lab of rice biology, institute of nuclearagriculture sciences, zhejiang university, hangzhou, china, 2rice research and extension center. Rice germplasm in korea and association mapping intechopen.
Association mapping and genetic dissection of drought. Association mapping and marker development of genes for starch lpl synthesis in rice 289 lingshui, hainan province, china, in 2010 and 2011 included 20 nonwaxy rice accessions g01g20, of which 8 belong to japonica subspecies, 8 indica subspecies and 4 the aus group xu et al, 2014. Rice is grown on 82 % of the agricultural area, which corresponds to 7. Association mapping of yield and its components in rice cultivars h. Association mapping of quantitative trait loci for mineral element contents in whole grain rice oryza sativa l. Genomewide association mapping of virulence gene in rice. Pdf genomewide association mapping in a rice magic plus. Discovers linked markers associated linked to gene controlling the trait major goal. Genomewide association studies gwas, by contrast, are used to identify genes or qtls that underlie traits of importance to breeding such.
Genomewide association mapping in a rice magic plus population detects qtls and genes useful for biofortification. Original article genomewide association mapping for phenotypic plasticity in rice shinjikikuchi 1, raju bheemanahalli 2,6,krishnas. Association mapping of four important traits using the. Association mapping of quantitative trait loci for mineral. Genome wide association mapping for grain shape traits in.
Here, we conducted a genomewide association study gwas of salt tolerance based on exome sequencing of the thai rice accessions. Vietnam is a tropical country in southeast asia with a ricebased agricultural economy. The platform provides an immortal collection of diverse germplasm, a highdensity singlenucleotide. Many qtl affecting rice ecq and pc have been identified through linkage mapping,14,15,16 and association studies 17,18,19,20, but qtl cloning is still a major challenge to plant geneticists and. Association mapping of yield and its components in rice. Association mapping am an alternative to traditional qtl mapping. Rice oryza sativa is a staple food that feeds 3 billion people 1,2. Genomic selection and association mapping in rice oryza. Association mapping and marker development of genes for. Pdf association mapping for aluminum tolerance in a core. Association mapping analyzes loci in diverse populations and associates them with both one another and with phenotypes.
It has the largest, publicly available, singlespecies germplasm collection in the world 3, and a rich omics toolkit. Genomea wide association mapping for phenotypic plasticity. Many of the associated markers were located in regions where qtl had previously been identified. The use of resistant cultivars is the only practical way to control the disease in developing countries where most farmers cannot afford fungicides. Genomewide association study for salinity tolerance at. Association mapping for aluminum tolerance in a core. Dissecting the genetic loci controlling salt tolerance in rice for improving productivity, especially at the flowering stage, remains challenging. More recently, employing candidate genebased association mapping approach, 11 snps mined in. Association mapping of resistance to rice blast in upland. A new rice panel, the bengal and assam aus panel baap of 266 aus accessions was generated with. Association analysis was applied to a panel of accessions of embrapa rice core collection ericc with 86 ssr and field data from two experiments. The genetic architecture of plant height was investigated in a set of 358 recent european winter wheat varieties plus 14 spring wheat varieties based on field data in eight environments.
Introduction one of the many goals of plant geneticists and breeders pertains to the explanation of. Materials and methods included in this study were 92 blastresistant rice germplasm accessions from seven different regions of africa, asia, and latin america table 1. An association mapping for starch quality traits using both candidate genebased association mapping and genomewide. In the last decade, association mapping am has become a wellestablished method to detect genes and quantitative trait loci qtls. The mixed linear model method was used to disclose markertrait associations. An extra advantage of the gwas design for rice is the homozygous nature of most rice varieties, which makes it possible to employ. The identification of a large number of single nucleotide polymorphisms snps from genome sequencing and concurrent development of highthroughput genotyping platforms has led to am being widely used for a range of crops. The development of rice genotypes with micronutrientdense grains and disease resistance is one of the major priorities in rice improvement programs. Association mapping of stigma and spikelet characteristics. We discovered 11 significant markertrait associations and identified candidate genes potentially involved in. Association mapping allows the detection of markers linked to target genes without having to generate a mapping population. Pdf in the last decade, association mapping am has become a well established method to detect genes and quantitative trait loci qtls.
Genomewide association mapping of salinity tolerance in. In rice breeding programs, the selection for desirable traits is completed based on the evaluation of phenotypes. This study presents the development of a panel of rice varieties from vietnam for. Therefore, we employed an association mapping approach in this study. Planta october 2016, volume 244, issue 4, pp 819830 cite as genome wide association mapping for grain shape traits in indica rice authorsauthors and affiliations yue fengqing lurongrong zhaimengchen zhangqun xuyaolong yangshan wangxiaoping yuanhanyong yuyiping wangxinghua wei open access original article first online. We performed an association mapping study for root traits in the rice japonica group using a mediumthroughput hydroponic root phenotyping system with glass beads and marker data obtained by gbs. Whole genome association mapping of plant height in winter.
Varioius strategey involved in association mapping is discussed in this presentation. Association mapping of yield and yieldrelated traits under. Abstractin the last decade, association mapping am has become a wellestablished method to detect genes and quantitative trait loci qtls associated with agronomically important traits. Frontiers genomewide association mapping in a rice. Allelic analysis of sheath blight resistance with association mapping in rice limeng jia1,2,3, wengui yan3, chengsong zhu4, hesham a. Pdf in the last decade, association mapping am has become a wellestablished method to detect genes and quantitative trait loci qtls associated. Association mapping of resistance to rice blast in upland field conditions louismarie raboin1, elsa ballini2, didier tharreau3, alain ramanantsoanirina4, julien frouin5, brigitte courtois5 and nourollah ahmadi5 abstract background. Association mapping for important agronomic traits in core. In that study, a highdensity rice haplotype map was constructed with 3. Genomewide association mapping of root traits in a.
Genome wide association studies gwas allow high resolution exploration of rice genetic diversity for quantitative and qualitative resistance alleles. Discover the causative snp in a gene exploits the natural variation found in a species. Genomewide and genebased association mapping for rice. Genomewide association study gwas mapping makes it possible to simultaneously screen a very large number of accessions for genetic variation underlying diverse complex traits. Among different rice ecosystems, rainfed upland and rainfed lowland rice occupy 30% of total rice area but. Characterization of a panel of vietnamese rice varieties. Sotocerda 1,2 and sylvie cloutier 1 1cereal research center, agriculture and agrifood canada 2agriaquaculture nutritional genomic center, cgna r10c1001 genomics and bioinformatics unit 1canada 2chile 1. Pdf open access resources for genomewide association. Association mapping of quantitative trait loci for yieldrelated. It is important to note that nested association mapping unlike association mapping is a specific technique that cannot be performed outside of a specifically designed population such as. Critical considerations shift from genotyping to experimental design sean myles,a,1 jason peiffer,a patrick j. Results of the present study demonstrated that genomewide association mapping in the usda rice minicore collection could complement and enhance the information from linkagebased qtl studies, and help increase yield through improvement of these related traits by markerassisted selection either directly or.
We used a core collection of rice landraces, while two biparental segregation mapping populations and a rice panel consisting of 383 diverse rice accessions, which was not developed as a core collection, were used in the study of famoso et al. Genomewide association mapping in a rice magic plus. Salt stress, a major plant environmental stress, is a critical constraint for rice productivity. Pdf in the last decade, association mapping am has become a wellestablished method to detect genes and quantitative trait loci qtls. Preliminary genomewide association mapping of rice bacterial leaf blight resistance loci using major korean races of xoo xanthomonas oryzae.
Rice blast is one of the most damaging disease of rice. Association mapping for yield and grain quality traits in rice oryza satival. Pdf association mapping for yield and grain quality. It is a powerful genetic mapping tool for crops and provides highresolution, broad allele coverage, and costeffective gene tagging for the evaluation of plant germplasm resources.