Mogga m, sibiya j, shimelis h, lamo j, yao n 2018 diversity analysis and genome wide association studies of grain shape and eating quality traits. Apr 04, 2018 genome wide association study using whole genome sequencing rapidly identifies new genes influencing agronomic traits in rice. To identify the morphological and genetic determinants of panicle architecture, we performed a detailed phenotypic analysis and a genome wide association study gwas using an original panel of vietnamese landraces. Panicle architecture is one of the key components of rice yield and exhibits a large diversity. Studies on panicle architecture, number of spikelets. Mogga m, sibiya j, shimelis h, lamo j, yao n 2018 diversity analysis and genomewide association studies of grain shape and eating quality traits. Genomewide association study of 12 agronomic traits in. Nov 20, 2018 the agronomic traits, including morphological and yield component traits, are important in barley breeding programs.
Zhao et al 2011 genotyped 44 100 snp variants across 4 diverse accessions systematically and phenotyped 34 traits, and they have identified dozens of common variants influencing numerous complex traits. Identification of loci for agronomic traits and characterization of their genetic architecture are crucial in markerassisted selection mas. A genomewide association study gwas of i traits and traditional dr traits identified 470 association loci, some containing known drrelated genes. Here, we describe a comprehensive study of the genetic architecture of the variation in the rice ionome performed using genomewide association studies. Mapping quantitative trait loci through the use of linkage disequilibrium ld in populations of unrelated individuals provides a valuable approach for dissecting the genetic basis of complex traits in soybean glycine max. Yu j, pressoir g, briggs wh, bi iv, yamasaki m, doebley jf, et al. Genomewide association mapping for yield and other. Genomewide association studies of 14 agronomic traits in rice landraces article pdf available in nature genetics 4211. Huang x, wei x, sang t, zhao q, feng q, zhao y, et al. Advances in genomewide association studies of complex. Several gwas have been performed in a search for genes involved in traits affecting yield. Han b 2010 genomewide studies of 14 agronomic traits in rice landraces.
Olsen d a institute of crop sciences, chinese academy of agricultural sciences, beijing, 81, p. Genomewide association studies gwas, genetic surveys of the whole genome to detect variants associated with a trait in natural populations, are a powerful approach for dissecting complex traits. Some loci were mapped at close to gene resolution, indicating that gwas of rice landraces could provide an effective approach for gene. In human genetics, genomewide association study gwas is a commonly used method for discovering genes and genetic variants contributing to human traits, usually through statistical examination of the associations between wholegenome sequence variants and one specific trait. Oct 24, 2010 we performed genomewide association studies gwas for 14 agronomic traits in the population of oryza sativa indica subspecies. Genomewide association study of blast resistance in indica rice.
Genome wide association study for drought, aflatoxin resistance, and important agronomic traits of maize hybrids in the subtropics ivan d. Here, we describe an integrated omics knowledgebase for molecular breeding mbkbase. In human genetics, genomewide association study gwas is a commonly used method for discovering genes and genetic variants contributing to human traits, usually through statistical examination of the associations between wholegenome sequence. Identification of loci for agronomic traits and characterization of their genetic architecture are crucial. Rice landraces are the groups of lineages that originated and evolved in the field over millennia through selective breeding by generations of. The intersubspecific crossing between indica and japonica subspecies in rice have been utilized to improve the yield potential of temperate rice. A genomewide association study of 23 agronomic traits in.
Nov 14, 2018 yield improvement is an important issue for rice breeding. Genomewide association study of important agronomic. Genomewide association study of agronomic traits in bread. Compared with the traditional biparental mapping strategy, the genetic background of the population for. Further, it is also considered as a model crop for studying agronomic, nutritional and biofuel traits. Genomewide association mapping reveals a rich genetic. Genomewide association studies were performed to uncover the genotypic and phenotypic. Genome wide association study using whole genome sequencing rapidly identifies new genes influencing agronomic traits in rice. Extremely high resolution can be achieved by dense snps identified in diverse germplasm panels based on the 2nd generation genome sequencing or snp array approaches 29 35. Genomewide association studies of 14 agronomic traits in rice landraces xuehui huang 1,2 10, xinghua wei 3, tao sang 4,10, qiang zhao 12, qi feng, yan zhao, canyang li. The first effort in human gwas, using genotyping data of 96 patients and 50 healthy controls, successfully identified. Pdf genomewide association studies of 14 agronomic traits. This genetic mapping approach has been applied in rice over the last 10 years.
In the present study, a gwas of 12 rice agronomic traits was carried out using. This study demonstrated that dartseq markers were useful genomic resources for genome wide association studies of rice grain quality traits to accelerate varietal development and release. A genomewide association study gwas performed with emmax for 12 agronomic traits measured in both guangzhou and hangzhou was carried out using 150 accessions of tings core collection selected based on. Mapping approaches can be extended to dissect adaptive genetic variation from structured background variation in an ecological context. We extensively examined 16 rice blast strains and a further genome wide association study based on genotyping 0. Genomewide association study of major agronomic traits in. Genome wide association studies of 14 agronomic traits in rice landraces.
Association mapping of quantitative trait loci for yield. A genomewide association study gwas performed with emmax for 12 agronomic traits measured in both guangzhou and hangzhou was carried out using 150 accessions of tings core collection selected based on 48 phenotypic traits from 2262 accessions of tings collection, the gwas included more than 3. The introduction of new adaptive alleles in the diverse genetic backgrounds may help to improve grain yield of old or. Genomewide association study of four yieldrelated traits. Genetic diversity is the main source of variability in any crop improvement program. Genotype environment interactions for agronomic traits of. Most resistance genes were identified by linkage mapping using genetic populations. Starch and protein are two major components of polished rice, and the amylose and protein contents affect eating and cooking qualities ecqs. The genetic basis underlying the variations in the mineral composition, the ionome, in rice remains largely unknown. A genomewide association study of 23 agronomic traits in chinese wheat landraces yaxi liu1, yu lin1, shang gao1, zhanyi li1, jian ma1, mei deng1, guoyue chen1, yuming wei1 and youliang zheng1, 1 triticeae research institute, sichuan agricultural university, wenjiang, chengdu 611, peoples republic of china. Sep 11, 2015 huang xh, wei xh, sang t, zhao q, feng q, zhao y, et al. Jul 29, 2019 linkage mapping lm and genome wide association studies gwas are the two most popular methods to decipher genetic architectures of complex traits in crops.
Foxtail millet setaria italica, the second largest cultivated millet crop after pearl millet, is utilized for food and forage globally. Supplementary information for genomewide association studies of 14 agronomic traits in rice landraces xuehui huang, xinghua wei, tao sang, qiang zhao, qi feng, yan zhao, canyang li, chuanrang zhu, tingting lu, zhiwu zhang, meng li, danlin fan, yunli guo, ahong wang, lu wang, liuwei deng, wenjun li, yiqi lu, qijun weng, kunyan liu, tao huang. Genomewide association studies reveal new genetic targets for. Genomewide association studies dissect the genetic networks. Xiaoming zheng, a d tingting gong, a b hongling ou, c dayuan xue, b weihua qiao, a junrui wang, a sha liu, a qingwen yang, a kenneth m. Genomewide association study on agronomic traits of temperate. In the present study, a genomewide association study gwas was performed for ten important agronomic traits in 142 foxtail millet core ecogeographically. Genomewide association studies dissect the genetic. Genome wide association study for drought, aflatoxin. We genotyped genome wide association studies of 14 agronomic traits in rice landraces.
Genomewide association studies across simulated 26 seasonal environments was used to identify candidate genes and pathways tied 27 to key life history and agronomic traits under current and future climatic 28 conditions. Using both the general linear model and the mixed linear model, 149 significant markers were identified for 21 agronomic traits based on best linear unbiased prediction values. The haplotypebased genome wide association study gwas has now been proposed as a complementary approach to intensify benefits from ld, which enable to assess the. A haplotype map of genomic variations and genomewide association studies of agronomic traits in foxtail millet setaria. Of these 470 loci, 443 loci 94% were identified using i traits, 437 loci 93% colocalized with previously reported drrelated quantitative trait loci, and 3 loci 66. It has been shown that abundant elite genes exist in rice landraces in previous studies. We performed genomewide association studies gwas for 14 agronomic traits in the population of oryza sativa indica subspecies. Genomewide association study of rice grain width variation. However, to our knowledge, an association mapping with a high. To manage blast disease effectively and in an environmentally friendly way, it is important to continually discover diverse resistant resources for breeding.
Genomewide association mapping of complex traits in rice. A genome wide association study was conducted for these traits using 52 303 dartseq markers to identify markertrait associations and candidate genes. Using wholegenome sequencing data generated from 129 peach accessions, here we perform a comprehensive genomewide association study for 12 key agronomic traits. In human genetics, genome wide association study gwas is a commonly used method for discovering genes and genetic variants contributing to human traits, usually through statistical examination of the associations between whole genome sequence variants and one specific trait. Huang x1, wei x, sang t, zhao q, feng q, zhao y, li c, zhu c. Genomewide association study of eating and cooking.
Genomewide snp variation reveals relationships among landraces and modern varieties of rice. Thus, compared with maize and rice, less is known about the genetic basis of. In the present study, genomewide association study with highquality resequencing data was performed for 10 ecqs in a panel of 227 nonglutinous rice accessions and four derived panels. Genomewide association study of important agronomic traits within. Jan 08, 20 in addition, genome wide association studies gwas have been used to elucidate the genetic basis of agronomic traits in rice and maize. A genomewide association study using a vietnamese landrace. The genomewide association study gwas method based on the highdensity snp markers has recently been established in plants such as maize yu et al.
A genomewide association study was conducted for these traits using 52 303 dartseq markers to identify markertrait associations and candidate genes. Population structure of the brachypodium species complex. Genomewide association studies of 14 agronomic traits in rice landraces. It serves as a reservoir for identifying superior alleles controlling key agronomic and quality traits through allele mining association mapping. Estimation of a significance threshold for genomewide. During the last decade, gwas was used to identify the loci underlying tens of rice traits, and several important. Recently, 3000 rice accessions were systematically sequenced, and around 18. Genomewide association study gwas of mesocotyl elongation. In this study, genomewide association study gwas was used to map genesloci resistant to rice blast in the openaccess rice. In addition, genomewide association studies gwas have been used to elucidate the genetic basis of agronomic traits in rice and maize. In this study, a comparative study of the genomic regions in the eight highyielding varieties hyvs was conducted with those of the four nonhyvs.
Population structure accounted for high phenotypic. Gwas has been widely conducted in each of the important crops and model plant systems like wheat, rice, maize, arabidopsis for several traits. Genomewide association studies of 14 agronomic traits in rice. Association mapping for important agronomic traits in core. Nucleotide diversity scans, 14 and association studies 5, 15 have been carried out in sorghum, but the resolution and sensitivity of these studies has been limited by the small number of markers 14. Murray, 1 thomas isakeit, 2 peicheng huang, 2 marilyn warburton, 3 paul williams, 3 gary l. Nucleotide diversity scans , 14 and association studies 5, 15 have been carried out in sorghum, but the resolution and sensitivity of these studies has been limited by the small number of markers. Diversity analysis and genomewide association studies of. A total of 8, 22 and 47 qtls were identified for flowering time, early 29 vigour and energy traits, respectively. Genomewide association study using wholegenome sequencing rapidly identifies new genes influencing agronomic traits in rice. Genomewide association study on agronomic traits of. Genomewide association studies of 11 agronomic traits in cassava manihot esculenta crantz shengkui zhang 1,2, xin chen 2, cheng lu 2, jianqiu ye 3, meiling zou 2, kundian lu 4, subin feng 2, jinli pei 2, chen liu 2, xincheng zhou 2, pingan ma 2, zhaogui li 4, cuijuan liu 5, qi liao 5, zhiqiang xia 2 and wenquan wang 2.
In this study, a total of 517 landraces were selected and comprehensively phenotyped see online methods. Rice blast, caused by the fungal pathogen magnaporthe oryzae, is a destructive disease of rice that reduces yields from 10 to 30 % annually skamnioti and gurr 2009. Genomewide association study of agronomic traits in rice cultivated. Genomewide association study of rice genes and loci. Genetic variation and association mapping for 12 agronomic traits in. The loci identified through gwas explained 36% of the phenotypic variance, on average. During the last decade, gwas was used to identify the loci underlying tens of rice traits, and several important genes. Rice blast, caused by magnaporthe oryzae, is an important rice disease occurring in all rice growing areas. In this study, a genomewide association study gwas was performed using specificlocus amplified fragment sequencing slafseq. Sequencingbased genomewide association study in rice. Advances in genomewide association studies of complex traits. Huang x, wei x, sang t et al 2010 genomewide association studies of 14 agronomic traits in rice landraces.
Rice, which has a modest genome size, is a wonderful model crop that has been comprehensively studied in functional genomics. The agronomic traits, including morphological and yield component traits, are important in barley breeding programs. More than 500 diverse rice landraces were used to construct a highdensity rice haplotype map and perform gwas for 14 agronomic traits, which identified a sub stantial number of potential loci. A genomewide association study for agronomic traits in. With advancements in high throughput genotyping and sequencing technologies, single nucleotide polymorphisms snps provide relatively low cost and dense marker coverage across various genomes.
Oct 28, 2011 genome wide association studies gwas have been even more successful in plants than in humans. Pdf genomewide association studies of 14 agronomic. With vast germplasm resources and reduced sequencing cost, genome wide association study gwas has been feasible to explore the allelic variation underlying agronomic traits in rice. Genomewide association studies of 14 agronomic traits in. Genomewide association studies of image traits reveal. Genomewide associations and epistatic interactions for. In human genetics, genomewide association study gwas is a commonly used method. Results a genome wide association study gwas performed with emmax for 12 agronomic traits measured in. Here, we describe a comprehensive study of the genetic architecture of the variation in the rice ionome performed using genome wide association studies. A soybean subdatabase will be released in 3 months and wheat and maize will. A haplotype map of genomic variations and genomewide association studies of agronomic traits in foxtail millet setaria italica. Results a genomewide association study gwas performed with emmax for 12 agronomic traits measured in. Multilocus genomewide association studies for 14 main. Genomewide association study gwas based on ssr or single nucleotide polymorphism snp markers 2933 has been widely used in model plant species including rice.
Genomewide association studies of 11 agronomic traits in. A genomewide association study of field resistance to. Phenotypic characters of rice landraces reveal independent lineages of shortgrain aromatic indica rice avik ray. In this study, three models were adopted and tested. The nextgeneration sequencing ngs mapping on the nipponbare reference genome identified a total. This study demonstrated that dartseq markers were useful genomic resources for genomewide association studies of rice grain quality traits to accelerate varietal development and release. Genomewide association study of 12 agronomic traits in peach. Genomewide association studies reveal the genetic basis of. Association mapping based on ld linkage disequilibrium, nonrandom associations between causative loci and phenotype in natural population is highly useful in.
Phenotypic characters of rice landraces reveal independent. In comparison to qtlmapping, gwas help accelerates the assessment of a more representative set of individuals in both time and costeffective way 14. Genomewide association studies reveal the genetic basis. A genome wide association study gwas of i traits and traditional dr traits identified 470 association loci, some containing known drrelated genes. In order to reveal the genetic foundation of agronomic traits of interest, in this study 122 doubled haploid lines from a cross between cultivars huaai 11 sixrowed and dwarf and huadamai 6 tworowed were genotyped by 9680 snps and phenotyped 14 agronomic traits. Nov 18, 2014 rice blast disease is one of the most serious and recurrent problems in rice growing regions worldwide. Genes free fulltext characterization of the common. Rice oryza sativa is an important dietary source of both essential micronutrients and toxic trace elements for humans. Pdf genomewide association studies of 14 agronomic traits in.
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