Genome-wide Association Studies Dissect Magnesium Nutrition Related Loci In Arabidopsis Thaliana And Homologous Genes In Rice

Open GWAS algorithm?OATH?:In line with the open-source movement in genetics,we report a novel linear regression technique for genome-wide association studies?GWAS?,called Open GWAS algorithm?OATH?-when individual level data are not available,using naive summary statistics?NSS? only OATH can not only completely reproduce the reported results from an experimental model but also recover underreported results from other alternative models.Using NSS only,one can i)reproduce reported GWAS results as precise as those estimated from individual-level data;ii)recover an underreported results with any combination of covariates;and iii)deep evaluation for the results,such as analyzing the variance of p-values and leading to a much more reliable evaluation of all the results,as demonstrated for 42 Arabidopsis phenotypes under 3 magnesium conditions.In addition,OATH can be used for consortium-driven genome-wide association meta-analyses?GWAMA?,and greatly improve the flexibility of GWAMA.A prototype of OATH has been realized in software GEnetic Analysis Repository?GEAR,https://github.com/gc5k/GEAR?.High magnesium related lociHigh magnesium?Mg?in some extreme serpentine soils or semi-arid regions is an important obstruct for crop growth and development.Specific loci that form the genetic framework underlying high Mg homeostasis,however,are not well understood.By using GWA mapping on 388 accessions of Arabidopsis thaliana selected from a worldwide collection and genotyped at approximately 250,00 SNPs,we successfully identified 109 and 74 putative genetic regions associated in nutrient traits under normal?1,000 ?M?and high Mg?10,000 ?M?,respectively.Above 90%SNPs associated with nutrient and only two SNPs shared between normal and high Mg.A single strong peak of SNPs associated with Ca concentration corresponding to candidate gene At1g60420 under high Mg was further determined.Compared with wildtype,Atnrx1 mutant supplied with high Mg had high cytosolic Ca²⁺ concentrations([Ca²⁺]c)during root elongation and Ca concentrations in plants,developed longer primary root and accumulated equivalent fresh weight.This suggests that AtNRX1 gene specially and negatively regulates Ca uptake and probably plant growth.Besides,the use of GWAS-identified SNPs as candidate loci also helps to identify biomarkers for incipient mineral nutrition and to develop molecular markers for breeding nutrient-efficient crops.Rice homologus genes related with MgAccording to the Mg-related gene loci located in Arabidopsis thaliana,we further indentied the rice homologous genes basing on rice genomic information.GWAS results found a total of 613 significant SNP loci corresponding to 431 candidate genes in Arabidopsis,which had 424 rice homologous genes by direct homologous comparison.Among this,some already cloned and tested genes indicated that the phenotypically associated genes found by our GWAS results were at least partially able to find similar genes in rice by homologous alignment analysis.In addition,further analysis of the uncloned genes in and the relationship between then and the phenotypes,it was found that homologous genes are more likely to related to seed germination,hypocotyl length,fresh weight and concent of sodium and calcium ion.