Genome Wide Association Analysis Of Important Agronomic Traits In Peanut (Arachis Hypogaea L.)Based On The Axiom＿Arachis2 48K SNP Array

Peanut is the main oil crop and cash crop in China.It is rich in oil,protein and other nutrients.It has been widely planted in many countries around the world.Cultivated peanut(Arachis hypogaea L.)is an allotetraploid with a narrow genetic basis.At present,there are few studies on the genetic characteristics of the cultivated peanut population.The research and reports on the linkage loci related to important agronomic traits of peanuts are not comprehensive.Most of them focus on seed size,plant type,leaf spots,etc.Testa color,peel thickness and testa oil spots are important indicators that affect the quality of peanut products.However,there are few studies about them in peanuts.In present study,the Axiom＿Arachis2SNP array was used to genotype 178 representative varieties from different provinces in China and 9 other countries.Traits phenotype and genotype statistical analysis,population structure analysis and Genome wide association study(GWAS)were used to study the genetic basis of these peanut varieties.The results provide markers for distinguishing and utilizing variety resources,identifying candidate loci and genes related to importat agronomic traits.The result also provides valuable information for further fine mapping and improving peanut quality and yield using molecular-assisted breeding methods.The main conclusions are as follows:1.Phenotypic identification and statistical analysis:The phenotypic analysis of 38 agronomic traits of 178 peanut materials has been completed.The statistical results showed that these peanuts displayed rich phenotypic variation,such as the average number of total branches from 2.6 to 16.4.The average variation range of one hundred seed weight is 29.5 g to 113.0 g.Most traits are normally distributed,suggesting that these traits may be controlled by quantitative trait locus(QTL).The correlations of these phenotypic traits were analyzed and many traits were found to be significantly correlated.2.Statistical analysis of genotyping:The peanut varieties were genotyped by Axiom＿Arachis2 48 K SNP array.After filtering out SNPs with missing data rates(>10%)and minor allele frequencies(<5%),13,125 SNPs showed polymorphisms in the peanut population,accounting for 27.43% of the total SNPs on the array.These SNPs were distributed on 20 chromosomes in the peanut genome with an average density of 4.69 SNPs/Mb.Arahy.14 had the largest number of SNPs.Arahy.07(8.47 SNPs/Mb))had the highest density.Arahy.12(3.74 SNPs/Mb)had the lowest density.A total of six SNP variant types of "T/C","A/G","A/C","T/G","C/G" and "A/T" were observed,among which the most abundant SNP type is "T/C",accounting for 39.43% of the total SNPs."A/G" accounting for39.05% of the total SNPs."A/C" and "T/G" accounted for 10.71% and 10.37% of the total SNPs,respectively."C/G" accounted for 0.29% of the total SNPs.And "A/T" was the least,accounting for only 0.15% of the total SNPs.3.Population structure analysis:The population structure of these 178 peanut varieties was further studied and verified by PCA.The optimal K(number of groups)is 7.According to genotyping results,peanut samples can be divided into 7 groups,group 1(G1)to group 7(G7),and the number of peanut varieties in each group ranges from 5 to 72.G1 containing 72 peanut varieties,was the largest group,followed by G6,containing 53 peanut varieties.In addition,the results of population structure and phylogenetic analysis also indicated the existence of two subgroups,G1(G1-1)and G2(G2-1).These groupings show a geographic distribution pattern.Peanut varieties from the same planting area usually being in the same grouping.Most of the native varieties of northern provinces such as Shandong,Henan,and Hebei belong to G1,and the varieties of southern provinces(Fujian,Guangdong,Guangxi)belong to G6.4.GWAS analysis:GWAS analysis was performed on 12 agronomic traits.It was found that two candidate genes(Arahy.9SIV6 F,Arahy.4TTF80)about one-hundred seed weight were detected on Arahy.16 with a threshold of-log10(P)> 5.4.A candidate gene(Arahy.N1NJX0)related to the total number of branches was detected in the 97.90-98.98 Mb region of Arahy.05.In the downstream 111.93-115.81 Mb region of this chromosome,SNP＿Chr05:111936057,which is associated with testa oil spots,was detected on the exon encoding the peroxidase superfamily protein gene(Arahy.7X9WBQ).In addition,a total of 13 candidate regions related to pod shape were obtained.Peel thickness candidate regions were obtained in 86.18-89.45 Mb study on Arahy.02.Testa color is also a complex trait which correlated candidate intervals detected in most chromosomes including Arahy.03 and Arahy.10,where genes controlling red and black testa have been identified in previous studies determined separately.For main stem height,there was only one SNP identified on Arahy.06.A total of two candidate genes related to behenic acid content were obtained on Arahy.10,namely Arahy.H2 NMKM and Arahy.4RN93 K.In addition,the research results obtained a total of44 SNP loci related to linoleic acid content.And 14 SNP loci related to oleic acid content,which were distributed on 6 chromosomes of Chr6,Chr9,Chr14,Chr7,Chr18,and Chr20.The Arahy.FVV1 VG gene was located and correlated with the content of linoleic acid,oleic acid and palmitic acid.7 SNP loci that jointly control these three traits and 5 SNP loci that jointly control the content of oleic acid and palmitic acid.In addition,5 SNP loci are related to sucrose content were detected on Arahy.09 the SNP site.