| Sichuan has a long history of peanut planting and processing.It is the largest peanut production and consumption area in southwest China and is famous for its unique medium-sized peanuts.In the present study,seventy peanut materials from Sichuan province were collected and grow across two environments in Sichuan province,China.All of them were genotyped using SLAF-seq technology.The cultivated peanut genome was used as the reference for enzyme digestion prediction during SLAF-seq.The resulted SNP genotype data was used for phylogenetic tree constructing and the population structure analyzing within the 70 peanut materials.Moreover,it was used to detect SNPs that were significantly correlated with important agronomy and seed quality traits.Annotated genes nearby the significantly SNPs were also analyzed.The present results was wish to provide a theoretical basis for further improvement the yield and quality and molecular marker-assisted breeding of Sichuan peanut.The main results are as follows:(1)Seven traits,including plant height,branch number,100-fruit weight,seed coat color,seed protein content,seed fat content and seed total soluble sugar content,were evaluated.Of these,plant height,branch number and seed protein content were skewed distribution within the seventy peanuts.and the rest of the traits had no normality.The main materials exhibited a medium and low plant height(20-50 cm),medium branch number(6-10),medium and large grain type(140-200 g),and pink peanuts with high protein content(23-27%),medium fat content(51-56%),and low total soluble sugar content(3.5-5.5%).(2)The enzymatic cleavage efficiency of Hae Ⅲ in the experiment was 92.71%,and a total of 213.91 Mb reads was obtained.The average Q30 of sequencing was 94.44%,and the average GC content was 42.70%.A number of 206,506 SLAF tags were developed in average for each sample.The average sequencing depth of the sample SLAF tags was14.36 x,and a total of 184,034 population SNPs were obtained.In total of 3,313high-quality SNP markers with less than 10% of heterozygosity and deletion ratio and MAF greater than or equal to 0.05 were used in further analysis.(3)The phylogenetic tree was constructed based on the selected SNP markers.Seventy peanut materials can be divided into 5 groups,which respectively contain 17,5,20,7 and 21 members.The Tianfu series of approved varieties were concentrated in the first groups,and have sporadic distribution in the second,third and fourth groups.The fifth group is the largest group,and is relatively distant from others.Groups Ⅲ and Ⅴ showed the trend of classification by seed coat color.The results of the population structure show that with the increase of K value,different subgroups of Tianfu series cultivars are separated,the common varieties in production have multiple subgroup classifications such as seed coat color material type and nutrients.When K = 8,the cross-validation error rate reaches the lowest value,and the resource similarity in the subgroup is the largest.Compared with the phylogenetic tree,the overall structure of the two is similar,and only a few materials will be divided into different groups or subgroups.(4)With-lg(P)> 4.5 as the threshold,a total of 6 SNP markers were detected,which were associated with agronomic traits,including 5 extremely significant sites.With-lg(P)> 4.0 as the threshold,2 SNP markers related to quality traits were associated,including2 extremely significant sites.The detected significant association sites were distributed on7 chromosomes,and the marker SNP8 was simultaneously associated with fat and total soluble sugar content. |
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