Genome-wide Variation Identification in Peanut and Development of InDel Markers for Genetic Research
This study aimed to identify genetic variations on the whole genome level using genome resequencing data of 13 peanut cultivars,clarify their distribution characteristic,develop and verify InDel markers,and evaluate the efficiency of InDel markers in peanut cultivar identification.A total of 313432 high-quality SNPsand38777high-quality InDel weredetected,with an average distribution density of 123/Mb and 15.23/Mb,respectively.The InDels and SNPs were mainly distributed in intergenic regions,with a frequency of 52.35％and 60.08％of the total SNP and InDel,respectively.Primers were designed using InDel with insertion or deletion length ≥10 bp,and 3675 InDel could be used to develop InDel markers.These InDel locus were unevenly distributed on the 20 chromosomes of peanut with an average density of 1.48/Mb.Using electronic PCR,the InDel primers amplified mainly with 1 locus and 2561 effective primers(69.69％)could amplified 3133 effective loci in the peanut reference genome.The physical map of amplification loci was drawn according to the loci position in cultivated peanut genome.Among 100 pairs of random primers,31 pairs amplified different bands in the 4 varieties with distant relatives.The 31 InDel primer pairs amplified 62 alleles in 47 peanut cultivars(or breeding lines),the frequency of major genes ranged from 0.51 to 0.98 with an average of 0.77,and the polymorphic information content ranged from 0.04 to 0.37,with an average of 0.24.Both cluster analysis and population structure analysis could divide the 47 peanut cultivars(breeding lines)into two groups,and the 47 materials could be distinguished by at least 7 markers,indicating that the developed InDel markers could be effectively used for the assessment of genetic diversity and variety identification of peanut.The research results enriched the molecular markers of peanut,and was beneficial for the use of InDel markers in genetic studies of peanut resource genetic diversity,variety identification,fingerprint construction.
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