The application of short and highly polymorphic microhaplotypes based on nonbinary-SNPs in kinship testing of extremely degraded samples

Kinship testing becomes more difficult in extremely degraded samples. But commonly used genetic markers cannot completely solved this problem. Microhaplotype combining the advantages of STR and SNP may be a promising genetic marker for kinship testing in extremely degraded samples. Therefore, in this study, 36 short and highly polymorphism microhaplotype loci with length smaller than 100 bp and Ae greater than 3.0 were developed, of which 29 loci met the Hardy-Weinberg and linkage equilibrium. The CPD and CPE of these 29 loci were 0.99999999999999999999999997036 and 0.9999999945, respectively. Allele dropout of these loci was not observed in extremely degraded samples. Through simulated kinship analysis, the effectiveness of paternity testing reached 98.39% at threshold of 4/-4, and effectiveness of full-sibling testing reached 93.01% at threshold of 2/-2, which were greater than that of 15 STR loci. After combining with other 50 short and highly polymorphic microhaplotype loci, the effectiveness of half-sibling testing also reached 82.42% at the threshold of 2/-2. Our developed short and highly polymorphic microhaplotype loci may be useful for paternity testing and full-sibling testing in extremely degraded samples, and after combining with other short and highly polymorphic microhaplotype loci, may be helpful to analyze the more distant kinship relationship.