More affordable and effective noninvasive single nucleotide polymorphism genotyping using high-throughput amplicon sequencing

被引:31
作者
Eriksson, Charlotte E. [1 ]
Ruprecht, Joel [1 ]
Levi, Taal [1 ]
机构
[1] Oregon State Univ, Dept Fisheries & Wildlife, Corvallis, OR 97331 USA
关键词
faecal DNA; individual identification; next-generation sequencing; noninvasive samples; single nucleotide polymorphisms; SNP genotyping; BLACK BEARS; MICROSATELLITES; CONSERVATION; ASSIGNMENT; MANAGEMENT; GENOMICS; ECOLOGY; SNP;
D O I
10.1111/1755-0998.13208
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Noninvasive genotyping methods have become key elements of wildlife research over the last two decades, but their widespread adoption is limited by high costs, low success rates and high error rates. The information lost when genotyping success is low may lead to decreased precision in animal population densities, which could misguide conservation and management actions. Single nucleotide polymorphisms (SNPs) provide a promising alternative to traditionally used microsatellites as SNPs allow amplification of shorter DNA fragments, are less prone to genotyping errors and produce results that are easily shared among laboratories. Here, we outline a detailed protocol for cost-effective and accurate noninvasive SNP genotyping using multiplexed amplicon sequencing optimized for degraded DNA. We validated this method for individual identification by genotyping 216 scats, 18 hairs and 15 tissues from coyotes (Canis latrans) using 26 SNPs. Our genotyping success rate for scat samples was 93%, and 100% for hair and tissue, representing a substantial increase compared to previous microsatellite-based studies while remaining at a low cost of under $5 per PCR replicate (excluding labour). The accuracy of the genotypes was further corroborated in that genotypes from scats matching known, GPS-collared coyotes were always located within the territory of the known individual. We also show that different levels of multiplexing produced similar results, but that PCR product cleanup strategies can have substantial effects on genotyping success. By making noninvasive genotyping more affordable, accurate and efficient, this research may allow for a substantial increase in the use of noninvasive methods to monitor and conserve free-ranging wildlife populations.
引用
收藏
页码:1505 / 1516
页数:12
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  • [1] [Anonymous], 2018, POPULATION GENOMICS
  • [2] From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome-wide approaches in Atlantic salmon Salmo salar
    Aykanat, T.
    Lindqvist, M.
    Pritchard, V. L.
    Primmer, C. R.
    [J]. JOURNAL OF FISH BIOLOGY, 2016, 89 (06) : 2658 - 2679
  • [3] Using non-invasively collected genetic data to estimate density and population size of tigers in the Bangladesh Sundarbans
    Aziz, M. Abdul
    Tollington, Simon
    Barlow, Adam
    Greenwood, Christina
    Goodrich, John M.
    Smith, Olutolani
    Shamsuddoha, Mohammad
    Islam, M. Anwarul
    Groombridge, Jim J.
    [J]. GLOBAL ECOLOGY AND CONSERVATION, 2017, 12 : 272 - 282
  • [4] Microhaplotypes provide increased power from short-read DNA sequences for relationship inference
    Baetscher, Diana S.
    Clemento, Anthony J.
    Ng, Thomas C.
    Anderson, Eric C.
    Garza, John C.
    [J]. MOLECULAR ECOLOGY RESOURCES, 2018, 18 (02) : 296 - 305
  • [5] Improving cost-efficiency of faecal genotyping: New tools for elephant species
    Bourgeois, Stephanie
    Kaden, Jenny
    Senn, Helen
    Bunnefeld, Nils
    Jeffery, Kathryn J.
    Akomo-Okoue, Etienne F.
    Ogden, Rob
    McEwing, Ross
    [J]. PLOS ONE, 2019, 14 (01):
  • [6] Quantifying genotyping errors in noninvasive population genetics
    Broquet, T
    Petit, E
    [J]. MOLECULAR ECOLOGY, 2004, 13 (11) : 3601 - 3608
  • [7] The elimination of primer-dimer accumulation in PCR
    Brownie, J
    Shawcross, S
    Theaker, J
    Whitcombe, D
    Ferrie, R
    Newton, C
    Little, S
    [J]. NUCLEIC ACIDS RESEARCH, 1997, 25 (16) : 3235 - 3241
  • [8] Genotyping-in-Thousands by sequencing (GT-seq): A cost effective SNP genotyping method based on custom amplicon sequencing
    Campbell, Nathan R.
    Harmon, Stephanie A.
    Narum, Shawn R.
    [J]. MOLECULAR ECOLOGY RESOURCES, 2015, 15 (04) : 855 - 867
  • [9] Genetic and genomic monitoring with minimally invasive sampling methods
    Carroll, Emma L.
    Bruford, Mike W.
    DeWoody, J. Andrew
    Leroy, Gregoire
    Strand, Alan
    Waits, Lisette
    Wang, Jinliang
    [J]. EVOLUTIONARY APPLICATIONS, 2018, 11 (07): : 1094 - 1119
  • [10] Assessing population structure and gene flow in Montana wolverines (Gulo gulo) using assignment-based approaches
    Cegelski, CC
    Waits, LP
    Anderson, NJ
    [J]. MOLECULAR ECOLOGY, 2003, 12 (11) : 2907 - 2918