Abstract
Potato has about 100 related wild Solanum species growing naturally in the Americas. The US Potato Genebank aims to keep samples useful for research and breeding to improve the crop, often in the form of botanical seed families. A key component of genebank efficiency is assessing diversity within and among populations, and DNA marker sequence diversity is a powerful proxy for trait diversity. We previously reported on three factors which can cause under-estimation of heterozygosity: ascertainment, allele frequency, and ploidy bias. We here report, using GBS data for four diploid potato species, that average percent of apparent heterozygosity increases as data is more complete—the maximum difference was 2% heterozygotes when only a few individuals are called, to 36% when nearly all individuals were called. However, there was evidence that estimates of average heterozygosity based only on loci for which every individual has data can also be biased upward. Implausibly high levels of heterozygosity suggest non-segregating non-homologous SNPs, which occurred as 5–9% of all loci with complete data. We propose that best estimates of average heterozygosity in unselected seedlings should be based on loci with data for all samples after eliminating those loci that appear to be artificially fixed as heterozygous, which reduces observed heterozygote frequency by 16–26%. On that basis, the wild species examined have similar heterozygosity to the cultivated phureja.
Resumen
La papa tiene alrededor de 100 especies silvestres relacionadas con Solanum que crecen naturalmente en las Américas. El banco de Germoplasma de Papa de los Estados Unidos tiene como objetivo mantener muestras útiles para la investigación y el mejoramiento para mejorar el cultivo, a menudo en forma de familias de semillas botánicas. Un componente clave de la eficiencia del banco de germoplasma es evaluar la diversidad dentro y entre las poblaciones, y la diversidad de secuencias de marcadores de ADN es un poderoso indicador de la diversidad de caractéres. Previamente informamos sobre tres factores que pueden causar una subestimación de la heterocigosidad: comprobación, frecuencia de alelos y sesgo de ploidía. Aquí informamos, utilizando datos de GBS para cuatro especies de papa diploides, que el porcentaje promedio de heterocigosidad aparente aumenta a medida que los datos son más completos: la diferencia máxima fue del 2% de heterocigotos cuando solo se consaidera a unos pocos individuos, al 36% cuando se incluye a casi todos los individuos. Sin embargo, hubo evidencia de que las estimaciones de la heterocigosidad promedio basadas solo en loci para los cuales cada individuo tiene datos también pueden estar sesgadas hacia arriba. Inverosimilmente, Los niveles altos de heterocigosidad sugieren SNP no segregantes no homólogos, que ocurrieron como 5–9% de todos los loci con datos completos. Proponemos que las mejores estimaciones de la heterocigosidad promedio en plántulas no seleccionadas deben basarse en loci con datos para todas las muestras después de eliminar aquellos loci que parecen estar fijados artificialmente como heterocigotos, lo que reduce la frecuencia de heterocigotos observada en un 16–26%. Sobre esa base, las especies silvestres examinadas tienen una heterocigosidad similar a la de phureja cultivada.
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Abbreviations
- USPG:
-
US Potato Genebank
- GRIN:
-
Germplasm Resources Information Network (https://npgsweb.ars-grin.gov/gringlobal/search)
- GBS:
-
Genotyping By Sequencing
References
Bamberg, J.B. 2019. Southwest 2019 Potato (Solanum) Collecting Trip Report. Online at: https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?id=2096809. Accessed 17 Aug 2021.
Bamberg, J.B., and A.H. del Rio. 2004. Genetic heterogeneity estimated by RAPD polymorphism of four tuber-bearing potato species differing by breeding system. American Journal of Potato Research 81: 377–383.
Bamberg, J.B., A.H. del Rio, J. Coombs, and D. Douches. 2015. Assessing SNPs versus RAPDs for predicting heterogeneity in wild potato species. American Journal of Potato Research 92: 276–283.
Bamberg, J.B., and A.H. del Rio. 2020. Assessing under-estimation of genetic diversity within wild potato (Solanum) species populations. American Journal of Potato Research 97: 547–553.
Bamberg, J.B., A.H. del Rio, and Rocio Moreyra. 2009. Genetic consequences of clonal versus seed sampling in model populations of two wild potato species indigenous to the USA. American Journal of Potato Research 86: 367–372.
Bamberg, J.B., A.H. del Rio, S.J. Jansky, and D. Ellis. 2018. Ensuring the genetic diversity of potatoes. In Achieving sustainable cultivation of potatoes No. 26, Vol.1, ed. Prof. Gefu Wang-Pruski, Chapter 3, pp 57–80. Cambridge, UK: Burleigh-Dodds Science Publishers.
Bryan, G.J., K. McLean, R. Waugh, and D.M. Spooner. 2017. Levels of intra-specific AFLP diversity in tuber-bearing potato species with different breeding systems and ploidy levels. Frontiers in Genetics 8: 119.
Jiang, H., R. Lei, S.W. Ding, and S. Zhu. 2014. Skewer: A fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics 15: 1–12. https://doi.org/10.1186/1471-2105-15-182.
Li, H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, and N. Homer. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25: 2078–2079. https://doi.org/10.1093/bioinformatics/btp352.
Lu, F., A.E. Lipka, J. Glaubitz, R. Elshire, J.H. Cherney, M.D. Casler, et al. 2013. Switchgrass genomic diversity, ploidy, and evolution: Novel insights from a network-based SNP discovery protocol. PLoS Genetics 9: e1003215. https://doi.org/10.1371/journal.pgen.1003215.
Melo, A.T.O., R. Bartaula, and I. Hale. 2016. GBS-SNP-CROP: A reference-optional pipeline for SNP discovery and plant germplasm characterization using variable length, paired-end genotyping-by-sequencing data. BMC Bioinformatics 17: 29. https://doi.org/10.1186/s12859-016-0879-y.
Qiao, Y., F. Guo, N. Huo, L. Zhan, J. Sun, X. Zuo, Z. Guo, Y.Q. Gu, and Y. Liu. 2020. Genotyping-by-sequencing to determine the genetic structure of a Tibetan medicinal plant Swertia mussotii Franch. Genetic Resources and Crop Evolution. https://doi.org/10.1007/s10722-020-00993-6 (Online 06 Aug 2020).
Revord, R.S., S.T. Lovell, P. Brown, J. Capik, and T.J. Molnar. 2020. Using genotyping-by-sequencing derived SNPs to examine the genetic structure and identify a core set of Corylus americana germplasm. Tree Genetics & Genomes 16: 65. https://doi.org/10.1007/s11295-020-01462-y.
Torkamaneh, D., and F. Belzile. 2015. Scanning and Filling: Ultra-Dense SNP Genotyping Combining Genotyping-By-Sequencing, SNP Array and Whole-Genome Resequencing Data. PLoS ONE 10 (7): e0131533. https://doi.org/10.1371/journal.pone.0131533.
Acknowledgements
Financial support for collection of S. jamesii samples was provided by the National Science Foundation, award no. BCS-1827414. The authors thank the University of Wisconsin Biotechnology Center DNA Sequencing Facility for providing GBS facilities and services.
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Bamberg, J., del Rio, A., Louderback, L. et al. Assessing SNP Heterozygosity in Potato (Solanum) Species— Bias Due to Missing and Non-allelic Genotypes. Am. J. Potato Res. 98, 328–332 (2021). https://doi.org/10.1007/s12230-021-09846-z
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DOI: https://doi.org/10.1007/s12230-021-09846-z