Using DNA markers to reconstruct the lifetime morphology of barley grains from carbonized cereal crop remains unearthed at Usvyaty Settlement

Authors

  • Tatiana Semilet Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources, Bol'shaya Morskaya ul., 42–44, Saint Petersburg, 190000, Russian Federation https://orcid.org/0000-0001-7275-3878
  • Natalia Shvachko Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources, Bol'shaya Morskaya ul., 42–44, Saint Petersburg, 190000, Russian Federation https://orcid.org/0000-0002-1958-5008
  • Natalia Smirnova Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources, Bol'shaya Morskaya ul., 42–44, Saint Petersburg, 190000, Russian Federation https://orcid.org/0000-0001-9480-8737
  • Lilia Shipilina Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources, Bol'shaya Morskaya ul., 42–44, Saint Petersburg, 190000, Russian Federation https://orcid.org/0000-0001-7590-3173
  • Elena Khlestkina Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources, Bol'shaya Morskaya ul., 42–44, Saint Petersburg, 190000, Russian Federation https://orcid.org/0000-0002-8470-8254

DOI:

https://doi.org/10.21638/spbu03.2023.101

Abstract

Research on taxonomic and genetic diversity of cultivated plants provides valuable data that help to clarify how the flora of cultivated plants was formed in a particular region. Paleogenetics, a discipline that developed at the intersection of molecular biology, archeology and genetics, helps to explore plant origin and changes in plant genotype during evolution. By the 12th century, the economy of medieval Northern Russia was based on a developed farming culture. Tracing the origin of its constituent agricultural traditions is an important fundamental task. The objective of this work was to study and identify the species affiliation of carbonized fossil remains of plants that grew in the Russian Northwest in the 12th century using morphological and molecular genetic methods. The results of the morphological analysis of grain fossils showed that most of the unearthed plant material was barley. Other cereals, such as wheat, rye and oat, were also observed. Molecular genetic studies helped to clarify the species affiliation of partially destroyed grains and reconstruct their lifetime morphology.

Keywords:

H. vulgare, barley, Nud, aDNA, naked

Downloads

Download data is not yet available.
 

References

Badr, A., Müller, K., Schäfer-Pregl, R., Rabey, H. E., Factorfgen, S., Ibrahim, H. H., Pozzi, C., Rohde, W., and Salamini, F. 2000. On the origin and domestication history of barley (Hordeum vulgare). Molecular Biology and Evolution 17(4):499–510. https://doi.org/10.1093/oxfordjournals.molbev.a026330

Bennett, K. D. and Parducci, L. 2006. DNA from pollen: principles and potential. The Holocene 16(8):1031–1034. https://doi.org/10.1177/0959683606069383

Blatter, R. H. E., Jacomet, S., and Schlumbaum, A. 2002. Little evidence for the preservation of a single-copy gene in charred archaeological wheat. Ancient Biomolecules 4(2):65–77. https://doi.org/10.1080/1358612021000010677

Brown, T. A., Allaby, R. G., Brown, K. A., O’Donoghue, K., and Sallares, R. 1994. DNA in wheat seeds from European archaeological sites. Experientia 50(6):571–575. https://doi.org/10.1007/bf01921727

Charles, M. and Bogaard, A. 2010. Charred plant macro-remains from Jeitun: implications for early cultivation and herding practices in western Central Asia; pp. 150–165 in Dr. Harris (ed.), Origins of agriculture in western Central Asia. An environmental-archaeological study. University of Pennsylvania Museum of Archaeology and Anthropology, Philadelphia.

Chen, H., Wanga, B., Zhouc, B., Qia, J., Tanga, N., Wanga, S., Tiana, Z., Wanga, M., Xua, S., Yua, N., Chena, D., Mahmoud, A. O., and Lia, D. Z. 2020. Characterization, phylogeny, and responses of leptin to different nutritional states in critically endangered yangtze sturgeon (Acipenser dabryanus). Aquaculture 525:1–10. https://doi.org/10.1016/j.aquaculture.2020.735296

Costantini, L. 1984. The beginning of agriculture in the Kachi plain: the evidence of Mehrgarh; pp. 29–33 in B. Allchin (ed.), South Asian Archaeology. Cambridge University Press. Cambridge.

Dabney, J., Knappb, M., Glocke, I., Gansaugea, M.-T., Weihmanna, A., Nickela, B., Valdioserad, C., Garcíad, N., Pääbo, S., Arsuaga, J.-L., and Meyer, M. 2013. Complete mitochondrial genome sequence of a middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proceedings of the National Academy of Sciences USA 110(39):15758–15763. https://doi.org/10.1073/pnas.1314445110

Dickin, E., Steele, K., Edwards-Jones, G., and Wright, D. 2012. Agronomic diversity of naked barley (Hordeum vulgare L.): a potential resource for breeding new food barley for Europe. Euphitica 184(1):85–99.

Eremeev, I. I. and Dzyuba, O. F. 2010. Essays on the historical geography of the forest part of the Way from the Varangians to the Greeks: Archaeological and paleogeographical studies between the Western Dvina and the Ilmen Lake. 670 pp. Nestor-Istoriia Publ. St. Petersburg. (In Russian)

Eremeev, I. I. 2021. A new stage of investigations in medieval town of Usvyat; pp. 447–467 in Collection of scientific articles in memory of Alexander Plavinsky "Expedition of a lifetime". Kolorgrad Publishing. Minsk. (In Russian)

Eremeev, I. and Furasiev, A. 2021. Medieval Usvyat: searching for the town of Yaroslav the Wise. 52 pp. Institute for the History of Material Culture of the Russian Academy of Sciences, St. Petersburg

Fedak, G., Tsuchiya, T., and Helgason, S. B. 1972. Use of monotelotrisomics for linkage mapping in barley. Canadian Journal of Genetics and Cytology 14:949–957. https://doi.org/10.1139/g72-117

Gerasimova, S. V., Hertig, C., Korotkova, A. M., Kolosovskaya, E. V., Otto, I., Hiekel, S., Кochetov, A. V., Khlestkina, E. K., and Kumlehn, J. 2020. Conversion of hulled into naked barley by Cas endonuclease-mediated knockout of the Nud gene. BMC Plant Biology 20:255. https://doi.org/10.1186/s12870-020-02454-9

Gustafsson, D. R. 2013. The origin of naked barley (Hordeum vulgare L. ssp. vulgare) studied bythe nud gene. PhD Thesis, Linköping, 17 p.

Harlan, H. 1920. Daily development of kernels of Hannchan barley from flowering to maturity at Aberdeen, Idaho. Journal of Agricultural Research 19:393–439.

Helback, H. 1959. Domestication of Food Plants in the Old World: Joint efforts by botanists and archeologists illuminate the obscure history of plant domestication. Science 130(3372):365–372. https://doi.org/10.1126/science.130.3372.365

Kikuchi, S., Taketa, S., Ichii, M., and Kawasaki, S. 2003. Efficient fine mapping of naked caryopsis gene (nud) by HEGS (High Efficiency Genome Scanning)/AFLP in barley. Theoretical and Applied Genetics 108:73–78. https://doi.org/10.1007/s00122-003-1413-y

Kiryanova, N. A. 1979. On the assortment of the cultivated plants in the ancient Russia of the X–XV centuries. Soviet Archeology 4:72–85. (In Russian)

Lister, D. L., Jones, H., Jones, M. K., O’Sullivan, D. M., and Cockram, J. 2013. Analysis of DNA polymorphism in ancient barley herbarium material: validation of the KASP SNP genotyping platform. Taxon 62(4):779–789. https://doi.org/10.12705/624.9

Lister, D. L., Jones, H., Oliveira, H. R., Petrie, C. A., Liu, X., Cockram, J., Catherine, J., Kovaleva, O., and Jones, M. K. 2018. Barley heads east: Genetic analyses reveal routes of spread through diverse Eurasian landscapes. PLoS ONE 13(7):e0196652. https://doi.org/10.1371/journal.pone.0196652

Mascher, M., Schuenemann, V. J., Davidovich, U., Marom, N., Himmelbach, A., Hübner, S., and Stein, N. 2016. Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley. Nature Genetics 48(9):1089–1093. https://doi.org/10.1038/ng.3611

Murphy, P. J. and Witcombe, J. R. 1986. Covered and naked barleys from the Himalaya. 1. Evidence of multivariate differences between two types. Theoretical and Applied Genetics 71:730–735. https://doi.org/10.1007/bf00263271

Nielsen, P. S., Kleinhofs, A., and Olsen. O.-A. 1997. Barley elongation factor 1α: genomic organization, DNA sequence, and phylogenetic implications. Genome 40(4):559–565. https://doi.org/10.1139/g97-073

Orlov, A. A. 1929. Barley of Abyssinia and Eritrea. Proceedings on Applied Botany, Genetics and Breeding 20:283–345. (In Russian)

Pankin, A. and Korff, M. V. 2017. Co-evolution of methods and thoughts in cereal domestication studies: a tale of barley (Hordeum vulgare). Current Opinion in Plant Biology 36:15–21. https://doi.org/10.1016/j.pbi.2016.12.001

Poinar, H. N., Kuch, M., Sobolik, K. D., Barnes, I., Stankiewicz, A. B., Kuder, T., Spaulding, W. G., Bryant, V. M., Cooper, A., and Pääbo, S. 2001. A molecular analysis of dietary diversity for three archaic Native Americans. Proceedings of the National Academy of Sciences USA 98(8):4317–4322. https://doi.org/10.1073/pnas.061014798

Rawlence, N. J., Lowe, D. J., Wood, J. R., Young, J. M., Churchman, G. J., Huang, Y.-T., and Cooper, A. 2014. Using palaeoenvironmental DNA to reconstruct past environments: progress and prospects. Journal of Quaternary Science 29(7):610–626. https://doi.org/10.1002/jqs.2740

Regel, R. E. 1922. Bread in Russia. Proceedings on Applied Botany, Genetics and Breeding 13:60. (In Russian)

Taketa, S., Amano, S., Tsujino, Y., Sato, T., Saisho, D., Kakeda, K., Nomura, M., Suzuki, T., Matsumoto, T., Sato, K., Kanamori, H., Kawasaki, S., and Takeda, K. 2008. Barley grain with adhering hulls is controlled by an ERF family transcription factor gene regulating a lipid biosynthesis pathway. Proceedings of the National Academy of Sciences USA 105:4062–4067. https://doi.org/10.1073/pnas.0711034105

Taketa, S., Kikuchi, S., Awayama, T., Yamamoto, S., Ichii, M., and Kawasaki, S. 2004. Monophyletic origin of naked barley inferred from molecular analyses of a marker closely linked to the naked caryopsis gene (nud). Theoretical and Applied Genetics 108:1236–1242. https://doi.org/10.1007/s00122-003-1560-1

Trofimova, S. S., Krylasova, N. B., and Sarapulov, A. N. 2016. Archaebotanical research in medieval Rozhdestvenskoye settlement (Perm krai). Natural science research. Perm Federal Research Centre Journal 3:23–29. (In Russian)

Vavilov, N. I. 1924a. About the eastern centers of origin of cultivated plants. Novyi Vostok 6:290–305. (In Russian)

Vavilov, N. I. 1924b. Patterns in the variability of plants. Izvestiia gosudarstvennogo instituta opytnoi agronomii 2(6):209–223. (In Russian)

Vavilov, N. I. 1929. The problem of the origin of cultivated plants, as conceived of at the present time. Progress and Perspectives within the field of applied botany, genetics and breeding; pp. 11–22 in Achievements and prospects in the field of applied botany, genetics and breeding. All-Russian Research Institute of Plant Industry and State Institute of Experimental Agronomy Press. Leningrad. (In Russian)

Wabila, С., Neumann, K., Kilian, B., Radchuk, V., and Graner, A. 2019. A tiered approach to genome-wide association analysis for the adherence of hulls to the caryopsis of barley seeds reveals footprints of selection Celestine. BMC Plant Biology 19:95. https://doi.org/10.1186/s12870-019-1694-1

Warren, P., Jarman, M. R., Jarman, H. N., Shackleton, N. J., and Evans, J. D. 1968. Knossos Neolithic, part II. Annual of the British School at Athens 63:239–276. https://doi.org/10.1017/S0068245400014374

Weyrich, L. S., Dobney, K., and Cooper, A. 2015. Ancient DNA analysis of dental calculus. Journal of Human Evolution 79:119–124. https://doi.org/10.1016/j.jhevol.2014.06.018

Yu, S., Long, H., Deng, G. Pan, Z., Liang, J., Zeng, X., Tang, Y., Tashi, N., and Yu, M. 2016. A single nucleotide polymorphism of Nud converts the caryopsis type of barley (Hordeum vulgare L.). Plant Molecular Biology Reporter 34:242–248. https://doi.org/10.1007/s11105-015-0911-9

Zhelesnov, A. V., Kukoeva, T. V., and Zheleznova, N. B. 2013. Naked barley: origin, distribution, and prospects of utilisation. Vavilov Journal of Genetics and Breeding 17(2):286–297.

Zhukovsky, P. M. 1964. Cultivated plants and their relatives. 745 p. Kolos Publ. Leningrad. (In Russian)

Zohary, D. and Hopf, M. 2000. Domestication of plants in the Old World. 316 pp. Oxford University Press. New York. https://doi.org/10.1006/anbo.2001.1505

Downloads

Published

2023-05-02

How to Cite

Semilet, T., Shvachko, N., Smirnova, N., Shipilina, L., & Khlestkina, E. (2023). Using DNA markers to reconstruct the lifetime morphology of barley grains from carbonized cereal crop remains unearthed at Usvyaty Settlement. Biological Communications, 68(1), 3–9. https://doi.org/10.21638/spbu03.2023.101

Issue

Section

Full communications

Categories