bioselБиотехнология и селекция растенийPlant Biotechnology and Breeding2658-62662658-6258VIR10.30901/2658-6266-2024-4-o7biosel-251Research ArticleКРАТКИЕ СООБЩЕНИЯBRIEF COMMUNICATIONSПЦР-тест для установления принадлежности разрушенных остатков карбонизированных семян к роду Hordeum L.PCR test to determine whether the destroyed remains of carbonized seeds belong to the genus Hordeum L.https://orcid.org/0000-0001-7275-3878СемилетТ. В.SemiletT. V.

Татьяна Вячеславовна Семилет, младший научный сотрудник, лаборатория постгеномных исследований, ВИР

190000 Россия, Санкт-Петербург, ул. Большая Морская, 42, 44

Tatiana V. Semilet, Junior Researcher, Laboratory of Postgenomic Research, VIR

42, 44, Bolshaya Morskaya Street, St. Petersburg, 190000 Russia

t.semilet@vir.nw.ruhttps://orcid.org/0000-0001-7590-3173ШипилинаЛ. Ю.ShipilinaL. Yu.

Лилия Юрьевна Шипилина, кандидат биологических наук, старший научный сотрудник, лаборатория мониторинга биоресурсов и археоботаники, ВИР

190000 Россия, Санкт-Петербург, ул. Большая Морская, 42, 44

Liliya Yu. Shipilina, Cand. Sci. (Biology), Senior Researcher, Laboratory of Bioresources Monitoring and Archaeobotany, VIR

42, 44, Bolshaya Morskaya Street, St. Petersburg, 190000 Russia

l.shipilina@vir.nw.ruhttps://orcid.org/0000-0002-8470-8254ХлесткинаЕ. К.KhlestkinaE. K.

Елена Константиновна Хлесткина, доктор биологических наук, профессор РАН, директор, ВИР

190000 Россия, Санкт-Петербург, ул. Большая Морская, 42, 44

Elena K. Khlestkina, Dr. Sci. (Biology), Professor of the Russian Academy of Sciences (RAS), Director, VIR

42, 44, Bolshaya Morskaya Street, St. Petersburg, 190000 Russia

director@vir.nw.ruhttps://orcid.org/0000-0002-1958-5008ШвачкоН. А.ShvachkoN. A.

Наталия Альбертовна Швачко, кандидат биологических наук, ведущий научный сотрудник, заведующая, лаборатория постгеномных исследований, ВИР

190000 Россия, Санкт-Петербург, ул. Большая Морская, 42, 44

Natalia A. Shvachko, Cand. Sci. (Biology), Leading Researcher, Head, Laboratory of Postgenomic Research, VIR

42, 44, Bolshaya Morskaya Street, St. Petersburg, 190000 Russia

n.shvachko@vir.nw.ruФедеральный исследовательский центр Всероссийский институт генетических ресурсов растений имени Н.И. ВавиловаРоссияN.I. Vavilov All-Russian Institute of Plant Genetic ResourcesRussian Federation20240302202574105113Copyright © Семилет Т.В., Шипилина Л.Ю., Хлесткина Е.К., Швачко Н.А., 20242024Семилет Т.В., Шипилина Л.Ю., Хлесткина Е.К., Швачко Н.А.Semilet T.V., Shipilina L.Y., Khlestkina E.K., Shvachko N.A.This work is licensed under a Creative Commons Attribution 4.0 License.https://biosel.elpub.ru/jour/article/view/251

Археологи во время раскопок исторических памятников находят разнообразные артефакты, свидетельствующие о жизни и быте наших далеких предков. Особое внимание уделяется останкам живых организмов. Они свидетельствуют не только о хозяйственной деятельности древних земледельцев, но и помогают выявлять филогенетические взаимоотношения и процессы доместикации в мировых центрах разнообразия. Зачастую из-за длительного нахождения палеообъектов в условиях, не способствующих их сохранности, они разрушаются и становится невозможным определить их видовую принадлежность. Поэтому археологи все чаще прибегают к помощи палеогенетиков. В России известны работы по изучению древней ДНК (дДНК) из останков человека и животных. Однако, палеогенетические исследования ископаемых остатков растений, таких как пыльца, семена, древесина, немногочисленны. На территории Усвятского городища (Псковская область) в 2019 году были найдены карбонизированные зерновки зерновых культур. Находка датируется XII веком. В результате морфологического анализа смеси семян были обнаружены зерновки, степень разрушенности которых не позволяет определить видовую принадлежность по анализу микрорельефа. Поэтому целью данного исследования послужила разработка таксон-специфичных праймеров, дающих короткий продукт амплификации, для анализа фрагментированной дДНК разрушенных зерновок ячменя. В результате был разработан ПЦР-тест HORDELF, который рекомендуется к использованию при идентификации растительных остатков (карбонизированных семян), принадлежащих роду Hordeum L.

During excavations of historical monuments, archaeologists find various artifacts that testify to the existence and everyday life of our distant ancestors. Particular attention is paid to the remains of living organisms. They not only provide evidence of the economic activity of ancient farmers, but also help to identify phylogenetic relationships and domestication processes in the world's centers of diversity. Due to the long-term presence of paleontological objects in the environment that is not conducive to preservation, they often get destroyed and it becomes impossible to determine which species they belong to. Therefore, archaeologists increasingly resort to the help of paleogeneticists. The works on studies of ancient DNA (aDNA) from human and animal remains are known in Russia. However, paleogenetic studies of fossil plant remains such as pollen, seeds, and timber are few. In 2019, carbonized grains of cereal crops were found on the territory of the Usvyaty settlement in Pskov Region. The findings date back to the 12th century. The morphological analysis of the seed mixture resulted in finding grains, the degree of destruction of which prevented determination of the species they belong to by analyzing their microrelief. Therefore, the aim of this study was to develop taxon-specific primers that yield a short amplification product for the analysis of fragmented aDNA from the destroyed barley caryopses. As a result, a PCR test named HORDELF was developed, which is recommended for the identification of plant residues (carbonized seeds) belonging to the genus Hordeum L.

Elf3HordeumУсвятыдревняя ДНКпалеогенетикаElf3HordeumUsvyatyancient DNApaleogeneticsРабота выполнена в рамках государственного задания ВИР согласно тематическому плану НИР по теме FGEM-2024-0002 «Исследование растительных биоресурсов в пространственном и временном аспекте с применением современных цифровых и генетических технологий».The work was carried out within the framework of the State Assignment of VIR in accordance with the thematic plan of research on the topic FGEM-2024-0002 «Study of plant bioresources in spatial and temporal aspects using modern digital and genetic technologies».ReferencesAdonina I.G., Orlovskaya O.A., Tereshchenko O.Yu., Korenb L.V., Khotyleva L.V., Shumnya V.K., Salina E.A. Development of commercially valuable traits in hexaploid Triticale lines with Aegilops introgressions as dependent on the genome composition. Russian Journal of Genetics. 2011;47(4):453-461. DOI: 10.1134/S1022795411040028Adonina I.G., Orlovskaya O.A., Tereshchenko O.Yu., Korenb L.V., Khotyleva L.V., Shumnya V.K., Salina E.A. Development of commercially valuable traits in hexaploid Triticale lines with Aegilops introgressions as dependent on the genome composition. Russian Journal of Genetics. 2011;47(4):453-461. DOI: 10.1134/S1022795411040028Antil S., Abraham J.S., Sripoorna S., Maurya S., Dagar J., Makhija S., Bhagat P., Gupta R., Sood U., Lal R., Toteja R. DNA barcoding, an effective tool for species identification: a review. Molecular Biology Reports. 2023;50(1):761-775. DOI: 10.1007/s11033-022-08015-7Antil S., Abraham J.S., Sripoorna S., Maurya S., Dagar J., Makhija S., Bhagat P., Gupta R., Sood U., Lal R., Toteja R. DNA barcoding, an effective tool for species identification: a review. Molecular Biology Reports. 2023;50(1):761-775. DOI: 10.1007/s11033-022-08015-7Benito C., Silva-Navas J., Fontecha G., Hernandez-Riquer M.V., Eguren M., Salvador N., Gallego F.J. From the rye Alt3 and Alt4 aluminum tolerance loci to orthologous genes in other cereals. Plant Soil. 2010;327:107-120.Benito C., Silva-Navas J., Fontecha G., Hernandez-Riquer M.V., Eguren M., Salvador N., Gallego F.J. From the rye Alt3 and Alt4 aluminum tolerance loci to orthologous genes in other cereals. Plant Soil. 2010;327:107-120.Bilgic H., Hakki E.E., Pandey A., Khan M.K., Akkaya M.S. Ancient DNA from 8400 year-old Çatalhöyük wheat: implications for the origin of neolithic agriculture. PLOS ONE. 2016;11(3):e0151974. DOI: 10.1371/journal.pone.0151974Bilgic H., Hakki E.E., Pandey A., Khan M.K., Akkaya M.S. Ancient DNA from 8400 year-old Çatalhöyük wheat: implications for the origin of neolithic agriculture. PLOS ONE. 2016;11(3):e0151974. DOI: 10.1371/journal.pone.0151974Boden S.A., Weiss D., Ross J.J., Davies N.W., Trevaskis B., Chandler P.M., Swain S.M. EARLY FLOWERING 3 regulates flowering in spring barley by mediating gibberellin production and FLOWERING LOCUS T expression. The Plant Cell. 2014;26(4):1557-1569. DOI: 10.1105/tpc.114.123794Boden S.A., Weiss D., Ross J.J., Davies N.W., Trevaskis B., Chandler P.M., Swain S.M. EARLY FLOWERING 3 regulates flowering in spring barley by mediating gibberellin production and FLOWERING LOCUS T expression. The Plant Cell. 2014;26(4):1557-1569. DOI: 10.1105/tpc.114.123794Bouby L. Lorge à deux range (Hordeum distichum) dans l’agriculture Gallo-Romaine: données archéobotaniques. Revue Archéométrie. 2001;25:35-44. [in French]Bouby L. Lorge à deux range (Hordeum distichum) dans l’agriculture Gallo-Romaine: données archéobotaniques. Revue Archéométrie. 2001;25:35-44. [in French]Bunning S.L., Jones G., Brown T.A. Next generation sequencing of DNA in 3300-year-old charred cereal grains. Journal Archaeology Science. 2012;39(8):2780-2784. DOI: 10.1016/j.jas.2012.04.012Bunning S.L., Jones G., Brown T.A. Next generation sequencing of DNA in 3300-year-old charred cereal grains. Journal Archaeology Science. 2012;39(8):2780-2784. DOI: 10.1016/j.jas.2012.04.012Charles M., Bogaard A. Charred plant macro-remains from Jeitun: implications for early cultivation and herding practices in western Central Asia. In: D.R. Harris (ed.) Origins of agriculture in western Central Asia. An environmental-archaeological study. Philadelphia: University of Pennsylvania Museum of Archaeology and Anthropology. 2011:150-165. DOI: 10.9783/9781934536513Charles M., Bogaard A. Charred plant macro-remains from Jeitun: implications for early cultivation and herding practices in western Central Asia. In: D.R. Harris (ed.) Origins of agriculture in western Central Asia. An environmental-archaeological study. Philadelphia: University of Pennsylvania Museum of Archaeology and Anthropology. 2011:150-165. DOI: 10.9783/9781934536513Deng W., Clausen J., Boden S., Oliver S.N., Casao M.C., Ford B., Anderssen R.S., Trevaskis B. Dawn and dusk set states of the circadian oscillator in sprouting barley (Hordeum vulgare) seedlings. PLoS One. 2015;10(6):1-18. DOI: 10.1371/journal.pone.0129781Deng W., Clausen J., Boden S., Oliver S.N., Casao M.C., Ford B., Anderssen R.S., Trevaskis B. Dawn and dusk set states of the circadian oscillator in sprouting barley (Hordeum vulgare) seedlings. PLoS One. 2015;10(6):1-18. DOI: 10.1371/journal.pone.0129781Faure S., Turner A.S., Gruszka D., Christodoulou V., Davis S.J., Korffet von M., Laurie D. Mutation at the circadian clock gene Early maturity 8 adapts domesticated barley (Hordeum vulgare) to short growing seasons. PNAS. 2012;109(21):8328-8333. DOI: 10.1073/pnas.1120496109Faure S., Turner A.S., Gruszka D., Christodoulou V., Davis S.J., Korffet von M., Laurie D. Mutation at the circadian clock gene Early maturity 8 adapts domesticated barley (Hordeum vulgare) to short growing seasons. PNAS. 2012;109(21):8328-8333. DOI: 10.1073/pnas.1120496109Fernandez E., Thaw S. Brown T.A., Arroyo-Pardo E., Buxo R., Serret M.D., Araus J.L. DNA analysis in charred grains of naked wheat from several archaeological sites in Spain. Journal of Archaeological Science. 2013;40(1):659-670. DOI: 10.1016/j.jas.2012.07.014Fernandez E., Thaw S. Brown T.A., Arroyo-Pardo E., Buxo R., Serret M.D., Araus J.L. DNA analysis in charred grains of naked wheat from several archaeological sites in Spain. Journal of Archaeological Science. 2013;40(1):659-670. DOI: 10.1016/j.jas.2012.07.014GeneBank NCBI, National Center for Biotechnology Information; 2024. Available from: https://www.ncbi.nlm.nih.gov/nucleotide/ [accessed Dec. 3, 2024].GeneBank NCBI, National Center for Biotechnology Information; 2024. Available from: https://www.ncbi.nlm.nih.gov/nucleotide/ [accessed Dec. 3, 2024].Grazina L., Amaral J.S., Mafra I. Botanical origin authentication of dietary supplements by DNA-based approaches. Comprehensive Reviews in Food Science and Food Safety. 2020;19:1080-1109. DOI: 10.1111/1541-4337.12551Grazina L., Amaral J.S., Mafra I. Botanical origin authentication of dietary supplements by DNA-based approaches. Comprehensive Reviews in Food Science and Food Safety. 2020;19:1080-1109. DOI: 10.1111/1541-4337.12551Helback B.H. Domestication of food plants in the old world: joint efforts by botanists and archeologists illuminate the obscure history of plant domestication. Science. 1959;130(3372):365-372. DOI: 10.1126/science.130.3372.365Helback B.H. Domestication of food plants in the old world: joint efforts by botanists and archeologists illuminate the obscure history of plant domestication. Science. 1959;130(3372):365-372. DOI: 10.1126/science.130.3372.365Hemming M.N., Walford S.A., Fieg S., Dennis E.S., Trevaskis B. Identification of high-temperature-responsive genes in cereals. Plant Physiology. 2012;158:1439-1450. DOI: 10.1104/pp.111.192013Hemming M.N., Walford S.A., Fieg S., Dennis E.S., Trevaskis B. Identification of high-temperature-responsive genes in cereals. Plant Physiology. 2012;158:1439-1450. DOI: 10.1104/pp.111.192013Hill C.B., Li C. Genetic Architecture of Flowering Phenology in Cereals and Opportunities for Crop Improvement. Frontiers in Plant Science. 2016;19(7):1-23. DOI: 10.3389/fpls.2016.01906Hill C.B., Li C. Genetic Architecture of Flowering Phenology in Cereals and Opportunities for Crop Improvement. Frontiers in Plant Science. 2016;19(7):1-23. DOI: 10.3389/fpls.2016.01906Huang H., Gehan M.A., Huss S.E., Alvarez S., Lizarraga C., Gruebbling E.L., Gierer J., Naldrett M.J., Bindbeutel R.K., Evans B.S., Mockler T.C., Nusinow D.A. Cross-species complementation reveals conserved functions for EARLY FLOWERING 3 between monocots and dicots. Plant Direct. 2017;1(14). DOI: 10.1002/pld3.18Huang H., Gehan M.A., Huss S.E., Alvarez S., Lizarraga C., Gruebbling E.L., Gierer J., Naldrett M.J., Bindbeutel R.K., Evans B.S., Mockler T.C., Nusinow D.A. Cross-species complementation reveals conserved functions for EARLY FLOWERING 3 between monocots and dicots. Plant Direct. 2017;1(14). DOI: 10.1002/pld3.18Jacomet S. Identification of cereal remains from archaeological sites. Basel: Basel University, Archaeobotany Lab IPAS; 2006.Jacomet S. Identification of cereal remains from archaeological sites. Basel: Basel University, Archaeobotany Lab IPAS; 2006.Khlestkina E.K., Than M.H., Pestsova E.G., Röder M.S., Malyshev S.V., Korzun V., Börner A. Mapping of 99 new microsatellite-derived loci in rye (Secale cereale L.) including 39 expressed sequence tags. Theoretical and Applied Genetics. 2004;109:725-732. DOI: 10.1007/s00122-004-1659-zKhlestkina E.K., Than M.H., Pestsova E.G., Röder M.S., Malyshev S.V., Korzun V., Börner A. Mapping of 99 new microsatellite-derived loci in rye (Secale cereale L.) including 39 expressed sequence tags. Theoretical and Applied Genetics. 2004;109:725-732. DOI: 10.1007/s00122-004-1659-zKhlestkina E.K., Tereshchenko O.Y., Salina E.A. Anthocyanin biosynthesis genes location and expression in wheat-rye hybrids. Molecular Genetics and Genomics. 2009;282:475-485. DOI: 10.1007/s00438-009-0479-xKhlestkina E.K., Tereshchenko O.Y., Salina E.A. Anthocyanin biosynthesis genes location and expression in wheat-rye hybrids. Molecular Genetics and Genomics. 2009;282:475-485. DOI: 10.1007/s00438-009-0479-xKhlestkina E.K., Shoeva O.Y. Intron loss in the chalcone-flavanone isomerase gene of rye. Molecular Breeding. 2014;33(4):953-959. DOI: 10.1007/s11032-013-0009-8Khlestkina E.K., Shoeva O.Y. Intron loss in the chalcone-flavanone isomerase gene of rye. Molecular Breeding. 2014;33(4):953-959. DOI: 10.1007/s11032-013-0009-8Kress W.J., Erickson D.L. DNA Barcodes Methods and Protocols. In: Kress W., Erickson D. (eds). DNA Barcodes. Methods in Molecular Biology. Vol 858. Humana Press, Totowa, NJ. Humana Press; 2012. p. 3-8. DOI: 10.1007/978-1-61779-591-6_1Kress W.J., Erickson D.L. DNA Barcodes Methods and Protocols. In: Kress W., Erickson D. (eds). DNA Barcodes. Methods in Molecular Biology. Vol 858. Humana Press, Totowa, NJ. Humana Press; 2012. p. 3-8. DOI: 10.1007/978-1-61779-591-6_1Li X., Yang Y., Henry R.J., Rossetto M., Wang Y., Chen S. Plant DNA barcoding: from gene to genome. Biological reviews of the Cambridge Philosophical Society. 2015;90(1):157-66. DOI: 10.1111/brv.12104Li X., Yang Y., Henry R.J., Rossetto M., Wang Y., Chen S. Plant DNA barcoding: from gene to genome. Biological reviews of the Cambridge Philosophical Society. 2015;90(1):157-66. DOI: 10.1111/brv.12104Lister D.L., Jones H., Jones M.K., O'Sullivan D.M., Cockram J. Analysis of DNA polymorphism in ancient barley herbarium material: validation of the KASP SNP genotyping platform. Taxon. 2013;62(4):779-89. DOI: 10.12705/624.9Lister D.L., Jones H., Jones M.K., O'Sullivan D.M., Cockram J. Analysis of DNA polymorphism in ancient barley herbarium material: validation of the KASP SNP genotyping platform. Taxon. 2013;62(4):779-89. DOI: 10.12705/624.9Pavlik B.M., del Rio A., Bamberg J., Louderback L.A. Evidence for human-caused founder effect in populations of Solanum jamesii at archaeological sites: II. Genetic sequencing establishes ancient transport across the Southwest USA. American Journal of Botany. 2024;111(7):e16365. DOI: 10.1002/ajb2.16365Pavlik B.M., del Rio A., Bamberg J., Louderback L.A. Evidence for human-caused founder effect in populations of Solanum jamesii at archaeological sites: II. Genetic sequencing establishes ancient transport across the Southwest USA. American Journal of Botany. 2024;111(7):e16365. DOI: 10.1002/ajb2.16365Pérez-Escobar O.A, Tusso S., Przelomska N.A.S., Wu S., Ryan P., Nesbitt M., Silber M.V., Preick M., Fei Z., Hofreiter M., Chomicki G., Renner S.S., Genome sequencing of up to 6,000-year-old Citrullus seeds reveals use of a bitter-fleshed species prior to watermelon domestication. Molecular Biology and Evolution. 2022;39(8):msac168. DOI: 10.1093/molbev/msac168Pérez-Escobar O.A, Tusso S., Przelomska N.A.S., Wu S., Ryan P., Nesbitt M., Silber M.V., Preick M., Fei Z., Hofreiter M., Chomicki G., Renner S.S., Genome sequencing of up to 6,000-year-old Citrullus seeds reveals use of a bitter-fleshed species prior to watermelon domestication. Molecular Biology and Evolution. 2022;39(8):msac168. DOI: 10.1093/molbev/msac168Phytozome 13, The Plant Genomic Resource; 2024. Available from: https://phytozome-next.jgi.doe.gov/report/transcript/HvulgareMorex_V3/ HORVU.MOREX.r3.3HG0292270.1 [accessed Dec. 3, 2024]Phytozome 13, The Plant Genomic Resource; 2024. Available from: https://phytozome-next.jgi.doe.gov/report/transcript/HvulgareMorex_V3/ HORVU.MOREX.r3.3HG0292270.1 [accessed Dec. 3, 2024]Pollmann B., Jacomet S., Schlumbaum A. Morphological and genetic studies of waterlogged Prunus species from the Roman vicus Tasgetium (Eschenz, Switzerland). Journal of Archaeological Science. 2005;32(10):1471-1480. DOI: 10.1016/j.jas.2005.04.002Pollmann B., Jacomet S., Schlumbaum A. Morphological and genetic studies of waterlogged Prunus species from the Roman vicus Tasgetium (Eschenz, Switzerland). Journal of Archaeological Science. 2005;32(10):1471-1480. DOI: 10.1016/j.jas.2005.04.002Richards S.M., Li L., Breen J., Hovhannisyan N., Estrada O., Gasparyan B., Gilliham M., Smith A., Cooper A., Zhang H. Recovery of chloroplast genomes from medieval millet grains excavated from the Areni-1 cave in Southern Armenia. Scientific reports. 2022;12(1). DOI: 10.1038/s41598-022-17931-4Richards S.M., Li L., Breen J., Hovhannisyan N., Estrada O., Gasparyan B., Gilliham M., Smith A., Cooper A., Zhang H. Recovery of chloroplast genomes from medieval millet grains excavated from the Areni-1 cave in Southern Armenia. Scientific reports. 2022;12(1). DOI: 10.1038/s41598-022-17931-4Riehl S., Pustovoytov K.E., Weippert H., Klett S., Hole F. Drought stress variability in ancient Near Eastern agricultural systems evidenced by δ13C in barley grain. Proceedings of the National Academy of Sciences. 2014;111(34):12348-12353. DOI: 10.1073/pnas.1409516111Riehl S., Pustovoytov K.E., Weippert H., Klett S., Hole F. Drought stress variability in ancient Near Eastern agricultural systems evidenced by δ13C in barley grain. Proceedings of the National Academy of Sciences. 2014;111(34):12348-12353. DOI: 10.1073/pnas.1409516111Sadder M., Brake M., Ayoub S., Abusini Y., Al-Amad I., Haddad N. Complete mitochondrial genome sequence of historical olive (Olea europaea Linnaeus 1753 subsp. europaea) cultivar Mehras in Jordan. Mitochondrial DNA Part B: Resourses. 2023;8(11):1205-1208. DOI: 10.1080/23802359.2023.2275828Sadder M., Brake M., Ayoub S., Abusini Y., Al-Amad I., Haddad N. Complete mitochondrial genome sequence of historical olive (Olea europaea Linnaeus 1753 subsp. europaea) cultivar Mehras in Jordan. Mitochondrial DNA Part B: Resourses. 2023;8(11):1205-1208. DOI: 10.1080/23802359.2023.2275828Semilet T., Shvachko N., Smirnova N., Shipilina L., Khlestkina E. Using DNA markers to reconstruct the lifetime morphology of barley grains from carbonized cereal crop remains unearthed at Usvyaty Settlement. Biological Communications. 2023;68(1):3-9. DOI: 10.21638/spbu03.2023.101Semilet T., Shvachko N., Smirnova N., Shipilina L., Khlestkina E. Using DNA markers to reconstruct the lifetime morphology of barley grains from carbonized cereal crop remains unearthed at Usvyaty Settlement. Biological Communications. 2023;68(1):3-9. DOI: 10.21638/spbu03.2023.101Schubert M., Ermini L., Sarkissian C., Jónsson H., Ginolhac A., Schaefer R., Martin M.D., Fernández R., Kircher M., McCue M., Willerslev E., Orlando L. Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX. Nature Protocols. 2014;9:1056-1082. DOI: 10.1038/nprot.2014.063Schubert M., Ermini L., Sarkissian C., Jónsson H., Ginolhac A., Schaefer R., Martin M.D., Fernández R., Kircher M., McCue M., Willerslev E., Orlando L. Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX. Nature Protocols. 2014;9:1056-1082. DOI: 10.1038/nprot.2014.063Vallebueno-Estrada M., Hernandez-Robles G.G., González-Orozco E., Lopez-Valdivia I., Rosales Tham T., Vasquez Sanchez V., Swarts K., Dillehay T.D., Vielle-Calzada J.P., Montiel R. Domestication and lowland adaptation of coastal preceramic maize from Paredones, Peru. Elife. 2023;12:e83149. DOI: 10.7554/eLife.83149. Erratum in: Elife. 2023;12:e91314.Vallebueno-Estrada M., Hernandez-Robles G.G., González-Orozco E., Lopez-Valdivia I., Rosales Tham T., Vasquez Sanchez V., Swarts K., Dillehay T.D., Vielle-Calzada J.P., Montiel R. Domestication and lowland adaptation of coastal preceramic maize from Paredones, Peru. Elife. 2023;12:e83149. DOI: 10.7554/eLife.83149. Erratum in: Elife. 2023;12:e91314.Wang X., Zhao X., Zhu J., Wu W. Genome-wide investigation of intron length polymorphisms and their potential as molecular markers in rice (Oryza sativa L.). DNA Research. 2005;12(6):417-427. DOI: 10.1093/dnares/dsi019Wang X., Zhao X., Zhu J., Wu W. Genome-wide investigation of intron length polymorphisms and their potential as molecular markers in rice (Oryza sativa L.). DNA Research. 2005;12(6):417-427. DOI: 10.1093/dnares/dsi019Wales N., Andersen K., Cappellini E., Ávila-Arcos M.C., Gilbert M.T.P. Optimization of DNA recovery and amplification from non-carbonized archaeobotanical remains. PLoS ONE. 2014;9(1):e86827. DOI: 10.1371/journal.pone.0086827Wales N., Andersen K., Cappellini E., Ávila-Arcos M.C., Gilbert M.T.P. Optimization of DNA recovery and amplification from non-carbonized archaeobotanical remains. PLoS ONE. 2014;9(1):e86827. DOI: 10.1371/journal.pone.0086827Wales N., Kistler L. Extraction of ancient DNA from plant remains. Methods Molecular Biology. 2019:45-55. DOI: 10.1007/978-1-4939-9176-1_6Wales N., Kistler L. Extraction of ancient DNA from plant remains. Methods Molecular Biology. 2019:45-55. DOI: 10.1007/978-1-4939-9176-1_6Zakhrabekova S., Gough S.P., Braumann I., Müller A.H., Lundqvist J., Ahmannet K., Dockter C., Matyszczak I., Kurowska M., Druka A., Waugh R., Graner A., Stein N., Steuernagel B., Lundqvist U., Hansson M. Induced mutations in circadian clock regulator Mat-a facilitated short-season adaptation and range extension in cultivated barley. PNAS USA. 2012;109(11):4326-4331. DOI: 10.1073/pnas.1113009109Zakhrabekova S., Gough S.P., Braumann I., Müller A.H., Lundqvist J., Ahmannet K., Dockter C., Matyszczak I., Kurowska M., Druka A., Waugh R., Graner A., Stein N., Steuernagel B., Lundqvist U., Hansson M. Induced mutations in circadian clock regulator Mat-a facilitated short-season adaptation and range extension in cultivated barley. PNAS USA. 2012;109(11):4326-4331. DOI: 10.1073/pnas.1113009109

The authors declare that there are no conflicts of interest present.