vavilovВавиловский журнал генетики и селекцииVavilov Journal of Genetics and Breeding2500-3259Institute of Cytology and Genetics of Siberian Branch of the RAS10.18699/VJ21.087vavilov-3180Research ArticleБИОТЕХНОЛОГИЯ В ПОСТГЕНОМНУЮ ЭРУBiotechnology in the postgenomic epoch BIOTECHNOLOGY IN THE POSTGENOMIC EPOCHРазработка панели маркеров для генотипирования отечественных сортов сои по генам, контролирующим срок вегетации и реакцию на фотопериодDevelopment of a marker panel for genotyping of domestic soybean cultivars for genes controlling the duration of vegetation and response to photoperiodПерфильевР. Н.Perfil’evR. N.

Новосибирск

Novosibirsk

PerfilyevRN@bionet.nsc.ruhttps://orcid.org/0000-0003-1000-8228ЩербаньА. Б.ShcherbanA. B.

Новосибирск

Novosibirsk

https://orcid.org/0000-0001-8590-847XСалинаЕ. А.SalinaE. A.

Новосибирск

Novosibirsk

Федеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наукРоссияInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of SciencesRussian Federation202103122021257761769Copyright © Перфильев Р.Н., Щербань А.Б., Салина Е.А., 20212021Перфильев Р.Н., Щербань А.Б., Салина Е.А.Perfil’ev R.N., Shcherban A.B., Salina E.A.This work is licensed under a Creative Commons Attribution 4.0 License.https://vavilov.elpub.ru/jour/article/view/3180Cоя (Glycine max L

Cоя (Glycine max L.) – одна из важнейших сельскохозяйственных культур, выращиваемая в большом диапазоне географической широты. В связи с этим в селекции сои необходимо обращать внимание на набор генов, контролирующих переход к фазе цветения, что позволит максимально точно адаптировать генотипы к локальным условиям произрастания. В настоящее время возможности селекции сои по данному признаку значительно расширились благодаря идентификации в ее геноме основных генов (E1–Е4, GmFT2a, GmFT5a), контролирующих процессы цветения и созревания в зависимости от длины дня. Целью нашей работы являлось создание панели маркеров к этим генам, которая может быть использована для быстрого и эффективного генотипирования отечественных сортов сои и отбора растительного материала по признакам чувствительности к длине дня и продолжительности вегетационного периода. Проведено тестирование 10 комбинаций праймеров (как ранее разработанных, так и собственных) для выявления различных аллельных состояний генов E1–Е4, GmFT2a и GmFT5a на выборке из 10 сортов сои из различных групп спелости. В итоге выявлено пять комбинаций доминантных и рецессивных аллелей по генам E1–E4: 1) е1-nl(e1-as)/e2-ns/е3-tr(e3-fs)/е4; 2) e1-as/e2-ns/е3-tr/Е4; 3) e1-as/e2-ns/Е3-На/е4; 4) E1/e2-ns/е3-tr/Е4; 5) е1-nl/e2-ns/Е3-На/Е4. Проанализированные сорта содержали наиболее распространенные аллели генов GmFT2a и GmFT5a, за исключением сорта Кассиди, у которого был обнаружен редкий доминантный аллель GmFT5a-H4. Степень скороспелости сортов положительно коррелировала с количеством рецессивных генов E1–Е4, что согласуется с данными зарубежных авторов, полученными на выборках сортов из Японии и Северного Китая. Таким образом, разработанная панель маркеров может успешно использоваться в селекции сои на скороспелость и чувствительность к фотопериоду.

 

 

Soybean, Glycine max L., is one of the most important agricultural crops grown in a wide range of latitude. In this regard, in soybean breeding, it is necessary to pay attention to the set of genes that control the transition to the flowering stage, which will make it possible to adapt genotypes to local growing conditions as accurately as possible. The possibilities of soybean breeding for this trait have now significantly expanded due to identification of the main genes (E1–E4, GmFT2a, GmFT5a) that control the processes of flowering and maturation in soybean, depending on the day length. The aim of this work was to develop a panel of markers for these genes, which could be used for a rapid and efficient genotyping of domestic soybean cultivars and selection of plant material based on sensitivity to photoperiod and the duration of vegetation. Combinations of 10 primers, both previously developed and our own, were tested to identify different alleles of the E1–E4, GmFT2a, and GmFT5a genes using 10 soybean cultivars from different maturity groups. As a result, 5 combinations of dominant and recessive alleles for the E1–E4 genes were identified: (1) e1-nl(e1-as)/ e2-ns/e3-tr(e3-fs)/e4; (2) e1-as/e2-ns/e3-tr/E4; (3) e1-as/e2-ns/E3-Ha/e4; (4) E1/e2-ns/e3-tr/E4; (5) e1-nl/e2-ns/E3-Ha/E4. The studied cultivars contained the most common alleles of the GmFT2a and GmFT5a genes, with the exception of the ‘Cassidi’ cultivar having a rare dominant allele GmFT5a-H4. The degree of earliness of cultivars positively correlated with the number of recessive genes E1–E4, which is consistent with the data of foreign authors on different sets of cultivars from Japan and North China. Thus, the developed panel of markers can

фотопериодсрок цветениямаркер генааллель-специфичные праймерынесинонимичная заменаиндельсортсоягруппа спелостиphotoperiodflowering periodgene markerallele-specific primersnonsynonymous substitutionindelcultivarsoybeanmaturity groupThis work was supported by the Russian Science Foundation, project 21-76-30003. Multiplication of plants was carried out in Laboratory of artificial plant growth (ICG SB RAS) in the framework of the budget project 0259-2021-0012ReferencesAgarkova S.N., Novikova N.E., Belyaeva R.V., Golovina E.V., Belyaeva Zh.A., Tsukanova Z.R., Mitkina N.I. Features of the formation of productivity and adaptive reactions in leguminous crop varieties with recessive alleles of genes. Trudy po Prikladnoy Botanike, Genetike i Selektsii = Proceedings on Applied Botany, Genetics and Breeding. 2016;177(2):22-39. DOI 10.30901/2227-8834-2016-222-39. (in Russian)Agarkova S.N., Novikova N.E., Belyaeva R.V., Golovina E.V., Belyaeva Zh.A., Tsukanova Z.R., Mitkina N.I. Features of the formation of productivity and adaptive reactions in leguminous crop varieties with recessive alleles of genes. Trudy po Prikladnoy Botanike, Genetike i Selektsii = Proceedings on Applied Botany, Genetics and Breeding. 2016;177(2):22-39. DOI 10.30901/2227-8834-2016-222-39. (in Russian)Gorissen S.H.M., Crombag J.J.R., Senden J.M.G., Waterval W.A.H., Bierau J., Verdijk L.B., Loon L.J.C. Protein content and amino acid composition of commercially available plant-based protein isolates. Amino Acids. 2018;50(12):1685-1695. DOI 10.1007/s00726-0182640-5.Gorissen S.H.M., Crombag J.J.R., Senden J.M.G., Waterval W.A.H., Bierau J., Verdijk L.B., Loon L.J.C. Protein content and amino acid composition of commercially available plant-based protein isolates. Amino Acids. 2018;50(12):1685-1695. DOI 10.1007/s00726-0182640-5.Guo G., Xu K., Zhang X., Zhu J., Lu M., Chen F., Liu L., Xi Z.Y., Bachmair A., Chen Q., Fu Y.F. Extensive analysis of GmFTL and GmCOL expression in northern soybean cultivars in field conditions. PLoS One. 2015;10(9):e0136601. DOI 10.1371/journal.pone.0136601.Guo G., Xu K., Zhang X., Zhu J., Lu M., Chen F., Liu L., Xi Z.Y., Bachmair A., Chen Q., Fu Y.F. Extensive analysis of GmFTL and GmCOL expression in northern soybean cultivars in field conditions. PLoS One. 2015;10(9):e0136601. DOI 10.1371/journal.pone.0136601.Hoffman J.R., Falvo M.J. Protein – which is best? J. Sports Sci. Med. 2004;3(3):118-130.Hoffman J.R., Falvo M.J. Protein – which is best? J. Sports Sci. Med. 2004;3(3):118-130.Jia H., Jiang B., Wu C., Lu W., Hou W., Sun S., Yan H., Han T. Maturity group classification and maturity locus genotyping of early-maturing soybean varieties from high-latitude cold regions. PLoS One. 2014;9(4):e94139. DOI 10.1371/journal.pone.0094139.Jia H., Jiang B., Wu C., Lu W., Hou W., Sun S., Yan H., Han T. Maturity group classification and maturity locus genotyping of early-maturing soybean varieties from high-latitude cold regions. PLoS One. 2014;9(4):e94139. DOI 10.1371/journal.pone.0094139.Jiang B., Nan H., Gao Y., Tang L., Yue Y., Lu S., Ma L., Cao D., Sun S., Wang J., Wu C., Yuan X., Hou W., Kong F., Han T., Liu B. Allelic combinations of soybean maturity loci E1, E2, E3 and E4 result in diversity of maturity and adaptation to different latitudes. PLoS One. 2014;9(8):e106042. DOI 10.1371/journal.pone.0106042.Jiang B., Nan H., Gao Y., Tang L., Yue Y., Lu S., Ma L., Cao D., Sun S., Wang J., Wu C., Yuan X., Hou W., Kong F., Han T., Liu B. Allelic combinations of soybean maturity loci E1, E2, E3 and E4 result in diversity of maturity and adaptation to different latitudes. PLoS One. 2014;9(8):e106042. DOI 10.1371/journal.pone.0106042.Jiang B., Yue Y., Gao Y., Ma L., Sun S., Wu C., Hou W., Lam H.M., Han T. GmFT2a polymorphism and maturity diversity in soybeans. PLoS One. 2013;8(10):e77474. DOI 10.1371/journal.pone.0077474.Jiang B., Yue Y., Gao Y., Ma L., Sun S., Wu C., Hou W., Lam H.M., Han T. GmFT2a polymorphism and maturity diversity in soybeans. PLoS One. 2013;8(10):e77474. DOI 10.1371/journal.pone.0077474.Jiang B., Zhang S., Song W., Khan M., Sun S., Zhang C., Wu T., Wu C., Han T. Natural variations of FT family genes in soybean varieties covering a wide range of maturity groups. BMC Genom. 2019; 20(1):230. DOI 10.1186/s12864-019-5577-5.Jiang B., Zhang S., Song W., Khan M., Sun S., Zhang C., Wu T., Wu C., Han T. Natural variations of FT family genes in soybean varieties covering a wide range of maturity groups. BMC Genom. 2019; 20(1):230. DOI 10.1186/s12864-019-5577-5.Kiseleva A.A., Shcherban A.B., Leonova I.N., Frenkel Z., Salina E.A. Identification of new heading date determinants in wheat 5B chromosome. BMC Plant Biol. 2016;16(8):35-46. DOI 10.1186/s12870015-0688-х.Kiseleva A.A., Shcherban A.B., Leonova I.N., Frenkel Z., Salina E.A. Identification of new heading date determinants in wheat 5B chromosome. BMC Plant Biol. 2016;16(8):35-46. DOI 10.1186/s12870015-0688-х.Kong F., Liu B., Xia Z., Sato S., Kim B.M., Watanabe S., Yamada T., Tabata S., Kanazawa A., Harada K., Abe J. Two coordinately regulated homologs of FLOWERING LOCUS T are involved in the control of photoperiodic flowering in soybean. Plant Physiol. 2010; 154(3):1220-1231. DOI 10.1104/pp.110.160796.Kong F., Liu B., Xia Z., Sato S., Kim B.M., Watanabe S., Yamada T., Tabata S., Kanazawa A., Harada K., Abe J. Two coordinately regulated homologs of FLOWERING LOCUS T are involved in the control of photoperiodic flowering in soybean. Plant Physiol. 2010; 154(3):1220-1231. DOI 10.1104/pp.110.160796.Korsakov N.I. Soybean Genetic Collection Catalog. Leningrad, 1973. (in Russian)Korsakov N.I. Soybean Genetic Collection Catalog. Leningrad, 1973. (in Russian)Liu B., Kanazawa A., Matsumura H., Takahashi R., Harada K., Abe J. Genetic redundancy in soybean photoresponses associated with duplication of phytochrome A gene. Genetics. 2008;180(2):995-1007. DOI 10.1534/genetics.108.092742.Liu B., Kanazawa A., Matsumura H., Takahashi R., Harada K., Abe J. Genetic redundancy in soybean photoresponses associated with duplication of phytochrome A gene. Genetics. 2008;180(2):995-1007. DOI 10.1534/genetics.108.092742.Saindon G., Voldeng H.D., Beversdorf W.D., Buzzell R.I. Genetic control of long daylength response in soybean. Crop Sci. 1989; 29(6):1436-1439. DOI 10.2135/cropsci1989.0011183X002900060021x.Saindon G., Voldeng H.D., Beversdorf W.D., Buzzell R.I. Genetic control of long daylength response in soybean. Crop Sci. 1989; 29(6):1436-1439. DOI 10.2135/cropsci1989.0011183X002900060021x.Samanfar B., Molnar S.J., Charette M., Schoenrock A., Dehne F., Golshani A., Belzile F., Cober E.R. Mapping and identification of a potential candidate gene for a novel maturity locus, E10, in soybean. Theor. Appl. Genet. 2017;130(2):377-390. DOI 10.1007/s00122016-2819-7.Samanfar B., Molnar S.J., Charette M., Schoenrock A., Dehne F., Golshani A., Belzile F., Cober E.R. Mapping and identification of a potential candidate gene for a novel maturity locus, E10, in soybean. Theor. Appl. Genet. 2017;130(2):377-390. DOI 10.1007/s00122016-2819-7.Takeshima R., Hayashi T., Zhu J., Zhao C., Xu M., Yamaguchi N., Sayama T., Ishimoto M., Kong L., Shi X., Liu B., Tian Z., Yamada T., Kong F., Abe J. A soybean quantitative trait locus that promotes flowering under long days is identified as FT5a, a FLOWERING LOCUS T ortholog. J. Exp. Bot. 2016;67(17):5247-5258. DOI 10.1093/jxb/erw283.Takeshima R., Hayashi T., Zhu J., Zhao C., Xu M., Yamaguchi N., Sayama T., Ishimoto M., Kong L., Shi X., Liu B., Tian Z., Yamada T., Kong F., Abe J. A soybean quantitative trait locus that promotes flowering under long days is identified as FT5a, a FLOWERING LOCUS T ortholog. J. Exp. Bot. 2016;67(17):5247-5258. DOI 10.1093/jxb/erw283.Tsubokura Y., Watanabe S., Xia Z., Kanamori H., Yamagata H., Kaga A., Katayose Y., Abe J., Ishimoto M., Harada K. Natural variation in the genes responsible for maturity loci E1, E2, E3 and E4 in soybean. Ann. Bot. 2014;13(3):429-441. DOI 10.1093/aob/mct269.Tsubokura Y., Watanabe S., Xia Z., Kanamori H., Yamagata H., Kaga A., Katayose Y., Abe J., Ishimoto M., Harada K. Natural variation in the genes responsible for maturity loci E1, E2, E3 and E4 in soybean. Ann. Bot. 2014;13(3):429-441. DOI 10.1093/aob/mct269.Vavilov N.I. Centers of origin of cultivated plants. Trudy po Prikladnoy Botanike, Genetike i Selektsii = Proceedings on Applied Botany, Genetics and Breeding. 1926;16(2):248. (in Russian)Vavilov N.I. Centers of origin of cultivated plants. Trudy po Prikladnoy Botanike, Genetike i Selektsii = Proceedings on Applied Botany, Genetics and Breeding. 1926;16(2):248. (in Russian)Wang F., Nan H., Chen L., Fang C., Zhang H., Su T., Li S., Cheng Q., Dong L., Liu B., Kong F., Lu S. A new dominant locus, E11, controls early flowering time and maturity in soybean. Mol. Breed. 2019; 39(5):70. DOI 10.1007/s11032-019-0978.Wang F., Nan H., Chen L., Fang C., Zhang H., Su T., Li S., Cheng Q., Dong L., Liu B., Kong F., Lu S. A new dominant locus, E11, controls early flowering time and maturity in soybean. Mol. Breed. 2019; 39(5):70. DOI 10.1007/s11032-019-0978.Watanabe S., Harada K., Abe J. Genetic and molecular bases of photoperiod responses of flowering in soybean. Breed Sci. 2012;61(5): 531-543. DOI 10.1270/jsbbs.61.531.Watanabe S., Harada K., Abe J. Genetic and molecular bases of photoperiod responses of flowering in soybean. Breed Sci. 2012;61(5): 531-543. DOI 10.1270/jsbbs.61.531.Watanabe S., Hideshima R., Xia Z., Tsubokura Y., Sato S., Nakamoto Y., Yamanaka N., Takahashi R., Ishimoto M., Anai T., Tabata S., Harada K. Map-based cloning of the gene associated with the soybean maturity locus E3. Genetics. 2009;182(4):1251-1262. DOI 10.1534/genetics.108.098772.Watanabe S., Hideshima R., Xia Z., Tsubokura Y., Sato S., Nakamoto Y., Yamanaka N., Takahashi R., Ishimoto M., Anai T., Tabata S., Harada K. Map-based cloning of the gene associated with the soybean maturity locus E3. Genetics. 2009;182(4):1251-1262. DOI 10.1534/genetics.108.098772.Watanabe S., Xia Z., Hideshima R, Tsubokura Y., Sato S., Yamanaka N., Takahashi R., Anai T., Tabata S., Kitamura K., Harada K. A map-based cloning strategy employing a residual heterozygous line reveals that the GIGANTEA gene is involved in soybean maturity and flowering. Genetics. 2011;188(2):395-407. DOI 10.1534/genetics.110.125062.Watanabe S., Xia Z., Hideshima R, Tsubokura Y., Sato S., Yamanaka N., Takahashi R., Anai T., Tabata S., Kitamura K., Harada K. A map-based cloning strategy employing a residual heterozygous line reveals that the GIGANTEA gene is involved in soybean maturity and flowering. Genetics. 2011;188(2):395-407. DOI 10.1534/genetics.110.125062.Wu F., Sedivy E.J., Price W.B., Haider W., Hanzawa Y. Evolutionary trajectories of duplicated FT homologues and their roles in soybean domestication. Plant J. 2017;90(5):941-953. DOI 10.1111/tpj.13521.Wu F., Sedivy E.J., Price W.B., Haider W., Hanzawa Y. Evolutionary trajectories of duplicated FT homologues and their roles in soybean domestication. Plant J. 2017;90(5):941-953. DOI 10.1111/tpj.13521.Xia Z., Watanabe S., Yamada T., Tsubokura Y., Nakashima H., Zhai H., Anai T., Sato S., Yamazaki T., Lü S., Wu H., Tabata S., Harada K. Positional cloning and characterization reveal the molecular basis for soybean maturity locus E1 that regulates photoperiodic flowering. Proc. Natl. Acad. Sci. USA. 2012;109(32):E2155-E2164. DOI 10.1073/pnas.1117982109.Xia Z., Watanabe S., Yamada T., Tsubokura Y., Nakashima H., Zhai H., Anai T., Sato S., Yamazaki T., Lü S., Wu H., Tabata S., Harada K. Positional cloning and characterization reveal the molecular basis for soybean maturity locus E1 that regulates photoperiodic flowering. Proc. Natl. Acad. Sci. USA. 2012;109(32):E2155-E2164. DOI 10.1073/pnas.1117982109.Xu M., Xu Z., Liu B., Kong F., Tsubokura Y., Watanabe S., Xia Z., Harada K., Kanazawa A., Yamada T., Abe J. Genetic variation in four maturity genes affects photoperiod insensitivity and PHYA-regulated post-flowering responses of soybean. BMC Plant Biol. 2013; 13:91. DOI 10.1186/1471-2229-13-91.Xu M., Xu Z., Liu B., Kong F., Tsubokura Y., Watanabe S., Xia Z., Harada K., Kanazawa A., Yamada T., Abe J. Genetic variation in four maturity genes affects photoperiod insensitivity and PHYA-regulated post-flowering responses of soybean. BMC Plant Biol. 2013; 13:91. DOI 10.1186/1471-2229-13-91.Xu M., Yamagishi N., Zhao C., Takeshima R., Kasai M., Watanabe S., Kanazawa A., Yoshikawa N., Liu B., Yamada T., Abe J. The soybean-specific maturity gene E1 family of floral repressors controls night-break responses through down-regulation of FLOWERING LOCUS T orthologs. Plant Physiol. 2015;168(4):1735-1746. DOI 10.1104/pp.15.00763.Xu M., Yamagishi N., Zhao C., Takeshima R., Kasai M., Watanabe S., Kanazawa A., Yoshikawa N., Liu B., Yamada T., Abe J. The soybean-specific maturity gene E1 family of floral repressors controls night-break responses through down-regulation of FLOWERING LOCUS T orthologs. Plant Physiol. 2015;168(4):1735-1746. DOI 10.1104/pp.15.00763.Zhai H., Lü S., Liang S., Wu H., Zhang X., Liu B., Kong F., Yuan X., Li J., Xia Z. GmFT4, a homolog of FLOWERING LOCUS T, is positively regulated by E1 and functions as a flowering repressor in soybean. PLoS One. 2014;9(2):e89030. DOI 10.1371/journal.pone.0089030.Zhai H., Lü S., Liang S., Wu H., Zhang X., Liu B., Kong F., Yuan X., Li J., Xia Z. GmFT4, a homolog of FLOWERING LOCUS T, is positively regulated by E1 and functions as a flowering repressor in soybean. PLoS One. 2014;9(2):e89030. DOI 10.1371/journal.pone.0089030.Zhao C., Takeshima R., Zhu J., Xu M., Sato M., Watanabe S., Kanazawa A., Liu B., Kong F., Yamada T., Abe J. A recessive allele for delayed flowering at the soybean maturity locus E9 is a leaky allele of FT2a, a FLOWERING LOCUS T ortholog. BMC Plant Biol. 2016; 16(1):1-15. DOI 10.1186/s12870-016-0704-9.Zhao C., Takeshima R., Zhu J., Xu M., Sato M., Watanabe S., Kanazawa A., Liu B., Kong F., Yamada T., Abe J. A recessive allele for delayed flowering at the soybean maturity locus E9 is a leaky allele of FT2a, a FLOWERING LOCUS T ortholog. BMC Plant Biol. 2016; 16(1):1-15. DOI 10.1186/s12870-016-0704-9.Zhu J., Takeshima R., Harigai K., Xu M., Kong F., Liu B., Kanazawa A., Yamada T., Abe J. Loss of function of the E1-Like-b gene associates with early flowering under long-day conditions in soybean. Front. Plant Sci. 2019;9:1867. DOI 10.3389/fpls.2018.01867.Zhu J., Takeshima R., Harigai K., Xu M., Kong F., Liu B., Kanazawa A., Yamada T., Abe J. Loss of function of the E1-Like-b gene associates with early flowering under long-day conditions in soybean. Front. Plant Sci. 2019;9:1867. DOI 10.3389/fpls.2018.01867.Zhukovsky P.M. Cultivated Plants and Their Relatives. Leningrad: Kolos Publ., 1964. (in Russian)Zhukovsky P.M. Cultivated Plants and Their Relatives. Leningrad: Kolos Publ., 1964. (in Russian)

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