Differentiation and evolution among geographic and seasonal eco-populations of soybean germplasm in Southern China
Zhipeng Zhang A , Weiying Zeng B , Zhaoyan Cai B , Zhenguang Lai B , Yanzhu Su A , Guangnan Xing A , Wubin Wang A , Zudong Sun B C and Junyi Gai
A C
+ Author Affiliations
- Author Affiliations
A Soybean Research Institute, Nanjing Agricultural University, MARA National Center for Soybean Improvement, MARA Key Laboratory of Biology and Genetic Improvement of Soybean, National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
B Institute of Economic Crops, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China.
C Corresponding authors. Email: sunzudong639@163.com; sri@njau.edu.cn
Crop and Pasture Science 70(2) 121-132 https://doi.org/10.1071/CP18459
Submitted: 11 April 2018 Accepted: 9 December 2018 Published: 4 February 2019
Abstract
Soybean (Glycine max (L.) Merrill) germplasm in Southern China is extremely diverse. In order to explore the differentiation and evolution among geographic sowing-seasonal ecotypes of the Southern China Soybean Germplasm Population (SCSGP), we tested a sample set of accessions comprising 359 of the spring-sowing (SP) ecotype and 341 of the summer–autumn-sowing (SA) ecotype for their flowering date and sensitivity to seasonal photo-thermal changes in Nanning, Guangxi, China. The sample set and another 175 wild annual accessions were genotyped with 60 representative simple sequence repeat (SSR) markers. The SCSGP is characterised by its geographic differentiation (four geo-regional ecotypes), especially its sowing-seasonal differentiation (SA and SP ecotypes), and their combinations (eight geo-seasonal eco-populations). The ecological differentiation coincided with genetic differentiation in terms of allele richness and genetic distance. Neighbour-joining clustering among accessions by using SSRs indicated SA varieties to be the primitive ecotype relative to SP. The SA ecotype of Eco-region III (SA-III) was the most primitive among the eight geo-seasonal eco-populations, from which evolved SA-IV, and then SA-VI and SA-V. The SP ecotype was mainly evolved from its older SA counterpart, starting from SP-III emerging from SA-III accompanied by its introduction to Eco-region IV and other boarder regions. The evolutionary relationship among the geo-seasonal eco-populations was validated further with the analysis of multi-population specific-present alleles, which supports the hypothesis of Southern China origin of cultivated soybeans.
Additional keywords: allele-richness, cluster analysis.
References
Carter TE, Hymowitz T, Nelson RL (2004) Biogeography, local adaptation, Vavilov, and genetic diversity in soybean. In ‘Biological resources and migration’. (Ed. D Werner) pp. 47–59. (Springer: Berlin)Dong YS, Zhao LM, Liu B, Wang ZW, Jin ZQ, Sun H (2004) The genetic diversity of cultivated soybean grown in China. Theoretical and Applied Genetics 108, 931–936.
| The genetic diversity of cultivated soybean grown in China.Crossref | GoogleScholarGoogle Scholar | 14595543PubMed |
Dong DK, Fu XJ, Yuan FJ, Chen PY, Zhu SL, Li BQ, Yang QH, Yu XM, Zhu DH (2014) Genetic diversity and population structure of vegetable soybean (Glycine max (L.) Merr.) in China as revealed by SSR markers. Genetic Resources and Crop Evolution 61, 173–183.
| Genetic diversity and population structure of vegetable soybean (Glycine max (L.) Merr.) in China as revealed by SSR markers.Crossref | GoogleScholarGoogle Scholar |
Doyle JJ, Doyle JL, Hortoriun LB (1990) Isolation of plant DNA from fresh tissue. Focus 12, 13–15.
Gai JY, Wang YS (2001) A study on the varietal eco-regions of soybeans in China. Scientia Agricultura 34, 139–145.
Gai JY, Xu DH, Gao Z, Shimamoto Y, Abe J, Fukushi H, Kitajima S (2000) Studies on the evolutionary relationship among eco-types of G. max and G. soja in China. Acta Agronomica Sinica 26, 513–520.
Gregory TR (2008) Understanding evolutionary trees. Evolution 1, 121–137.
| Understanding evolutionary trees.Crossref | GoogleScholarGoogle Scholar |
Guo J, Wang Y, Song C, Zhou J, Qiu L, Huang H, Wang Y (2010) A single origin and moderate bottleneck during domestication of soybean (Glycine max): implications from microsatellites and nucleotide sequences. Annals of Botany 106, 505–514.
| A single origin and moderate bottleneck during domestication of soybean (Glycine max): implications from microsatellites and nucleotide sequences.Crossref | GoogleScholarGoogle Scholar | 20566681PubMed |
Han Y, Zhao X, Liu D, Li Y, Lightfoot DA, Yang Z, Zhao L, Zhao G, Wang Z, Huang L, Zhang Z, Qiu L, Zheng H, Li W (2016) Domestication footprints anchor genomic regions of agronomic importance in soybeans. New Phytologist 209, 871–884.
| Domestication footprints anchor genomic regions of agronomic importance in soybeans.Crossref | GoogleScholarGoogle Scholar | 26479264PubMed |
Hartman GL, West ED, Herman TK (2011) Crops that feed the world 2. Soybean—worldwide production, use, and constraints caused by pathogens and pests. Food Security 3, 5–17.
| Crops that feed the world 2. Soybean—worldwide production, use, and constraints caused by pathogens and pests.Crossref | GoogleScholarGoogle Scholar |
Kim MY, Van K, Kang YJ, Kim KH, Lee SH (2012) Tracing soybean domestication history: from nucleotide to genome. Breeding Science 61, 445–452.
| Tracing soybean domestication history: from nucleotide to genome.Crossref | GoogleScholarGoogle Scholar | 23136484PubMed |
Kong F, Nan H, Cao D, Li Y, Wu F, Wang J, Lu S, Yuan X, Cober ER, Abe J, Liu B (2014) A new dominant gene E9 conditions early flowering and maturity in soybean. Crop Science 54, 2529–2535.
| A new dominant gene E9 conditions early flowering and maturity in soybean.Crossref | GoogleScholarGoogle Scholar |
Leamy LJ, Lee CR, Song Q, Mujacic I, Luo Y, Chen CY, Li C, Kjemtrup S, Song BH (2016) Environmental versus geographical effects on genomic variation in wild soybean (Glycine soja) across its native range in northeast Asia. Ecology and Evolution 6, 6332–6344.
| Environmental versus geographical effects on genomic variation in wild soybean (Glycine soja) across its native range in northeast Asia.Crossref | GoogleScholarGoogle Scholar | 27648247PubMed |
Lee GA, Crawford GW, Liu L, Sasaki Y, Chen X (2011) Archaeological soybean (Glycine max) in East Asia: does size matter? PLoS One 6, e26720
| Archaeological soybean (Glycine max) in East Asia: does size matter?Crossref | GoogleScholarGoogle Scholar | 22073186PubMed |
Li FS (1994) Study on origin and evolution of soybean. Soybean Science 13, 61–66.
Li Y, Gai JY (2017) Genetic basis for the development of soybean to the tropics. Chinese Bulletin of Botany 52, 389–393.
Li ZL, Nelson RL (2002) RAPD marker diversity among cultivated and wild soybean accessions from four Chinese provinces. Crop Science 42, 1737–1742.
| RAPD marker diversity among cultivated and wild soybean accessions from four Chinese provinces.Crossref | GoogleScholarGoogle Scholar |
Li Y, Guan R, Liu Z, Ma Y, Wang L, Li L, Lin F, Luan W, Chen P, Yan Z, Guan Y, Zhu L, Ning X, Smulders MJM, Li W, Piao R, Cui Y, Yu Z, Guan M, Chang R, Hou A, Shi A, Zhang B, Zhu S, Qiu L (2008) Genetic structure and diversity of cultivated soybean (Glycine max (L.) Merr.) landraces in China. Theoretical and Applied Genetics 117, 857–871.
| Genetic structure and diversity of cultivated soybean (Glycine max (L.) Merr.) landraces in China.Crossref | GoogleScholarGoogle Scholar | 18587557PubMed |
Li YH, Li W, Zhang C, Yang L, Chang RZ, Gaut BS, Qiu LJ (2010) Genetic diversity in domesticated soybean (Glycine max) and its wild progenitor (Glycine soja) for simple sequence repeat and single-nucleotide polymorphism loci. New Phytologist 188, 242–253.
| Genetic diversity in domesticated soybean (Glycine max) and its wild progenitor (Glycine soja) for simple sequence repeat and single-nucleotide polymorphism loci.Crossref | GoogleScholarGoogle Scholar | 20618914PubMed |
Li JY, Sun S, Han TF (2012) Methods and quantitative parameters for evaluating the adaptability of soybean varieties to environmental factors. Chinese Journal of Oil Crop Sciences 34, 671–677.
Liu KJ, Muse SV (2005) PowerMarker: An integrated analysis environment for genetic marker analysis. Bioinformatics 21, 2128–2129.
| PowerMarker: An integrated analysis environment for genetic marker analysis.Crossref | GoogleScholarGoogle Scholar |
Liu X, Wu J, Ren H, Qi Y, Li C, Cao J, Zhang X, Zhang Z, Cai Z, Gai J (2017) Genetic variation of world soybean maturity date and geographic distribution of maturity groups. Breeding Science 67, 221–232.
| Genetic variation of world soybean maturity date and geographic distribution of maturity groups.Crossref | GoogleScholarGoogle Scholar | 28744175PubMed |
Lu S, Zhao X, Hu Y, Liu S, Nan H, Li X, Fang C, Cao D, Shi X, Kong L, Su T, Zhang F, Li S, Wang Z, Yuan X, Cober ER, Weller JL, Liu B, Hou X, Tian Z, Kong F (2017) Natural variation at the soybean J locus improves adaptation to the tropics and enhances yield. Nature Genetics 49, 773–779.
| Natural variation at the soybean J locus improves adaptation to the tropics and enhances yield.Crossref | GoogleScholarGoogle Scholar | 28319089PubMed |
Meng S, He J, Zhao T, Xing G, Li Y, Yang S, Lu J, Wng Y, Gai J (2016) Detecting the QTL-allele system of seed isoflavone content in Chinese soybean landrace population for optimal cross design and gene system exploration. Theoretical and Applied Genetics 129, 1557–1576.
| Detecting the QTL-allele system of seed isoflavone content in Chinese soybean landrace population for optimal cross design and gene system exploration.Crossref | GoogleScholarGoogle Scholar | 27189002PubMed |
Piao RH, Liu ZX, Guan RX, Chang RZ, Hao ZB, Qiu LJ (2005) Genetic diversity of southern summer soybean in Chinese coastal revealed by SSR markers. Journal of Agricultural Biotechnology 13, 435–440.
Qu MN, Wu CX, Guo YH (2010) Advance in the establishment of experimental systems for the studies of photo-periodism in soybean. Soybean Science 29, 332–335.
Sedivy EJ, Wu F, Hanzawa Y (2017) Soybean domestication: the origin, genetic architecture and molecular bases. New Phytologist 214, 539–553.
| Soybean domestication: the origin, genetic architecture and molecular bases.Crossref | GoogleScholarGoogle Scholar | 28134435PubMed |
Shete S, Tiwari H, Elston RC (2000) On estimating the heterozygosity and polymorphism information content value. Theoretical Population Biology 57, 265–271.
| On estimating the heterozygosity and polymorphism information content value.Crossref | GoogleScholarGoogle Scholar | 10828218PubMed |
Song QJ, Marek LF, Shoemaker RC, Lark KG, Concibido VC, Delannay X, Specht JE, Cregan PB (2004) A new integrated genetic linkage map of the soybean. Theoretical and Applied Genetics 109, 122–128.
| A new integrated genetic linkage map of the soybean.Crossref | GoogleScholarGoogle Scholar | 14991109PubMed |
Song Q, Jia G, Zhu Y, Grant D, Nelson RT, Hwang EY, Hyten DL, Cregan PB (2010) Abundance of SSR motifs and development of candidate polymorphic SSR markers (BARCSOYSSR_1.0) in Soybean. Crop Science 50, 1950–1960.
| Abundance of SSR motifs and development of candidate polymorphic SSR markers (BARCSOYSSR_1.0) in Soybean.Crossref | GoogleScholarGoogle Scholar |
Tasma IM, Lorenzen LL, Green DE, Shoemaker RC (2001) Mapping genetic loci for flowering time, maturity, and photoperiod insensitivity in soybean. Molecular Breeding 8, 25–35.
| Mapping genetic loci for flowering time, maturity, and photoperiod insensitivity in soybean.Crossref | GoogleScholarGoogle Scholar |
Wang GX (1981) Ecological classification of the Chinese soybean cultivars. Scientia Agricultura Sinica 3, 39–46.
Wang YS, Zhang MC (2000) Response to short photoperiod of days to flowering of soybean ecotypes of China. Journal of Hebei Agricultural Sciences 4, 25–29.
Wang L, Guan R, Liu ZX, Chang R, Qiu L (2006) Genetic diversity of Chinese cultivated soybean revealed by SSR markers. Crop Science 46, 1032–1038.
| Genetic diversity of Chinese cultivated soybean revealed by SSR markers.Crossref | GoogleScholarGoogle Scholar |
Wen Z, Zhao T, Ding Y, Gai J (2009) Genetic diversity, geographic differentiation and evolutionary relationship among ecotypes of Glycine max and G. soja in China. Science Bulletin 54, 4393–4403.
| Genetic diversity, geographic differentiation and evolutionary relationship among ecotypes of Glycine max and G. soja in China.Crossref | GoogleScholarGoogle Scholar |
Xu DH, Abe J, Gai JY, Shimamoto Y (2002) Diversity of chloroplast DNA SSRs in wild and cultivated soybeans: evidence for multiple origins of cultivated soybean. Theoretical and Applied Genetics 105, 645–653.
| Diversity of chloroplast DNA SSRs in wild and cultivated soybeans: evidence for multiple origins of cultivated soybean.Crossref | GoogleScholarGoogle Scholar |
Zhang J, Zhao TJ, Gai JY (2009) Analysis of genetic structure differentiation of released soybean cultivar population and specificity of subpopulations in China. Scientia Agricultura Sinica 42, 1901–1910.
Zhang Y, He J, Wang Y, Xing G, Zhao J, Li Y, Yang S, Palmer RG, Zhao T, Gai J (2015) Establishment of a 100-seed weight quantitative trait locus-allele matrix of the germplasm population for optimal recombination design in soybean breeding programmes. Journal of Experimental Botany 66, 6311–6325.
| Establishment of a 100-seed weight quantitative trait locus-allele matrix of the germplasm population for optimal recombination design in soybean breeding programmes.Crossref | GoogleScholarGoogle Scholar | 26163701PubMed |
Zhang H, Zeng F, Zou Z, Zhang Z, Li Y (2017) Nitrogen uptake and transfer in a soybean/maize intercropping system in the karst region of southwest China. Ecology and Evolution 7, 8419–8426.
| Nitrogen uptake and transfer in a soybean/maize intercropping system in the karst region of southwest China.Crossref | GoogleScholarGoogle Scholar | 29075459PubMed |
Zhao TJ, Gai JY (2004) The origin and evolution of cultivated soybean [Glycine max (L.) Merr.]. Scientia Agricultura Sinica 37, 954–962.
Zhuang BC, Xu B, Lu QH (1986) Effect of day and night temperature on development of wild, semi-wild and cultivated soybean in China. Soybean Science 5, 289–298.
