Genome Re-sequencing of Semi-wild Soybean Reveals a Complex Soja Population Structure and Deep Introgression

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2014 Sep 30

PMID 25265539

Citations 12

Authors

Jie Qiu

Yu Wang

Sanling Wu

Ying-Ying Wang

Chu-Yu Ye

Xuefei Bai

Zefeng Li

Chenghai Yan

Weidi Wang

Ziqiang Wang

Qingyao Shu

Jiahua Xie

Suk-Ha Lee

Longjiang Fan

Affiliations

Soon will be listed here.

Abstract

Semi-wild soybean is a unique type of soybean that retains both wild and domesticated characteristics, which provides an important intermediate type for understanding the evolution of the subgenus Soja population in the Glycine genus. In this study, a semi-wild soybean line (Maliaodou) and a wild line (Lanxi 1) collected from the lower Yangtze regions were deeply sequenced while nine other semi-wild lines were sequenced to a 3-fold genome coverage. Sequence analysis revealed that (1) no independent phylogenetic branch covering all 10 semi-wild lines was observed in the Soja phylogenetic tree; (2) besides two distinct subpopulations of wild and cultivated soybean in the Soja population structure, all semi-wild lines were mixed with some wild lines into a subpopulation rather than an independent one or an intermediate transition type of soybean domestication; (3) high heterozygous rates (0.19-0.49) were observed in several semi-wild lines; and (4) over 100 putative selective regions were identified by selective sweep analysis, including those related to the development of seed size. Our results suggested a hybridization origin for the semi-wild soybean, which makes a complex Soja population structure.

Citing Articles

Circadian clock regulation in soybean senescence: a transcriptome analysis of early and late senescence types.

Basnet P, Lee S, Moon K, Park N, Lee G, Lee S BMC Genomics. 2025; 26(1):56.

PMID: 39838316 PMC: 11748321. DOI: 10.1186/s12864-024-11095-3.

Identification and Characterization of Key Genes Responsible for Weedy and Cultivar Growth Types in Soybean.

Basnet P, Um T, Roy N, Cho W, Park S, Park K Front Genet. 2022; 13:805347.

PMID: 35281824 PMC: 8907156. DOI: 10.3389/fgene.2022.805347.

Progress in soybean functional genomics over the past decade.

Zhang M, Liu S, Wang Z, Yuan Y, Zhang Z, Liang Q Plant Biotechnol J. 2021; 20(2):256-282.

PMID: 34388296 PMC: 8753368. DOI: 10.1111/pbi.13682.

Impacts of genomic research on soybean improvement in East Asia.

Li M, Wang Z, Jiang B, Kaga A, Wong F, Zhang G Theor Appl Genet. 2019; 133(5):1655-1678.

PMID: 31646364 PMC: 7214498. DOI: 10.1007/s00122-019-03462-6.

Is Chickpea a Potential Substitute for Soybean? Phenolic Bioactives and Potential Health Benefits.

de Camargo A, Favero B, Morzelle M, Franchin M, Alvarez-Parrilla E, de la Rosa L Int J Mol Sci. 2019; 20(11).

PMID: 31146372 PMC: 6600242. DOI: 10.3390/ijms20112644.

References

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

Chen K, Wallis J, McLellan M, Larson D, Kalicki J, Pohl C . BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods. 2009; 6(9):677-81. PMC: 3661775. DOI: 10.1038/nmeth.1363. View

Saski C, Lee S, Daniell H, Wood T, Tomkins J, Kim H . Complete chloroplast genome sequence of Gycine max and comparative analyses with other legume genomes. Plant Mol Biol. 2005; 59(2):309-22. DOI: 10.1007/s11103-005-8882-0. View

SMIT A . The origin of interspersed repeats in the human genome. Curr Opin Genet Dev. 1996; 6(6):743-8. DOI: 10.1016/s0959-437x(96)80030-x. View

Price A, Jones N, Pevzner P . De novo identification of repeat families in large genomes. Bioinformatics. 2005; 21 Suppl 1:i351-8. DOI: 10.1093/bioinformatics/bti1018. View

Close P, Shoemaker R, Keim P . Distribution of restriction site polymorphism within the chloroplast genome of the genus Glycine, subgenus Soja. Theor Appl Genet. 2013; 77(6):768-76. DOI: 10.1007/BF00268325. View

Hao D, Cheng H, Yin Z, Cui S, Zhang D, Wang H . Identification of single nucleotide polymorphisms and haplotypes associated with yield and yield components in soybean (Glycine max) landraces across multiple environments. Theor Appl Genet. 2011; 124(3):447-58. DOI: 10.1007/s00122-011-1719-0. View

Nei M, Miller J . A simple method for estimating average number of nucleotide substitutions within and between populations from restriction data. Genetics. 1990; 125(4):873-9. PMC: 1204113. DOI: 10.1093/genetics/125.4.873. View

Langmead B, Salzberg S . Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012; 9(4):357-9. PMC: 3322381. DOI: 10.1038/nmeth.1923. View

10.

Yang K, Jeong N, Moon J, Lee Y, Lee S, Kim H . Genetic analysis of genes controlling natural variation of seed coat and flower colors in soybean. J Hered. 2010; 101(6):757-68. DOI: 10.1093/jhered/esq078. View

11.

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N . The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16):2078-9. PMC: 2723002. DOI: 10.1093/bioinformatics/btp352. View

12.

Du Z, Zhou X, Ling Y, Zhang Z, Su Z . agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res. 2010; 38(Web Server issue):W64-70. PMC: 2896167. DOI: 10.1093/nar/gkq310. View

13.

Evanno G, Regnaut S, Goudet J . Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol. 2005; 14(8):2611-20. DOI: 10.1111/j.1365-294X.2005.02553.x. View

14.

Schmutz J, Cannon S, Schlueter J, Ma J, Mitros T, Nelson W . Genome sequence of the palaeopolyploid soybean. Nature. 2010; 463(7278):178-83. DOI: 10.1038/nature08670. View

15.

Xu H, Abe J, Gai Y, Shimamoto Y . Diversity of chloroplast DNA SSRs in wild and cultivated soybeans: evidence for multiple origins of cultivated soybean. Theor Appl Genet. 2003; 105(5):645-653. DOI: 10.1007/s00122-002-0972-7. View

16.

Hyten D, Song Q, Zhu Y, Choi I, Nelson R, Costa J . Impacts of genetic bottlenecks on soybean genome diversity. Proc Natl Acad Sci U S A. 2006; 103(45):16666-71. PMC: 1624862. DOI: 10.1073/pnas.0604379103. View

17.

Kelley D, Salzberg S . Detection and correction of false segmental duplications caused by genome mis-assembly. Genome Biol. 2010; 11(3):R28. PMC: 2864568. DOI: 10.1186/gb-2010-11-3-r28. View

18.

Axelsson E, Ratnakumar A, Arendt M, Maqbool K, Webster M, Perloski M . The genomic signature of dog domestication reveals adaptation to a starch-rich diet. Nature. 2013; 495(7441):360-4. DOI: 10.1038/nature11837. View

19.

Boetzer M, Pirovano W . Toward almost closed genomes with GapFiller. Genome Biol. 2012; 13(6):R56. PMC: 3446322. DOI: 10.1186/gb-2012-13-6-r56. View

20.

Rubin C, Zody M, Eriksson J, Meadows J, Sherwood E, Webster M . Whole-genome resequencing reveals loci under selection during chicken domestication. Nature. 2010; 464(7288):587-91. DOI: 10.1038/nature08832. View