Identification of domestication-related loci associated with flowering time and seed size in soybean with the RAD-seq genotyping method

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1 Wahl, V. et al. Regulation of flowering by trehalose-6-phosphate signaling in Arabidopsis thaliana. Science 339,704–707 (2013). 2 Adebisi, M. A. et al. Influence of different seed size fractions on seed germination, seedling emergence and seed yield characters in tropical soybean (Glycine max L. Merrill). J Int Pharm Res 8,26–33 (2013). 3 Sun, C. Q., Wang, X. K., Li, Z. C., Yoshimura, A. & Iwata, N. Comparison of the genetic diversity of common wild rice (Oryza rufipogon Griff.) and cultivated rice (O. sativa L.) using RFLP markers. Theor Appl Genet 102,157–162 (2001). 4 Li, Y. H. et al. Genetic diversity in domesticated soybean (Glycine max) and its wild progenitor (Glycine soja) for simple sequence repeat and single-nucleotide polymorphism loci. New Phytol 188,242–253 (2010). 5 Laidò, G. et al. Genetic diversity and population structure of tetraploid wheats (Triticum turgidum L.) estimated by SSR, DArT and pedigree data. PLoS ONE 8, e67280 (2013). 6 Gupta, P. K., Kulwal, P. L. & Mir, R. R. QTL mapping: methodology and applications in cereal breeding. In Gupta PK, Varshney RK (eds.), Cereal Genomics II pp319–340 (2013). 7 Olsen, K. M. & Wendel, J. F. A bountiful harvest: genomic insights into crop domestication phenotypes. Annu Rev Plant Biol 64,47–70 (2013). 8 Andersson, L. & Georges, M. Domestic-animal genomics: deciphering the genetics of complex traits. Nat Rev Genet 5,202-212 (2004). 9 Doebley, J., Stec, A. & Gustus, C. Teosinte branched1 and the origin of maize: evidence for epistasis and the evolution of dominance. Genetics 141,333–346 (1995). 10 Konishi, S. et al. An SNP caused loss of seed shattering during rice domestication. Science 312,1392–1396 (2006). 11 Grisart, B. et al. Positional candidate cloning of a QTL in dairy cattle: identification of a missense mutation in the bovine DGAT1 gene with major effect on milk yield and composition. Genome Res 12,222–231 (2002). 12 Wang, S. et al. Control of grain size, shape and quality by OsSPL16 in rice. Nat Genet 44,950–594 (2012). 13 Simons, K. J. et al. Molecular characterization of the major wheat domestication gene Q. Genetics 172, 547–555 (2006). 14 Komatsuda, T. et al. Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene. Proc Natl Acad Sci U S A 104,1424–1429 (2007). 15 Fujii, J. et al. Identification of a mutation in porcine ryanodine receptor associated with malignant hyperthermia. Science 253,448–451 (1991). 16 Kim, M. Y., Van, K., Kang, Y. J., Kim, K. H. & Lee, S. H. Tracing soybean domestication history: From nucleotide to genome. Breeding Sci 61,445–452 (2012). 17 Bactrian Camels Genome Sequencing and Analysis Consortium, Jirimutu. et al. Genome sequences of wild and domestic bactrian camels. Nat Commun 3,1202 (2012). 18 He, Z. et al. Two evolutionary histories in the genome of rice: the roles of domestication genes. PLoS Genet 7, e1002100 (2011). 19 Hufford, M. B. et al. Comparative population genomics of maize domestication and improvement. Nat Genet 44,808–811 (2012). 20 Andersson, L. How selective sweeps in domestic animals provide new insight into biological mechanisms. J Intern Med 271,1–14 (2012). 21 Lenser, T. & Theißen, G. Molecular mechanisms involved in convergent crop domestication. Trends Plant Sci 18, 704–714 (2013). 22 Millar, C.D. & Lambert, D.M. Towards a million-year-old genome. Nature 499,34–35 (2013). 23 Zhang, H. et al. Morphological and genetic evidence for early Holocene cattle management in northeastern China. Nat Commun 4,2755 (2013). 24 Moles, A. T. et al. A brief history of seed size. Science 576,307 (2005). 25 Carter, T. E., Nelson, J. R., Sneller, C. H. & Cui, Z. Genetic diversity in soybean. In Boerma HR, Specht JE (eds.) Soybeans: Improvement, Production and Uses, Am. Soc. of Agro, Madison, Wisconsin pp303–416 (2004). 26 Schmutz, J. et al. Genome sequence of the paleopolyploid soybean. Nature 463,178–183 (2010). 27 Li, Q.-G., Zhang, L., Li, C., Dunwell, J. M. & Zhang, Y.-M. Comparative genomics suggests that an ancestral polyploidy event leads to enhanced root nodule symbiosis in the Papilionoideae. Mol Biol Evol 30,2602–2611 (2013). 28 Liu, B. et al. QTL mapping of domestication-related traits in soybean (Glycine max). Ann Bot 100,1027–1038 (2007). 29 Liang, H. Z. et al. Mapping quantitative trait loci for six seed shape traits in soybean. Henan Agriculture Science 45,54–60 (2008). 30 Xu, Y. et al. Mapping quantitative trait loci for seed size traits in soybean (Glycine max L. Merr.). Theor Appl Genet 122,581–594 (2011). 31 Hu, Z. et al. Determination of the genetic architecture of seed size and shape via linkage and association analysis in soybean (Glycine max L. Merr.). Genetica 141,247–254 (2013). 32 Xie, F.-T. et al. Fine mapping of quantitative trait loci for seed size traits in soybean. Mol Breeding, online, DOI 10.1007/s11032-014-0171-7 (2014) 33 Niu, Y. et al. Association mapping for seed size and shape traits in soybean cultivars. Mol Breeding 31,785–794 (2013). 34 Liu, B. et al. Genetic redundancy in soybean photoresponses associated with duplication of the phytochrome A gene. Genetics 180,995–1007 (2008). 35 Watanabe, S. et al. Map-based cloning of the gene associated with the soybean maturity locus E3. Genetics 182, 1251–1262 (2009). 36 Watanabe, S. et al. A map-based cloning strategy employing a residual heterozygous line reveals that the GIGANTEA gene is involved in soybean maturity and flowering. Genetics 188,395–407 (2011). 37 Xia, Z. et al. Positional cloning and characterization reveal the molecular basis for soybean maturity locus E1 that regulates photoperiodic flowering. Proc Natl Acad Sci U S A 109,2155–2164 (2012). 38 Jung, C. H., Wong, C. E. & Singh, M. B. Comparative genomic analysis of soybean flowering genes. PLoS ONE 7,e38250 (2012). 39 Tian, Z. et al. Artificial selection for determinate growth habit in soybean. Proc Natl Acad Sci U S A 107, 8563–8568 (2010). 40 Chen, Y. W. & Nelson, R. L. Genetic variation and relationships among cultivated, wild, and semiwild soybean. Crop Sci 44,316–325 (2004). 41 Kim, M. Y. et al. Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. Proc Natl Acad Sci U S A 107,22032–22037 (2010). 42 Stupar, R. M. Into the wild: The soybean genome meets its undomesticated relative. Proc Natl Acad Sci U S A 107,21947–21948 (2010). 43 Kim, M. Y., Shin, J. H., Kang, Y. J., Shim, S. R. & Lee, S. H. Divergence of flowering genes in soybean. J. Biosciences 37,857–870 (2012).. 44 Chung, W. H. et al. Population structure and domestication revealed by high-depth resequencing of Korean cultivated and wild soybean genomes. DNA Res 21,153–167 (2014). 45 Li, Y. H. et al. Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing. BMC Genomics 14,579 (2013). 46 Krichevsky, A., Zaltsman, A., Lacroix, B. & Citovsky, V. Involvement of KDM1C histone demethylase-OTLD1 otubain-like histone deubiquitinase complexes in plant gene repression. Proc Natl Acad Sci U S A 108, 11157– 11162 (2011). 47 Zhang, X. Y. Chromatin modification in plants. In Wendel JF, et al. (eds), Plant Genome Diversity Volume I 15, 237–255 (2012). 48 Stekhoven, D. J. et al. Causal stability ranking. Bioinformatics 28,2819–2823 (2012). 49 Wang, L.et al. NOT2 proteins promote polymerase II–dependent transcription and interact with multiple micro RNA biogenesis factors in Arabidopsis. Plant Cell 25,715–727 (2013). 50 Sun, X., Shantharaj, D., Kang, X. & Ni, M. Transcriptional and hormonal signaling control of Arabidopsis seed development. Curr Opin Plant Biol 13,611–620 (2010). 51 Gao, M. J., Gropp, G., Wei, S., Hegedus, D. D. & Lydiate, D. J. Combinatorial networks regulating seed development and seed filling. In: KI Sato, ed, Embryogenesis. Rijeka, Croatia: InTech; ISBN 979-953-307-439-8 (2012). 52 Xiao, W. et al. Regulation of seed size by hypomethylation of maternal and paternal genomes. Plant Physiol 142,1160–1168 (2006). 53 Ohto, M. A., Floyd, S. K., Fischer, R. L., Goldberg, R. B. & Harada, J. J. Effects of APETALA2 on embryo, endosperm, and seed coat development determine seed size in Arabidopsis. Sex Plant Reprod 22,277–289 (2009). 54 Zhou, Y. et al. SHORT HYPOCOTYL UNDER BLUE1 associates with MINISEED3 and HAIKU2 promoters in vivo to regulate Arabidopsis seed development. Plant Cell 21,106–117 (2009). 55 Canales, C., Bhatt, A. M., Scott, R. & Dickinson, H. EXS, a putative LRR receptor kinase, regulates male germline cell number and tapetal identity and promotes seed development in Arabidopsis. Curr Biol 12,1718–1727 (2002). 56 Schruff, M. C. et al. The AUXIN RESPONSE FACTOR 2 gene of Arabidopsis links auxin signalling, cell division, and the size of seeds and other organs. Development 133,251–261 (2006). 57 Garcia, D., Fitz Gerald, J. N. & Berger, F. Maternal control of integument cell elongation and zygotic control of endosperm growth are coordinated to determine seed size in Arabidopsis. Plant Cell 17,52–60 (2005). 58 Mizukami, Y. & Fischer, R. L. Plant organ size control: AINTEGUMENTA regulates growth and cell numbers during organogenesis. Proc Natl Acad Sci U S A 97, 942–947 (2000). 59 Lam, H. M. et al. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet 42,1053–1059 (2010). 60 Baird, N. A. et al. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3, e3376 (2008). 61 Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25,1754–1760 (2009). 62 McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20,1297–1303 (2010). 63 Xia, Q. et al. Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science 326,433–436 (2009). 64 Rousset, F. Genepop’007: a complete re-implementation of the genepop software for Windows and Linux. Mol Ecol Resource 8,103–106 (2008). 65 Falush, D., Stephens, M. & Pritchard, J. K. Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol Ecol Notes 7,574–578 (2007). 66 Evanno, G., Regnaut, S. & Goudet, J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14,2611–2620 (2005).