1. Fried HG, Narayanan S, Fallen B. Evaluation of soybean [
Glycine max (L.) Merr.] genotypes for yield, water use efficiency, and root traits. PLoS One 2019;14:e0212700.
2. Shin DH. Utilization of soybean as food stuffs in Korea. (El-Shemy H, ed.). In: Soybean and Nutrition London: IntechOpen, 2011. pp. 81–110.
3. Zhang Y, Yu C, Lin J, Liu J, Liu B, Wang J,
et al. OsMPH1 regulates plant height and improves grain yield in rice. PLoS One 2017;12:e0180825.
4. Milach SC, Federizzi LC. Dwarfing genes in plant improvement. Adv Agron 2001;73:35–63.
5. Kuraparthy V, Sood S, Gill BS. Genomic targeting and mapping of tiller inhibition gene (tin3) of wheat using ESTs and synteny with rice. Funct Integr Genomics 2008;8:33–42.
6. Ku L, Wei X, Zhang S, Zhang J, Guo S, Chen Y. Cloning and characterization of a putative TAC1 ortholog associated with leaf angle in maize (
Zea mays L.). PLoS One 2011;6:e20621.
7. Dardick C, Callahan A, Horn R, Ruiz KB, Zhebentyayeva T, Hollender C,
et al. PpeTAC1 promotes the horizontal growth of branches in peach trees and is a member of a functionally conserved gene family found in diverse plants species. Plant J 2013;75:618–630.
8. Cooper RL, Martin RJ, Walker AK, Schmitthenner AF. Registration of ‘Hobbit’ soybean. Crop Sci 1991;31:231.
9. Egan AN, Schlueter J, Spooner DM. Applications of next-generation sequencing in plant biology. Am J Bot 2012;99:175–185.
10. Brautigam A, Gowik U. What can next generation sequencing do for you? Next generation sequencing as a valuable tool in plant research. Plant Biol (Stuttg) 2010;12:831–841.
11. Qi J, Liu X, Shen D, Miao H, Xie B, Li X,
et al. A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. Nat Genet 2013;45:1510–1515.
12. Li H, Peng Z, Yang X, Wang W, Fu J, Wang J,
et al. Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels. Nat Genet 2013;45:43–50.
13. Ossowski S, Schneeberger K, Clark RM, Lanz C, Warthmann N, Weigel D. Sequencing of natural strains of
Arabidopsis thaliana with short reads. Genome Res 2008;18:2024–2033.
14. Kim MY, Lee S, Van K, Kim TH, Jeong SC, Choi IY,
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 2010;107:22032–22037.
16. Tang W, Wu T, Ye J, Sun J, Jiang Y, Yu J,
et al. SNP-based analysis of genetic diversity reveals important alleles associated with seed size in rice. BMC Plant Biol 2016;16:93.
17. Xu X, Liu X, Ge S, Jensen JD, Hu F, Li X,
et al. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol 2011;30:105–111.
19. Mace ES, Tai S, Gilding EK, Li Y, Prentis PJ, Bian L,
et al. Whole-genome sequencing reveals untapped genetic potential in Africa's indigenous cereal crop sorghum. Nat Commun 2013;4:2320.
20. Lam HM, Xu X, Liu X, Chen W, Yang G, Wong FL,
et al. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet 2010;42:1053–1059.
21. Chung WH, Jeong N, Kim J, Lee WK, Lee YG, Lee SH,
et al. Population structure and domestication revealed by high-depth resequencing of Korean cultivated and wild soybean genomes. DNA Res 2014;21:153–167.
22. Maldonado dos Santos JV, Valliyodan B, Joshi T, Khan SM, Liu Y, Wang J,
et al. Evaluation of genetic variation among Brazilian soybean cultivars through genome resequencing. BMC Genomics 2016;17:110.
23. Zheng LY, Guo XS, He B, Sun LJ, Peng Y, Dong SS,
et al. Genome-wide patterns of genetic variation in sweet and grain sorghum (
Sorghum bicolor). Genome Biol 2011;12:R114.
24. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W,
et al. Genome sequence of the palaeopolyploid soybean. Nature 2010;463:178–183.
26. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A,
et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010;20:1297–1303.
28. Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L,
et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of
Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 2012;6:80–92.
29. Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R,
et al. The
Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res 2012;40:D1202–D1210.
30. Ramakrishna G, Kaur P, Nigam D, Chaduvula PK, Yadav S, Talukdar A,
et al. Genome-wide identification and characterization of InDels and SNPs in
Glycine max and
Glycine soja for contrasting seed permeability traits. BMC Plant Biol 2018;18:141.
31. Singh BD. Principles of Genetics. New Delhi: Kalyani Publishers, 1992.
32. Liu Y, Du H, Li P, Shen Y, Peng H, Liu S,
et al. Pan-genome of wild and cultivated soybeans. Cell 2020;182:162–176.
33. Xie M, Chung CY, Li MW, Wong FL, Wang X, Liu A,
et al. A reference-grade wild soybean genome. Nat Commun 2019;10:1216.
36. Shirano Y, Kachroo P, Shah J, Klessig DF. A gain-of-function mutation in an
Arabidopsis Toll Interleukin1 receptor-nucleotide binding site-leucine-rich repeat type R gene triggers defense responses and results in enhanced disease resistance. Plant Cell 2002;14:3149–3162.
37. van Wersch R, Li X, Zhang Y. Mighty dwarfs:
Arabidopsis autoimmune mutants and their usages in genetic dissection of plant immunity. Front Plant Sci 2016;7:1717.
38. Gao M, Wang X, Wang D, Xu F, Ding X, Zhang Z,
et al. Regulation of cell death and innate immunity by two receptor-like kinases in
Arabidopsis. Cell Host Microbe 2009;6:34–44.
40. Noutoshi Y, Ito T, Seki M, Nakashita H, Yoshida S, Marco Y,
et al. A single amino acid insertion in the WRKY domain of the
Arabidopsis TIR-NBS-LRR-WRKY-type disease resistance protein SLH1 (sensitive to low humidity 1) causes activation of defense responses and hypersensitive cell death. Plant J 2005;43:873–888.
41. Yoshioka K, Kachroo P, Tsui F, Sharma SB, Shah J, Klessig DF. Environmentally sensitive, SA-dependent defense responses in the cpr22 mutant of
Arabidopsis. Plant J 2001;26:447–459.
42. Zhou F, Menke FL, Yoshioka K, Moder W, Shirano Y, Klessig DF. High humidity suppresses ssi4-mediated cell death and disease resistance upstream of MAP kinase activation, H2O2 production and defense gene expression. Plant J 2004;39:920–932.
43. Marino G, Funk C. Matrix metalloproteinases in plants: a brief overview. Physiol Plant 2012;145:196–202.
44. Audonnet L, Shen Y, Zhou DX. JMJ24 antagonizes histone H3K9 demethylase IBM1/JMJ25 function and interacts with RNAi pathways for gene silencing. Gene Expr Patterns 2017;25-26:1–7.
45. Luttgeharm KD, Chen M, Mehra A, Cahoon RE, Markham JE, Cahoon EB. Overexpression of
Arabidopsis ceramide synthases differentially affects growth, sphingolipid metabolism, programmed cell death, and mycotoxin resistance. Plant Physiol 2015;169:1108–1117.
46. Miao Y, Jiang J, Ren Y, Zhao Z. The single-stranded DNA-binding protein WHIRLY1 represses WRKY53 expression and delays leaf senescence in a developmental stage-dependent manner in
Arabidopsis. Plant Physiol 2013;163:746–756.
47. Yonekura-Sakakibara K, Hanada K. An evolutionary view of functional diversity in family 1 glycosyltransferases. Plant J 2011;66:182–193.