GmHs1-1, encoding a calcineurin-like protein, controls hard-seededness in soybean

Nature Genetics

Volumn 47, Issue 8, 2015, Pages 939-943

  Sun, Lianjun ^a   Miao, Zhenyan ^a   Cai, Chunmei ^b   Zhang, Dajian ^a   Zhao, Meixia ^a   Wu, Yanyan ^b   Zhang, Xueling ^b   Swarm, Stephen A ^c   Zhou, Liwen ^d   Zhang, Zhanyuan J ^d   Nelson, Randall L ^c,e   Ma, Jianxin ^a,b  

^a PURDUE UNIVERSITY   (United States)

^b QINGDAO AGRICULTURAL UNIVERSITY   (China)

^c UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^d UNIVERSITY OF MISSOURI   (United States)

^e AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CALCINEURIN; CALCIUM; GMHS1 1 PROTEIN; MEMBRANE PROTEIN; METHIONINE; SOYBEAN PROTEIN; UNCLASSIFIED DRUG;

ALLELE; ARTICLE; ARTIFICIAL SELECTION; CHROMOSOME 2; CHROMOSOME 9; CONTROLLED STUDY; EXON; GENE FLOW; GENE LINKAGE DISEQUILIBRIUM; GENETIC ASSOCIATION; HAPLOTYPE; HARDNESS; INTROGRESSION; INTRON; LANDRACE; NONHUMAN; PERMEABILITY; PLANT CHROMOSOME; POINT MUTATION; PRIORITY JOURNAL; PROMOTER REGION; QUANTITATIVE TRAIT; QUANTITATIVE TRAIT LOCUS; SEED HUSK; SELECTIVE SWEEP; SIGNAL TRANSDUCTION; SOYBEAN; TRANSGENE; WILD PLANT; CHROMOSOME MAP; CLASSIFICATION; GENE EXPRESSION REGULATION; GENETIC COMPLEMENTATION; GENETICS; IN SITU HYBRIDIZATION; METABOLISM; MOLECULAR GENETICS; MUTATION; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT SEED; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; TRANSGENIC PLANT;

GLYCINE MAX; GLYCINE SOJA;

BASE SEQUENCE; CALCINEURIN; CALCIUM; CHROMOSOME MAPPING; CHROMOSOMES, PLANT; GENE EXPRESSION REGULATION, PLANT; GENETIC COMPLEMENTATION TEST; IN SITU HYBRIDIZATION; MOLECULAR SEQUENCE DATA; MUTATION; PHYLOGENY; PLANTS, GENETICALLY MODIFIED; PROMOTER REGIONS, GENETIC; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEEDS; SEQUENCE HOMOLOGY, NUCLEIC ACID; SOYBEAN PROTEINS; SOYBEANS; SPECIES SPECIFICITY;

EID: 84938287526     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.3339     Document Type: Article

References (45)

1. Fuller, D.Q. & Allaby, R. Seed dispersal and crop domestication: Shattering, germination and seasonality in evolution under cultivation. Annual Plant Reviews 38, 238-295 (2009).
2. Abbo, S. et al. Plant domestication versus crop evolution: A conceptual framework for cereals and grain legumes. Trends Plant Sci. 19, 351-360 (2014).
3. Rolston, M.P. Water impermeable seed dormancy. Bot. Rev. 44, 365-396 (1978).
4. Foley, M.E. Seed dormancy: An update on terminology, physiological genetics, and quantitative trait loci regulating germinability. Weed Sci. 49, 305-317 (2001).
5. Ladizinsky, G. The origin of lentil and its wild gene pool. Euphytica 28, 179-187 (1979).
6. Gepts, P. & Debouck, D.G. In Common Beans: Research for Crop Improvement Origin, domestication, and evolution of the common bean, Phaseolus vulgaris. (eds. Voysest, O. & Van Schoonhoven, A.) pp. 7-53 (CAB International, 1991).
7. Abbo, S., Shtienberg, D., Lichtenzveig, J., Lev-Yadun, S. & Gopher, A. The chickpea, summer cropping, and a new model for pulse domestication in the ancient near east. Q. Rev. Biol. 78, 435-448 (2003).
8. Liu, B. et al. QTL Mapping of domestication-related traits in soybean (Glycine max). Ann. Bot. 100, 1027-1038 (2007).
9. Weeden, N.F. Genetic changes accompanying the domestication of Pisum sativum: Is there a common genetic basis to the "domestication syndrome" for legumes? Ann. Bot. 100, 1017-1025 (2007).
10. Andargie, M., Pasquet, R.S., Gowda, B.S., Muluvi, G.M. & Timko, M.P. Molecular mapping of QTLs for domestication-related traits in cowpea (V. unguiculata (L.) Walp.). Euphytica 200, 401-412 (2014).
11. Keim, P., Diers, B.W. & Shoemaker, R.C. Genetic analysis of soybean hard seededness with molecular markers. Theor. Appl. Genet. 79, 465-469 (1990).
12. Carter, T., Nelson, R., Sneller, C. & Cui, Z. Genetic diversity in soybean. In Soybeans: Improvement Production and Uses 3rd edn. (eds. Boerma, H.R. & Specht, J.E.) pp. 303-416 (American Society of Agronomy-Crop Science Society of America-Soil Science Society of America, 2004).
13. Li, Y. et al. Genetic structure and diversity of cultivated soybean (Glycine max (L.) Merr.) landraces in China. Theor. Appl. Genet. 117, 857-871 (2008).
14. Potts, H.C., Duangpatra, J., Hairston, W.G. & Delouche, J.C. Some influences of hardseededness on soybean seed quality. Crop Sci. 18, 221-224 (1978).
15. Saio, K., Arai, K. & Watanabe, T. Fine structure of soybean seed coat and its changes on cooking. Cereal Science Today 18, 197-201 (1973).
16. Saio, K. Soybeans resistant to water absorption. Cereal Foods World 21, 168-173 (1976).
17. Zhang, B. et al. Quantitative trait loci mapping of seed hardness in soybean. Crop Sci. 48, 1341-1349 (2008).
18. Watanabe, S., Tajuddin, T., Yamanaka, N., Hayashi, M. & Harada, K. Analysis of QTLs for reproductive development and seed quality traits in soybean using recombinant inbred lines. Breed. Sci. 54, 399-407 (2004).
19. Schmutz, J. et al. Genome sequence of the paleopolyploid soybean (Glycine max (L.) Merr.). Nature 463, 178-183 (2010).
20. 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. USA 107, 22032-22037 (2010).
21. Li, Y.H. et al. De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nat. Biotechnol. 32, 1045-1052 (2014).
22. Lush, W.M. & Evan, L.T. The seed coats of cowpeas and other grain legumes: Structure in relation to function. Field Crops Res. 3, 267-286 (1980).
23. Miller, S.S., Bowman, L.A., Gijzen, M. & Miki, B.L.A. Early development of the seed coat of soybean (Glycine max). Ann. Bot. 84, 297-304 (1999).
24. Harris, W.H. Comparative ultrastructure of developing seed coats of 'hard-seeded' and 'soft-seeded' varieties of soybean, Glycine max (L.) Merril. Bot. Gaz. 148, 324-331 (1987).
25. Russi, L., Cocks, P.S. & Roberts, E.H. Coat thickness and hard-seededness in some Medicago and Trifolium species. Seed Sci. Res. 2, 243-249 (1992).
26. Valenti, G.S., Melone, L., Ferro, M. & Bozzini, A. Comparative studies on testa structure of 'hard-seeded' and 'soft-seeded' varieties of Lupinus angustifolius L. (Leguminosae) and on mechanisms of water entry. Seed Science and Technology 17, 563-581 (1989).
27. Kingsbury, T.J. & Cunningham, K.W. A conserved family of calcineurin regulators. Genes Dev. 14, 1595-1604 (2000).
28. Rusnak, F. & Mertz, P. Calcineurin: Form and function. Physiol. Rev. 80, 1483-1521 (2000).
29. Aramburu, J., Heitman, J. & Crabtree, G.R. Calcineurin: A central controller of signaling in eukaryotes. EMBO Rep. 5, 343-348 (2004).
30. Zhou, Z. et al. Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat. Biotechnol. 33, 408-414 (2015).
31. Hyten, D.L. et al. Impacts of genetic bottlenecks on soybean genome diversity. Proc. Natl. Acad. Sci. USA 103, 16666-16671 (2006).
32. Tian, Z. et al. Artificial selection for determinate growth habit in soybean. Proc. Natl. Acad. Sci. USA 107, 8563-8568 (2010).
33. Nakamura, T., Yang, D., Kalaiselvi, S., Uematsu, Y. & Takahashi, R. Genetic analysis of net-like cracking in soybean seed coats. Euphytica 133, 179-184 (2003).
34. Ma, F., Cholewa, E., Mohamed, T., Peterson, C.A. & Gijzen, M. Cracks in the palisade cuticle of soybean seed coats correlate with their permeability to water. Ann. Bot. 94, 213-228 (2004).
35. Ping, J. et al. Dt2 is a gain-of-function MADS-domain factor gene that specifies semideterminacy in soybean. Plant Cell 26, 2831-2842 (2014).
36. Edgar, R.C. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797 (2004).
37. Flores, T. et al. Silencing of GmFAD3 gene by siRNA leads to low ?-linolenic acids (18:3) of fad3-mutant phenotype in soybean [Glycine max (Merr.)]. Transgenic Res. 17, 839-850 (2008).
38. Shi, H. et al. BR-SIGNALING KINASE1 physically associates with FLAGELLIN SENSING2 and regulates plant innate immunity in Arabidopsis. Plant Cell 25, 1143-1157 (2013).
39. Yang, J. et al. The I-TASSER Suite: Protein structure and function prediction. Nat. Methods 12, 7-8 (2015).
40. Krogh, A., Larsson, B., von Heijne, G. & Sonnhammer, E.L. Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J. Mol. Biol. 305, 567-580 (2001).
41. Ziegler, G. et al. Ionomic screening of field-grown soybean identifies mutants with altered seed elemental composition. Plant Genome doi:10.3835/plantgenome2012.07.0012 (2013).
42. Bradbury, P.J. et al. TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23, 2633-2635 (2007).
43. Olsen, K.M. et al. Selection under domestication: Evidence for a sweep in the rice waxy genomic region. Genetics 173, 975-983 (2006).
44. Bosse, M. et al. Genomic analysis reveals selection for Asian genes in European pigs following human-mediated introgression. Nat. Commun. 5, 4392 (2014).
45. Chia, J.M. et al. Maize HapMap2 identifies extant variation from a genome in flux. Nat. Genet. 44, 803-807 (2012).