A platform for soybean molecular breeding: The utilization of core collections for food security

Plant Molecular Biology

Volumn 83, Issue 1-2, 2013, Pages 41-50

  Qiu, Li Juan ^a   Xing, Li Li ^a   Guo, Yong ^a   Wang, Jun ^a   Jackson, Scott A ^b   Chang, Ru Zhen ^a  

^a INSTITUTE OF PLANT PROTECTION   (China)

^b UNIVERSITY OF GEORGIA   (United States)

Author keywords

Food security; Molecular breeding; Plant genetic resources; Soybean; Utilization of core collection

Indexed keywords

MICROSATELLITE DNA;

ALLELE; ARTICLE; CATERING SERVICE; DATA MINING; DNA SHUFFLING; GENETICS; GENOTYPE; INBREEDING; METHODOLOGY; PHENOTYPE; PHYSIOLOGY; PLANT GENE; PLANT SEED; SINGLE NUCLEOTIDE POLYMORPHISM; SOYBEAN;

ALLELES; DATA MINING; DNA SHUFFLING; FOOD SUPPLY; GENES, PLANT; GENOTYPE; INBREEDING; MICROSATELLITE REPEATS; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; SEEDS; SOYBEANS;

GLYCINE MAX; GLYCINE SOJA;

EID: 84883252302     PISSN: 01674412     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11103-013-0076-6     Document Type: Article

References (82)

1. Balfourier F, Roussel V, Strelchenko P, Exbrayat-Vinson F, Sourdille P, Boutet G, Koenig J, Ravel C, Mitrofanova O, Beckert M, Charmet G (2007) A worldwide bread wheat core collection arrayed in a 384-well plate. Theor Appl Genet 114: 1265-1275.
2. Blair MW, Diaz LM, Buendia HF, Duque MC (2009) Genetic diversity, seed size associations and population structure of a core collection of common beans (Phaseolus vulgaris L.). Theor Appl Genet 119: 955-972.
3. Brown AHD (1989) Core collections: a practical approach to genetic resources management. Genome 31: 818-824.
4. Brown AHD, Grace JP, Speer SS (1987) Designation of a "core" collection of perennial Glycine. Soyb Genet Newsl 14: 59-70.
5. Bruulsema T, Heffer P, Welch R, Cakmak I, Moran K (2012) Fertilizing crops to improve human health: a scientific review. IPNI/IFA, Norcross, GA.
6. Chen S-Y, Zheng G-J, Yang Z-L, Liu R-M, Zhi H-J (2009) Evaluation of resistance to SMV of soybean core collection from Southern China. Chin J Oil Crop Sci 31: 513-516.
7. Cho GT, Yoon MS, Lee J, Baek HJ, Kang JH, Kim TS, Paek NC (2008) Development of a core set of Korean soybean landraces [Glycine max (L.) Merr.]. J Crop Sci Biotech 11: 157-162.
8. Chu Y, Ramos L, Holbrook CC, Ozias-Akins P (2007) Frequency of a loss-of-function mutation in oleoyl-PC desaturase (ahFAD2A) in the mini-core of the US peanut germplasm collection. Crop Sci 47: 2372-2378.
9. Cui Y-H, Qiu L-J, Chang R-Z, Lv W-H (2003) Examination of representativeness of the primary core collection in Huanghuai summer sowing soybean (Glycine max) using SSR. J Plant Genet Resour 4: 9-15.
10. Cui Y-H, Qiu L-J, Chang R-Z, Lv W-H (2004) Representative test for primary core collection of summer sowing soybeans in Huanghuai region of China. Acta Agron Sin 1: 284-288.
11. Duan Y-X, Zhou B, Chen L-J, Wu H-Y (2008) Representative analysis of the establishment of a core collection focused on race 3 of soybean cyst nematode. Soybean Sci 27: 366-372.
12. Fan C, Xing Y, Mao H, Lu T, Han B, Xu C, Li X, Zhang Q (2006) GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet 112: 1164-1171.
13. FAO (2003) Trade reforms and food security: conceptualizing the linkages. Food and Agriculture Organization of the United Nations, Rome.
14. Frankel OH, Brown AHD (1984) Current plant genetic resources-a critical appraisal. Genetics: New Frontiers Vol. IV. Oxford and IBH Publishing, New Delhi.
15. Guo Y, Qiu L-J (2013) Allele-specific marker development and selection efficiencies for both flavonoid 3′-hydroxylase and flavonoid 3′, 5′-hydroxylase genes in soybean subgenus soja. Theor Appl Genet. doi: 10. 1007/s00122-013-2063-3.
16. Guo J-J, Chang R-Z, Zhang J-X, Zhang J-S, Guan R-X, Qiu L-J (2007) Contribution analysis of Japanese soybean germplasm Tokachi-Nagaha to Chinese soybean cultivars. Soybean Sci 26: 807-819.
17. Guo Y, Li Y-H, Hong H-L, Qiu L-J (2013) Establishment of the integrated applied core collection and its comparison with mini core collection in soybean (Glycine max). Crop J (accepted).
18. Hao C-Y, Dong Y-C, Wang L-F, You G-X, Zhang H-N, Gai H-M, Jia J-Z, Zhang X-Y (2008) Establishment and genetic analysis of a wheat core collection in China. Chin Sci Bull 53: 908-915.
19. Hao D, Cheng H, Yin Z, Cui S, Zhang D, Wang H, Yu D (2012) Identification of single nucleotide polymorphisms and haplotypes associated with yield and yield components in soybean (Glycine max) landraces across multiple environments. Theor Appl Genet 124: 447-458.
20. 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 Secur 3: 5-17.
21. Holbrook C, Dong W (2005) Development and evaluation of a mini core collection for the US peanut germplasm collection. Crop Sci 45: 1540-1544.
22. Hu G-Y, Zhang L, Zhang L-Y, Huang Z-P, Li J-K, Hu C (2009) Agronomic characteristics and adaptability of Chinese soybean (Glycine max) core collection in Huanghuai summer sowing ecological region. J Plant Genet Resour 10: 448-452.
23. Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, Li C, Zhu C, Lu T, Zhang Z, Li M, Fan D, Guo Y, Wang A, Wang L, Deng L, Li W, Lu Y, Weng Q, Liu K, Huang T, Zhou T, Jing Y, Lin Z, Buckler ES, Qian Q, Zhang QF, Li J, Han B (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42: 961-967.
24. Huang X, Zhao Y, Wei X, Li C, Wang A, Zhao Q, Li W, Guo Y, Deng L, Zhu C, Fan D, Lu Y, Weng Q, Liu K, Zhou T, Jing Y, Si L, Dong G, Huang T, Lu T, Feng Q, Qian Q, Li J, Han B (2012) Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat Genet 44: 32-39.
25. Hymowitz T, Newell CA (1980) Toxonomy, speciation, domestication, dissemination, germplasm resources, and variation in the genus Glycine. In: Summerfeld RJ, Bunting AH (eds) Advances in legume science. Royal Botanic Gardens, Kew, pp 251-264.
26. Jeong N, Suh SJ, Kim MH, Lee S, Moon JK, Kim HS, Jeong SC (2012) Ln is a key regulator of leaflet shape and number of seeds per pod in soybean. Plant Cell 24: 4807-4818.
27. Jian S, Lu W-G, Wen Z-X, Li H-C, Yuan D-H, Li J-Y, ZHang H, Ye Y-Z (2012) Analysis of protein subunit variation in the mini core collection of cultivated soybean. J Henan Agric Sci 41: 42-45.
28. Jiang H-W, Li C-D, Liu C-Y, Zhang W-B, Qiu P-C, Li W-F, Gao Y-L, Hu G-H, Chen Q-S (2009) Genotype analysis and QTL mapping for tolerance to low temperature in germination by introgression lines in soybean. Acta Agron Sin 35: 1268-1273.
29. Jiao Y, Wang Y, Xue D, Wang J, Yan M, Liu G, Dong G, Zeng D, Lu Z, Zhu X, Qian Q, Li J (2010) Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat Genet 42: 541-544.
30. Jin J, Huang W, Gao JP, Yang J, Shi M, Zhu MZ, Luo D, Lin HX (2008) Genetic control of rice plant architecture under domestication. Nat Genet 40: 1365-1369.
31. Kaga A, Shimizu T, Watanabe S, Tsubokura Y, Katayose Y, Harada K, Vaughan DA, Tomooka N (2012) Evaluation of soybean germplasm conserved in NIAS genebank and development of mini core collections. Breed Sci 61: 566-592.
32. Kashiwagi J, Krishnamurthy L, Upadhyaya HD, Krishna H, Chandra S, Vadez V, Serraj R (2005) Genetic variability of drought-avoidance root traits in the mini-core germplasm collection of chickpea (Cicer arietinum L.). Euphytica 146: 213-222.
33. Kilian B, Graner A (2012) NGS technologies for analyzing germplasm diversity in genebanks. Brief Funct Genomics 11: 38-50.
34. Kim MY, Lee S, van K, Kim TH, Jeong SC, Choi IY, Kim DS, Lee YS, Park D, Ma J, Kim WY, Kim BC, Park S, Lee KA, Kim DH, Kim KH, Shin JH, Jang YE, Kim KD, Liu WX, Chaisan T, Kang YJ, Lee YH, Moon JK, Schmutz J, Jackson SA, Bhak J, Lee SH (2010) Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. Proc Natl Acad Sci USA 107: 22032-22037.
35. Kumar GR, Sakthivel K, Sundaram RM, Neeraja CN, Balachandran SM, Rani NS, Viraktamath BC, Madhav MS (2010) Allele mining in crops: prospects and potentials. Biotechnol Adv 28: 451-461.
36. Lam HM, Xu X, Liu X, Chen W, Yang G, Wong FL, Li MW, He W, Qin N, Wang B, Li J, Jian M, Wang J, Shao G, Sun SS, Zhang G (2010) Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet 42: 1053-1059.
37. Li Y, Shi Y, Cao Y, Wang T (2004) Establishment of a core collection for maize germplasm preserved in Chinese National Genebank using geographic distribution and characterization data. Genet Resour Crop Evol 51: 845-852.
38. Li C-D, Jiang H-W, Liu C-Y, Qiu P-C, Zhang W-B, Li W-F, Gao Y-L, Chen Q-S, Hu G-H (2009) Genotype and QTL analysis of drought tolerance loci for directional population in soybean. Chin J Oil Crop Sci 31: 285-292.
39. 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 Phytol 188: 242-253.
40. Li J, Zhang H, Wang D, Tang B, Chen C, Zhang D, Zhang M, Duan J, Xiong H, Li Z (2011) Rice omics and biotechnology in China. Plant Omics 4: 302-317.
41. Li Y-H, Zhao S-C, Ma J-X, Li D, Yan L, Li J, Qi X-T, Guo X-S, Zhang L, He W-M, Chang R-Z, Liang Q-S, Guo Y, Ye C, Wang X-B, Tao Y, Guan R-X, Wang J-Y, Liu Y-L, Jin L-G, Zhang X-Q, Liu Z-X, Zhang L-J, Chen J, Wang K-J, Nielsen R, Li R-Q, Chen P-Y, Li W-B, Reif JC, Purugganan M, Wang J, Zhang M-C, Wang J, Qiu L-J (2013) Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing. BMC Genomics (accepted).
42. Liu K (2008) Food use of whole soybeans. In: Johnson L, White PJ, Galloway R (eds) Soybeans: chemistry, production, processing, and utilization. AOCS Press, Urbana, IL, pp 441-482.
43. Liu Y, Li X, Wang K (2009) Analysis of the genetic variability for the mini-core collection of Chinese wild soybean (Glycine soja) collection in the National Gene Bank based on SSR markers. J Plant Genet Resour 10: 211-217.
44. Liu Z-X, Yang C-Y, Rea Xu (2011) Analysis of adaptability of soybean mini core collection in huang-huai rivers region in China. Acta Agron Sin 37: 443-451.
45. Long P, Yang H, Yu S-B, Mei H-W, Li Z-K, Luo L-J (2009) Development and conservation of introgression lines in rice. J Plant Genet Resour 10: 51-54.
46. Ma Y-S, Wang W-H, Wang L-X, Ma F-M, Wang P-W, Chang R-Z, Qiu L-J (2006) Genetic diversity of soybean and the establishment of a core collection focused on resistance to soybean cyst nematode. J Integr Plant Biol 48: 722-731.
47. Mi S-J, Qiu L-J, Chang R-Z, Hao Z-B, Guan R-X (2004) Genetic diversity analysis of varieties of Glycine max L. Merr resistant to soybean mosaic virus by SSR fingerprints. Acta Phytopathol Sin 34: 244-253.
48. Oliveira MF, Nelson RL, Geraldi IO, Cruz CD, de Toledo JFF (2010) Establishing a soybean germplasm core collection. Field Crops Res 119: 277-289.
49. Qiu L-J, Cao Y-S, Chang R-Z, Zhou X-A, Wang G-X, Sun J-Y, Xie H, Zhang B, Li X-H, Xu Z-Y, Liu L-F (2003) Establishment of Chinese soybean (G. max) core collection: sampling strategy. Sci Agri Sin 36: 1442-1449.
50. Qiu L-J, Li Y-H, Guan R-X, Liu Z-X, Wang L-X, Chang R-Z (2009) Establishment representative testing and research progress of soybean core collection and mini core collection. Acta Agron Sin 35: 571-579.
51. Qiu L-J, Chen P-Y, Liu Z-X, Li Y-H, Guan R-X, Wang L-H, Chang R-Z (2011a) The worldwide utilization of the Chinese soybean germplasm collection. Plant Genet Resour Charact 9: 109-122.
52. Qiu P-C, Zhang W-B, Li C-D, Jiang H-W, Liu C-Y, Fan D-M, Zeng Q-L, Hu G-H, Chen Q-S (2011b) Genetic overlap of drought-tolerance loci between germination stage and seedling stage analyzed using introgression lines in soybean. Acta Agron Sin 37: 477-483.
53. Schmidt MR, Wei W (2006) Loss of agro-biodiversity, uncertainty, and perceived control: a comparative risk perception study in Austria and China. Risk Anal 26: 455-470.
54. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang XC, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA (2010) Genome sequence of the palaeopolyploid soybean. Nature 463: 178-183.
55. Sharma M, Rathore A, Mangala UN, Ghosh R, Sharma S, Upadhyay HD, Pande S (2012) New sources of resistance to fusarium wilt and sterility mosaic disease in a mini-core collection of pigeonpea germplasm. Eur J Plant Pathol 133: 707-714.
56. Singh G (2010) The soybean: botany, production and uses. CABI Publishing, Wallingford.
57. Song X-E, Li Y-H, Chang R-Z, Guo P-Y, Qiu L-J (2010) Population structure and genetic diversity of mini core collection of cultivated soybean (Glycine max (L.) Merr.) in China. Sci Agric Sin 43: 2209-2219.
58. Tan L, Li X, Liu F, Sun X, Li C, Zhu Z, Fu Y, Cai H, Wang X, Xie D, Sun C (2008) Control of a key transition from prostrate to erect growth in rice domestication. Nat Genet 40: 1360-1364.
59. Tian Z, Wang X, Lee R, Li Y, Specht JE, Nelson RL, McClean PE, Qiu L, Ma J (2010) Artificial selection for determinate growth habit in soybean. Proc Natl Acad Sci USA 107: 8563-8568.
60. Upadhyaya HD, Oritz R (2001) A mini core subset for capturing diversity and promoting utilization of chickpea genetic resources in crop improvement. Theor Appl Genet 102: 1292-1298.
61. Upadhyaya HD, Bramel PJ, Singh S (2001) Development of a chickpea core subset using geographic distribution and quantitative traits. Crop Sci 41: 206-210.
62. Upadhyaya HD, Reddy KN, Gowda CLL, Singh S (2007) Phenotypic diversity in the pigeonpea (Cajanus cajan) core collection. Genet Resour Crop Evol 54: 1167-1184.
63. Upadhyaya HD, Gowda CLL, Sastry DVSSR (2008) Plant genetic resources management: collection, characterization, conservation and utilization. J SAT Agric Res 6: 1-15.
64. Wang B, Chang R-Z, Tao L, Guan R-X, Yan L, Zhang M-H, Feng Z-F, Qiu L-J (2003) Identification of SSR primer numbers for analyzing genetic diversity of Chinese soybean cultivated soybean. Mol Plant Breed 1: 82-88.
65. Wang L-X, Guan Y, Guan R-X, Li Y-H, Ma Y-S, Dong Z-M, Liu X, Zhang H-Y, Zhang Y-Q, Liu Z-X, Chang R-Z, Xu H-M, Li L-H, Lin F-Y, Luan W-J, Ya N-Z, Ning X-C, Zhu L, Cui Y-H, Piao R-H, Liu Y, Chen P-Y, Qiu L-J (2006) Establishment of Chinese soybean (Glycine max) core collections with agronomic traits and SSR markers. Euphytica 151: 215-223.
66. Wang L-L, Guan R-X, Qi Z, Qiu L-J, Luo S-P (2008) Analysis of 11S/7S ratio between soybean mini core collection and cultivars. J Plant Genet Resour 9: 68-72.
67. Wang L-L, Duan C-X, Shuang S-M, Ren G-X (2011a) Determine the isoflavones content in soybean and analysis by near-infrared reflectance spectroscopy (NIRS). Food Sci Technol 36: 242-246.
68. Wang X, Fu G, Yuan S, Zhang H (2011b) Genetic diversity analysis of seed appearance quality of Chinese soybean mini core collection. Procedia Eng 18: 392-397.
69. Wei X, Xu J, Guo H, Jiang L, Chen S, Yu C, Zhou Z, Hu P, Zhai H, Wan J (2010) DTH8 suppresses flowering in rice, influencing plant height and yield potential simultaneously. Plant Physiol 153: 1747-1758.
70. Xia Z, Watanabe S, Yamada T, Tsubokura Y, Nakashima H, Zhai H, Anai T, Sato S, Yamazaki T, Lu S, Wu H, Tabata S, Harada K (2012) Positional cloning and characterization reveal the molecular basis for soybean maturity locus E1 that regulates photoperiodic flowering. Proc Natl Acad Sci USA 109: E2155-E2164.
71. Xie H, Chang R-Z, Cao Y-S, Zhang M-H, Feng Z-F, Qiu L-J (2003) Selection of core SSR loci by using Chinese autumn soybean. Sci Agric Sin 36: 360-366.
72. Yaklich RW, Helm RM, Cockrell G, Herman EM (1999) Analysis of the distribution of the major soybean seed allergens in a core collection of Glycine max accessions. Crop Sci 39: 1444-1447.
73. Yan Z, Chang R-Z, Guan R-X, Liu Z-X, Qiu L-J (2003) Analysis of similarity and difference of various collections of soybean variety Mancangjin by using agronomic traits and SSR markers. J Plant Genet Resour 4: 128-133.
74. Yan L, Feng Y, Yang C-Y, Shi X-L, Zhang M-C (2012) The character of protein and oil content distribution among introgression lines using Jidou12 as recipient parent. Acta Agric Boreali Sin 27: 87-92.
75. Young VR (1991) Soy protein in relation to human protein and amino acid nutrition. J Am Diet Assoc 91: 828-835.
76. Yuan F-J, Jiang Y, Dong D-K, Zhu D-H, Li B-Q, Zhu S-L, Fu X-J (2011) Analysis of isoflavone content in soybean core collection. J Chin Cereals Oils Association 26: 5-8.
77. Zhang X-Y, Pang B-S, You G-X, Wang L-F, Jia J-Z, Dong Y-C (2002) Allelic variation and genetic diversity at Glu-1 loci in Chinese wheat (Triticum aestivum L.) germplasms. Sci Agri Sin 35: 1302-1310.
78. Zhang Y-Q, Guan R-X, Liu Z-X, Chang R-Z, Yao Y-S, Qiu L-J (2006) Identification of Gly m Bd 28 K and Gly m Bd 30 K lacking soybean by random sampling of core collection in soybean. Acta Agron Sin 32: 324-329.
79. Zhang H, Zhang D, Wang M, Sun J, Qi Y, Li J, Wei X, Han L, Qiu Z, Tang S, Li Z (2011a) A core collection and mini core collection of Oryza sativa L. in China. Theor Appl Genet 122: 49-61.
80. Zhang J-W, Han F-X, Sun J-M, Yu F-K, Ma L, Chen M-Y, Zhang J-Y, Yan S-R, Yang H (2011b) Genetic variation of the protein content and correlation between protein content and main agronomic characters of soybean. J Plant Genet Resour 12: 501-506.
81. Zhao J, Fu J-B, Liao H, He Y, Nian H, Hu Y-M, Qiu L-J, Dong Y-S, Yan X-L (2004) Characterization of root architecture in an applied core collection for phosphorus efficiency of soybean germplasm. Chinese Sci Bull 49: 1611-1620.
82. Zhao L, Dong Y, Liu B, Hao S, Wang K, Li X (2005) Establishment of a core collection for the Chinese annual wild soybean (Glycine Soja). Chin Sci Bul 50: 989-996.