Genetic variation and genetic complexity of nodule occupancy in soybean inoculated with USDA110 and USDA123 rhizobium strains.
GWAS
Nodulation restriction
Soybean
USDA110
USDA123
rhizobium
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
04 Sep 2023
04 Sep 2023
Historique:
received:
14
04
2023
accepted:
26
08
2023
medline:
6
9
2023
pubmed:
5
9
2023
entrez:
4
9
2023
Statut:
epublish
Résumé
Symbiotic nitrogen fixation differs among Bradyrhizobium japonicum strains. Soybean inoculated with USDA123 has a lower yield than strains known to have high nitrogen fixation efficiency, such as USDA110. In the main soybean-producing area in the Midwest of the United States, USDA123 has a high nodule incidence in field-grown soybean and is competitive but inefficient in nitrogen fixation. In this study, a high-throughput system was developed to characterize nodule number among 1,321 Glycine max and 69 Glycine soja accessions single inoculated with USDA110 and USDA123. Seventy-three G. max accessions with significantly different nodule number of USDA110 and USDA123 were identified. After double inoculating 35 of the 73 accessions, it was observed that PI189939, PI317335, PI324187B, PI548461, PI562373, and PI628961 were occupied by USDA110 and double-strain nodules but not by USDA123 nodules alone. PI567624 was only occupied by USDA110 nodules, and PI507429 restricted all strains. Analysis showed that 35 loci were associated with nodule number in G. max when inoculated with strain USDA110 and 35 loci with USDA123. Twenty-three loci were identified in G. soja when inoculated with strain USDA110 and 34 with USDA123. Only four loci were common across two treatments, and each locus could only explain 0.8 to 1.5% of phenotypic variation. High-throughput phenotyping systems to characterize nodule number and occupancy were developed, and soybean germplasm restricting rhizobium strain USDA123 but preferring USDA110 was identified. The larger number of minor effects and a small few common loci controlling the nodule number indicated trait genetic complexity and strain-dependent nodulation restriction. The information from the present study will add to the development of cultivars that limit USDA123, thereby increasing nitrogen fixation efficiency and productivity.
Sections du résumé
BACKGROUND
BACKGROUND
Symbiotic nitrogen fixation differs among Bradyrhizobium japonicum strains. Soybean inoculated with USDA123 has a lower yield than strains known to have high nitrogen fixation efficiency, such as USDA110. In the main soybean-producing area in the Midwest of the United States, USDA123 has a high nodule incidence in field-grown soybean and is competitive but inefficient in nitrogen fixation. In this study, a high-throughput system was developed to characterize nodule number among 1,321 Glycine max and 69 Glycine soja accessions single inoculated with USDA110 and USDA123.
RESULTS
RESULTS
Seventy-three G. max accessions with significantly different nodule number of USDA110 and USDA123 were identified. After double inoculating 35 of the 73 accessions, it was observed that PI189939, PI317335, PI324187B, PI548461, PI562373, and PI628961 were occupied by USDA110 and double-strain nodules but not by USDA123 nodules alone. PI567624 was only occupied by USDA110 nodules, and PI507429 restricted all strains. Analysis showed that 35 loci were associated with nodule number in G. max when inoculated with strain USDA110 and 35 loci with USDA123. Twenty-three loci were identified in G. soja when inoculated with strain USDA110 and 34 with USDA123. Only four loci were common across two treatments, and each locus could only explain 0.8 to 1.5% of phenotypic variation.
CONCLUSIONS
CONCLUSIONS
High-throughput phenotyping systems to characterize nodule number and occupancy were developed, and soybean germplasm restricting rhizobium strain USDA123 but preferring USDA110 was identified. The larger number of minor effects and a small few common loci controlling the nodule number indicated trait genetic complexity and strain-dependent nodulation restriction. The information from the present study will add to the development of cultivars that limit USDA123, thereby increasing nitrogen fixation efficiency and productivity.
Identifiants
pubmed: 37667205
doi: 10.1186/s12864-023-09627-4
pii: 10.1186/s12864-023-09627-4
pmc: PMC10478483
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
520Subventions
Organisme : U.S. Department of Agriculture-Agricultural Research Service
ID : 8042-21000-289-00D and 8042-21000-285-00D
Informations de copyright
© 2023. BioMed Central Ltd., part of Springer Nature.
Références
BMC Genomics. 2014 Jan 02;15:1
pubmed: 24382143
Appl Environ Microbiol. 1987 Nov;53(11):2631-5
pubmed: 16347482
New Phytol. 2020 Oct;228(2):651-666
pubmed: 32521047
Bioinformatics. 2007 Oct 1;23(19):2633-5
pubmed: 17586829
G3 (Bethesda). 2015 Jul 28;5(10):1999-2006
pubmed: 26224783
New Phytol. 2020 Oct;228(2):667-681
pubmed: 32533710
Plant Dis. 2021 Sep;105(9):2426-2434
pubmed: 33560880
Plant Biol (Stuttg). 2016 May;18(3):537-41
pubmed: 26848549
Bioinformatics. 2005 Jan 15;21(2):263-5
pubmed: 15297300
BMC Genomics. 2016 Jan 06;17:33
pubmed: 26739042
Appl Environ Microbiol. 2013 Apr;79(7):2459-62
pubmed: 23354704
Mol Genet Genomics. 2019 Aug;294(4):1049-1058
pubmed: 30982151
Mol Plant Microbe Interact. 2002 Mar;15(3):225-32
pubmed: 11952125
Appl Environ Microbiol. 1992 Feb;58(2):720-3
pubmed: 16348655
Proc Natl Acad Sci U S A. 1987 Nov;84(21):7428-32
pubmed: 16593884
Science. 1978 Aug 4;201(4354):448-50
pubmed: 17729899
Plant J. 2006 Oct;48(2):261-73
pubmed: 17018035
Appl Environ Microbiol. 1989 Apr;55(4):862-5
pubmed: 16347891
Plant Dis. 2022 May;106(5):1486-1491
pubmed: 34879726
AMB Express. 2019 Apr 10;9(1):47
pubmed: 30969386
Appl Environ Microbiol. 1988 Mar;54(3):803-808
pubmed: 16347589
Hereditas. 2013 Jun;150(2-3):17-25
pubmed: 23865962
J Appl Microbiol. 2007 Nov;103(5):1355-65
pubmed: 17953546
New Phytol. 2020 Jun;226(5):1413-1428
pubmed: 32119117
Appl Environ Microbiol. 1995 Jun;61(6):2378-83
pubmed: 16535054
Appl Environ Microbiol. 1990 Jun;56(6):1768-74
pubmed: 16348217
Arch Microbiol. 2007 Jul;188(1):1-14
pubmed: 17497134
Breed Sci. 2012 Jan;61(5):544-53
pubmed: 23136493
Mol Plant Microbe Interact. 2012 Mar;25(3):321-30
pubmed: 22074348
Appl Microbiol Biotechnol. 2018 Jan;102(1):485-497
pubmed: 29110071
Stand Genomic Sci. 2017 Mar 4;12:26
pubmed: 28270909
Nucleic Acids Res. 2012 Jan;40(Database issue):D1178-86
pubmed: 22110026
Front Plant Sci. 2017 Aug 23;8:1466
pubmed: 28878798
Genome Res. 2009 Sep;19(9):1655-64
pubmed: 19648217
Appl Environ Microbiol. 1984 Apr;47(4):607-12
pubmed: 16346501
J Bacteriol. 1943 Jun;45(6):523-7
pubmed: 16560662
Am J Bot. 2012 Dec;99(12):1930-41
pubmed: 23204487
Mol Gen Genet. 1988 Nov;214(3):420-4
pubmed: 3146016
Plant Physiol. 1990 Nov;94(3):899-905
pubmed: 16667870
Mol Ecol. 2017 Mar;26(6):1641-1651
pubmed: 28139080
Plant Cell Physiol. 2014 Sep;55(9):1679-89
pubmed: 25059584
BMC Genomics. 2007 Aug 14;8:275
pubmed: 17697334
Nucleic Acids Res. 2017 Jul 3;45(W1):W122-W129
pubmed: 28472432
J Appl Microbiol. 2012 Nov;113(5):1014-26
pubmed: 22747964