Sequence-based unique DNA marker for simultaneous genotyping of all three β-conglycinin subunit genes in soybean
Kiwoung YangSenthil Kumar ThamilarasanJong-Min KoJungmin HaIn-Youl BaekYeong Hoon LeeJong‐Koo KangMi-Young ChungIll–Sup Nou
0
Citation
18
Reference
20
Related Paper
Abstract:
Soybean ( Glycine max [L.] Merr.) seed is about 40% protein, most of which is accounted for by the major storage proteins β-conglycinin (7S globulin) and glycinin (11S globulin). β-conglycinin, which consists of three subunits, α, α', and β, is the main allergen in soybean. Accordingly, elimination of β-conglycinin from seed is one of the goals of soybean breeding programs. Soybean accessions PI 200485 and CS 1150 lack the α'- and α-subunits of β-conglycinin, respectively. In this study, we developed a 3-betacon marker that could simultaneously identify genotypes for the three subunit genes of β-conglycinin. Interestingly, the three subunit genes were amplified with three distinct bands representing varied amplicon sizes. Mutant alleles could be identified in progeny of a three-way cross, and the corresponding α- and α'-subunit proteins were clearly absent in each mutant accession. 3-betacon marker will be highly useful for soybean breeding programs to develop soybean cultivars with decreased β-conglycinin contents. The online version of this article (doi: 10.5073/JABFQ.2015.088.041) contains supplementary files .Keywords:
Amplicon
Five sets of synthetic oligonucleotide (20-to 24-mers containing no intenal repeats) primers of known gene sequences [yellow lupin nodule specific (hydroxyl) proline-rich protein, pearl millet alcohol dehydrogenase, Pisum sativum heat shock proteins, Drosophila homeobox, and tRNA] were used to differentiate 73 soybean accessions, including 56 Glycine max (L.) Merr. and 17 G. soja Zucc. & Sieb. The amplified genetic markers revealed polymorphic bands for most genotypes studied. The χ2-analyses of the results showed that several fragments produced with these gene primers were associated non-randomly with resistance to Phytophothora, maturity, seed size, flower colour, seed coat colour, seed hilum colour, growth type, and leaf shape. These markers appear to be valuable for differentiation of G. max and G. soja species and genotypes within these species.
Glycine soja
Germ plasm
Cite
Citations (7)
Reducing the content of phytic acid(PA,myo-inositol 1,2,3,4,5,6 hexakisphosphate) is important for improvement of the nutritional quality of soybean.By radiation,one novel soybean [(Glycine max L.(Merr.)] mutant with low PA content,Gm-lpa-ZC-2,was isolated and characterized.Classic genetic study has shown that the lpa mutation was determined by a single recessive gene and was mapped on linkage group B2.Following preliminary mapping of Gm-lpa-ZC-2,in this study,we constructed large genetic populations,developed some new position-specific microsatellite markers by using soybean whole genome sequence and bioinformatics tools,and fine mapped the mutant gene based on soybean genomics and methods of traditional mapping.The results showed that the genetic distance between mutant gene Gm-lpa-ZC-2 and SSR marker Satt168 and Satt416 was much larger than the prediction in our previous study,which should be 18.2 cM.Based on these results,9 pairs of position-specific microsatellite marker which had polymorphism between the two parental lines Zhexiandou 4 and Gm-lpa-ZC-2 were developed in a 4 900-8 200 kb region between target gene and satt168 in LG B2.The lpa mutation gene was fine mapped on LG B2,closely linked with microsatellite loci psm lpa-224,psm lpa-225 and psm lpa-226,at genetic distances of 0.8cM.
Cite
Citations (1)
摘要:
Germ plasm
Identification
Alpha (finance)
Alpha globulin
Cite
Citations (1)
Germ plasm
Inbred strain
Cite
Citations (76)
Soybean is the most important oil crop in the world,which oil production accounts for more than a quarter of global vegetable oil production,thus increasing the oil content and oil composition in soybean seed is essential for soybean breeding.However,there are limited molecular markers derived from functional genes in soybean breeding program. Two soybean genes that are homologous to known proteins involved in oil metabolic pathways were chosen to develop molecular markers in this study,including genes encoding a diacylglycerol kinase 7( DGK7) and a pentatricopeptide repeat-containing protein( TPR),respectively. Based on the position and type of mutation of the single nucleotide polymorphisms( SNPs) within these two genes,we selected SNP1 located in the 5'- untranslated region( 5'-UTR) of Gm DGK7 and SNP2 located in the Gm TPR exon to design d CAPS markers. Association mapping of SNP1 and SNP2 with the oil related traits among 200 soybean released cultivars showed that SNP1 in Gm DGK7 is significantly( P = 6. 21 × 10- 5) associated with oil content,SNP2 in Gm TPR is significantly associated with the content of oil,stearic acid,oleic acid and linoleic acid( P values were 4. 9 × 10- 11,1. 6 × 10- 6,3. 4 × 10- 5and 4. 09 × 10- 8,respectively). Fourteen soybean cultivars with high oil content( 23%) and 5 cultivars with high oleic acid( 33%) were identified in this mapping population. These cultivars and d CAPS markers could be used in marker-assisted breeding to improve soybean oil content and quality.
Soybean oil
Cite
Citations (0)
Kwang-Ho Jeong, Man-Soo Choi, Seuk-Ki Lee, Min-Jung Seo, Tae-Young Hwang, Hong-Tai Yun, Hong-Sig Kim, Jung-Tae Kim, Young-Up Kwon, and Yul-Ho Kim. Plant Breeding and Biotechnology 2013;1:298-306. https://doi.org/10.9787/PBB.2013.1.3.298
Molecular marker
Cite
Citations (10)
During ongoing proteomic analysis of the soybean (Glycine max (L.) Merr) germplasm collection, PI 603408 was identified as a landrace whose seeds lack accumulation of one of the major seed storage glycinin protein subunits. Whole genomic resequencing was used to identify a two-base deletion affecting glycinin 5 The newly discovered deletion was confirmed to be causative through immunological, genetic, and proteomic analysis, and no significant differences in total seed protein content were found to be due to the glycinin 5 loss-of-function mutation per se In addition to focused studies on this one specific glycinin subunit-encoding gene, a total of 1,858,185 nucleotide variants were identified, of which 39,344 were predicted to affect protein coding regions. In order to semiautomate analysis of a large number of soybean gene variants, a new SIFT 4G (Sorting Intolerant From Tolerated 4 Genomes) database was designed to predict the impact of nonsynonymous single nucleotide soybean gene variants, potentially enabling more rapid analysis of soybean resequencing data in the future.
Cite
Citations (8)
Genetic linkage
genomic DNA
Cite
Citations (21)
Abstract Soybean mosaic virus ( SMV ) commonly affects soybean production worldwide, and the SC 18 strain has been widespread in C hina. This study aimed to characterize and map the SC 18 resistance genes present in soybean cultivars ‘ K efeng N o. 1’ and ‘ Q ihuang 22’. Inheritance analysis revealed that two independent single dominant genes in K efeng No. 1 and Q ihuang 22 confer resistance to SC 18. Using simple sequence repeat ( SSR ) markers and bulked segregant analysis, the K efeng No. 1 and Q ihuang 22 resistance genes were located on soybean chromosomes 2 and 13, respectively. We further screened two populations of recombinant inbred lines with 32 SSR markers in the target region, where the resistance gene in K efeng No. 1 was fine mapped to an 80‐kb region containing six putative genes. Sequence and expression analyses of these genes revealed that SMV resistance in K efeng No. 1 was probably attributable to three of the candidate genes (i.e. Glyma.02G127800 , Glyma.02G128200 and Glyma.02G128300 ). Collectively, the results of this study will greatly facilitate the cloning of SC 18 resistance genes and marker‐assisted breeding of SMV ‐resistant soybean cultivars.
Soybean mosaic virus
Bulked segregant analysis
Candidate gene
Cloning (programming)
Cite
Citations (31)
Molecular marker
Multiplex
Null allele
Sequence-tagged site
Marker-Assisted Selection
Cite
Citations (4)